[1] "ofn"        "-oTUCEC-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/UCEC-TP/15094079/UCEC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UCEC-TP/15106276/transformed.cor.cli.txt"

nPatients in clinical file=537, in cluster file=539, common to both=528
[1]  82 528
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               49               479 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               49               479 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              182               346 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              182               346 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               93               435 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               93               435 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               78               450 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               78               450 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               46               482 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               46               482 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               81               447 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               81               447 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               14               514 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               14               514 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                8               520 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                8               520 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               50               478 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               50               478 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               19               509 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               19               509 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               78               450 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               78               450 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               62               466 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               62               466 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               65               463 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               65               463 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               64               464 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               64               464 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              117               411 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              117               411 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              157               371 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              157               371 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               21               507 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               21               507 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                8               520 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                8               520 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               115                413 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               115                413 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               108                420 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               108                420 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                22                506 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                22                506 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                18                510 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                18                510 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                70                458 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                70                458 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                53                475 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                53                475 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                29                499 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                29                499 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                36                492 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                36                492 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                10                518 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                10                518 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                27                501 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                27                501 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                10                518 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                10                518 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                12                516 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                12                516 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                30                498 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                30                498 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                71                457 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                71                457 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                44                484 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                44                484 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                52                476 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                52                476 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                55                473 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                55                473 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               110                418 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               110                418 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               130                398 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               130                398 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                38                490 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                38                490 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                31                497 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                31                497 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               64               464 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               64               464 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               63               465 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               63               465 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               25               503 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               25               503 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               14               514 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               14               514 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               11               517 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               11               517 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               17               511 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               17               511 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               50               478 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               50               478 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               30               498 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               30               498 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              100               428 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              100               428 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              101               427 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              101               427 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               54               474 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               54               474 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               73               455 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               73               455 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               17               511 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               17               511 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               25               503 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               25               503 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               43               485 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               43               485 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               41               487 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               41               487 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               78               450 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               78               450 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               24               504 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               24               504 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              101               427 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              101               427 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              120               408 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              120               408 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                42                486 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                42                486 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                39                489 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                39                489 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                73                455 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                73                455 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                72                456 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                72                456 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                42                486 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                42                486 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                35                493 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                35                493 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                89                439 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                89                439 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                59                469 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                59                469 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               105                423 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               105                423 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                96                432 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                96                432 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               136                392 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               136                392 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               125                403 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               125                403 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                89                439 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                89                439 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                50                478 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                50                478 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                63                465 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                63                465 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                59                469 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                59                469 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                56                472 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                56                472 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                18                510 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                18                510 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 9                519 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 9                519 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                53                475 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                53                475 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               106                422 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               106                422 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               80               448 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               80               448 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               69               459 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               69               459 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "HISTOLOGICAL_TYPE"                     
[16] "RADIATIONS_RADIATION_REGIMENINDICATION"
[17] "COMPLETENESS_OF_RESECTION"             
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCH_NUMBER"                          

Input Data has 20 rows and 528 columns.

[1] "Batch" "20"   
[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=67,	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=422,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE excluded in the analysis because there is no case of (both >= 3) in the table below"
              ENDOMETRIAL OTHER  SPECIFY
freq.values   "527"       "1"           
freq.contrast "1"         "527"         
both >= 3     "FALSE"     "FALSE"       
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "NEOPLASM_DISEASESTAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_T_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_N_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "GENDER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH_NUMBER':	nDistinctValues=35,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 528 columns, 1 survival variables, and 6 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"                        
[2] "HISTOLOGICAL_TYPE"                     
[3] "RADIATIONS_RADIATION_REGIMENINDICATION"
[4] "COMPLETENESS_OF_RESECTION"             
[5] "RACE"                                  
[6] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=59, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS_OF_RESECTION, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=5, 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    37  12
  1P GAIN WILD-TYPE 420  57
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               49               477 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               12                57 
$`1P GAIN MUTATED`
TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A0GA TCGA-A5-A1OG TCGA-A5-A1OK TCGA-A5-A3LP 
       36.69        37.02        17.85        11.44         8.02        14.96 
TCGA-AJ-A3BD TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A8CW TCGA-AP-A052 
       34.16        20.81        10.19        16.87         0.13        21.99 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A0IW TCGA-AX-A1CI TCGA-AX-A3FX TCGA-AX-A3G1 
       21.90        36.13        37.78        72.56        43.82        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A18C TCGA-BG-A222 
        1.38         0.30        29.65        34.13        15.45         9.57 
TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-D1-A16I TCGA-D1-A16S 
       10.16        16.64        61.87        67.20        11.51        18.67 
TCGA-D1-A177 TCGA-D1-A17R TCGA-DI-A1NO TCGA-E6-A2P9 TCGA-EO-A3AS TCGA-EO-A3KU 
       18.02        11.15         9.37         6.67        34.39        22.26 
TCGA-EY-A212 TCGA-EY-A2ON TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-JU-AAVI 
       10.19        20.05        14.70        39.95        59.01         7.76 
TCGA-KJ-A3U4 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-QS-A744 
        2.43         9.47        26.10        23.97        12.92        14.83 
TCGA-SL-A6J9 
        0.07 

$`1P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GB 
       41.06        10.29       106.88       149.56        83.51        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
      112.54       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH 
       24.62        29.06        42.35        15.95         7.92        36.33 
TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
        9.60        91.04        46.32        28.64         5.33         5.16 
TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
        7.33         1.18        14.43        10.26         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI 
       29.39         2.40        34.36         1.12         0.76        18.90 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
        1.68         1.64        14.66        22.49        22.26        17.06 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       36.99        20.65        21.21        15.62        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
       14.76        16.87        22.32        12.82        20.78         2.70 
TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
       83.67         5.95        23.31        86.07         8.22        63.91 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       57.80        45.53        36.89        23.87        12.20        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       33.40        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        60.36        55.89        31.30        35.54        46.78 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        30.90        10.42        27.85        16.24 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       28.54        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       16.96        13.55        15.25        20.28        12.43        20.05 
TCGA-AX-A1CF TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR 
       76.83        54.12        67.50        25.12        36.39        11.08 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
        4.77        30.12        71.24        40.80        61.18        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       34.32        46.49        19.36        26.33        17.75        30.74 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
        2.96        31.13        64.93         0.23         0.20         0.56 
TCGA-AX-A3FZ TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.20         0.26         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
        0.39        80.38        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        27.29        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       11.01         4.11         8.71       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
       75.72        54.44        45.90        43.96        40.50        36.82 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU 
       18.41        17.36        16.57       191.84       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 
       14.40        14.70        11.70        11.87        15.29        12.79 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH 
      116.25        96.30        78.81        62.14        33.11        14.27 
TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       41.06        34.95        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98        22.06        38.37        36.49        28.27 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       14.27         1.81        20.02        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B 
        6.81        35.90        34.98         6.21        10.22        31.76 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.99        24.13        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ 
       23.47        85.55        78.21         4.80        77.95        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       96.49        30.74        97.41        88.34        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        72.72        73.25        59.51        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       49.55        63.16        66.48        16.83        19.79        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       36.10        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V 
       29.92        31.07        33.63        10.65         0.69         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A179 
        3.65        17.49        19.53         6.64        30.15        14.73 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S 
       28.08        26.37        10.22         1.51         1.78        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
        2.33        22.92         1.41        13.22         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.52        41.42         8.48        44.88         0.26         4.27 
TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        4.11        16.93        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QU 
       39.29        36.62        24.30        35.38        12.39        31.10 
TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A8L9 
      110.10        23.38        48.36        17.06         2.37        27.32 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       16.04         7.36        16.80        10.92        49.15        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       51.42        19.40        26.43        35.15        17.19        27.16 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 
       17.88        26.96        16.34        14.53        24.89         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99         4.54        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       23.34        23.90        22.78        13.97         6.90        19.27 
TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       18.84        17.88        17.62        15.09        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 
       15.81        11.08         6.48        19.33        12.59        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 
       18.87        22.82        45.76        31.04        29.10        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 
       13.84        11.38        17.92        14.14        19.89        16.96 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 
        5.88        40.01        41.06        39.88         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 
        8.98        96.69         9.07        28.93        28.96        25.02 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KP-A3VZ 
       29.23        41.06        45.01         1.74        14.04        23.74 
TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A915 TCGA-PG-A916 
       13.28        18.21        23.24        15.45         7.00        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A8F1 
        6.97        18.84        39.95        12.92        23.64         4.44 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       14.07        18.28         0.23 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.07              0.20 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            72.56            191.84 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            17.85             23.90 
[1] "0.1 - 72.6 (17.9)"  "0.2 - 191.8 (23.9)"
[1] "hr=" "2.9"
D1V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  1P GAIN MUTATED                                        21
  1P GAIN WILD-TYPE                                     374
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  1P GAIN MUTATED                               2
  1P GAIN WILD-TYPE                            19
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  1P GAIN MUTATED                                  26
  1P GAIN WILD-TYPE                                86
D1V3, multiclass
                                         clus
vv                                        1P GAIN MUTATED 1P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              21               374
  MIXED SEROUS AND ENDOMETRIOID                         2                19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    26                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V4, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     6  43
  1P GAIN WILD-TYPE 135 344
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      6   43
  1P GAIN WILD-TYPE  135  344
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                6               135
  YES              43               344
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1P GAIN MUTATED    31   0   2   7
  1P GAIN WILD-TYPE 332  23  15  28
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              31               332
  R1               0                23
  R2               2                15
  RX               7                28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  0     1
  1P GAIN WILD-TYPE                                4    19
                   vv
clus                BLACK OR AFRICAN AMERICAN
  1P GAIN MUTATED                          17
  1P GAIN WILD-TYPE                        84
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1P GAIN MUTATED                                           2    26
  1P GAIN WILD-TYPE                                         7   340
D1V6, multiclass
                                           clus
vv                                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   1                19
  BLACK OR AFRICAN AMERICAN                              17                84
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               2                 7
  WHITE                                                  26               340
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     1  38
  1P GAIN WILD-TYPE  13 329
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1   38
  1P GAIN WILD-TYPE   13  329
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                13
  NOT HISPANIC OR LATINO              38               329
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED   153  29
  1Q GAIN WILD-TYPE 304  40
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              182               344 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               29                40 
$`1Q GAIN MUTATED`
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GG 
       36.69        10.29        83.51        17.85        32.78        87.32 
TCGA-A5-A0GI TCGA-A5-A0GN TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GX TCGA-A5-A1OG 
       57.53        60.53        28.27        20.81        68.65        11.44 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A3LP TCGA-AJ-A23O 
       36.33         9.60         8.02        46.32        14.96        10.26 
TCGA-AJ-A3BD TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NF 
       34.16         1.64        22.26        20.81        36.99        21.21 
TCGA-AJ-A3NH TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       10.19        14.76        16.87         0.13        83.67        21.99 
TCGA-AP-A054 TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LH TCGA-AP-A0LI 
       23.31        20.91       117.99       110.37        36.36        97.71 
TCGA-AP-A0LL TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1E1 TCGA-AP-A1E4 
       83.97        55.89        31.30        35.54        10.42        16.24 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       21.90        36.13        13.58        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A0IS TCGA-AX-A0IW TCGA-AX-A0J1 
       35.34        66.58        34.98        35.01        37.78        65.88 
TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A2HA 
       13.55        20.28        72.56        54.12        67.50        81.37 
TCGA-AX-A2HH TCGA-AX-A2IN TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 
       17.75        31.13        43.82        20.52         1.38         0.30 
TCGA-AX-A3G6 TCGA-AX-A3G8 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JT 
        0.26         1.18        14.47         0.39        56.91        43.13 
TCGA-B5-A0JV TCGA-B5-A0K0 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       40.67        28.34        17.88        13.74        17.10        11.01 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11Z TCGA-B5-A1MU 
       36.82        32.09        33.50        27.35        17.36        50.89 
TCGA-B5-A1MZ TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-BG-A0LX TCGA-BG-A0M0 
       15.29        14.27        29.65        41.06        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0MO TCGA-BG-A0MQ 
       20.94        35.21        34.98        22.06        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0W1 
       30.81        21.17        20.28        15.42        24.39        52.83 
TCGA-BG-A186 TCGA-BG-A18C TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A3EW TCGA-BK-A0C9 
       13.78        15.45         1.81         9.57        11.31        35.90 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A26L TCGA-BS-A0TI TCGA-BS-A0U7 TCGA-BS-A0U9 
       10.16        31.76        24.13        61.87        30.74        67.20 
TCGA-BS-A0UT TCGA-BS-A0V4 TCGA-BS-A0VI TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       72.72        59.51        63.16        16.83         8.55         0.56 
TCGA-D1-A102 TCGA-D1-A160 TCGA-D1-A165 TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A16V 
        4.44         3.68         0.66        11.51        18.67         3.95 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17L TCGA-D1-A17M 
       30.15        18.02         1.58         7.00        26.37        10.22 
TCGA-D1-A17R TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA 
       11.15        16.87        18.02        41.42         8.48         0.26 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1NO TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1QX 
       27.16        16.31         9.37         6.67        27.32         7.36 
TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EY-A1G7 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GF 
       51.52        34.39         6.21         4.54        53.88        27.16 
TCGA-EY-A1GK TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       22.78        19.27        17.88        15.09        16.11        12.43 
TCGA-EY-A1GX TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
        6.48        10.19        14.40        20.05        45.76        31.04 
TCGA-EY-A4KR TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2D2 TCGA-FI-A2EW 
       11.38        19.89        14.70        16.96        39.95        59.01 
TCGA-FI-A2F4 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-JU-AAVI TCGA-KJ-A3U4 TCGA-KP-A3W0 
       28.96        41.06        45.01         7.76         2.43        13.28 
TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A917 TCGA-QS-A744 TCGA-QS-A8F1 
       26.10        23.97        12.92         6.97        14.83         4.44 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

$`1Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0GD TCGA-A5-A0GE 
       41.06       106.88       149.56        37.02       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       74.10        65.75        60.53        46.55        38.37        36.82 
TCGA-A5-A0GW TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       23.21        19.96        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A2K5 
       42.35        15.95         7.92        91.04        28.64         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QL 
        5.16         7.33         1.18        14.43         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI 
       29.39         2.40        34.36         1.12         0.76        18.90 
TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NE TCGA-AJ-A3NG 
        1.68        14.66        22.49        17.06        20.65        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.35        15.95        16.87        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AP-A053 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D 
        2.70         5.95        86.07         8.22        63.91        57.80 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A0L8 TCGA-AP-A0L9 
       45.53        36.89        23.87        12.20        48.79       125.42 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
        3.39        63.16        31.73        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E3 
       60.36        46.78        49.15         6.71        30.90        27.85 
TCGA-AW-A1PO TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A062 TCGA-AX-A06B TCGA-AX-A06D 
        0.56        19.82        29.69        45.99        53.92        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IU TCGA-AX-A0IZ 
       51.09        27.39        30.02        60.66        28.54        43.82 
TCGA-AX-A0J0 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C9 TCGA-AX-A1CC 
       40.11        13.28        19.20        16.96        15.25        12.43 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 
       20.05        76.83        25.12        36.39        11.08         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HC TCGA-AX-A2HD 
       30.12        71.24        40.80        61.18        34.32        46.49 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FS 
       19.36        26.33        30.74         2.96        64.93         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G7 TCGA-AX-A3G9 TCGA-B5-A0JN 
        0.20         0.56         0.20         0.30        18.35        80.38 
TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K1 
       46.75        48.76        44.71        32.55        28.64        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F 
       25.91        27.29        17.85         4.11         8.71       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A121 
       40.50        16.73        19.56        19.50        18.41        16.57 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      191.84       102.31        14.40        14.70        11.70        11.87 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       12.79       116.25        96.30        78.81        62.14        33.11 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       34.13        34.95        18.61        38.37        36.49        28.27 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0VV 
       10.72        41.52        48.56        23.47        43.30        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       16.34        34.29        52.64        56.58        14.83        12.56 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A2AD TCGA-BG-A2AE 
       14.73        14.01        15.45        14.27        20.02        23.70 
TCGA-BG-A2L7 TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13C 
       20.12         6.81        34.98         6.21        10.22        24.99 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       16.64        13.18        10.03         9.86        46.95        23.47 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 
       85.55        78.21         4.80        77.95        67.99        96.49 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV 
       97.41        88.34        85.84        82.39        81.57        73.25 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZO TCGA-D1-A0ZP 
       62.79        63.58        49.55        66.48        19.79        29.95 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 
        4.87        28.67        23.93        22.55         1.74        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A161 TCGA-D1-A163 
       39.48        30.08        29.88         1.91        29.33        32.58 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       27.42        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A179 TCGA-D1-A17C 
        3.65        17.49        19.53         6.64        14.73         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17N TCGA-D1-A17Q 
       30.44         1.28        28.01        28.08         1.51         1.78 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW 
       24.30         2.33        22.92         1.41        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       18.25         2.07        15.06         1.05         3.95         3.52 
TCGA-D1-A2G7 TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY 
       44.88         4.27         4.11        16.93        89.33        10.92 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QU 
       39.29        36.62        24.30        35.38        12.39        31.10 
TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-EC-A1NJ 
      110.10        23.38        48.36        17.06         2.37        16.04 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
       16.80        10.92        49.15        37.71        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU 
       66.90        46.26        57.60        51.42        19.40        26.43 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU 
       35.15        17.19        27.16        17.88        26.96        22.26 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GE TCGA-EY-A1GH 
       16.34        14.53        24.89        14.99        24.36        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GR 
       23.34        23.90        13.97         6.90        18.84        17.62 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A215 TCGA-EY-A2OM 
       15.81        11.08        19.33        12.59        18.87        22.82 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A72D 
       29.10        27.35        13.84        17.92        14.14         5.88 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       40.01        41.06        39.88         7.99        13.84         8.98 
TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-H5-A2HR 
       96.69         9.07        28.93        25.02        29.23         1.74 
TCGA-K6-A3WQ TCGA-KP-A3VZ TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       14.04        23.74         9.47        18.21        23.24        15.45 
TCGA-PG-A915 TCGA-PG-A916 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
        7.00        11.24        18.84        39.95        12.92        23.64 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       14.07        18.28 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.07              0.20 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           117.99            191.84 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           20.925            23.915 
[1] "0.1 - 118.0 (20.9)" "0.2 - 191.8 (23.9)"
[1] "hr=" "1.6"
D2V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  1Q GAIN MUTATED                                       137
  1Q GAIN WILD-TYPE                                     258
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  1Q GAIN MUTATED                               5
  1Q GAIN WILD-TYPE                            16
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  1Q GAIN MUTATED                                  40
  1Q GAIN WILD-TYPE                                72
D2V3, multiclass
                                         clus
vv                                        1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             137               258
  MIXED SEROUS AND ENDOMETRIOID                         5                16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    40                72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V4, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    46 136
  1Q GAIN WILD-TYPE  95 251
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     46  136
  1Q GAIN WILD-TYPE   95  251
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               46                95
  YES             136               251
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1Q GAIN MUTATED   124   7   6  12
  1Q GAIN WILD-TYPE 239  16  11  23
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0             124               239
  R1               7                16
  R2               6                11
  RX              12                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  1     4
  1Q GAIN WILD-TYPE                                3    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  1Q GAIN MUTATED                          39
  1Q GAIN WILD-TYPE                        62
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1Q GAIN MUTATED                                           2   131
  1Q GAIN WILD-TYPE                                         7   235
D2V6, multiclass
                                           clus
vv                                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 3
  ASIAN                                                   4                16
  BLACK OR AFRICAN AMERICAN                              39                62
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               2                 7
  WHITE                                                 131               235
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     2 134
  1Q GAIN WILD-TYPE  12 233
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2  134
  1Q GAIN WILD-TYPE   12  233
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                12
  NOT HISPANIC OR LATINO             134               233
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    69  23
  2P GAIN WILD-TYPE 388  46
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               92               434 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               23                46 
$`2P GAIN MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0GN TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0R7 TCGA-A5-A1OG 
      149.56        60.53        28.27        20.81        17.59        11.44 
TCGA-A5-A1OH TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3BK 
       36.33        28.64        14.96         1.18        14.43         1.68 
TCGA-AJ-A3EJ TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A05A 
        1.64        20.81        10.19        16.87        16.87        63.91 
TCGA-AP-A0L8 TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05W 
       48.79        97.71        46.78        21.90        36.13        68.35 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CK TCGA-AX-A2H2 TCGA-AX-A2H7 
       28.54        37.78        16.96        67.50         4.77        40.80 
TCGA-AX-A2HH TCGA-AX-A2HK TCGA-AX-A3G3 TCGA-AX-A3G6 TCGA-B5-A0JT TCGA-B5-A0K7 
       17.75         2.96         1.38         0.26        43.13        17.10 
TCGA-B5-A0K9 TCGA-B5-A11I TCGA-B5-A1MU TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-BG-A0M0 
       11.01        75.72        50.89        12.79        29.65        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A2AE 
       20.94        22.06        36.49        15.42        24.39        23.70 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TE 
        6.81        35.90        10.16        24.13        16.64         4.80 
TCGA-BS-A0TI TCGA-BS-A0UT TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-D1-A0ZO TCGA-D1-A0ZP 
       61.87        72.72        63.58        49.55        19.79        29.95 
TCGA-D1-A168 TCGA-D1-A16I TCGA-D1-A17R TCGA-D1-A1NW TCGA-D1-A2G6 TCGA-D1-A3DH 
       36.10        11.51        11.15         0.72         8.48         4.11 
TCGA-D1-A3JP TCGA-DI-A1NN TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A2CG 
       16.93        35.38       110.10        48.36        27.32        51.42 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1G7 TCGA-EY-A1GH TCGA-EY-A1GM TCGA-EY-A1GO 
       26.96        22.26         6.21        23.34         6.90        19.27 
TCGA-EY-A1GS TCGA-EY-A214 TCGA-EY-A54A TCGA-EY-A72D TCGA-FI-A2D2 TCGA-FI-A2D4 
       15.09        14.40        14.70         5.88        39.95         7.99 
TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3VZ TCGA-KP-A3W1 TCGA-PG-A7D5 
       45.01         7.76        14.04        23.74         9.47        23.97 
TCGA-QS-A8F1 TCGA-SL-A6J9 
        4.44         0.07 

$`2P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       57.53        65.75        60.53        46.55        38.37        36.82 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       23.21        68.65        19.96        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 
       42.35        15.95         7.92         9.60         8.02        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23O TCGA-AJ-A2QK 
       46.32         5.33         5.16         7.33        10.26         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF 
       19.79        29.39         2.40        34.36        34.16         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
        0.76        18.90        14.66        22.49        22.26        17.06 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       36.99        20.65        21.21        15.62        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW 
       14.76        22.32        12.82        20.78         2.70         0.13 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       83.67        21.99         5.95        23.31        86.07         8.22 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       57.80        45.53        36.89        23.87        12.20        20.91 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
      125.42       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       31.73        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       55.89        31.30        35.54        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       10.42        27.85        16.24         0.56        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       34.98        53.92        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       60.66        35.01        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       19.20        13.55        15.25        20.28        12.43        20.05 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR 
       76.83        72.56        54.12        25.12        36.39        11.08 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       30.12        71.24        61.18        81.37        34.32        46.49 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       19.36        26.33        30.74        31.13        64.93         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 
        0.20         0.56        43.82         0.20        20.52         0.30 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN 
        0.30         1.18        18.35        14.47         0.39        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       56.91        46.75        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        27.29        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       13.74        17.85         4.11         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
       88.34        54.44        45.90        43.96        40.50        36.82 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV 
       18.41        17.36        16.57       191.84       102.31        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA 
       14.70        11.70        11.87        15.29       116.25        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD 
       78.81        62.14        33.11        14.27        41.06        34.13 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       34.95        18.61        20.19        35.21        34.98        38.37 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VV 
       43.04        39.32        30.81        21.17        20.28        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW 
       14.27         1.81         9.57        20.02        20.12        11.31 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F 
       34.98         6.21        10.22        31.76        24.99        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        23.47        85.55        78.21 
TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       77.95        67.99        96.49        30.74        97.41        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV TCGA-BS-A0V4 
       88.34        85.84        82.39        81.57        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       62.79        63.16        66.48        16.83         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A169 TCGA-D1-A16B 
       29.33        32.58         0.66        15.72        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       37.51        36.79        27.42        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       10.65         0.69        18.67         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T 
       26.37        10.22         1.51         1.78        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
       22.92         1.41        13.22        18.25        16.87        18.02 
TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 
        2.07        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
       44.88         0.26         4.27        89.33        10.92        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT 
       16.31        39.29        36.62        24.30         9.37        12.39 
TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       31.10        23.38        17.06         2.37         6.67        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
        7.36        16.80        10.92        49.15        37.71        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH 
       61.55        66.90        46.26        57.60        51.52        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       34.39        26.43        35.15        17.19        27.16        17.88 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       16.34        14.53        24.89        14.99         4.54        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL 
       24.36        27.16        23.34        23.90        22.78        13.97 
TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       18.84        17.88        17.62        16.11        12.43        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A215 
       11.08         6.48        19.33        12.59        10.19        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 
       22.82        20.05        45.76        31.04        29.10        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 
       13.84        11.38        17.92        14.14        19.89        16.96 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       40.01        41.06        39.88        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 
       59.01         9.07        28.93        28.96        25.02        29.23 
TCGA-FI-A3PV TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 
       41.06         1.74         2.43        13.28        26.10        18.21 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 
       23.24        15.45        12.92         7.00        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI 
       18.84        39.95        12.92        23.64        14.83        14.07 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.07              0.13 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           149.56            191.84 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           20.810            23.885 
[1] "0.1 - 149.6 (20.8)" "0.1 - 191.8 (23.9)"
[1] "hr=" "2.6"
D3V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  2P GAIN MUTATED                                        42
  2P GAIN WILD-TYPE                                     353
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  2P GAIN MUTATED                               5
  2P GAIN WILD-TYPE                            16
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  2P GAIN MUTATED                                  46
  2P GAIN WILD-TYPE                                66
D3V3, multiclass
                                         clus
vv                                        2P GAIN MUTATED 2P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              42               353
  MIXED SEROUS AND ENDOMETRIOID                         5                16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    46                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V4, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    20  73
  2P GAIN WILD-TYPE 121 314
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     20   73
  2P GAIN WILD-TYPE  121  314
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               20               121
  YES              73               314
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2P GAIN MUTATED    65   3   5   7
  2P GAIN WILD-TYPE 298  20  12  28
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0              65               298
  R1               3                20
  R2               5                12
  RX               7                28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P GAIN MUTATED                                  0     5
  2P GAIN WILD-TYPE                                4    15
                   vv
clus                BLACK OR AFRICAN AMERICAN
  2P GAIN MUTATED                          19
  2P GAIN WILD-TYPE                        82
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2P GAIN MUTATED                                           2    64
  2P GAIN WILD-TYPE                                         7   302
D3V6, multiclass
                                           clus
vv                                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   5                15
  BLACK OR AFRICAN AMERICAN                              19                82
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               2                 7
  WHITE                                                  64               302
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     0  68
  2P GAIN WILD-TYPE  14 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0   68
  2P GAIN WILD-TYPE   14  299
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                14
  NOT HISPANIC OR LATINO              68               299
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    58  19
  2Q GAIN WILD-TYPE 399  50
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               77               449 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               19                50 
$`2Q GAIN MUTATED`
TCGA-5B-A90C TCGA-A5-A0GN TCGA-A5-A0GV TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OH 
       36.69        60.53        20.81        17.59        11.44        36.33 
TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       28.64        14.96         1.18        14.43         1.68         1.64 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3TW TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 
       20.81        10.19        16.87        97.71        46.78        21.90 
TCGA-AP-A5FX TCGA-AX-A05W TCGA-AX-A0IW TCGA-AX-A2HH TCGA-AX-A2HK TCGA-AX-A3G3 
       36.13        68.35        37.78        17.75         2.96         1.38 
TCGA-B5-A0JT TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11I TCGA-B5-A1MU TCGA-B5-A3S1 
       43.13        17.10        11.01        75.72        50.89        29.65 
TCGA-BG-A0M2 TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A2AE 
       20.94        22.06        36.49        15.42        24.39        23.70 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TE 
        6.81        35.90        10.16        24.13        16.64         4.80 
TCGA-BS-A0UT TCGA-BS-A0V7 TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A168 TCGA-D1-A16I 
       72.72        63.58        19.79        29.95        36.10        11.51 
TCGA-D1-A17R TCGA-D1-A2G6 TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DI-A1NN TCGA-DI-A2QY 
       11.15         8.48         4.11        16.93        35.38       110.10 
TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A2CG TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1G7 
       48.36        27.32        51.42        26.96        22.26         6.21 
TCGA-EY-A1GH TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A214 TCGA-EY-A54A 
       23.34         6.90        19.27        15.09        14.40        14.70 
TCGA-EY-A72D TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ 
        5.88        39.95         7.99        45.01         7.76        14.04 
TCGA-KP-A3VZ TCGA-KP-A3W1 TCGA-PG-A7D5 TCGA-QS-A8F1 TCGA-SL-A6J9 
       23.74         9.47        23.97         4.44         0.07 

$`2Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       57.53        65.75        60.53        46.55        38.37        36.82 
TCGA-A5-A0GU TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 
       28.27        23.21        68.65        19.96        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK 
       29.06        42.35        15.95         7.92         9.60         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23O 
       91.04        46.32         5.33         5.16         7.33        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
        0.39        19.79        29.39         2.40        34.36        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
        1.12         0.76        18.90        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       17.06        36.99        20.65        21.21        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.95        14.76        16.87        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        2.70         0.13        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        63.91        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       23.87        12.20        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37         3.39        63.16        36.36        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       35.54        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y 
       16.24         0.56        13.58        19.82        29.69        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       28.54        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       16.96        13.55        15.25        20.28        12.43        20.05 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       76.83        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       11.08         4.77        30.12        71.24        40.80        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HJ 
       81.37        34.32        46.49        19.36        26.33        30.74 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        64.93         0.23         0.20         0.56        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.20        20.52         0.30         0.26         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       18.35        14.47         0.39        80.38        56.91        46.75 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K8 
       30.51        25.91        27.29        17.88        13.74        17.85 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J 
        4.11         8.71       185.79       113.36        88.34        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R 
       45.90        43.96        40.50        36.82        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       16.57       191.84       102.31        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       11.87        15.29        12.79       116.25        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       62.14        33.11        14.27        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       18.61        20.19        19.33        35.21        34.98        38.37 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VV 
       43.04        39.32        30.81        21.17        20.28        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW 
       14.27         1.81         9.57        20.02        20.12        11.31 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F 
       34.98         6.21        10.22        31.76        24.99        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        23.47        85.55        78.21 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV 
       67.20        88.34        85.84        82.39        81.57        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       59.51        62.79        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J 
       37.32        36.36        37.51        36.79        27.42        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
       31.07        33.63        10.65         0.69        18.67         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW 
       24.30         2.33        22.92         1.41        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
       18.25        16.87        18.02         2.07        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.95         3.52        41.42        44.88         0.26         4.27 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 
       24.30         9.37        12.39        31.10        23.38        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37         6.67        16.04         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       49.15        37.71        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       57.60        51.52        19.40        34.39        26.43        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       17.19        27.16        17.88        16.34        14.53        24.89 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GI 
       14.99         4.54        53.88        24.36        27.16        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR 
       23.90        22.78        13.97        18.84        17.88        17.62 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        12.43        15.81        11.08         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       12.59        10.19        18.87        22.82        20.05        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 
       31.04        29.10        27.35        13.84        11.38        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
       14.14        19.89        16.96        40.01        41.06        39.88 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       13.84         8.98        96.69        59.01         9.07        28.93 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-KJ-A3U4 
       28.96        25.02        29.23        41.06         1.74         2.43 
TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 
       13.28        26.10        18.21        23.24        15.45        12.92 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        7.00        11.24         6.97        18.84        39.95        12.92 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       23.64        14.83        14.07        18.28         0.23 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.07              0.13 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           110.10            191.84 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            20.81             23.90 
[1] "0.1 - 110.1 (20.8)" "0.1 - 191.8 (23.9)"
[1] "hr=" "2.7"
D4V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  2Q GAIN MUTATED                                        37
  2Q GAIN WILD-TYPE                                     358
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  2Q GAIN MUTATED                               4
  2Q GAIN WILD-TYPE                            17
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  2Q GAIN MUTATED                                  37
  2Q GAIN WILD-TYPE                                75
D4V3, multiclass
                                         clus
vv                                        2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              37               358
  MIXED SEROUS AND ENDOMETRIOID                         4                17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    37                75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V4, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    15  63
  2Q GAIN WILD-TYPE 126 324
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     15   63
  2Q GAIN WILD-TYPE  126  324
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               15               126
  YES              63               324
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2Q GAIN MUTATED    52   2   5   7
  2Q GAIN WILD-TYPE 311  21  12  28
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0              52               311
  R1               2                21
  R2               5                12
  RX               7                28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q GAIN MUTATED                                  0     4
  2Q GAIN WILD-TYPE                                4    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  2Q GAIN MUTATED                          15
  2Q GAIN WILD-TYPE                        86
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2Q GAIN MUTATED                                           1    55
  2Q GAIN WILD-TYPE                                         8   311
D4V6, multiclass
                                           clus
vv                                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   4                16
  BLACK OR AFRICAN AMERICAN                              15                86
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 8
  WHITE                                                  55               311
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     0  57
  2Q GAIN WILD-TYPE  14 310
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0   57
  2Q GAIN WILD-TYPE   14  310
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                14
  NOT HISPANIC OR LATINO              57               310
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    36  10
  3P GAIN WILD-TYPE 421  59
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               46               480 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               10                59 
$`3P GAIN MUTATED`
TCGA-A5-A2K2 TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3IA TCGA-AJ-A3QS TCGA-AJ-A8CW 
       91.04        34.16        18.90        20.81        16.87         0.13 
TCGA-AP-A0LO TCGA-AP-A1DO TCGA-AX-A05W TCGA-AX-A06D TCGA-AX-A1CA TCGA-AX-A2H4 
       33.40        31.30        68.35        12.26        20.28        30.12 
TCGA-AX-A2H7 TCGA-AX-A3G6 TCGA-B5-A0K4 TCGA-B5-A11R TCGA-B5-A1MR TCGA-B5-A1MY 
       40.80         0.26        17.88        33.50       191.84        11.87 
TCGA-BG-A0M4 TCGA-BG-A0RY TCGA-BG-A0W1 TCGA-BS-A0U9 TCGA-BS-A0UV TCGA-BS-A0V8 
       34.98        15.42        52.83        67.20        73.25        49.55 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DI-A2QY TCGA-E6-A8L9 
       41.42         8.48         4.11        16.93       110.10        27.32 
TCGA-EO-A22Y TCGA-EO-A3B1 TCGA-EY-A1GC TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS 
       51.52        26.96         4.54        17.88        17.62        15.09 
TCGA-EY-A1GW TCGA-EY-A212 TCGA-EY-A4KR TCGA-EY-A72D TCGA-FI-A2EW TCGA-FI-A2EX 
       11.08        10.19        11.38         5.88        59.01         9.07 
TCGA-FI-A3PX TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A744 
       45.01        12.92         7.00        14.83 

$`3P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       38.37        36.82        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       19.96        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK 
       15.95         7.92        11.44        36.33         9.60         8.02 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       46.32        28.64         5.33         5.16         7.33        14.96 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM 
        1.18        14.43        10.26         0.39        19.79        29.39 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EJ 
        2.40        34.36         1.12         0.76         1.68         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE 
       14.66        22.49        22.26        17.06        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       21.21        15.62        10.19        15.35        15.95        14.76 
TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AP-A051 
       16.87        22.32        12.82        20.78         2.70        83.67 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
       21.99         5.95        23.31        86.07         8.22        63.91 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       57.80        45.53        36.89        23.87        12.20        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        83.97        27.12        82.52 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       60.36        55.89        35.54        46.78        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
       30.90        10.42        27.85        16.24        21.90        36.13 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z 
        0.56        13.58        19.82        29.69        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06F 
       35.34        45.99        66.58        34.98        53.92        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        35.01        28.54        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        65.88        13.28        19.20        16.96 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       13.55        15.25        12.43        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 
       54.12        67.50        25.12        36.39        11.08         4.77 
TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       71.24        61.18        81.37        34.32        46.49        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       26.33        17.75        30.74         2.96        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
        0.23         0.20         0.56        43.82         0.20        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        1.38         0.30         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
        0.39        80.38        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       25.91        27.29        13.74        17.10        17.85        11.01 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
        4.11         8.71       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q 
       54.44        45.90        43.96        40.50        36.82        32.09 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       16.57       102.31        50.89        14.40        14.70        11.70 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       15.29        12.79       116.25        96.30        78.81        62.14 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       33.11        14.27        29.65        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M6 
       18.61        20.19        19.33        20.94        35.21        22.06 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       38.37        36.49        28.27        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       23.47        43.30        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        24.39        26.66        16.34        34.29        52.64 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       15.45        15.45        14.27         1.81         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31         6.81        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
        6.21        10.22        10.16        31.76        24.99        24.13 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       16.64        13.18        10.03         9.86        46.95        23.47 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       96.49        30.74        97.41        88.34        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI 
       81.57        72.72        59.51        62.79        63.58        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       36.36        37.51        36.79        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
       31.07        33.63        10.65         0.69        18.67         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
        0.72        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        1.05         3.95         3.52        44.88         0.26         4.27 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX 
       24.30        35.38         9.37        12.39        31.10        23.38 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       48.36        17.06         2.37         6.67        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
       16.80        10.92        49.15        37.71        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       66.90        46.26        57.60        51.42        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KU 
       26.43        35.15        17.19        27.16        17.88        22.26 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD 
       16.34        14.53        24.89         6.21        14.99        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK 
       24.36        27.16        23.34        23.34        23.90        22.78 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU 
       13.97         6.90        19.27        18.84        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A215 
       15.81         6.48        19.33        12.59        14.40        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 
       22.82        20.05        45.76        31.04        29.10        27.35 
TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
       13.84        17.92        14.14        19.89        14.70        16.96 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
       40.01        41.06        39.88        39.95         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 
        8.98        96.69        28.93        28.96        25.02        29.23 
TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       41.06         1.74         7.76        14.04         2.43        23.74 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       13.28         9.47        26.10        18.21        23.24        15.45 
TCGA-PG-A7D5 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       23.97        11.24         6.97        18.84        39.95        12.92 
TCGA-QS-A5YR TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       23.64         4.44        14.07        18.28         0.07         0.23 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.13              0.07 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           191.84            185.79 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           19.590            23.425 
[1] "0.1 - 191.8 (19.6)" "0.1 - 185.8 (23.4)"
[1] "hr=" "1.7"
D5V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  3P GAIN MUTATED                                        26
  3P GAIN WILD-TYPE                                     369
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  3P GAIN MUTATED                               0
  3P GAIN WILD-TYPE                            21
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  3P GAIN MUTATED                                  20
  3P GAIN WILD-TYPE                                92
D5V3, multiclass
                                         clus
vv                                        3P GAIN MUTATED 3P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              26               369
  MIXED SEROUS AND ENDOMETRIOID                         0                21
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    20                92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V4, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     6  40
  3P GAIN WILD-TYPE 135 347
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      6   40
  3P GAIN WILD-TYPE  135  347
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                6               135
  YES              40               347
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3P GAIN MUTATED    32   4   2   3
  3P GAIN WILD-TYPE 331  19  15  32
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              32               331
  R1               4                19
  R2               2                15
  RX               3                32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P GAIN MUTATED                                  0     0
  3P GAIN WILD-TYPE                                4    20
                   vv
clus                BLACK OR AFRICAN AMERICAN
  3P GAIN MUTATED                          14
  3P GAIN WILD-TYPE                        87
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3P GAIN MUTATED                                           3    27
  3P GAIN WILD-TYPE                                         6   339
D5V6, multiclass
                                           clus
vv                                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   0                20
  BLACK OR AFRICAN AMERICAN                              14                87
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               3                 6
  WHITE                                                  27               339
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     1  38
  3P GAIN WILD-TYPE  13 329
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1   38
  3P GAIN WILD-TYPE   13  329
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                13
  NOT HISPANIC OR LATINO              38               329
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    63  18
  3Q GAIN WILD-TYPE 394  51
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               81               445 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               18                51 
$`3Q GAIN MUTATED`
TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A3LP 
       36.69        37.02        11.44        36.33        91.04        14.96 
TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3IA TCGA-AJ-A3QS TCGA-AJ-A8CW 
       34.16        18.90         1.64        20.81        16.87         0.13 
TCGA-AP-A0L8 TCGA-AP-A0LO TCGA-AP-A1DO TCGA-AX-A05W TCGA-AX-A06D TCGA-AX-A1CA 
       48.79        33.40        31.30        68.35        12.26        20.28 
TCGA-AX-A1CF TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A3FW TCGA-AX-A3G6 
       76.83        11.08        30.12        40.80         0.56         0.26 
TCGA-B5-A0K4 TCGA-B5-A11I TCGA-B5-A11R TCGA-B5-A1MR TCGA-B5-A1MY TCGA-B5-A1N2 
       17.88        75.72        33.50       191.84        11.87        12.79 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0RY TCGA-BG-A0W1 TCGA-BG-A0YV TCGA-BK-A0CC 
       34.98        22.06        15.42        52.83        12.56        10.22 
TCGA-BS-A0TE TCGA-BS-A0U9 TCGA-BS-A0UV TCGA-BS-A0V8 TCGA-D1-A168 TCGA-D1-A16G 
        4.80        67.20        73.25        49.55        36.10        27.42 
TCGA-D1-A1NW TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DI-A2QY 
        0.72        41.42         8.48         4.11        16.93       110.10 
TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EC-A1QX TCGA-EO-A1Y5 TCGA-EO-A22Y TCGA-EO-A2CG 
       48.36        27.32         7.36        10.92        51.52        51.42 
TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GM TCGA-EY-A1GQ TCGA-EY-A1GR 
       26.96        16.34         4.54         6.90        17.88        17.62 
TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A212 TCGA-EY-A2ON TCGA-EY-A3QX TCGA-EY-A4KR 
       15.09        11.08        10.19        20.05        13.84        11.38 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A3PX 
        5.88        40.01        59.01         9.07        28.93        45.01 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-PG-A914 
        7.76        14.04         9.47        26.10        23.97        12.92 
TCGA-PG-A915 TCGA-QS-A744 TCGA-SL-A6J9 
        7.00        14.83         0.07 

$`3Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA 
       41.06        10.29       106.88       149.56        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       32.78       112.54       105.37        87.32        74.10        57.53 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       65.75        60.53        60.53        46.55        38.37        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        20.81        23.21        68.65        19.96        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       19.59        24.62        29.06        42.35        15.95         7.92 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
        9.60         8.02        46.32        28.64         5.33         5.16 
TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
        7.33         1.18        14.43        10.26         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK 
       29.39         2.40        34.36         1.12         0.76         1.68 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE 
       14.66        22.49        22.26        17.06        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       21.21        15.62        10.19        15.35        15.95        14.76 
TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AP-A051 
       16.87        22.32        12.82        20.78         2.70        83.67 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
       21.99         5.95        23.31        86.07         8.22        63.91 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       57.80        45.53        36.89        23.87        12.20        20.91 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
      125.42       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP 
       97.71        31.73        83.97        27.12        82.52        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       55.89        35.54        46.78        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
       10.42        27.85        16.24        21.90        36.13         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       13.58        19.82        29.69        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06F TCGA-AX-A06H 
       45.99        66.58        34.98        53.92        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        35.01        28.54        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        65.88        13.28        19.20        16.96        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       15.25        12.43        20.05        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HA 
       25.12        36.39         4.77        71.24        61.18        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       34.32        46.49        19.36        26.33        17.75        30.74 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FX 
        2.96        31.13        64.93         0.23         0.20        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.20        20.52         1.38         0.30         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       18.35        14.47         0.39        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 
       28.34        30.51        25.91        27.29        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.85        11.01         4.11         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
       88.34        54.44        45.90        43.96        40.50        36.82 
TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       32.09        27.35        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW 
       17.36        16.57       102.31        50.89        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       11.70        15.29       116.25        96.30        78.81        62.14 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       33.11        14.27        29.65        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M7 
       18.61        20.19        19.33        20.94        35.21        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       36.49        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       43.30        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 
       24.39        26.66        16.34        34.29        52.64        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 
       11.31         6.81        35.90        34.98         6.21        10.16 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
       31.76        24.99        24.13        16.64        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG 
        9.86        46.95        23.47        85.55        78.21        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA 
       61.87        67.99        96.49        30.74        97.41        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0V4 TCGA-BS-A0V6 
       85.84        82.39        81.57        72.72        59.51        62.79 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        63.16        66.48        16.83        19.79        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16I TCGA-D1-A16J 
       37.32        36.36        37.51        36.79        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
       31.07        33.63        10.65         0.69        18.67         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
       18.25        16.87        18.02         2.07        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KV 
        3.95         3.52        44.88         0.26         4.27        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 
       35.38         9.37        12.39        31.10        23.38        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 
        2.37         6.67        16.04        16.80        49.15        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CH 
       61.74        61.55        66.90        46.26        57.60        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       34.39        26.43        35.15        17.19        27.16        17.88 
TCGA-EO-A3KU TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD 
       22.26        14.53        24.89         6.21        14.99        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK 
       24.36        27.16        23.34        23.34        23.90        22.78 
TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       13.97        19.27        18.84        16.11        12.43        15.81 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM 
        6.48        19.33        12.59        14.40        18.87        22.82 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A547 TCGA-EY-A548 
       45.76        31.04        29.10        27.35        17.92        14.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
       19.89        14.70        16.96        41.06        39.88        39.95 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2F4 TCGA-FI-A2F8 
        7.99        13.84         8.98        96.69        28.96        25.02 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 
       29.23        41.06         1.74         2.43        23.74        13.28 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       18.21        23.24        15.45        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       39.95        12.92        23.64         4.44        14.07        18.28 
TCGA-SL-A6JA 
        0.23 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.07              0.20 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           191.84            185.79 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            17.88             23.70 
[1] "0.1 - 191.8 (17.9)" "0.2 - 185.8 (23.7)"
[1] "hr=" "2.1"
D6V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  3Q GAIN MUTATED                                        35
  3Q GAIN WILD-TYPE                                     360
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  3Q GAIN MUTATED                               4
  3Q GAIN WILD-TYPE                            17
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  3Q GAIN MUTATED                                  42
  3Q GAIN WILD-TYPE                                70
D6V3, multiclass
                                         clus
vv                                        3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              35               360
  MIXED SEROUS AND ENDOMETRIOID                         4                17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    42                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V4, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    17  64
  3Q GAIN WILD-TYPE 124 323
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     17   64
  3Q GAIN WILD-TYPE  124  323
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               17               124
  YES              64               323
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3Q GAIN MUTATED    55   5   5   6
  3Q GAIN WILD-TYPE 308  18  12  29
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              55               308
  R1               5                18
  R2               5                12
  RX               6                29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q GAIN MUTATED                                  0     3
  3Q GAIN WILD-TYPE                                4    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  3Q GAIN MUTATED                          26
  3Q GAIN WILD-TYPE                        75
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3Q GAIN MUTATED                                           3    44
  3Q GAIN WILD-TYPE                                         6   322
D6V6, multiclass
                                           clus
vv                                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   3                17
  BLACK OR AFRICAN AMERICAN                              26                75
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               3                 6
  WHITE                                                  44               322
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     2  63
  3Q GAIN WILD-TYPE  12 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      2   63
  3Q GAIN WILD-TYPE   12  304
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                12
  NOT HISPANIC OR LATINO              63               304
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    11   3
  4P GAIN WILD-TYPE 446  66
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               14               512 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3                66 
$`4P GAIN MUTATED`
TCGA-A5-A0G5 TCGA-A5-A1OG TCGA-AJ-A23N TCGA-AP-A0LI TCGA-B5-A0JN TCGA-BG-A0M6 
       37.02        11.44        14.43        97.71        80.38        22.06 
TCGA-BK-A139 TCGA-BK-A4ZD TCGA-D1-A3DH TCGA-EO-A1Y5 TCGA-EO-A2CG TCGA-EY-A1GW 
       10.16        16.64         4.11        10.92        51.42        11.08 
TCGA-EY-A72D TCGA-PG-A914 
        5.88        12.92 

$`4P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88       149.56        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       36.82        28.27        20.81        23.21        68.65        19.96 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 
        7.92        36.33         9.60         8.02        91.04        46.32 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M 
       28.64         5.33         5.16         7.33        14.96         1.18 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
       10.26         0.39        19.79        29.39         2.40        34.36 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       34.16         1.12         0.76        18.90         1.68         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC 
       14.66        22.49        22.26        17.06        20.81        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       20.65        21.21        15.62        10.19        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       14.76        16.87        16.87        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        2.70         0.13        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        63.91        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       23.87        12.20        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37         3.39        63.16        36.36        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        46.78        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       27.85        16.24        21.90        36.13         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       45.99        66.58        34.98        53.92        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        35.01        28.54        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        65.88        13.28        19.20        16.96 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       13.55        15.25        20.28        12.43        20.05        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR 
       72.56        54.12        67.50        25.12        36.39        11.08 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
        4.77        30.12        71.24        40.80        61.18        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       34.32        46.49        19.36        26.33        17.75        30.74 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
        2.96        31.13        64.93         0.23         0.20         0.56 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 
       43.82         0.20        20.52         1.38         0.30         0.26 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR 
        0.30         1.18        18.35        14.47         0.39        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       46.75        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        27.29        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E 
       13.74        17.10        17.85        11.01         4.11         8.71 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L 
      185.79       113.36        88.34        75.72        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       43.96        40.50        36.82        32.09        33.50        27.35 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
      191.84       102.31        50.89        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       11.87        15.29        12.79       116.25        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       62.14        33.11        14.27        29.65        41.06        34.13 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       34.98        38.37        36.49        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        52.64        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 
       13.78        14.73        14.01        15.45        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
        1.81         9.57        20.02        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B 
        6.81        35.90        34.98         6.21        10.22        31.76 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.99        24.13        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        67.20        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       62.79        63.58        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       36.79        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       10.65         0.69        18.67         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
        2.33        22.92         1.41        13.22         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.52        41.42         8.48        44.88         0.26         4.27 
TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
       16.93        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU 
       36.62        24.30        35.38         9.37        12.39        31.10 
TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
      110.10        23.38        48.36        17.06         2.37         6.67 
TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       27.32        16.04         7.36        16.80        49.15        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       19.40        34.39        26.43        35.15        17.19        27.16 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       17.88        26.96        22.26        16.34        14.53        24.89 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
        6.21        14.99         4.54        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       23.34        23.34        23.90        22.78        13.97         6.90 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT 
       19.27        18.84        17.88        17.62        15.09        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 
       12.43        15.81         6.48        19.33        12.59        10.19 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       14.40        18.87        22.82        20.05        45.76        31.04 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 
       29.10        27.35        13.84        11.38        17.92        14.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
       19.89        14.70        16.96        40.01        41.06        39.88 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       39.95         7.99        13.84         8.98        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV 
        9.07        28.93        28.96        25.02        29.23        41.06 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       45.01         1.74         7.76        14.04         2.43        23.74 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       13.28         9.47        26.10        18.21        23.24        15.45 
TCGA-PG-A7D5 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       23.97         7.00        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       12.92        23.64        14.83         4.44        14.07        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             4.11              0.07 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            97.71            191.84 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           13.675            23.470 
[1] "4.1 - 97.7 (13.7)"  "0.1 - 191.8 (23.5)"
[1] "hr=" "2.1"
D7V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  4P GAIN MUTATED                                         5
  4P GAIN WILD-TYPE                                     390
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  4P GAIN MUTATED                               0
  4P GAIN WILD-TYPE                            21
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  4P GAIN MUTATED                                   9
  4P GAIN WILD-TYPE                               103
D7V3, multiclass
                                         clus
vv                                        4P GAIN MUTATED 4P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               5               390
  MIXED SEROUS AND ENDOMETRIOID                         0                21
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     9               103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V4, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     4  10
  4P GAIN WILD-TYPE 137 377
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      4   10
  4P GAIN WILD-TYPE  137  377
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                4               137
  YES              10               377
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4P GAIN MUTATED    10   1   2   0
  4P GAIN WILD-TYPE 353  22  15  35
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0              10               353
  R1               1                22
  R2               2                15
  RX               0                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P GAIN MUTATED                                  0     2
  4P GAIN WILD-TYPE                                4    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  4P GAIN MUTATED                           6
  4P GAIN WILD-TYPE                        95
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4P GAIN MUTATED                                           0     5
  4P GAIN WILD-TYPE                                         9   361
D7V6, multiclass
                                           clus
vv                                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   2                18
  BLACK OR AFRICAN AMERICAN                               6                95
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 9
  WHITE                                                   5               361
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     1   8
  4P GAIN WILD-TYPE  13 359
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1    8
  4P GAIN WILD-TYPE   13  359
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                13
  NOT HISPANIC OR LATINO               8               359
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     7   1
  4Q GAIN WILD-TYPE 450  68
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                8               518 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                68 
$`4Q GAIN MUTATED`
TCGA-A5-A0G5 TCGA-AX-A3G3 TCGA-B5-A0K8 TCGA-BK-A139 TCGA-BK-A4ZD TCGA-EO-A1Y5 
       37.02         1.38        17.85        10.16        16.64        10.92 
TCGA-EO-A2CG TCGA-EY-A1GW 
       51.42        11.08 

$`4Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88       149.56        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       36.82        28.27        20.81        23.21        68.65        19.96 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 
        7.92        11.44        36.33         9.60         8.02        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       46.32        28.64         5.33         5.16         7.33        14.96 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM 
        1.18        14.43        10.26         0.39        19.79        29.39 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI 
        2.40        34.36        34.16         1.12         0.76        18.90 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
        1.68         1.64        14.66        22.49        22.26        17.06 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH 
       20.81        36.99        20.65        21.21        15.62        10.19 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV 
       15.35        15.95        14.76        16.87        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       12.82        20.78         2.70         0.13        83.67        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D 
        5.95        23.31        86.07         8.22        63.91        57.80 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 
       45.53        36.89        23.87        12.20        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
      125.42       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       60.36        55.89        31.30        35.54        46.78        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        30.90        10.42        27.85        16.24        21.90 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       36.13         0.56        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       53.92        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       35.01        28.54        37.78        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       13.28        19.20        16.96        13.55        15.25        20.28 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       12.43        20.05        76.83        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       25.12        36.39        11.08         4.77        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       40.80        61.18        81.37        34.32        46.49        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       26.33        17.75        30.74         2.96        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
        0.23         0.20         0.56        43.82         0.20        20.52 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.30         0.26         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
        0.39        80.38        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       25.91        27.29        17.88        13.74        17.10        11.01 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
        4.11         8.71       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q 
       54.44        45.90        43.96        40.50        36.82        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       33.50        27.35        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV 
       17.36        16.57       191.84       102.31        50.89        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       14.70        11.70        11.87        15.29        12.79       116.25 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 
       96.30        78.81        62.14        33.11        14.27        29.65 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       41.06        34.13        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98        22.06        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       15.45        15.45        14.27         1.81         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31         6.81        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F 
        6.21        10.22        31.76        24.99        24.13        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        23.47        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        67.20        88.34        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       72.72        73.25        59.51        62.79        63.58        49.55 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.16        66.48        16.83        19.79        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        4.44        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I 
       37.32        36.36        37.51        36.79        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02        14.73         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 
       13.22         0.72        18.25        16.87        18.02         2.07 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV 
       44.88         0.26         4.27         4.11        16.93        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX 
       35.38         9.37        12.39        31.10       110.10        23.38 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ 
       48.36        17.06         2.37         6.67        27.32        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
        7.36        16.80        49.15        37.71        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS 
       66.90        46.26        57.60        51.52        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 
       26.43        35.15        17.19        27.16        17.88        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       22.26        16.34        14.53        24.89         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.90        22.78        13.97         6.90        19.27        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       17.88        17.62        15.09        16.11        12.43        15.81 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 
        6.48        19.33        12.59        10.19        14.40        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 
       22.82        20.05        45.76        31.04        29.10        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       13.84        11.38        17.92        14.14        19.89        14.70 
TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
       16.96         5.88        40.01        41.06        39.88        39.95 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
        7.99        13.84         8.98        96.69        59.01         9.07 
TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
       28.93        28.96        25.02        29.23        41.06        45.01 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 
        1.74         7.76        14.04         2.43        23.74        13.28 
TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 
        9.47        26.10        18.21        23.24        15.45        23.97 
TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       12.92         7.00        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       12.92        23.64        14.83         4.44        14.07        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             1.38              0.07 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            51.42            191.84 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           13.860            23.425 
[1] "1.4 - 51.4 (13.9)"  "0.1 - 191.8 (23.4)"
[1] "hr=" "1.5"
D8V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  4Q GAIN MUTATED                                         3
  4Q GAIN WILD-TYPE                                     392
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  4Q GAIN MUTATED                               0
  4Q GAIN WILD-TYPE                            21
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  4Q GAIN MUTATED                                   5
  4Q GAIN WILD-TYPE                               107
D8V3, multiclass
                                         clus
vv                                        4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               3               392
  MIXED SEROUS AND ENDOMETRIOID                         0                21
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     5               107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V4, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1   7
  4Q GAIN WILD-TYPE 140 380
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1    7
  4Q GAIN WILD-TYPE  140  380
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                1               140
  YES               7               380
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4Q GAIN MUTATED     5   1   0   0
  4Q GAIN WILD-TYPE 358  22  17  35
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0               5               358
  R1               1                22
  R2               0                17
  RX               0                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q GAIN MUTATED                                  0     1
  4Q GAIN WILD-TYPE                                4    19
                   vv
clus                BLACK OR AFRICAN AMERICAN
  4Q GAIN MUTATED                           2
  4Q GAIN WILD-TYPE                        99
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4Q GAIN MUTATED                                           0     4
  4Q GAIN WILD-TYPE                                         9   362
D8V6, multiclass
                                           clus
vv                                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   1                19
  BLACK OR AFRICAN AMERICAN                               2                99
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 9
  WHITE                                                   4               362
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1   3
  4Q GAIN WILD-TYPE  13 364
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1    3
  4Q GAIN WILD-TYPE   13  364
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                13
  NOT HISPANIC OR LATINO               3               364
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    36  14
  5P GAIN WILD-TYPE 421  55
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               50               476 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               14                55 
$`5P GAIN MUTATED`
TCGA-A5-A0G5 TCGA-A5-A1OH TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A3IA 
       37.02        36.33        14.96        14.43         0.39        20.81 
TCGA-AJ-A3NH TCGA-AP-A0LH TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AX-A0IS TCGA-AX-A0IW 
       10.19        36.36        31.30        46.78        35.01        37.78 
TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2HK TCGA-AX-A3G3 TCGA-AX-A3GI TCGA-B5-A1MY 
        4.77        71.24         2.96         1.38         0.39        11.87 
TCGA-B5-A5OD TCGA-BG-A0M3 TCGA-BG-A0M6 TCGA-BG-A0VT TCGA-BG-A18C TCGA-BK-A139 
       34.13        35.21        22.06        24.39        15.45        10.16 
TCGA-BS-A0TE TCGA-BS-A0TI TCGA-D1-A16N TCGA-D1-A1NW TCGA-D1-A3DH TCGA-DI-A1NN 
        4.80        61.87        31.07         0.72         4.11        35.38 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
        9.37        12.39       110.10        48.36        10.92        37.71 
TCGA-EO-A3B1 TCGA-EY-A1GC TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A2ON TCGA-EY-A547 
       26.96         4.54        17.62        15.09        20.05        17.92 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-JU-AAVI 
       39.95        59.01         9.07        28.93        25.02         7.76 
TCGA-KP-A3VZ TCGA-PG-A915 
       23.74         7.00 

$`5P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88       149.56        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       36.82        28.27        20.81        23.21        68.65        19.96 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 
        7.92        11.44         9.60         8.02        91.04        46.32 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23O 
       28.64         5.33         5.16         7.33         1.18        10.26 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF 
       19.79        29.39         2.40        34.36        34.16         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76        18.90         1.68         1.64        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       22.26        17.06        36.99        20.65        21.21        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV 
       15.35        15.95        14.76        16.87        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       12.82        20.78         2.70         0.13        83.67        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D 
        5.95        23.31        86.07         8.22        63.91        57.80 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 
       45.53        36.89        23.87        12.20        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LI 
      125.42       117.99       110.37         3.39        63.16        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       31.73        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       55.89        35.54        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       27.85        16.24        21.90        36.13         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       45.99        66.58        34.98        53.92        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 
       27.39        30.02        60.66        28.54        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       65.88        13.28        19.20        16.96        13.55        15.25 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       20.28        12.43        20.05        76.83        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H7 
       67.50        25.12        36.39        11.08        30.12        40.80 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       61.18        81.37        34.32        46.49        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       17.75        30.74        31.13        64.93         0.23         0.20 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 
        0.56        43.82         0.20        20.52         0.30         0.26 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR 
        0.30         1.18        18.35        14.47        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       46.75        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        27.29        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E 
       13.74        17.10        17.85        11.01         4.11         8.71 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L 
      185.79       113.36        88.34        75.72        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       43.96        40.50        36.82        32.09        33.50        27.35 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
      191.84       102.31        50.89        14.40        14.70        11.70 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       15.29        12.79       116.25        96.30        78.81        62.14 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW 
       33.11        14.27        29.65        41.06        34.95        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.19        19.33        20.94        34.98        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       11.31         6.81        35.90        34.98         6.21        10.22 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
       31.76        24.99        24.13        16.64        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG 
        9.86        46.95        23.47        85.55        78.21        77.95 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        67.20        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       62.79        63.58        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q 
       36.79        27.42        11.51        29.92        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
        0.69        18.67         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
       22.92         1.41        13.22        18.25        16.87        18.02 
TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 
        2.07        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JP TCGA-DF-A2KV 
        8.48        44.88         0.26         4.27        16.93        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 
       31.10        23.38        17.06         2.37         6.67        27.32 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S 
       16.04         7.36        16.80        49.15        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH 
       66.90        46.26        57.60        51.52        51.42        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       34.39        26.43        35.15        17.19        27.16        17.88 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       22.26        16.34        14.53        24.89         6.21        14.99 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ 
       22.78        13.97         6.90        19.27        18.84        17.88 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        12.43        15.81        11.08         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO 
       12.59        10.19        14.40        18.87        22.82        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 
       31.04        29.10        27.35        13.84        11.38        14.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY 
       19.89        14.70        16.96         5.88        40.01        41.06 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2F4 
       39.88         7.99        13.84         8.98        96.69        28.96 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 
       29.23        41.06        45.01         1.74        14.04         2.43 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       13.28         9.47        26.10        18.21        23.24        15.45 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       23.97        12.92        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       12.92        23.64        14.83         4.44        14.07        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.39              0.07 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           110.10            191.84 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           20.430            23.425 
[1] "0.4 - 110.1 (20.4)" "0.1 - 191.8 (23.4)"
[1] "hr=" "3"  
D9V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  5P GAIN MUTATED                                        16
  5P GAIN WILD-TYPE                                     379
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  5P GAIN MUTATED                               3
  5P GAIN WILD-TYPE                            18
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  5P GAIN MUTATED                                  31
  5P GAIN WILD-TYPE                                81
D9V3, multiclass
                                         clus
vv                                        5P GAIN MUTATED 5P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              16               379
  MIXED SEROUS AND ENDOMETRIOID                         3                18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    31                81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V4, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     7  43
  5P GAIN WILD-TYPE 134 344
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      7   43
  5P GAIN WILD-TYPE  134  344
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                7               134
  YES              43               344
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5P GAIN MUTATED    35   2   5   4
  5P GAIN WILD-TYPE 328  21  12  31
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0              35               328
  R1               2                21
  R2               5                12
  RX               4                31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P GAIN MUTATED                                  1     1
  5P GAIN WILD-TYPE                                3    19
                   vv
clus                BLACK OR AFRICAN AMERICAN
  5P GAIN MUTATED                          15
  5P GAIN WILD-TYPE                        86
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5P GAIN MUTATED                                           0    30
  5P GAIN WILD-TYPE                                         9   336
D9V6, multiclass
                                           clus
vv                                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 3
  ASIAN                                                   1                19
  BLACK OR AFRICAN AMERICAN                              15                86
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 9
  WHITE                                                  30               336
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     2  36
  5P GAIN WILD-TYPE  12 331
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2   36
  5P GAIN WILD-TYPE   12  331
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                12
  NOT HISPANIC OR LATINO              36               331
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    15   4
  5Q GAIN WILD-TYPE 442  65
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               19               507 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                4                65 
$`5Q GAIN MUTATED`
TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AX-A0IS TCGA-AX-A3G3 TCGA-B5-A1MY TCGA-BG-A0VT 
       31.30        46.78        35.01         1.38        11.87        24.39 
TCGA-BG-A18C TCGA-BS-A0TE TCGA-D1-A16N TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       15.45         4.80        31.07        35.38        48.36        10.92 
TCGA-EO-A3B1 TCGA-EY-A1GC TCGA-EY-A1GR TCGA-EY-A1GS TCGA-FI-A2EW TCGA-FI-A2EY 
       26.96         4.54        17.62        15.09        59.01        28.93 
TCGA-JU-AAVI 
        7.76 

$`5Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       38.37        36.82        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       19.96        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK 
       15.95         7.92        11.44        36.33         9.60         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
       91.04        46.32        28.64         5.33         5.16         7.33 
TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       14.96         1.18        14.43        10.26         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG 
       29.39         2.40        34.36        34.16         1.12         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       18.90         1.68         1.64        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       17.06        20.81        36.99        20.65        21.21        15.62 
TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW 
       10.19        15.35        15.95        14.76        16.87        16.87 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       22.32        12.82        20.78         2.70         0.13        83.67 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
       21.99         5.95        23.31        86.07         8.22        63.91 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       57.80        45.53        36.89        23.87        12.20        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       33.40        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       71.67        60.36        55.89        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
       30.90        10.42        27.85        16.24        21.90        36.13 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IU 
       12.26        51.09        27.39        30.02        60.66        28.54 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       16.96        13.55        15.25        20.28        12.43        20.05 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       76.83        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       11.08         4.77        30.12        71.24        40.80        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       81.37        34.32        46.49        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       30.74         2.96        31.13        64.93         0.23         0.20 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 
        0.56        43.82         0.20        20.52         0.30         0.26 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN 
        0.30         1.18        18.35        14.47         0.39        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        46.75        43.13        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB 
       17.88        13.74        17.10        17.85        11.01         4.11 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
        8.71       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R 
       45.90        43.96        40.50        36.82        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW 
       16.57       191.84       102.31        50.89        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       11.70        15.29        12.79       116.25        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       62.14        33.11        14.27        29.65        41.06        34.13 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       34.98        22.06        38.37        36.49        28.27        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       30.81        21.17        20.28        15.42        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        52.64        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 
       13.78        14.73        14.01        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        9.57        20.02        23.70        20.12        11.31         6.81 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       35.90        34.98         6.21        10.22        10.16        31.76 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       24.99        24.13        16.64        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TI 
       46.95        23.47        85.55        78.21        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        67.20        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       62.79        63.58        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q 
       36.79        27.42        11.51        29.92        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
        0.69        18.67         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
       22.92         1.41        13.22         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       18.02         2.07        15.06         1.05         3.95         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
       41.42         8.48        44.88         0.26         4.27         4.11 
TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
       16.93        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY 
       36.62        24.30         9.37        12.39        31.10       110.10 
TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ 
       23.38        17.06         2.37         6.67        27.32        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
        7.36        16.80        49.15        37.71        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH 
       66.90        46.26        57.60        51.52        51.42        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       34.39        26.43        35.15        17.19        27.16        17.88 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       22.26        16.34        14.53        24.89         6.21        14.99 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ 
       22.78        13.97         6.90        19.27        18.84        17.88 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        12.43        15.81        11.08         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
       12.59        10.19        14.40        18.87        22.82        20.05 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       45.76        31.04        29.10        27.35        13.84        11.38 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D 
       17.92        14.14        19.89        14.70        16.96         5.88 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
       40.01        41.06        39.88        39.95         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 
        8.98        96.69         9.07        28.96        25.02        29.23 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       41.06        45.01         1.74        14.04         2.43        23.74 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       13.28         9.47        26.10        18.21        23.24        15.45 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       23.97        12.92         7.00        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       39.95        12.92        23.64        14.83         4.44        14.07 
TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       18.28         0.07         0.23 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             1.38              0.07 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            59.01            191.84 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            24.39             23.34 
[1] "1.4 - 59.0 (24.4)"  "0.1 - 191.8 (23.3)"
[1] "hr=" "2"  
D10V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  5Q GAIN MUTATED                                         8
  5Q GAIN WILD-TYPE                                     387
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  5Q GAIN MUTATED                               0
  5Q GAIN WILD-TYPE                            21
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  5Q GAIN MUTATED                                  11
  5Q GAIN WILD-TYPE                               101
D10V3, multiclass
                                         clus
vv                                        5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               8               387
  MIXED SEROUS AND ENDOMETRIOID                         0                21
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    11               101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V4, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     3  16
  5Q GAIN WILD-TYPE 138 371
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      3   16
  5Q GAIN WILD-TYPE  138  371
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                3               138
  YES              16               371
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5Q GAIN MUTATED    13   1   2   1
  5Q GAIN WILD-TYPE 350  22  15  34
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              13               350
  R1               1                22
  R2               2                15
  RX               1                34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q GAIN MUTATED                                  0     1
  5Q GAIN WILD-TYPE                                4    19
                   vv
clus                BLACK OR AFRICAN AMERICAN
  5Q GAIN MUTATED                           6
  5Q GAIN WILD-TYPE                        95
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5Q GAIN MUTATED                                           0    10
  5Q GAIN WILD-TYPE                                         9   356
D10V6, multiclass
                                           clus
vv                                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   1                19
  BLACK OR AFRICAN AMERICAN                               6                95
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 9
  WHITE                                                  10               356
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     0  13
  5Q GAIN WILD-TYPE  14 354
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0   13
  5Q GAIN WILD-TYPE   14  354
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                14
  NOT HISPANIC OR LATINO              13               354
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    64  14
  6P GAIN WILD-TYPE 393  55
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               78               448 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               14                55 
$`6P GAIN MUTATED`
TCGA-5B-A90C TCGA-A5-A1OG TCGA-A5-A1OH TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AJ-A3BF 
       36.69        11.44        36.33         1.18        34.16         1.12 
TCGA-AJ-A3BI TCGA-AJ-A3IA TCGA-AJ-A8CW TCGA-AP-A0L8 TCGA-AP-A0LI TCGA-AP-A0LO 
       18.90        20.81         0.13        48.79        97.71        33.40 
TCGA-AP-A1DQ TCGA-AP-A5FX TCGA-AX-A06J TCGA-AX-A0IW TCGA-AX-A1CA TCGA-AX-A1CC 
       46.78        36.13        30.02        37.78        20.28        12.43 
TCGA-AX-A1CF TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G3 
       76.83        40.80        81.37        43.82        20.52         1.38 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11I TCGA-B5-A11R 
        0.39        80.38         4.11         8.71        75.72        33.50 
TCGA-B5-A11S TCGA-B5-A1MU TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A0M8 
       27.35        50.89        12.79        29.65        34.13        36.49 
TCGA-BG-A18C TCGA-BK-A0C9 TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0U9 
       15.45        35.90        10.22        24.13        16.64        67.20 
TCGA-BS-A0V8 TCGA-D1-A168 TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A2G5 TCGA-D1-A3DH 
       49.55        36.10        31.07        18.67        41.42         4.11 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QY TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3B1 
       35.38         9.37       110.10        51.52        51.42        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GR 
       22.26        16.34         4.54        19.27        17.88        17.62 
TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A54A TCGA-FI-A2CX 
       14.40        20.05        27.35        13.84        14.70        40.01 
TCGA-FI-A2D0 TCGA-FI-A2EW TCGA-FI-A2EY TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-K6-A3WQ 
       39.88        59.01        28.93        29.23        45.01        14.04 
TCGA-KP-A3VZ TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-PG-A915 TCGA-QS-A8F1 TCGA-SL-A6J9 
       23.74        26.10        23.97         7.00         4.44         0.07 

$`6P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       36.82        28.27        20.81        23.21        68.65        19.96 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 
        7.92         9.60         8.02        91.04        46.32        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O 
        5.33         5.16         7.33        14.96        14.43        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG 
        0.39        19.79        29.39         2.40        34.36         0.76 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
        1.68         1.64        14.66        22.49        22.26        17.06 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ 
       36.99        20.65        21.21        15.62        10.19        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.95        14.76        16.87        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       20.78         2.70        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        63.91        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        12.20        20.91       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
        3.39        63.16        36.36        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR 
       71.67        60.36        55.89        31.30        35.54        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        30.90        10.42        27.85        16.24        21.90 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       12.26        51.09        27.39        60.66        35.01        28.54 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        65.88        13.28        19.20        16.96 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       13.55        15.25        20.05        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       25.12        36.39        11.08         4.77        30.12        71.24 
TCGA-AX-A2H8 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       61.18        34.32        46.49        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       30.74         2.96        31.13        64.93         0.23         0.20 
TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.56         0.20         0.30         0.26         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       18.35        14.47        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        27.29        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
       11.01       185.79       113.36        88.34        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11U TCGA-B5-A11V 
       43.96        40.50        36.82        32.09        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS 
       19.50        18.41        17.36        16.57       191.84       102.31 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 
       14.40        14.70        11.70        11.87        15.29       116.25 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC 
       96.30        78.81        62.14        33.11        14.27        41.06 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       34.98        22.06        38.37        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        52.64        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 
       13.78        14.73        14.01        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        9.57        20.02        23.70        20.12        11.31         6.81 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F 
       34.98         6.21        10.16        31.76        24.99        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        23.47        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       97.41        88.34        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ 
       73.25        59.51        62.79        63.58        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
       32.58         0.66        15.72        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q 
       36.79        27.42        11.51        29.92        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
        0.69         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02        14.73         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
        1.41        13.22         0.72        18.25        16.87        18.02 
TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 
        2.07        15.06         1.05         3.95         3.52         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY 
       44.88         0.26         4.27        16.93        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT 
       27.16        16.31        39.29        36.62        24.30        12.39 
TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       31.10        23.38        48.36        17.06         2.37         6.67 
TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       27.32        16.04         7.36        16.80        10.92        49.15 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       37.71        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       19.40        34.39        26.43        35.15        17.19        27.16 
TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD 
       17.88        14.53        24.89         6.21        14.99        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK 
       24.36        27.16        23.34        23.34        23.90        22.78 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       13.97         6.90        18.84        15.09        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 
       15.81        11.08         6.48        19.33        12.59        10.19 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A4KR 
       18.87        22.82        45.76        31.04        29.10        11.38 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CY 
       17.92        14.14        19.89        16.96         5.88        41.06 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EX 
       39.95         7.99        13.84         8.98        96.69         9.07 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KJ-A3U4 
       28.96        25.02        41.06         1.74         7.76         2.43 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 
       13.28         9.47        18.21        23.24        15.45        12.92 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       11.24         6.97        18.84        39.95        12.92        23.64 
TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       14.83        14.07        18.28         0.23 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.07              0.20 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           110.10            191.84 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           27.155            22.870 
[1] "0.1 - 110.1 (27.2)" "0.2 - 191.8 (22.9)"
[1] "hr=" "1.5"
D11V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  6P GAIN MUTATED                                        37
  6P GAIN WILD-TYPE                                     358
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  6P GAIN MUTATED                               1
  6P GAIN WILD-TYPE                            20
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  6P GAIN MUTATED                                  40
  6P GAIN WILD-TYPE                                72
D11V3, multiclass
                                         clus
vv                                        6P GAIN MUTATED 6P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              37               358
  MIXED SEROUS AND ENDOMETRIOID                         1                20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    40                72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V4, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    18  60
  6P GAIN WILD-TYPE 123 327
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     18   60
  6P GAIN WILD-TYPE  123  327
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               18               123
  YES              60               327
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6P GAIN MUTATED    46   2   3   9
  6P GAIN WILD-TYPE 317  21  14  26
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0              46               317
  R1               2                21
  R2               3                14
  RX               9                26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P GAIN MUTATED                                  0     2
  6P GAIN WILD-TYPE                                4    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  6P GAIN MUTATED                          25
  6P GAIN WILD-TYPE                        76
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6P GAIN MUTATED                                           2    46
  6P GAIN WILD-TYPE                                         7   320
D11V6, multiclass
                                           clus
vv                                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   2                18
  BLACK OR AFRICAN AMERICAN                              25                76
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               2                 7
  WHITE                                                  46               320
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     1  54
  6P GAIN WILD-TYPE  13 313
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      1   54
  6P GAIN WILD-TYPE   13  313
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                13
  NOT HISPANIC OR LATINO              54               313
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    51  11
  6Q GAIN WILD-TYPE 406  58
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               62               464 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               11                58 
$`6Q GAIN MUTATED`
TCGA-AJ-A23M TCGA-AJ-A3BI TCGA-AJ-A8CW TCGA-AP-A0L8 TCGA-AP-A0LI TCGA-AP-A0LO 
        1.18        18.90         0.13        48.79        97.71        33.40 
TCGA-AP-A1DQ TCGA-AP-A5FX TCGA-AX-A06J TCGA-AX-A0IW TCGA-AX-A1CC TCGA-AX-A2H7 
       46.78        36.13        30.02        37.78        12.43        40.80 
TCGA-AX-A2HA TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3GI TCGA-B5-A0JN 
       81.37         0.56        43.82        20.52         0.39        80.38 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11I TCGA-B5-A11R TCGA-B5-A1MU TCGA-B5-A1N2 
        4.11         8.71        75.72        33.50        50.89        12.79 
TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A0M8 TCGA-BG-A18C TCGA-BK-A0C9 TCGA-BK-A0CC 
       29.65        34.13        36.49        15.45        35.90        10.22 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A168 TCGA-D1-A16N 
       24.13        16.64        67.20        49.55        36.10        31.07 
TCGA-D1-A16S TCGA-D1-A2G5 TCGA-DI-A1NN TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A22Y 
       18.67        41.42        35.38       110.10        48.36        51.52 
TCGA-EO-A2CG TCGA-EO-A3KU TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GR 
       51.42        22.26         4.54        19.27        17.88        17.62 
TCGA-EY-A1GS TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A3L3 TCGA-EY-A54A TCGA-FI-A2CX 
       15.09        14.40        20.05        27.35        14.70        40.01 
TCGA-FI-A2D0 TCGA-FI-A2EW TCGA-FI-A2F8 TCGA-FI-A3PX TCGA-KP-A3VZ TCGA-PG-A915 
       39.88        59.01        25.02        45.01        23.74         7.00 
TCGA-QS-A8F1 TCGA-SL-A6J9 
        4.44         0.07 

$`6Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       38.37        36.82        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       19.96        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK 
       15.95         7.92        11.44        36.33         9.60         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
       91.04        46.32        28.64         5.33         5.16         7.33 
TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM 
       14.96        14.43        10.26         0.39        19.79        29.39 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK 
        2.40        34.36        34.16         1.12         0.76         1.68 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA 
        1.64        14.66        22.49        22.26        17.06        20.81 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ 
       36.99        20.65        21.21        15.62        10.19        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.95        14.76        16.87        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       20.78         2.70        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        63.91        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        12.20        20.91       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
        3.39        63.16        36.36        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR 
       71.67        60.36        55.89        31.30        35.54        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        30.90        10.42        27.85        16.24        21.90 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       12.26        51.09        27.39        60.66        35.01        28.54 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        65.88        13.28        19.20        16.96 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       13.55        15.25        20.28        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 
       54.12        67.50        25.12        36.39        11.08         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       30.12        71.24        61.18        34.32        46.49        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       26.33        17.75        30.74         2.96        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 
        0.23         0.20         0.20         1.38         0.30         0.26 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS 
        0.30         1.18        18.35        14.47        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        27.29        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.10        17.85        11.01       185.79       113.36        88.34 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q 
       54.44        45.90        43.96        40.50        36.82        32.09 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       16.57       191.84       102.31        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       11.87        15.29       116.25        96.30        78.81        62.14 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       33.11        14.27        41.06        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98        22.06        38.37 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        20.02        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 
       20.12        11.31         6.81        34.98         6.21        10.16 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       31.76        24.99        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        30.74        97.41        88.34        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        62.79 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        63.16        66.48        16.83        19.79        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I 
       37.32        36.36        37.51        36.79        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X 
       29.92        33.63        10.65         0.69         3.95         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
       17.49        19.53         6.64        30.15        18.02        14.73 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW 
       24.30         2.33        22.92         1.41        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
       18.25        16.87        18.02         2.07        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.95         3.52         8.48        44.88         0.26         4.27 
TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        4.11        16.93        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU 
       39.29        36.62        24.30         9.37        12.39        31.10 
TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ 
       23.38        17.06         2.37         6.67        27.32        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
        7.36        16.80        10.92        49.15        37.71        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CH TCGA-EO-A3AS 
       61.55        66.90        46.26        57.60        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 
       26.43        35.15        17.19        27.16        17.88        26.96 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD 
       16.34        14.53        24.89         6.21        14.99        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK 
       24.36        27.16        23.34        23.34        23.90        22.78 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       13.97         6.90        18.84        16.11        12.43        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A215 
       11.08         6.48        19.33        12.59        10.19        18.87 
TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A4KR 
       22.82        45.76        31.04        29.10        13.84        11.38 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CY 
       17.92        14.14        19.89        16.96         5.88        41.06 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EX 
       39.95         7.99        13.84         8.98        96.69         9.07 
TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI 
       28.93        28.96        29.23        41.06         1.74         7.76 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 
       14.04         2.43        13.28         9.47        26.10        18.21 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 
       23.24        15.45        23.97        12.92        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI 
       18.84        39.95        12.92        23.64        14.83        14.07 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.07              0.20 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           110.10            191.84 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           29.835            22.870 
[1] "0.1 - 110.1 (29.8)" "0.2 - 191.8 (22.9)"
[1] "hr=" "1.3"
D12V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  6Q GAIN MUTATED                                        32
  6Q GAIN WILD-TYPE                                     363
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  6Q GAIN MUTATED                               1
  6Q GAIN WILD-TYPE                            20
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  6Q GAIN MUTATED                                  29
  6Q GAIN WILD-TYPE                                83
D12V3, multiclass
                                         clus
vv                                        6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              32               363
  MIXED SEROUS AND ENDOMETRIOID                         1                20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    29                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V4, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    17  45
  6Q GAIN WILD-TYPE 124 342
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     17   45
  6Q GAIN WILD-TYPE  124  342
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               17               124
  YES              45               342
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6Q GAIN MUTATED    35   1   3   8
  6Q GAIN WILD-TYPE 328  22  14  27
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              35               328
  R1               1                22
  R2               3                14
  RX               8                27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q GAIN MUTATED                                  0     1
  6Q GAIN WILD-TYPE                                4    19
                   vv
clus                BLACK OR AFRICAN AMERICAN
  6Q GAIN MUTATED                          23
  6Q GAIN WILD-TYPE                        78
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6Q GAIN MUTATED                                           2    35
  6Q GAIN WILD-TYPE                                         7   331
D12V6, multiclass
                                           clus
vv                                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   1                19
  BLACK OR AFRICAN AMERICAN                              23                78
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               2                 7
  WHITE                                                  35               331
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     1  43
  6Q GAIN WILD-TYPE  13 324
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1   43
  6Q GAIN WILD-TYPE   13  324
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                13
  NOT HISPANIC OR LATINO              43               324
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    51  13
  7P GAIN WILD-TYPE 406  56
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               64               462 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               13                56 
$`7P GAIN MUTATED`
TCGA-2E-A9G8 TCGA-A5-A0GV TCGA-A5-A3LO TCGA-AJ-A2QN TCGA-AJ-A3BF TCGA-AJ-A3BI 
       41.06        20.81         7.33         2.40         1.12        18.90 
TCGA-AJ-A3EJ TCGA-AJ-A3IA TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AP-A0L9 
        1.64        20.81        15.62        10.19        57.80       125.42 
TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A3K1 TCGA-AX-A05W TCGA-AX-A3FZ TCGA-AX-A3G1 
       97.71        33.40        21.90        68.35         0.20        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G6 TCGA-B5-A0JR TCGA-B5-A0JT TCGA-B5-A0K0 TCGA-B5-A0K4 
        1.38         0.26        56.91        43.13        28.34        17.88 
TCGA-B5-A1MV TCGA-B5-A1MY TCGA-BG-A0M3 TCGA-BG-A0MS TCGA-BG-A0RY TCGA-BG-A0VT 
       14.40        11.87        35.21        30.81        15.42        24.39 
TCGA-BG-A0YV TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD 
       12.56        23.70        35.90        10.16        24.13        16.64 
TCGA-BS-A0TE TCGA-BS-A0TI TCGA-BS-A0UT TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A17C 
        4.80        61.87        72.72        49.55        22.55         0.99 
TCGA-D1-A17R TCGA-D1-A1NY TCGA-D1-A2G6 TCGA-D1-A3JP TCGA-EO-A1Y5 TCGA-EO-A22Y 
       11.15        16.87         8.48        16.93        10.92        51.52 
TCGA-EY-A1G7 TCGA-EY-A1GH TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GW TCGA-EY-A1GX 
        6.21        23.34        13.97        19.27        11.08         6.48 
TCGA-EY-A2ON TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A72D TCGA-FI-A2D2 TCGA-FI-A2EU 
       20.05        19.89        14.70         5.88        39.95        96.69 
TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-PG-A914 
       45.01        14.04         9.47        12.92 

$`7P GAIN WILD-TYPE`
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       36.69        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       36.82        28.27        23.21        68.65        19.96        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       19.59        24.62        29.06        42.35        15.95         7.92 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 
       11.44        36.33         9.60         8.02        91.04        46.32 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N 
       28.64         5.33         5.16        14.96         1.18        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QO TCGA-AJ-A3BD 
       10.26         0.39        19.79        29.39        34.36        34.16 
TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
        0.76         1.68        14.66        22.49        22.26        17.06 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       36.99        20.65        21.21        15.35        15.95        14.76 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
       16.87        16.87        22.32        12.82        20.78         2.70 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        0.13        83.67        21.99         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
        8.22        63.91        45.53        36.89        23.87        12.20 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       20.91        48.79       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP 
       36.36        31.73        83.97        27.12        82.52        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       55.89        31.30        35.54        46.78        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO 
       30.90        10.42        27.85        16.24        36.13         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       13.58        19.82        29.69        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       45.99        66.58        34.98        53.92        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        35.01        28.54        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        65.88        13.28        19.20        16.96 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       13.55        15.25        20.28        12.43        20.05        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR 
       72.56        54.12        67.50        25.12        36.39        11.08 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
        4.77        30.12        71.24        40.80        61.18        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       34.32        46.49        19.36        26.33        17.75        30.74 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
        2.96        31.13        64.93         0.23         0.20         0.56 
TCGA-AX-A3FX TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
       43.82         0.30         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
        0.39        80.38        46.75        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 
       32.55        28.64        30.51        25.91        27.29        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F 
       17.10        17.85        11.01         4.11         8.71       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       40.50        36.82        32.09        33.50        27.35        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       191.84 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 
      102.31        50.89        14.70        11.70        15.29        12.79 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH 
      116.25        96.30        78.81        62.14        33.11        14.27 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       29.65        41.06        34.13        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       19.33        20.94        34.98        22.06        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VV TCGA-BG-A0VW 
       43.04        39.32        21.17        20.28        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 
       14.73        14.01        15.45        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0CA 
        9.57        20.02        20.12        11.31         6.81        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 
        6.21        10.22        31.76        24.99        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG 
        9.86        46.95        23.47        85.55        78.21        77.95 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        67.20        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       85.84        82.39        81.57        73.25        59.51        62.79 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        63.16        66.48        16.83        19.79        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 
        8.55         0.56         4.87        28.67        23.93         1.74 
TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        4.44        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I 
       37.32        36.36        37.51        36.79        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17D TCGA-D1-A17F 
       18.02        14.73         1.58         7.00        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW 
       24.30         2.33        22.92         1.41        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       18.25        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
        3.52        41.42        44.88         0.26         4.27         4.11 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY 
       24.30        35.38         9.37        12.39        31.10       110.10 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 
       23.38        48.36        17.06         2.37         6.67        27.32 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
       16.04         7.36        16.80        49.15        37.71        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A2CH 
       61.55        66.90        46.26        57.60        51.42        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       34.39        26.43        35.15        17.19        27.16        17.88 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 
       26.96        22.26        16.34        14.53        24.89        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GI TCGA-EY-A1GJ 
        4.54        53.88        24.36        27.16        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS 
       22.78         6.90        18.84        17.88        17.62        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 
       16.11        12.43        15.81        19.33        12.59        10.19 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       14.40        18.87        22.82        45.76        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A5W2 
       27.35        13.84        11.38        17.92        14.14        16.96 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       40.01        41.06        39.88         7.99        13.84         8.98 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 
       59.01         9.07        28.93        28.96        25.02        29.23 
TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 
       41.06         1.74         7.76         2.43        23.74        13.28 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A915 
       26.10        18.21        23.24        15.45        23.97         7.00 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       11.24         6.97        18.84        39.95        12.92        23.64 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83         4.44        14.07        18.28         0.07         0.23 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.20              0.07 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           125.42            191.84 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           18.390            24.135 
[1] "0.2 - 125.4 (18.4)" "0.1 - 191.8 (24.1)"
[1] "hr=" "2.1"
D13V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  7P GAIN MUTATED                                        41
  7P GAIN WILD-TYPE                                     354
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  7P GAIN MUTATED                               4
  7P GAIN WILD-TYPE                            17
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  7P GAIN MUTATED                                  20
  7P GAIN WILD-TYPE                                92
D13V3, multiclass
                                         clus
vv                                        7P GAIN MUTATED 7P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              41               354
  MIXED SEROUS AND ENDOMETRIOID                         4                17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    20                92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V4, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    13  52
  7P GAIN WILD-TYPE 128 335
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     13   52
  7P GAIN WILD-TYPE  128  335
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               13               128
  YES              52               335
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7P GAIN MUTATED    45   2   3   2
  7P GAIN WILD-TYPE 318  21  14  33
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0              45               318
  R1               2                21
  R2               3                14
  RX               2                33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P GAIN MUTATED                                  0     2
  7P GAIN WILD-TYPE                                4    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  7P GAIN MUTATED                           9
  7P GAIN WILD-TYPE                        92
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7P GAIN MUTATED                                           1    49
  7P GAIN WILD-TYPE                                         8   317
D13V6, multiclass
                                           clus
vv                                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   2                18
  BLACK OR AFRICAN AMERICAN                               9                92
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 8
  WHITE                                                  49               317
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     1  50
  7P GAIN WILD-TYPE  13 317
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      1   50
  7P GAIN WILD-TYPE   13  317
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                13
  NOT HISPANIC OR LATINO              50               317
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    47  16
  7Q GAIN WILD-TYPE 410  53
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               63               463 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               16                53 
$`7Q GAIN MUTATED`
TCGA-2E-A9G8 TCGA-A5-A0GV TCGA-A5-A3LP TCGA-AJ-A2QN TCGA-AJ-A3BI TCGA-AJ-A3EJ 
       41.06        20.81        14.96         2.40        18.90         1.64 
TCGA-AJ-A3IA TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI 
       20.81        15.62        10.19        48.79       125.42        97.71 
TCGA-AP-A0LO TCGA-AP-A3K1 TCGA-AX-A05W TCGA-AX-A2HJ TCGA-AX-A3FZ TCGA-AX-A3G1 
       33.40        21.90        68.35        30.74         0.20        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JT TCGA-B5-A0K0 
        1.38         0.26         0.39        56.91        43.13        28.34 
TCGA-B5-A0K4 TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MY TCGA-BG-A0M3 TCGA-BG-A0MS 
       17.88        50.89        14.40        11.87        35.21        30.81 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A4ZD TCGA-BS-A0TE 
       15.42        24.39        23.70        35.90        16.64         4.80 
TCGA-BS-A0TI TCGA-BS-A0UT TCGA-D1-A0ZN TCGA-D1-A0ZZ TCGA-D1-A17C TCGA-D1-A17R 
       61.87        72.72        16.83        22.55         0.99        11.15 
TCGA-D1-A1NY TCGA-D1-A2G6 TCGA-D1-A3JP TCGA-EC-A1NJ TCGA-EO-A22Y TCGA-EY-A1G7 
       16.87         8.48        16.93        16.04        51.52         6.21 
TCGA-EY-A1GH TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A549 
       23.34        13.97        19.27        11.08         6.48        19.89 
TCGA-EY-A54A TCGA-EY-A72D TCGA-FI-A2D2 TCGA-FI-A2EY TCGA-JU-AAVI TCGA-K6-A3WQ 
       14.70         5.88        39.95        28.93         7.76        14.04 
TCGA-KP-A3VZ TCGA-KP-A3W1 TCGA-QS-A8F1 
       23.74         9.47         4.44 

$`7Q GAIN WILD-TYPE`
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       36.69        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       36.82        28.27        23.21        68.65        19.96        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       19.59        24.62        29.06        42.35        15.95         7.92 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 
       11.44        36.33         9.60         8.02        91.04        46.32 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N 
       28.64         5.33         5.16         7.33         1.18        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QO TCGA-AJ-A3BD 
       10.26         0.39        19.79        29.39        34.36        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
        1.12         0.76         1.68        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       17.06        36.99        20.65        21.21        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       14.76        16.87        16.87        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        2.70         0.13        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        63.91        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       23.87        12.20        20.91       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       63.16        36.36        31.73        83.97        27.12        82.52 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       60.36        55.89        31.30        35.54        46.78        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX 
        6.71        30.90        10.42        27.85        16.24        36.13 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z 
        0.56        13.58        19.82        29.69        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D 
       35.34        45.99        66.58        34.98        53.92        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       51.09        27.39        30.02        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       16.96        13.55        15.25        20.28        12.43        20.05 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       76.83        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       11.08         4.77        30.12        71.24        40.80        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       81.37        34.32        46.49        19.36        26.33        17.75 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
        2.96        31.13        64.93         0.23         0.20         0.56 
TCGA-AX-A3FX TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
       43.82         0.30         0.30         1.18        18.35        14.47 
TCGA-B5-A0JN TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       80.38        46.75        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 
       28.64        30.51        25.91        27.29        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.85        11.01         4.11         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       36.82        32.09        33.50        27.35        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS 
       19.50        18.41        17.36        16.57       191.84       102.31 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       14.70        11.70        15.29        12.79       116.25        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       78.81        62.14        33.11        14.27        29.65        41.06 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       34.13        34.95        18.61        20.19        19.33        20.94 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       34.98        22.06        38.37        36.49        28.27        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        39.32 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       21.17        20.28        26.66        16.34        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.01        15.45        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A0CB 
       20.02        20.12        11.31         6.81        34.98         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F 
       10.22        10.16        31.76        24.99        24.13        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        23.47        85.55        78.21 
TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       77.95        67.99        96.49        30.74        97.41        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV TCGA-BS-A0V4 
       88.34        85.84        82.39        81.57        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZO 
       62.79        63.58        49.55        63.16        66.48        19.79 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       36.10        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       18.67         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17D 
       30.15        18.02        14.73         1.58         7.00        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
        1.78        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
        0.72        18.25        18.02         2.07        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.95         3.52        41.42        44.88         0.26         4.27 
TCGA-D1-A3DH TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
        4.11        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU 
       36.62        24.30        35.38         9.37        12.39        31.10 
TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
      110.10        23.38        48.36        17.06         2.37         6.67 
TCGA-E6-A8L9 TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       27.32         7.36        16.80        10.92        49.15        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG 
       61.74        61.55        66.90        46.26        57.60        51.42 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       19.40        34.39        26.43        35.15        17.19        27.16 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       17.88        26.96        22.26        16.34        14.53        24.89 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GI 
       14.99         4.54        53.88        24.36        27.16        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR 
       23.90        22.78         6.90        18.84        17.88        17.62 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1H0 TCGA-EY-A210 
       15.09        16.11        12.43        15.81        19.33        12.59 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       10.19        14.40        18.87        22.82        20.05        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 
       31.04        29.10        27.35        13.84        11.38        17.92 
TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
       14.14        16.96        40.01        41.06        39.88         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 
       13.84         8.98        96.69        59.01         9.07        28.96 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-KJ-A3U4 
       25.02        29.23        41.06        45.01         1.74         2.43 
TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 
       13.28        26.10        18.21        23.24        15.45        23.97 
TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       12.92         7.00        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       12.92        23.64        14.83        14.07        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.20              0.07 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           125.42            191.84 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            17.88             24.13 
[1] "0.2 - 125.4 (17.9)" "0.1 - 191.8 (24.1)"
[1] "hr=" "2.8"
D14V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  7Q GAIN MUTATED                                        41
  7Q GAIN WILD-TYPE                                     354
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  7Q GAIN MUTATED                               4
  7Q GAIN WILD-TYPE                            17
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  7Q GAIN MUTATED                                  19
  7Q GAIN WILD-TYPE                                93
D14V3, multiclass
                                         clus
vv                                        7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              41               354
  MIXED SEROUS AND ENDOMETRIOID                         4                17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    19                93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V4, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    12  52
  7Q GAIN WILD-TYPE 129 335
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     12   52
  7Q GAIN WILD-TYPE  129  335
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               12               129
  YES              52               335
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7Q GAIN MUTATED    43   1   2   2
  7Q GAIN WILD-TYPE 320  22  15  33
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0              43               320
  R1               1                22
  R2               2                15
  RX               2                33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q GAIN MUTATED                                  0     3
  7Q GAIN WILD-TYPE                                4    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  7Q GAIN MUTATED                          11
  7Q GAIN WILD-TYPE                        90
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7Q GAIN MUTATED                                           0    48
  7Q GAIN WILD-TYPE                                         9   318
D14V6, multiclass
                                           clus
vv                                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   3                17
  BLACK OR AFRICAN AMERICAN                              11                90
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 9
  WHITE                                                  48               318
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     1  49
  7Q GAIN WILD-TYPE  13 318
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      1   49
  7Q GAIN WILD-TYPE   13  318
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                13
  NOT HISPANIC OR LATINO              49               318
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    95  21
  8P GAIN WILD-TYPE 362  48
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              116               410 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               21                48 
$`8P GAIN MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0GE TCGA-A5-A0GW TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OJ 
       37.02       105.37        23.21        17.59        11.44         9.60 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A3BD 
        7.33        14.96         0.39        19.79         2.40        34.16 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NE TCGA-AJ-A3NG 
        1.68         1.64        22.26        20.81        20.65        15.62 
TCGA-AJ-A3NH TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A8CW TCGA-AP-A0L9 TCGA-AP-A0LD 
       10.19        14.76        16.87         0.13       125.42       117.99 
TCGA-AP-A0LO TCGA-AP-A1DO TCGA-AP-A1E0 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A1CA 
       33.40        31.30        30.90        21.90        36.13        20.28 
TCGA-AX-A1CI TCGA-AX-A1CK TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
       72.56        67.50         4.77        40.80        81.37        34.32 
TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G6 TCGA-B5-A0JT TCGA-B5-A0K4 
        0.20         0.20        20.52         0.26        43.13        17.88 
TCGA-B5-A11E TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11V TCGA-B5-A1MR 
        8.71        32.09        33.50        27.35        19.56       191.84 
TCGA-B5-A1MW TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OE TCGA-BG-A0M0 TCGA-BG-A0M2 
       14.70       116.25        33.11        34.95        19.33        20.94 
TCGA-BG-A0M4 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MQ TCGA-BG-A18C TCGA-BG-A221 
       34.98        28.27        10.72        39.32        15.45         1.81 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A4ZD TCGA-BS-A0T9 
       23.70        35.90         6.21        10.22        16.64        46.95 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0U9 TCGA-BS-A0UV TCGA-BS-A0VI TCGA-D1-A0ZU 
        4.80        77.95        67.20        73.25        63.16        28.67 
TCGA-D1-A102 TCGA-D1-A15V TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16I 
        4.44        39.48         0.66        36.10        37.32        11.51 
TCGA-D1-A16N TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A17R TCGA-D1-A1O0 TCGA-D1-A2G0 
       31.07         0.69        18.67        11.15         2.07         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-DI-A1C3 TCGA-DI-A2QU TCGA-E6-A1M0 TCGA-E6-A8L9 
       41.42         8.48        24.30        31.10        17.06        27.32 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22T TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AZ 
       10.92        37.71        66.90        51.52        19.40        27.16 
TCGA-EO-A3B0 TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GM TCGA-EY-A1GO 
       17.88        24.89        14.99         4.54         6.90        19.27 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2ON 
       17.88        17.62         6.48        19.33        22.82        20.05 
TCGA-EY-A2OQ TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2D4 TCGA-FI-A2F9 TCGA-K6-A3WQ 
       29.10        19.89         5.88         7.99        29.23        14.04 
TCGA-KP-A3W0 TCGA-QS-A744 
       13.28        14.83 

$`8P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88       149.56        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       17.85        32.78       112.54        87.32        74.10        57.53 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       65.75        60.53        60.53        46.55        38.37        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 
       28.27        20.81        68.65        19.96        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OK 
       29.06        42.35        15.95         7.92        36.33         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23M 
       91.04        46.32        28.64         5.33         5.16         1.18 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QM TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG 
       14.43        10.26        29.39        34.36         1.12         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NF 
       18.90        14.66        22.49        17.06        36.99        21.21 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.35        15.95        16.87        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        2.70        83.67        21.99         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        63.91        57.80        45.53        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       12.20        20.91        48.79       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        83.97        27.12        82.52 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       60.36        55.89        35.54        46.78        49.15         6.71 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       10.42        27.85        16.24         0.56        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       66.58        34.98        53.92        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        35.01        28.54        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        65.88        13.28        19.20        16.96        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CJ TCGA-AX-A1CN 
       15.25        12.43        20.05        76.83        54.12        25.12 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HD 
       36.39        11.08        30.12        71.24        61.18        46.49 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       19.36        26.33        17.75        30.74         2.96        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G3 TCGA-AX-A3G4 
       64.93         0.23         0.56        43.82         1.38         0.30 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN 
        0.30         1.18        18.35        14.47         0.39        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       56.91        46.75        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 
       28.64        28.34        30.51        25.91        27.29        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11F TCGA-B5-A11G 
       17.10        17.85        11.01         4.11       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       36.82        16.73        19.50        18.41        17.36        16.57 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
      102.31        50.89        14.40        11.70        11.87        15.29 
TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 
       12.79        96.30        78.81        62.14        14.27        29.65 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M3 TCGA-BG-A0M6 
       41.06        34.13        18.61        20.19        35.21        22.06 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       38.37        36.49        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       43.04        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A220 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
       14.27         9.57        20.02        20.12        11.31         6.81 
TCGA-BK-A0CA TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F 
       34.98        10.16        31.76        24.99        24.13        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TI 
       10.03         9.86        23.47        85.55        78.21        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        30.74        97.41        88.34        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       82.39        81.57        72.72        59.51        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       49.55        66.48        16.83        19.79        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 
        0.56         4.87        23.93        22.55         1.74        21.99 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A167 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J 
       15.72        36.36        37.51        36.79        27.42        29.92 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       33.63        10.65         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
       10.22         1.51         1.78        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
        1.41        13.22         0.72        18.25        16.87        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
       15.06         1.05         3.95        44.88         0.26         4.27 
TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        4.11        16.93        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY 
       39.29        36.62        35.38         9.37        12.39       110.10 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       23.38        48.36         2.37         6.67        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22U TCGA-EO-A22X 
       16.80        49.15        61.74        61.55        46.26        57.60 
TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B1 
       51.42        34.39        26.43        35.15        17.19        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EY-A1G7 TCGA-EY-A1GD TCGA-EY-A1GE 
       22.26        16.34        14.53         6.21        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL 
       27.16        23.34        23.34        23.90        22.78        13.97 
TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       18.84        15.09        16.11        12.43        15.81        11.08 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OO TCGA-EY-A2OP 
       12.59        10.19        14.40        18.87        45.76        31.04 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A54A 
       27.35        13.84        11.38        17.92        14.14        14.70 
TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D5 
       16.96        40.01        41.06        39.88        39.95        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 
        8.98        96.69        59.01         9.07        28.93        28.96 
TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KJ-A3U4 
       25.02        41.06        45.01         1.74         7.76         2.43 
TCGA-KP-A3VZ TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       23.74         9.47        26.10        18.21        23.24        15.45 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       23.97        12.92         7.00        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       39.95        12.92        23.64         4.44        14.07        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.13              0.07 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           191.84            185.79 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            19.97             24.05 
[1] "0.1 - 191.8 (20.0)" "0.1 - 185.8 (24.0)"
[1] "hr=" "1.7"
D15V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  8P GAIN MUTATED                                        87
  8P GAIN WILD-TYPE                                     308
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  8P GAIN MUTATED                               6
  8P GAIN WILD-TYPE                            15
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  8P GAIN MUTATED                                  24
  8P GAIN WILD-TYPE                                88
D15V3, multiclass
                                         clus
vv                                        8P GAIN MUTATED 8P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              87               308
  MIXED SEROUS AND ENDOMETRIOID                         6                15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    24                88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V4, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    24  93
  8P GAIN WILD-TYPE 117 294
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     24   93
  8P GAIN WILD-TYPE  117  294
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               24               117
  YES              93               294
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8P GAIN MUTATED    82   1   5   8
  8P GAIN WILD-TYPE 281  22  12  27
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0              82               281
  R1               1                22
  R2               5                12
  RX               8                27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0     7
  8P GAIN WILD-TYPE                                4    13
                   vv
clus                BLACK OR AFRICAN AMERICAN
  8P GAIN MUTATED                          22
  8P GAIN WILD-TYPE                        79
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8P GAIN MUTATED                                           3    79
  8P GAIN WILD-TYPE                                         6   287
D15V6, multiclass
                                           clus
vv                                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   7                13
  BLACK OR AFRICAN AMERICAN                              22                79
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               3                 6
  WHITE                                                  79               287
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     2  87
  8P GAIN WILD-TYPE  12 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      2   87
  8P GAIN WILD-TYPE   12  280
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                12
  NOT HISPANIC OR LATINO              87               280
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   124  31
  8Q GAIN WILD-TYPE 333  38
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              155               371 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               31                38 
$`8Q GAIN MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A0GE TCGA-A5-A0GJ TCGA-A5-A0GW 
       41.06        36.69        37.02       105.37        65.75        23.21 
TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K4 TCGA-A5-A3LO 
       17.59        11.44        36.33         9.60        28.64         7.33 
TCGA-A5-A3LP TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A3BD TCGA-AJ-A3BI 
       14.96         0.39        19.79         2.40        34.16        18.90 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NE 
        1.68         1.64        22.26        17.06        20.81        20.65 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A8CW TCGA-AP-A05A 
       15.62        10.19        14.76        16.87         0.13        63.91 
TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LF TCGA-AP-A0LO 
       45.53        48.79       125.42       117.99         3.39        33.40 
TCGA-AP-A1DO TCGA-AP-A1E0 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A0IW 
       31.30        30.90        21.90        36.13         0.56        37.78 
TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CI TCGA-AX-A1CK TCGA-AX-A2H2 
       13.55        20.28        12.43        72.56        67.50         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A3FT TCGA-AX-A3FZ 
       30.12        40.80        81.37        34.32         0.20         0.20 
TCGA-AX-A3G1 TCGA-B5-A0JT TCGA-B5-A0K4 TCGA-B5-A11E TCGA-B5-A11H TCGA-B5-A11Q 
       20.52        43.13        17.88         8.71        88.34        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11V TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MW 
       33.50        27.35        19.56       191.84       102.31        14.70 
TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M0 TCGA-BG-A0M2 
      116.25        33.11        34.13        34.95        19.33        20.94 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MT 
       34.98        22.06        36.49        28.27        10.72        21.17 
TCGA-BG-A18C TCGA-BG-A221 TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CB TCGA-BK-A0CC 
       15.45         1.81        23.70        35.90         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0T9 TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0U9 
       10.16        16.64        46.95         4.80        77.95        67.20 
TCGA-BS-A0UV TCGA-BS-A0VI TCGA-D1-A0ZP TCGA-D1-A0ZU TCGA-D1-A0ZZ TCGA-D1-A102 
       73.25        63.16        29.95        28.67        22.55         4.44 
TCGA-D1-A15V TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16N 
       39.48         0.66        36.10        37.32        11.51        31.07 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A17R TCGA-D1-A1NU TCGA-D1-A1O0 TCGA-D1-A2G0 
        0.69        18.67        11.15        13.22         2.07         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DI-A1C3 TCGA-DI-A2QU 
       41.42         8.48        44.88         4.11        24.30        31.10 
TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y7 
      110.10        48.36        17.06        27.32        10.92        49.15 
TCGA-EO-A1Y8 TCGA-EO-A22T TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AZ TCGA-EO-A3B0 
       37.71        66.90        51.52        19.40        27.16        17.88 
TCGA-EO-A3B1 TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GM TCGA-EY-A1GO 
       26.96        24.89        14.99         4.54         6.90        19.27 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM 
       17.88        17.62        15.81         6.48        19.33        22.82 
TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2D4 
       20.05        29.10        17.92        19.89         5.88         7.99 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 
       29.23        41.06         7.76        14.04        13.28         9.47 
TCGA-KP-A3W4 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A744 TCGA-SL-A6J9 
       18.21        12.92         7.00        14.83         0.07 

$`8Q GAIN WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
       10.29       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GN 
      112.54        87.32        74.10        57.53        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GX 
       46.55        38.37        36.82        28.27        20.81        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       19.96        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 
        7.92         8.02        91.04        46.32         5.33         5.16 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QM TCGA-AJ-A2QO TCGA-AJ-A3BF 
        1.18        14.43        10.26        29.39        34.36         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3NC TCGA-AJ-A3NF TCGA-AJ-A3OJ 
        0.76        14.66        22.49        36.99        21.21        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
       15.95        16.87        22.32        12.82        20.78         2.70 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       83.67        21.99         5.95        23.31        86.07         8.22 
TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LE 
       57.80        36.89        23.87        12.20        20.91       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       71.67        60.36        55.89        35.54        46.78        49.15 
TCGA-AP-A1DV TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AX-A05S TCGA-AX-A05T 
        6.71        10.42        27.85        16.24        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       66.58        34.98        53.92        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        35.01        28.54        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C9 TCGA-AX-A1CE 
       65.88        13.28        19.20        16.96        15.25        20.05 
TCGA-AX-A1CF TCGA-AX-A1CJ TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H5 
       76.83        54.12        25.12        36.39        11.08        71.24 
TCGA-AX-A2H8 TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       61.18        46.49        19.36        26.33        17.75        30.74 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FW TCGA-AX-A3FX 
        2.96        31.13        64.93         0.23         0.56        43.82 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        1.38         0.30         0.26         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU 
       14.47         0.39        80.38        56.91        46.75        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       25.91        27.29        13.74        17.10        17.85        11.01 
TCGA-B5-A0KB TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L 
        4.11       185.79       113.36        75.72        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y 
       43.96        40.50        36.82        16.73        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MX TCGA-B5-A1MY 
       17.36        16.57        50.89        14.40        11.70        11.87 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH 
       15.29        12.79        96.30        78.81        62.14        14.27 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M3 TCGA-BG-A0M7 
       29.65        41.06        18.61        20.19        35.21        38.37 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       30.81        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        52.64        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A222 
       13.78        14.73        14.01        15.45        14.27         9.57 
TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A13B 
       20.02        20.12        11.31         6.81        34.98        31.76 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0TA 
       24.99        24.13        13.18        10.03         9.86        23.47 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
       85.55        78.21        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       97.41        88.34        85.84        82.39        81.57        72.72 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       59.51        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZV TCGA-D1-A101 
       19.79         8.55         0.56         4.87        23.93         1.74 
TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       21.99        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       32.58        15.72        36.36        37.51        36.79        27.42 
TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       29.92        33.63        10.65         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T 
       26.37        10.22         1.51         1.78        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
       22.92         1.41         0.72        18.25        16.87        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JP 
       15.06         1.05         3.95         0.26         4.27        16.93 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A2P8 TCGA-E6-A2P9 
       35.38         9.37        12.39        23.38         2.37         6.67 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22U 
       16.04         7.36        16.80        61.74        61.55        46.26 
TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       57.60        51.42        34.39        26.43        35.15        17.19 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EY-A1G7 TCGA-EY-A1GD TCGA-EY-A1GE 
       22.26        16.34        14.53         6.21        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL 
       27.16        23.34        23.34        23.90        22.78        13.97 
TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A210 
       18.84        15.09        16.11        12.43        11.08        12.59 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 
       10.19        14.40        18.87        45.76        31.04        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX 
       13.84        11.38        14.14        14.70        16.96        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       41.06        39.88        39.95        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PX 
       59.01         9.07        28.93        28.96        25.02        45.01 
TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W3 TCGA-PG-A5BC TCGA-PG-A6IB 
        1.74         2.43        23.74        26.10        23.24        15.45 
TCGA-PG-A7D5 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       23.97        11.24         6.97        18.84        39.95        12.92 
TCGA-QS-A5YR TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       23.64         4.44        14.07        18.28         0.23 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.07              0.23 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           191.84            185.79 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            20.65             23.97 
[1] "0.1 - 191.8 (20.6)" "0.2 - 185.8 (24.0)"
[1] "hr=" "2.1"
D16V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  8Q GAIN MUTATED                                       102
  8Q GAIN WILD-TYPE                                     293
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  8Q GAIN MUTATED                               8
  8Q GAIN WILD-TYPE                            13
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  8Q GAIN MUTATED                                  47
  8Q GAIN WILD-TYPE                                65
D16V3, multiclass
                                         clus
vv                                        8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             102               293
  MIXED SEROUS AND ENDOMETRIOID                         8                13
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    47                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V4, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    32 125
  8Q GAIN WILD-TYPE 109 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     32  125
  8Q GAIN WILD-TYPE  109  262
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               32               109
  YES             125               262
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8Q GAIN MUTATED   112   3   7  12
  8Q GAIN WILD-TYPE 251  20  10  23
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0             112               251
  R1               3                20
  R2               7                10
  RX              12                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q GAIN MUTATED                                  0     7
  8Q GAIN WILD-TYPE                                4    13
                   vv
clus                BLACK OR AFRICAN AMERICAN
  8Q GAIN MUTATED                          33
  8Q GAIN WILD-TYPE                        68
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8Q GAIN MUTATED                                           3   105
  8Q GAIN WILD-TYPE                                         6   261
D16V6, multiclass
                                           clus
vv                                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   7                13
  BLACK OR AFRICAN AMERICAN                              33                68
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               3                 6
  WHITE                                                 105               261
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     2 117
  8Q GAIN WILD-TYPE  12 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      2  117
  8Q GAIN WILD-TYPE   12  250
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                12
  NOT HISPANIC OR LATINO             117               250
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    18   3
  9P GAIN WILD-TYPE 439  66
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               21               505 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3                66 
$`9P GAIN MUTATED`
TCGA-A5-A1OG TCGA-AJ-A2QK TCGA-AX-A05Z TCGA-AX-A06B TCGA-AX-A2HK TCGA-AX-A3G3 
       11.44         0.39        46.45        53.92         2.96         1.38 
TCGA-B5-A11H TCGA-B5-A11I TCGA-BG-A0YV TCGA-BS-A0U9 TCGA-D1-A1NW TCGA-E6-A1M0 
       88.34        75.72        12.56        67.20         0.72        17.06 
TCGA-EO-A1Y8 TCGA-EO-A22X TCGA-EY-A1GW TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3QX 
       37.71        57.60        11.08        20.05        29.10        13.84 
TCGA-FI-A3PX TCGA-PG-A7D5 TCGA-SL-A6J9 
       45.01        23.97         0.07 

$`9P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       38.37        36.82        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       19.96        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 
       15.95         7.92        36.33         9.60         8.02        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       46.32        28.64         5.33         5.16         7.33        14.96 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
        1.18        14.43        10.26        19.79        29.39         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
       34.36        34.16         1.12         0.76        18.90         1.68 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA 
        1.64        14.66        22.49        22.26        17.06        20.81 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ 
       36.99        20.65        21.21        15.62        10.19        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.95        14.76        16.87        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       20.78         2.70         0.13        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
       23.31        86.07         8.22        63.91        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       36.89        23.87        12.20        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      117.99       110.37         3.39        63.16        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       31.73        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       55.89        31.30        35.54        46.78        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
       30.90        10.42        27.85        16.24        21.90        36.13 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F 
       35.34        45.99        66.58        34.98        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        35.01        28.54        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        65.88        13.28        19.20        16.96 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       13.55        15.25        20.28        12.43        20.05        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR 
       72.56        54.12        67.50        25.12        36.39        11.08 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
        4.77        30.12        71.24        40.80        61.18        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       34.32        46.49        19.36        26.33        17.75        30.74 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        64.93         0.23         0.20         0.56        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.20        20.52         0.30         0.26         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       18.35        14.47         0.39        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        27.29        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F 
       17.10        17.85        11.01         4.11         8.71       185.79 
TCGA-B5-A11G TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
      113.36        54.44        45.90        43.96        40.50        36.82 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU 
       18.41        17.36        16.57       191.84       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 
       14.40        14.70        11.70        11.87        15.29        12.79 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH 
      116.25        96.30        78.81        62.14        33.11        14.27 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       29.65        41.06        34.13        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98        22.06        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       36.49        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       43.30        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       15.45        15.45        14.27         1.81         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31         6.81        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
        6.21        10.22        10.16        31.76        24.99        24.13 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       16.64        13.18        10.03         9.86        46.95        23.47 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       96.49        30.74        97.41        88.34        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        72.72        73.25        59.51        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       49.55        63.16        66.48        16.83        19.79        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       36.10        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       18.67         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02        14.73         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 
        1.41        13.22        18.25        16.87        18.02         2.07 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV 
       44.88         0.26         4.27         4.11        16.93        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX 
       35.38         9.37        12.39        31.10       110.10        23.38 
TCGA-E6-A1LZ TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       48.36         2.37         6.67        27.32        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       16.80        10.92        49.15        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       46.26        51.52        51.42        19.40        34.39        26.43 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU 
       35.15        17.19        27.16        17.88        26.96        22.26 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC 
       16.34        14.53        24.89         6.21        14.99         4.54 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ 
       22.78        13.97         6.90        19.27        18.84        17.88 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX 
       17.62        15.09        16.11        12.43        15.81         6.48 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM 
       19.33        12.59        10.19        14.40        18.87        22.82 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 
       45.76        31.04        27.35        11.38        17.92        14.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY 
       19.89        14.70        16.96         5.88        40.01        41.06 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       39.88        39.95         7.99        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 
       59.01         9.07        28.93        28.96        25.02        29.23 
TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       41.06         1.74         7.76        14.04         2.43        23.74 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       13.28         9.47        26.10        18.21        23.24        15.45 
TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       12.92         7.00        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       12.92        23.64        14.83         4.44        14.07        18.28 
TCGA-SL-A6JA 
        0.23 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.07              0.13 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            88.34            191.84 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            20.05             23.34 
[1] "0.1 - 88.3 (20.1)"  "0.1 - 191.8 (23.3)"
[1] "hr=" "1.2"
D17V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  9P GAIN MUTATED                                        12
  9P GAIN WILD-TYPE                                     383
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  9P GAIN MUTATED                               1
  9P GAIN WILD-TYPE                            20
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  9P GAIN MUTATED                                   8
  9P GAIN WILD-TYPE                               104
D17V3, multiclass
                                         clus
vv                                        9P GAIN MUTATED 9P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              12               383
  MIXED SEROUS AND ENDOMETRIOID                         1                20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     8               104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V4, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     3  18
  9P GAIN WILD-TYPE 138 369
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      3   18
  9P GAIN WILD-TYPE  138  369
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                3               138
  YES              18               369
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9P GAIN MUTATED    13   2   1   2
  9P GAIN WILD-TYPE 350  21  16  33
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              13               350
  R1               2                21
  R2               1                16
  RX               2                33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P GAIN MUTATED                                  0     1
  9P GAIN WILD-TYPE                                4    19
                   vv
clus                BLACK OR AFRICAN AMERICAN
  9P GAIN MUTATED                           4
  9P GAIN WILD-TYPE                        97
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9P GAIN MUTATED                                           1    12
  9P GAIN WILD-TYPE                                         8   354
D17V6, multiclass
                                           clus
vv                                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   1                19
  BLACK OR AFRICAN AMERICAN                               4                97
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 8
  WHITE                                                  12               354
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     3  12
  9P GAIN WILD-TYPE  11 355
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      3   12
  9P GAIN WILD-TYPE   11  355
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                11
  NOT HISPANIC OR LATINO              12               355
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED     7   1
  9Q GAIN WILD-TYPE 450  68
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                8               518 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                1                68 
$`9Q GAIN MUTATED`
TCGA-A5-A1OG TCGA-AX-A3G3 TCGA-B5-A11H TCGA-BS-A0U9 TCGA-D1-A1NW TCGA-E6-A1M0 
       11.44         1.38        88.34        67.20         0.72        17.06 
TCGA-EY-A1GW TCGA-SL-A6J9 
       11.08         0.07 

$`9Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       38.37        36.82        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       19.96        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 
       15.95         7.92        36.33         9.60         8.02        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       46.32        28.64         5.33         5.16         7.33        14.96 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM 
        1.18        14.43        10.26         0.39        19.79        29.39 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI 
        2.40        34.36        34.16         1.12         0.76        18.90 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
        1.68         1.64        14.66        22.49        22.26        17.06 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH 
       20.81        36.99        20.65        21.21        15.62        10.19 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV 
       15.35        15.95        14.76        16.87        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       12.82        20.78         2.70         0.13        83.67        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D 
        5.95        23.31        86.07         8.22        63.91        57.80 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 
       45.53        36.89        23.87        12.20        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
      125.42       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       60.36        55.89        31.30        35.54        46.78        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        30.90        10.42        27.85        16.24        21.90 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       36.13         0.56        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       53.92        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       35.01        28.54        37.78        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       13.28        19.20        16.96        13.55        15.25        20.28 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       12.43        20.05        76.83        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       25.12        36.39        11.08         4.77        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       40.80        61.18        81.37        34.32        46.49        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       26.33        17.75        30.74         2.96        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
        0.23         0.20         0.56        43.82         0.20        20.52 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.30         0.26         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
        0.39        80.38        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        27.29        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11I 
       11.01         4.11         8.71       185.79       113.36        75.72 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q 
       54.44        45.90        43.96        40.50        36.82        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       33.50        27.35        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV 
       17.36        16.57       191.84       102.31        50.89        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       14.70        11.70        11.87        15.29        12.79       116.25 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 
       96.30        78.81        62.14        33.11        14.27        29.65 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       41.06        34.13        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98        22.06        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       15.45        15.45        14.27         1.81         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31         6.81        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
        6.21        10.22        10.16        31.76        24.99        24.13 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       16.64        13.18        10.03         9.86        46.95        23.47 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       96.49        30.74        97.41        88.34        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        72.72        73.25        59.51        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       49.55        63.16        66.48        16.83        19.79        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       36.10        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       18.67         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02        14.73         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 
        1.41        13.22        18.25        16.87        18.02         2.07 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV 
       44.88         0.26         4.27         4.11        16.93        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX 
       35.38         9.37        12.39        31.10       110.10        23.38 
TCGA-E6-A1LZ TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       48.36         2.37         6.67        27.32        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
       16.80        10.92        49.15        37.71        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH 
       66.90        46.26        57.60        51.52        51.42        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       34.39        26.43        35.15        17.19        27.16        17.88 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 
       26.96        22.26        16.34        14.53        24.89         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99         4.54        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       23.34        23.90        22.78        13.97         6.90        19.27 
TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       18.84        17.88        17.62        15.09        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 
       15.81         6.48        19.33        12.59        10.19        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       18.87        22.82        20.05        45.76        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       27.35        13.84        11.38        17.92        14.14        19.89 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
       14.70        16.96         5.88        40.01        41.06        39.88 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       39.95         7.99        13.84         8.98        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV 
        9.07        28.93        28.96        25.02        29.23        41.06 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       45.01         1.74         7.76        14.04         2.43        23.74 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       13.28         9.47        26.10        18.21        23.24        15.45 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       23.97        12.92         7.00        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       39.95        12.92        23.64        14.83         4.44        14.07 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.07              0.13 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            88.34            191.84 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           11.260            23.425 
[1] "0.1 - 88.3 (11.3)"  "0.1 - 191.8 (23.4)"
[1] "hr=" "1.4"
D18V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  9Q GAIN MUTATED                                         5
  9Q GAIN WILD-TYPE                                     390
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  9Q GAIN MUTATED                               1
  9Q GAIN WILD-TYPE                            20
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  9Q GAIN MUTATED                                   2
  9Q GAIN WILD-TYPE                               110
D18V3, multiclass
                                         clus
vv                                        9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               5               390
  MIXED SEROUS AND ENDOMETRIOID                         1                20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     2               110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V4, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     1   7
  9Q GAIN WILD-TYPE 140 380
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1    7
  9Q GAIN WILD-TYPE  140  380
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                1               140
  YES               7               380
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9Q GAIN MUTATED     3   1   0   2
  9Q GAIN WILD-TYPE 360  22  17  33
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0               3               360
  R1               1                22
  R2               0                17
  RX               2                33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q GAIN MUTATED                                  0     1
  9Q GAIN WILD-TYPE                                4    19
                   vv
clus                BLACK OR AFRICAN AMERICAN
  9Q GAIN MUTATED                           1
  9Q GAIN WILD-TYPE                       100
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9Q GAIN MUTATED                                           1     5
  9Q GAIN WILD-TYPE                                         8   361
D18V6, multiclass
                                           clus
vv                                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   1                19
  BLACK OR AFRICAN AMERICAN                               1               100
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 8
  WHITE                                                   5               361
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     1   5
  9Q GAIN WILD-TYPE  13 362
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1    5
  9Q GAIN WILD-TYPE   13  362
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                13
  NOT HISPANIC OR LATINO               5               362
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    99  16
  10P GAIN WILD-TYPE 358  53
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               115                411 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                16                 53 
$`10P GAIN MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0GE TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0R9 TCGA-A5-A1OG 
       37.02       105.37        28.27        20.81        24.62        11.44 
TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A3LP TCGA-AJ-A23O TCGA-AJ-A3BI TCGA-AJ-A3EJ 
        9.60        91.04        14.96        10.26        18.90         1.64 
TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW 
       22.26        20.81        36.99        10.19        16.87        16.87 
TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LF TCGA-AP-A0LJ TCGA-AP-A0LN TCGA-AP-A0LQ 
       20.91       117.99         3.39        31.73        82.52        80.78 
TCGA-AP-A1DQ TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       46.78        27.85        16.24        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A06D TCGA-AX-A06J TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C4 
       68.35        12.26        30.02        28.54        37.78        13.28 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CJ TCGA-AX-A2HH TCGA-AX-A3FX TCGA-B5-A0JT 
       20.28        12.43        54.12        17.75        43.82        43.13 
TCGA-B5-A0JX TCGA-B5-A11F TCGA-B5-A11L TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A1MV 
       44.71       185.79        45.90        33.50        27.35        14.40 
TCGA-BG-A0LX TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0MG 
       20.19        20.94        35.21        34.98        22.06        48.56 
TCGA-BG-A0MS TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0W2 TCGA-BG-A187 TCGA-BG-A18A 
       30.81        15.42        24.39        56.58        14.73        14.01 
TCGA-BG-A221 TCGA-BK-A0C9 TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0T9 TCGA-BS-A0U7 
        1.81        35.90        10.16        16.64        46.95        30.74 
TCGA-BS-A0UV TCGA-BS-A0V7 TCGA-BS-A0WQ TCGA-D1-A0ZQ TCGA-D1-A0ZU TCGA-D1-A102 
       73.25        63.58        66.48         8.55        28.67         4.44 
TCGA-D1-A15V TCGA-D1-A15Z TCGA-D1-A161 TCGA-D1-A165 TCGA-D1-A169 TCGA-D1-A16S 
       39.48         1.91        29.33         0.66        37.32        18.67 
TCGA-D1-A17T TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A2G5 TCGA-D1-A3DH TCGA-DI-A2QY 
        2.33        18.25         2.07        41.42         4.11       110.10 
TCGA-E6-A1M0 TCGA-E6-A2P9 TCGA-EO-A1Y7 TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3B1 
       17.06         6.67        49.15        51.52        51.42        26.96 
TCGA-EO-A3KU TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1GC TCGA-EY-A1GH TCGA-EY-A1GK 
       22.26        24.89         6.21         4.54        23.34        22.78 
TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       19.27        17.88        16.11        11.08         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A72D TCGA-FI-A2D4 
       12.59        14.40        45.76        31.04         5.88         7.99 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-KP-A3W1 TCGA-PG-A7D5 TCGA-QS-A744 TCGA-QS-A8F1 
       59.01         9.07         9.47        23.97        14.83         4.44 
TCGA-SJ-A6ZJ 
       18.28 

$`10P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88       149.56        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       17.85        32.78       112.54        87.32        74.10        57.53 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       65.75        60.53        60.53        46.55        38.37        36.82 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0RA 
       23.21        68.65        19.96        17.59        19.59        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OK TCGA-A5-A2K3 
       42.35        15.95         7.92        36.33         8.02        46.32 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N 
       28.64         5.33         5.16         7.33         1.18        14.43 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
        0.39        19.79        29.39         2.40        34.36        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 
        1.12         0.76         1.68        14.66        22.49        17.06 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65        21.21        15.62        15.35        15.95        14.76 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       22.32        12.82        20.78         2.70         0.13        83.67 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
       21.99         5.95        23.31        86.07         8.22        63.91 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A0L8 
       57.80        45.53        36.89        23.87        12.20        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LL 
      125.42       110.37        63.16        36.36        97.71        83.97 
TCGA-AP-A0LM TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       27.12        33.40        61.64        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR 
       71.67        60.36        55.89        31.30        35.54        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
        6.71        30.90        10.42        21.90        36.13         0.56 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ 
       53.92        51.09        27.39        60.66        35.01        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       40.11        65.88        19.20        16.96        13.55        15.25 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       20.05        76.83        72.56        67.50        25.12        36.39 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       11.08         4.77        30.12        71.24        40.80        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HJ 
       81.37        34.32        46.49        19.36        26.33        30.74 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
        2.96        31.13        64.93         0.23         0.20         0.56 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
        0.20        20.52         1.38         0.30         0.26         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR 
        1.18        18.35        14.47         0.39        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       46.75        48.76        40.67        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        27.29        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11G TCGA-B5-A11H 
       17.85        11.01         4.11         8.71       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q 
       75.72        54.44        43.96        40.50        36.82        32.09 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      191.84       102.31        50.89        14.70        11.70        11.87 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       15.29        12.79       116.25        96.30        78.81        62.14 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       33.11        14.27        29.65        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0M0 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       18.61        19.33        38.37        36.49        28.27        10.72 
TCGA-BG-A0MC TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        23.47        43.30        43.04        39.32        21.17 
TCGA-BG-A0MU TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       20.28        26.66        16.34        34.29        52.64        52.83 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 
       14.83        12.56        13.78        15.45        15.45        14.27 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        9.57        20.02        23.70        20.12        11.31         6.81 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
       34.98         6.21        10.22        31.76        24.99        24.13 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       13.18        10.03         9.86        23.47        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U8 
        4.80        77.95        61.87        67.99        96.49        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       67.20        88.34        85.84        82.39        81.57        72.72 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-D1-A0ZN TCGA-D1-A0ZO 
       59.51        62.79        49.55        63.16        16.83        19.79 
TCGA-D1-A0ZP TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
       29.95         0.56         4.87        23.93        22.55         1.74 
TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A160 TCGA-D1-A163 TCGA-D1-A167 
       21.99        30.08        29.88         3.68        32.58        15.72 
TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I 
       36.10        36.36        37.51        36.79        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V 
       29.92        31.07        33.63        10.65         0.69         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW 
       11.15        24.30        22.92         1.41        13.22         0.72 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       16.87        18.02        15.06         1.05         3.95         3.52 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JP TCGA-DF-A2KV 
        8.48        44.88         0.26         4.27        16.93        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ 
       35.38         9.37        12.39        31.10        23.38        48.36 
TCGA-E6-A2P8 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37        27.32        16.04         7.36        16.80        10.92 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       37.71        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       19.40        34.39        26.43        35.15        17.19        27.16 
TCGA-EO-A3B0 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       17.88        16.34        14.53        14.99        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP 
       27.16        23.34        23.90        13.97         6.90        18.84 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A212 TCGA-EY-A215 
       17.62        15.09        12.43        15.81        10.19        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       22.82        20.05        29.10        27.35        13.84        11.38 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX 
       17.92        14.14        19.89        14.70        16.96        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       41.06        39.88        39.95        13.84         8.98        96.69 
TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
       28.93        28.96        25.02        29.23        41.06        45.01 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 
        1.74         7.76        14.04         2.43        23.74        13.28 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A915 
       26.10        18.21        23.24        15.45        12.92         7.00 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       11.24         6.97        18.84        39.95        12.92        23.64 
TCGA-SJ-A6ZI TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.07         0.07         0.23 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.66               0.07 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            185.79             191.84 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             20.94              23.70 
[1] "0.7 - 185.8 (20.9)" "0.1 - 191.8 (23.7)"
[1] "hr=" "1.1"
D19V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  10P GAIN MUTATED                                        86
  10P GAIN WILD-TYPE                                     309
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  10P GAIN MUTATED                               3
  10P GAIN WILD-TYPE                            18
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  10P GAIN MUTATED                                  26
  10P GAIN WILD-TYPE                                86
D19V3, multiclass
                                         clus
vv                                        10P GAIN MUTATED 10P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               86                309
  MIXED SEROUS AND ENDOMETRIOID                          3                 18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     26                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V4, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    27  88
  10P GAIN WILD-TYPE 114 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     27   88
  10P GAIN WILD-TYPE  114  299
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                27                114
  YES               88                299
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10P GAIN MUTATED    90   6   4   5
  10P GAIN WILD-TYPE 273  17  13  30
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               90                273
  R1                6                 17
  R2                4                 13
  RX                5                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P GAIN MUTATED                                  1     6
  10P GAIN WILD-TYPE                                3    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  10P GAIN MUTATED                          16
  10P GAIN WILD-TYPE                        85
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10P GAIN MUTATED                                           3    85
  10P GAIN WILD-TYPE                                         6   281
D19V6, multiclass
                                           clus
vv                                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  3
  ASIAN                                                    6                 14
  BLACK OR AFRICAN AMERICAN                               16                 85
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                3                  6
  WHITE                                                   85                281
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     1  86
  10P GAIN WILD-TYPE  13 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1   86
  10P GAIN WILD-TYPE   13  281
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 13
  NOT HISPANIC OR LATINO               86                281
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    92  16
  10Q GAIN WILD-TYPE 365  53
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               108                418 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                16                 53 
$`10Q GAIN MUTATED`
TCGA-A5-A0GE TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0R9 TCGA-A5-A1OG TCGA-A5-A1OJ 
      105.37        28.27        20.81        24.62        11.44         9.60 
TCGA-A5-A2K2 TCGA-AJ-A23O TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3NC 
       91.04        10.26        18.90         1.64        22.26        36.99 
TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LF TCGA-AP-A0LJ 
       10.19        16.87        20.91       117.99         3.39        31.73 
TCGA-AP-A0LN TCGA-AP-A0LQ TCGA-AP-A1DQ TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AX-A05S 
       82.52        80.78        46.78        27.85        16.24        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A06D TCGA-AX-A06J TCGA-AX-A0IU 
       19.82        29.69        68.35        12.26        30.02        28.54 
TCGA-AX-A0IW TCGA-AX-A1C4 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CJ TCGA-AX-A2HH 
       37.78        13.28        20.28        12.43        54.12        17.75 
TCGA-AX-A3FX TCGA-B5-A0JT TCGA-B5-A0JX TCGA-B5-A11F TCGA-B5-A11L TCGA-B5-A11R 
       43.82        43.13        44.71       185.79        45.90        33.50 
TCGA-B5-A11S TCGA-B5-A1MV TCGA-BG-A0LX TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M6 
       27.35        14.40        20.19        20.94        35.21        22.06 
TCGA-BG-A0MG TCGA-BG-A0MS TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0W2 TCGA-BG-A187 
       48.56        30.81        15.42        24.39        56.58        14.73 
TCGA-BG-A18A TCGA-BK-A0C9 TCGA-BK-A0CC TCGA-BK-A4ZD TCGA-BS-A0T9 TCGA-BS-A0TI 
       14.01        35.90        10.22        16.64        46.95        61.87 
TCGA-BS-A0U7 TCGA-BS-A0UV TCGA-BS-A0V7 TCGA-BS-A0WQ TCGA-D1-A0ZQ TCGA-D1-A0ZU 
       30.74        73.25        63.58        66.48         8.55        28.67 
TCGA-D1-A15V TCGA-D1-A15Z TCGA-D1-A161 TCGA-D1-A165 TCGA-D1-A169 TCGA-D1-A16S 
       39.48         1.91        29.33         0.66        37.32        18.67 
TCGA-D1-A17T TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A2G5 TCGA-DI-A2QT TCGA-E6-A1M0 
        2.33        18.25         2.07        41.42        12.39        17.06 
TCGA-E6-A2P9 TCGA-EO-A1Y7 TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3B1 TCGA-EO-A3L0 
        6.67        49.15        51.52        51.42        26.96        24.89 
TCGA-EY-A1G7 TCGA-EY-A1GC TCGA-EY-A1GH TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GS 
        6.21         4.54        23.34        19.27        17.88        15.09 
TCGA-EY-A1GT TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 
       16.11        11.08         6.48        19.33        12.59        14.40 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A72D TCGA-FI-A2D4 TCGA-FI-A2EW TCGA-FI-A2EX 
       45.76        31.04         5.88         7.99        59.01         9.07 
TCGA-FI-A2EY TCGA-KP-A3W1 TCGA-PG-A7D5 TCGA-PG-A915 TCGA-QS-A744 TCGA-SJ-A6ZJ 
       28.93         9.47        23.97         7.00        14.83        18.28 

$`10Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GR TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       36.82        23.21        68.65        19.96        17.59        19.59 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OK 
       29.06        42.35        15.95         7.92        36.33         8.02 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       46.32        28.64         5.33         5.16         7.33        14.96 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
        1.18        14.43         0.39        19.79        29.39         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK 
       34.36        34.16         1.12         0.76         1.68        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       22.49        17.06        20.81        20.65        21.21        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.35        15.95        14.76        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       20.78         2.70         0.13        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
       23.31        86.07         8.22        63.91        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LE 
       36.89        23.87        12.20        48.79       125.42       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LO 
       63.16        36.36        97.71        83.97        27.12        33.40 
TCGA-AP-A0LP TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       61.64        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       55.89        31.30        35.54        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05Y TCGA-AX-A05Z 
       10.42        21.90        36.13         0.56        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06F 
       35.34        45.99        66.58        34.98        53.92        51.09 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       27.39        60.66        35.01        43.82        40.11        65.88 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CF 
       19.20        16.96        13.55        15.25        20.05        76.83 
TCGA-AX-A1CI TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 
       72.56        67.50        25.12        36.39        11.08         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       30.12        71.24        40.80        61.18        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       46.49        19.36        26.33        30.74         2.96        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G1 
       64.93         0.23         0.20         0.56         0.20        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        1.38         0.30         0.26         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU 
       14.47         0.39        80.38        56.91        46.75        48.76 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       40.67        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        17.88        13.74        17.10        17.85        11.01 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
        4.11         8.71       113.36        88.34        75.72        54.44 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11U TCGA-B5-A11V 
       43.96        40.50        36.82        32.09        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS 
       19.50        18.41        17.36        16.57       191.84       102.31 
TCGA-B5-A1MU TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 
       50.89        14.70        11.70        11.87        15.29        12.79 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH 
      116.25        96.30        78.81        62.14        33.11        14.27 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0M0 
       29.65        41.06        34.13        34.95        18.61        19.33 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       34.98        38.37        36.49        28.27        10.72        41.52 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.30        43.04        39.32        21.17        20.28 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0YU 
       26.66        16.34        34.29        52.64        52.83        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 
       12.56        13.78        15.45        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        9.57        20.02        23.70        20.12        11.31         6.81 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
       34.98         6.21        10.16        31.76        24.99        24.13 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       13.18        10.03         9.86        23.47        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U8 TCGA-BS-A0U9 
        4.80        77.95        67.99        96.49        97.41        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0V4 
       88.34        85.84        82.39        81.57        72.72        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       62.79        49.55        63.16        16.83        19.79        29.95 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        0.56         4.87        23.93        22.55         1.74         4.44 
TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A160 TCGA-D1-A163 TCGA-D1-A167 
       21.99        30.08        29.88         3.68        32.58        15.72 
TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I 
       36.10        36.36        37.51        36.79        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V 
       29.92        31.07        33.63        10.65         0.69         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW 
       11.15        24.30        22.92         1.41        13.22         0.72 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       16.87        18.02        15.06         1.05         3.95         3.52 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP 
        8.48        44.88         0.26         4.27         4.11        16.93 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX 
       24.30        35.38         9.37        31.10       110.10        23.38 
TCGA-E6-A1LZ TCGA-E6-A2P8 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       48.36         2.37        27.32        16.04         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       10.92        37.71        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       57.60        19.40        34.39        26.43        35.15        17.19 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EY-A1G8 
       27.16        17.88        22.26        16.34        14.53        14.99 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK 
       53.88        24.36        27.16        23.34        23.90        22.78 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GU TCGA-EY-A1GV 
       13.97         6.90        18.84        17.62        12.43        15.81 
TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 
       10.19        18.87        22.82        20.05        29.10        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       13.84        11.38        17.92        14.14        19.89        14.70 
TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D5 
       16.96        40.01        41.06        39.88        39.95        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV 
        8.98        96.69        28.96        25.02        29.23        41.06 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       45.01         1.74         7.76        14.04         2.43        23.74 
TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 
       13.28        26.10        18.21        23.24        15.45        12.92 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       11.24         6.97        18.84        39.95        12.92        23.64 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44        14.07         0.07         0.23 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.66               0.07 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            185.79             191.84 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             21.50              23.47 
[1] "0.7 - 185.8 (21.5)" "0.1 - 191.8 (23.5)"
[1] "hr=" "1.2"
D20V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  10Q GAIN MUTATED                                        81
  10Q GAIN WILD-TYPE                                     314
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  10Q GAIN MUTATED                               3
  10Q GAIN WILD-TYPE                            18
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  10Q GAIN MUTATED                                  24
  10Q GAIN WILD-TYPE                                88
D20V3, multiclass
                                         clus
vv                                        10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               81                314
  MIXED SEROUS AND ENDOMETRIOID                          3                 18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     24                 88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V4, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    26  82
  10Q GAIN WILD-TYPE 115 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     26   82
  10Q GAIN WILD-TYPE  115  305
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                26                115
  YES               82                305
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED    84   6   6   4
  10Q GAIN WILD-TYPE 279  17  11  31
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0               84                279
  R1                6                 17
  R2                6                 11
  RX                4                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q GAIN MUTATED                                  2     6
  10Q GAIN WILD-TYPE                                2    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  10Q GAIN MUTATED                          17
  10Q GAIN WILD-TYPE                        84
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10Q GAIN MUTATED                                           3    77
  10Q GAIN WILD-TYPE                                         6   289
D20V6, multiclass
                                           clus
vv                                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  2
  ASIAN                                                    6                 14
  BLACK OR AFRICAN AMERICAN                               17                 84
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                3                  6
  WHITE                                                   77                289
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     3  79
  10Q GAIN WILD-TYPE  11 288
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3   79
  10Q GAIN WILD-TYPE   11  288
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 11
  NOT HISPANIC OR LATINO               79                288
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    17   5
  11P GAIN WILD-TYPE 440  64
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                22                504 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                 64 
$`11P GAIN MUTATED`
TCGA-A5-A3LO TCGA-AJ-A23N TCGA-AJ-A3TW TCGA-AP-A0L8 TCGA-AX-A0IU TCGA-AX-A0IW 
        7.33        14.43        16.87        48.79        28.54        37.78 
TCGA-AX-A2H2 TCGA-B5-A0JT TCGA-B5-A0K4 TCGA-B5-A1MU TCGA-B5-A5OE TCGA-BG-A0VT 
        4.77        43.13        17.88        50.89        34.95        24.39 
TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BS-A0U9 TCGA-D1-A169 TCGA-D1-A16I 
       15.45         6.81        10.22        67.20        37.32        11.51 
TCGA-DI-A1NN TCGA-FI-A3PX TCGA-KP-A3W3 TCGA-PG-A915 
       35.38        45.01        26.10         7.00 

$`11P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       38.37        36.82        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       19.96        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK 
       15.95         7.92        11.44        36.33         9.60         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP 
       91.04        46.32        28.64         5.33         5.16        14.96 
TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
        1.18        10.26         0.39        19.79        29.39         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
       34.36        34.16         1.12         0.76        18.90         1.68 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA 
        1.64        14.66        22.49        22.26        17.06        20.81 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ 
       36.99        20.65        21.21        15.62        10.19        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.95        14.76        16.87        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        2.70         0.13        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        63.91        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        12.20        20.91       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        46.78        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       27.85        16.24        21.90        36.13         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       45.99        66.58        34.98        53.92        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 
       27.39        30.02        60.66        35.01        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       65.88        13.28        19.20        16.96        13.55        15.25 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       20.28        12.43        20.05        76.83        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H5 
       67.50        25.12        36.39        11.08        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       40.80        61.18        81.37        34.32        46.49        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       26.33        17.75        30.74         2.96        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
        0.23         0.20         0.56        43.82         0.20        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        1.38         0.30         0.26         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU 
       14.47         0.39        80.38        56.91        46.75        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       25.91        27.29        13.74        17.10        17.85        11.01 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
        4.11         8.71       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q 
       54.44        45.90        43.96        40.50        36.82        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       33.50        27.35        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV TCGA-B5-A1MW 
       17.36        16.57       191.84       102.31        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       11.70        11.87        15.29        12.79       116.25        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       78.81        62.14        33.11        14.27        29.65        41.06 
TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.13        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       34.98        22.06        38.37        36.49        28.27        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       30.81        21.17        20.28        15.42        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        52.64        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 
       13.78        14.73        14.01        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 
        9.57        20.02        23.70        20.12        11.31        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
       34.98         6.21        10.16        31.76        24.99        24.13 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       16.64        13.18        10.03         9.86        46.95        23.47 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       96.49        30.74        97.41        88.34        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        72.72        73.25        59.51        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       49.55        63.16        66.48        16.83        19.79        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J 
       36.10        36.36        37.51        36.79        27.42        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
       31.07        33.63        10.65         0.69        18.67         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
        0.72        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 
        1.05         3.95         3.52        41.42         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY 
        0.26         4.27         4.11        16.93        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO 
       27.16        16.31        39.29        36.62        24.30         9.37 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
       12.39        31.10       110.10        23.38        48.36        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
        2.37         6.67        27.32        16.04         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       10.92        49.15        37.71        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       46.26        57.60        51.52        51.42        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 
       26.43        35.15        17.19        27.16        17.88        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       22.26        16.34        14.53        24.89         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.90        22.78        13.97         6.90        19.27        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       17.88        17.62        15.09        16.11        12.43        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 
       11.08         6.48        19.33        12.59        10.19        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       18.87        22.82        20.05        45.76        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       27.35        13.84        11.38        17.92        14.14        19.89 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
       14.70        16.96         5.88        40.01        41.06        39.88 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       39.95         7.99        13.84         8.98        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV 
        9.07        28.93        28.96        25.02        29.23        41.06 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 
        1.74         7.76        14.04         2.43        23.74        13.28 
TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 
        9.47        18.21        23.24        15.45        23.97        12.92 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       11.24         6.97        18.84        39.95        12.92        23.64 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83         4.44        14.07        18.28         0.07         0.23 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              4.77               0.07 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             67.20             191.84 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            25.245             23.325 
[1] "4.8 - 67.2 (25.2)"  "0.1 - 191.8 (23.3)"
[1] "hr=" "1.9"
D21V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  11P GAIN MUTATED                                         7
  11P GAIN WILD-TYPE                                     388
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  11P GAIN MUTATED                               0
  11P GAIN WILD-TYPE                            21
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  11P GAIN MUTATED                                  15
  11P GAIN WILD-TYPE                                97
D21V3, multiclass
                                         clus
vv                                        11P GAIN MUTATED 11P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                7                388
  MIXED SEROUS AND ENDOMETRIOID                          0                 21
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     15                 97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V4, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     5  17
  11P GAIN WILD-TYPE 136 370
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      5   17
  11P GAIN WILD-TYPE  136  370
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 5                136
  YES               17                370
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11P GAIN MUTATED    14   0   1   3
  11P GAIN WILD-TYPE 349  23  16  32
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0               14                349
  R1                0                 23
  R2                1                 16
  RX                3                 32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     0
  11P GAIN WILD-TYPE                                4    20
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  11P GAIN MUTATED                           6
  11P GAIN WILD-TYPE                        95
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11P GAIN MUTATED                                           1    14
  11P GAIN WILD-TYPE                                         8   352
D21V6, multiclass
                                           clus
vv                                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    0                 20
  BLACK OR AFRICAN AMERICAN                                6                 95
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   14                352
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1  15
  11P GAIN WILD-TYPE  13 352
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   15
  11P GAIN WILD-TYPE   13  352
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 13
  NOT HISPANIC OR LATINO               15                352
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    12   6
  11Q GAIN WILD-TYPE 445  63
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                18                508 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 6                 63 
$`11Q GAIN MUTATED`
TCGA-A5-A3LO TCGA-AJ-A23N TCGA-AX-A0IW TCGA-AX-A1CA TCGA-AX-A2H2 TCGA-AX-A2HK 
        7.33        14.43        37.78        20.28         4.77         2.96 
TCGA-B5-A0JT TCGA-B5-A0K4 TCGA-B5-A1MU TCGA-B5-A5OE TCGA-BG-A0M2 TCGA-BG-A0VT 
       43.13        17.88        50.89        34.95        20.94        24.39 
TCGA-BG-A18C TCGA-BS-A0U9 TCGA-D1-A16I TCGA-D1-A1O0 TCGA-FI-A2EY TCGA-FI-A3PX 
       15.45        67.20        11.51         2.07        28.93        45.01 

$`11Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       38.37        36.82        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       19.96        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK 
       15.95         7.92        11.44        36.33         9.60         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP 
       91.04        46.32        28.64         5.33         5.16        14.96 
TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
        1.18        10.26         0.39        19.79        29.39         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
       34.36        34.16         1.12         0.76        18.90         1.68 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA 
        1.64        14.66        22.49        22.26        17.06        20.81 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ 
       36.99        20.65        21.21        15.62        10.19        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.95        14.76        16.87        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       20.78         2.70         0.13        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
       23.31        86.07         8.22        63.91        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       36.89        23.87        12.20        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      117.99       110.37         3.39        63.16        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       31.73        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       55.89        31.30        35.54        46.78        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
       30.90        10.42        27.85        16.24        21.90        36.13 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       28.54        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       16.96        13.55        15.25        12.43        20.05        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR 
       72.56        54.12        67.50        25.12        36.39        11.08 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       30.12        71.24        40.80        61.18        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN 
       46.49        19.36        26.33        17.75        30.74        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       64.93         0.23         0.20         0.56        43.82         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
       20.52         1.38         0.30         0.26         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       18.35        14.47         0.39        80.38        56.91        46.75 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       30.51        25.91        27.29        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       11.01         4.11         8.71       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
       75.72        54.44        45.90        43.96        40.50        36.82 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV 
       18.41        17.36        16.57       191.84       102.31        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       14.70        11.70        11.87        15.29        12.79       116.25 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 
       96.30        78.81        62.14        33.11        14.27        29.65 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M3 
       41.06        34.13        18.61        20.19        19.33        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       34.98        22.06        38.37        36.49        28.27        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       30.81        21.17        20.28        15.42        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        52.64        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 
       13.78        14.73        14.01        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        9.57        20.02        23.70        20.12        11.31         6.81 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       35.90        34.98         6.21        10.22        10.16        31.76 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       24.99        24.13        16.64        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA 
       61.87        67.99        96.49        30.74        97.41        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       62.79        63.58        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       36.79        27.42        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
        0.69        18.67         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
       22.92         1.41        13.22         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 
       18.02        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP 
        8.48        44.88         0.26         4.27         4.11        16.93 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY 
       24.30        35.38         9.37        12.39        31.10       110.10 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 
       23.38        48.36        17.06         2.37         6.67        27.32 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       16.04         7.36        16.80        10.92        49.15        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       51.42        19.40        34.39        26.43        35.15        17.19 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX 
       27.16        17.88        26.96        22.26        16.34        14.53 
TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       24.89         6.21        14.99         4.54        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL 
       27.16        23.34        23.34        23.90        22.78        13.97 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS 
        6.90        19.27        18.84        17.88        17.62        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        12.43        15.81        11.08         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
       12.59        10.19        14.40        18.87        22.82        20.05 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       45.76        31.04        29.10        27.35        13.84        11.38 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D 
       17.92        14.14        19.89        14.70        16.96         5.88 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
       40.01        41.06        39.88        39.95         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F8 
        8.98        96.69        59.01         9.07        28.96        25.02 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 
       29.23        41.06         1.74         7.76        14.04         2.43 
TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
       23.74        13.28         9.47        26.10        18.21        23.24 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 
       15.45        23.97        12.92         7.00        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 
       18.84        39.95        12.92        23.64        14.83         4.44 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.07        18.28         0.07         0.23 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              2.07               0.07 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             67.20             191.84 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             20.61              23.36 
[1] "2.1 - 67.2 (20.6)"  "0.1 - 191.8 (23.4)"
[1] "hr=" "3.2"
D22V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  11Q GAIN MUTATED                                         9
  11Q GAIN WILD-TYPE                                     386
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  11Q GAIN MUTATED                               0
  11Q GAIN WILD-TYPE                            21
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  11Q GAIN MUTATED                                   9
  11Q GAIN WILD-TYPE                               103
D22V3, multiclass
                                         clus
vv                                        11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                9                386
  MIXED SEROUS AND ENDOMETRIOID                          0                 21
  SEROUS ENDOMETRIAL ADENOCARCINOMA                      9                103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V4, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     4  14
  11Q GAIN WILD-TYPE 137 373
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      4   14
  11Q GAIN WILD-TYPE  137  373
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 4                137
  YES               14                373
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN MUTATED    10   1   1   2
  11Q GAIN WILD-TYPE 353  22  16  33
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0               10                353
  R1                1                 22
  R2                1                 16
  RX                2                 33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q GAIN MUTATED                                  0     0
  11Q GAIN WILD-TYPE                                4    20
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  11Q GAIN MUTATED                           3
  11Q GAIN WILD-TYPE                        98
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11Q GAIN MUTATED                                           1    13
  11Q GAIN WILD-TYPE                                         8   353
D22V6, multiclass
                                           clus
vv                                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    0                 20
  BLACK OR AFRICAN AMERICAN                                3                 98
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   13                353
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     0  12
  11Q GAIN WILD-TYPE  14 355
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0   12
  11Q GAIN WILD-TYPE   14  355
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 14
  NOT HISPANIC OR LATINO               12                355
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    63   6
  12P GAIN WILD-TYPE 394  63
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                69                457 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 6                 63 
$`12P GAIN MUTATED`
TCGA-5B-A90C TCGA-A5-A0G2 TCGA-A5-A0GE TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A2K3 
       36.69       149.56       105.37        17.59        11.44        46.32 
TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A05P 
       14.96         1.18        34.16        20.81        10.19        20.91 
TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AP-A1E4 TCGA-AX-A05W TCGA-AX-A0IW TCGA-AX-A0J1 
       31.30        46.78        16.24        68.35        37.78        65.88 
TCGA-AX-A1CA TCGA-AX-A2HA TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-AX-A3GI TCGA-B5-A0JN 
       20.28        81.37        19.36         1.38         0.39        80.38 
TCGA-B5-A11R TCGA-B5-A11V TCGA-B5-A1N2 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0M2 
       33.50        19.56        12.79        41.06        34.13        20.94 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MG TCGA-BG-A0W1 TCGA-BG-A18C TCGA-BG-A2AE 
       22.06        36.49        48.56        52.83        15.45        23.70 
TCGA-BG-A3PP TCGA-BS-A0TE TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-BS-A0V7 TCGA-D1-A16O 
        6.81         4.80        61.87        67.20        63.58        33.63 
TCGA-D1-A17K TCGA-D1-A1NY TCGA-D1-A1O0 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-DI-A1C3 
       28.08        16.87         2.07        41.42        16.93        24.30 
TCGA-DI-A1NN TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A2CG TCGA-EO-A3AV 
       35.38       110.10        48.36        27.32        51.42        35.15 
TCGA-EO-A3AZ TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GR TCGA-EY-A1H0 TCGA-EY-A210 
       27.16         4.54        19.27        17.62        19.33        12.59 
TCGA-EY-A72D TCGA-FI-A2D2 TCGA-FI-A2D6 TCGA-FI-A2EY TCGA-FI-A3PX TCGA-JU-AAVI 
        5.88        39.95         8.98        28.93        45.01         7.76 
TCGA-KP-A3VZ TCGA-PG-A7D5 TCGA-PG-A914 
       23.74        23.97        12.92 

$`12P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
       41.06        10.29       106.88        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
       32.78       112.54        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 
       20.81        23.21        68.65        19.96        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ 
       29.06        42.35        15.95         7.92        36.33         9.60 
TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
        8.02        91.04        28.64         5.33         5.16         7.33 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
       14.43        10.26         0.39        19.79        29.39         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       34.36         1.12         0.76        18.90         1.68         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE 
       14.66        22.49        22.26        17.06        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       21.21        15.62        15.35        15.95        14.76        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW 
       16.87        22.32        12.82        20.78         2.70         0.13 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       83.67        21.99         5.95        23.31        86.07         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       63.91        57.80        45.53        36.89        23.87        12.20 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       33.40        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       71.67        60.36        55.89        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
       30.90        10.42        27.85        21.90        36.13         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       13.58        19.82        29.69        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       45.99        66.58        34.98        53.92        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ 
       27.39        30.02        60.66        35.01        28.54        43.82 
TCGA-AX-A0J0 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       40.11        13.28        19.20        16.96        13.55        15.25 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       12.43        20.05        76.83        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       25.12        36.39        11.08         4.77        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       40.80        61.18        34.32        46.49        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       30.74         2.96        31.13        64.93         0.23         0.20 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 
        0.56        43.82         0.20        20.52         0.30         0.26 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS 
        0.30         1.18        18.35        14.47        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        27.29        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F 
       17.10        17.85        11.01         4.11         8.71       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11W 
       40.50        36.82        32.09        27.35        16.73        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU 
       18.41        17.36        16.57       191.84       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 
       14.40        14.70        11.70        11.87        15.29       116.25 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 
       96.30        78.81        62.14        33.11        14.27        29.65 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M3 TCGA-BG-A0M4 
       34.95        18.61        20.19        19.33        35.21        34.98 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MI TCGA-BG-A0MK 
       38.37        28.27        10.72        41.52        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 
       24.39        26.66        16.34        34.29        52.64        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW 
       14.27         1.81         9.57        20.02        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       35.90        34.98         6.21        10.22        10.16        31.76 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       24.99        24.13        16.64        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TJ 
       46.95        23.47        85.55        78.21        77.95        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       96.49        30.74        97.41        88.34        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V8 
       81.57        72.72        73.25        59.51        62.79        49.55 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.16        66.48        16.83        19.79        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        4.44        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I 
       37.32        36.36        37.51        36.79        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
       29.92        31.07        10.65         0.69        18.67         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.01        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW 
       24.30         2.33        22.92         1.41        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       18.25        18.02        15.06         1.05         3.95         3.52 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KV 
        8.48        44.88         0.26         4.27         4.11        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1NO 
       10.92        27.16        16.31        39.29        36.62         9.37 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       12.39        31.10        23.38        17.06         2.37         6.67 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       16.04         7.36        16.80        10.92        49.15        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 
       19.40        34.39        26.43        17.19        17.88        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       22.26        16.34        14.53        24.89         6.21        14.99 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GS 
       22.78        13.97         6.90        18.84        17.88        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A212 
       16.11        12.43        15.81        11.08         6.48        10.19 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       14.40        18.87        22.82        20.05        45.76        31.04 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 
       29.10        27.35        13.84        11.38        17.92        14.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
       19.89        14.70        16.96        40.01        41.06        39.88 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 
        7.99        13.84        96.69        59.01         9.07        28.96 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 
       25.02        29.23        41.06         1.74        14.04         2.43 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       13.28         9.47        26.10        18.21        23.24        15.45 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        7.00        11.24         6.97        18.84        39.95        12.92 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       23.64        14.83         4.44        14.07        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.39               0.07 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            149.56             191.84 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             24.30              23.21 
[1] "0.4 - 149.6 (24.3)" "0.1 - 191.8 (23.2)"
[1] "hr=" "1.8"
D23V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  12P GAIN MUTATED                                        36
  12P GAIN WILD-TYPE                                     359
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  12P GAIN MUTATED                               3
  12P GAIN WILD-TYPE                            18
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  12P GAIN MUTATED                                  31
  12P GAIN WILD-TYPE                                81
D23V3, multiclass
                                         clus
vv                                        12P GAIN MUTATED 12P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               36                359
  MIXED SEROUS AND ENDOMETRIOID                          3                 18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     31                 81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V4, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    13  57
  12P GAIN WILD-TYPE 128 330
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     13   57
  12P GAIN WILD-TYPE  128  330
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                13                128
  YES               57                330
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12P GAIN MUTATED    52   1   2   4
  12P GAIN WILD-TYPE 311  22  15  31
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               52                311
  R1                1                 22
  R2                2                 15
  RX                4                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P GAIN MUTATED                                  0     6
  12P GAIN WILD-TYPE                                4    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  12P GAIN MUTATED                          18
  12P GAIN WILD-TYPE                        83
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12P GAIN MUTATED                                           2    42
  12P GAIN WILD-TYPE                                         7   324
D23V6, multiclass
                                           clus
vv                                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    6                 14
  BLACK OR AFRICAN AMERICAN                               18                 83
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                2                  7
  WHITE                                                   42                324
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     0  57
  12P GAIN WILD-TYPE  14 310
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      0   57
  12P GAIN WILD-TYPE   14  310
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 14
  NOT HISPANIC OR LATINO               57                310
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    50   3
  12Q GAIN WILD-TYPE 407  66
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                53                473 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                 66 
$`12Q GAIN MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0GE TCGA-A5-A0R7 TCGA-A5-A2K3 TCGA-AJ-A23M TCGA-AJ-A3BD 
      149.56       105.37        17.59        46.32         1.18        34.16 
TCGA-AJ-A3EM TCGA-AP-A05P TCGA-AP-A1DO TCGA-AP-A1E4 TCGA-AX-A05W TCGA-AX-A0IW 
       22.26        20.91        31.30        16.24        68.35        37.78 
TCGA-AX-A0J1 TCGA-AX-A1CA TCGA-AX-A2H4 TCGA-AX-A2HA TCGA-B5-A0JN TCGA-B5-A11R 
       65.88        20.28        30.12        81.37        80.38        33.50 
TCGA-B5-A11V TCGA-B5-A1N2 TCGA-B5-A5OC TCGA-BG-A0M2 TCGA-BG-A0M8 TCGA-BG-A0MG 
       19.56        12.79        41.06        20.94        36.49        48.56 
TCGA-BG-A0W1 TCGA-BG-A18C TCGA-BG-A2AE TCGA-BG-A3PP TCGA-BS-A0TE TCGA-BS-A0U9 
       52.83        15.45        23.70         6.81         4.80        67.20 
TCGA-BS-A0V7 TCGA-D1-A16O TCGA-D1-A1NY TCGA-D1-A1O0 TCGA-D1-A2G5 TCGA-D1-A3JP 
       63.58        33.63        16.87         2.07        41.42        16.93 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-E6-A8L9 TCGA-EO-A2CG TCGA-EO-A3AV TCGA-EO-A3AZ 
       24.30        35.38        27.32        51.42        35.15        27.16 
TCGA-EY-A1GO TCGA-EY-A1GR TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A72D TCGA-FI-A2D2 
       19.27        17.62        19.33        12.59         5.88        39.95 
TCGA-FI-A2D6 TCGA-FI-A2EY TCGA-FI-A3PX TCGA-KP-A3VZ TCGA-PG-A7D5 
        8.98        28.93        45.01        23.74        23.97 

$`12Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       17.85        32.78       112.54        87.32        74.10        57.53 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       65.75        60.53        60.53        46.55        38.37        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 
       28.27        20.81        23.21        68.65        19.96        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95         7.92        11.44 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A2K5 
       36.33         9.60         8.02        91.04        28.64         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
        5.16         7.33        14.96        14.43        10.26         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG 
       19.79        29.39         2.40        34.36         1.12         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 
       18.90         1.68         1.64        14.66        22.49        17.06 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH 
       20.81        36.99        20.65        21.21        15.62        10.19 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV 
       15.35        15.95        14.76        16.87        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       12.82        20.78         2.70         0.13        83.67        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D 
        5.95        23.31        86.07         8.22        63.91        57.80 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A0L8 TCGA-AP-A0L9 
       45.53        36.89        23.87        12.20        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      117.99       110.37         3.39        63.16        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       31.73        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       55.89        35.54        46.78        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       10.42        27.85        21.90        36.13         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       19.82        29.69        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       66.58        34.98        53.92        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        35.01        28.54        43.82        40.11 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC 
       13.28        19.20        16.96        13.55        15.25        12.43 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       20.05        76.83        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       36.39        11.08         4.77        71.24        40.80        61.18 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       34.32        46.49        19.36        26.33        17.75        30.74 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
        2.96        31.13        64.93         0.23         0.20         0.56 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 
       43.82         0.20        20.52         1.38         0.30         0.26 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR 
        0.30         1.18        18.35        14.47         0.39        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       46.75        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        27.29        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E 
       13.74        17.10        17.85        11.01         4.11         8.71 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L 
      185.79       113.36        88.34        75.72        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U 
       43.96        40.50        36.82        32.09        27.35        16.73 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS 
       19.50        18.41        17.36        16.57       191.84       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        14.40        14.70        11.70        11.87        15.29 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH 
      116.25        96.30        78.81        62.14        33.11        14.27 
TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       29.65        34.13        34.95        18.61        20.19        19.33 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       35.21        34.98        22.06        38.37        28.27        10.72 
TCGA-BG-A0MC TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       41.52        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       34.29        52.64        56.58        14.83        12.56        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.73        14.01        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.02        20.12        11.31        35.90        34.98         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD 
       10.22        10.16        31.76        24.99        24.13        16.64 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        23.47        85.55 
TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
       78.21        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       97.41        88.34        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ 
       73.25        59.51        62.79        49.55        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       37.51        36.79        27.42        11.51        29.92        31.07 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       10.65         0.69        18.67         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
        2.33        22.92         1.41        13.22         0.72        18.25 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 
       18.02        15.06         1.05         3.95         3.52         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KV TCGA-DF-A2KY 
       44.88         0.26         4.27         4.11        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1NO TCGA-DI-A2QT 
       27.16        16.31        39.29        36.62         9.37        12.39 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       31.10       110.10        23.38        48.36        17.06         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
        6.67        16.04         7.36        16.80        10.92        49.15 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       37.71        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3B0 
       51.52        19.40        34.39        26.43        17.19        17.88 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 
       26.96        22.26        16.34        14.53        24.89         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99         4.54        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP 
       23.34        23.90        22.78        13.97         6.90        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       17.88        15.09        16.11        12.43        15.81        11.08 
TCGA-EY-A1GX TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
        6.48        10.19        14.40        18.87        22.82        20.05 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       45.76        31.04        29.10        27.35        13.84        11.38 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX 
       17.92        14.14        19.89        14.70        16.96        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2EU TCGA-FI-A2EW 
       41.06        39.88         7.99        13.84        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR 
        9.07        28.96        25.02        29.23        41.06         1.74 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 
        7.76        14.04         2.43        13.28         9.47        26.10 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 
       18.21        23.24        15.45        12.92         7.00        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        18.84        39.95        12.92        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44        14.07        18.28         0.07         0.23 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              1.18               0.07 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            149.56             191.84 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             27.32              22.82 
[1] "1.2 - 149.6 (27.3)" "0.1 - 191.8 (22.8)"
[1] "hr=" "2.8"
D24V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  12Q GAIN MUTATED                                        32
  12Q GAIN WILD-TYPE                                     363
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  12Q GAIN MUTATED                               3
  12Q GAIN WILD-TYPE                            18
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  12Q GAIN MUTATED                                  18
  12Q GAIN WILD-TYPE                                94
D24V3, multiclass
                                         clus
vv                                        12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               32                363
  MIXED SEROUS AND ENDOMETRIOID                          3                 18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     18                 94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V4, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     9  44
  12Q GAIN WILD-TYPE 132 343
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      9   44
  12Q GAIN WILD-TYPE  132  343
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 9                132
  YES               44                343
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN MUTATED    40   1   3   3
  12Q GAIN WILD-TYPE 323  22  14  32
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               40                323
  R1                1                 22
  R2                3                 14
  RX                3                 32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q GAIN MUTATED                                  0     5
  12Q GAIN WILD-TYPE                                4    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  12Q GAIN MUTATED                          12
  12Q GAIN WILD-TYPE                        89
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12Q GAIN MUTATED                                           2    32
  12Q GAIN WILD-TYPE                                         7   334
D24V6, multiclass
                                           clus
vv                                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    5                 15
  BLACK OR AFRICAN AMERICAN                               12                 89
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                2                  7
  WHITE                                                   32                334
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     0  42
  12Q GAIN WILD-TYPE  14 325
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0   42
  12Q GAIN WILD-TYPE   14  325
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 14
  NOT HISPANIC OR LATINO               42                325
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    24   5
  13Q GAIN WILD-TYPE 433  64
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                29                497 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                 64 
$`13Q GAIN MUTATED`
TCGA-A5-A1OG TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF 
       11.44         1.18        14.43        48.79       125.42         3.39 
TCGA-AX-A0IW TCGA-B5-A0JN TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A1MS TCGA-B5-A5OD 
       37.78        80.38        17.85        75.72       102.31        34.13 
TCGA-BK-A26L TCGA-D1-A15V TCGA-D1-A165 TCGA-D1-A16I TCGA-D1-A16S TCGA-DI-A2QY 
       24.13        39.48         0.66        11.51        18.67       110.10 
TCGA-EO-A1Y5 TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3B1 TCGA-EY-A1GO TCGA-EY-A210 
       10.92        51.52        51.42        26.96        19.27        12.59 
TCGA-EY-A214 TCGA-EY-A54A TCGA-FI-A2F9 TCGA-PG-A914 TCGA-PG-A915 
       14.40        14.70        29.23        12.92         7.00 

$`13Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       38.37        36.82        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       19.96        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 
       15.95         7.92        36.33         9.60         8.02        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       46.32        28.64         5.33         5.16         7.33        14.96 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
       10.26         0.39        19.79        29.39         2.40        34.36 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       34.16         1.12         0.76        18.90         1.68         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC 
       14.66        22.49        22.26        17.06        20.81        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       20.65        21.21        15.62        10.19        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       14.76        16.87        16.87        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        2.70         0.13        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        63.91        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       23.87        12.20        20.91       117.99       110.37        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       33.40        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        60.36        55.89        31.30        35.54        46.78 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        30.90        10.42        27.85        16.24 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       21.90        36.13         0.56        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       34.98        53.92        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        35.01        28.54        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       13.28        19.20        16.96        13.55        15.25        20.28 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       12.43        20.05        76.83        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       25.12        36.39        11.08         4.77        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       40.80        61.18        81.37        34.32        46.49        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       26.33        17.75        30.74         2.96        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
        0.23         0.20         0.56        43.82         0.20        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        1.38         0.30         0.26         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       14.47         0.39        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       25.91        27.29        17.88        13.74        17.10        11.01 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J 
        4.11         8.71       185.79       113.36        88.34        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R 
       45.90        43.96        40.50        36.82        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       16.57       191.84        50.89        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       11.87        15.29        12.79       116.25        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE 
       62.14        33.11        14.27        29.65        41.06        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       22.06        38.37        36.49        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        52.64        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 
       13.78        14.73        14.01        15.45        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
        1.81         9.57        20.02        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
        6.81        35.90        34.98         6.21        10.22        10.16 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       31.76        24.99        16.64        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ 
       59.51        62.79        63.58        49.55        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        21.99 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       27.42        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02        14.73         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 
       13.22         0.72        18.25        16.87        18.02         2.07 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV 
       44.88         0.26         4.27         4.11        16.93        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ 
       35.38         9.37        12.39        31.10        23.38        48.36 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       17.06         2.37         6.67        27.32        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       16.80        49.15        37.71        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       46.26        57.60        19.40        34.39        26.43        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX 
       17.19        27.16        17.88        22.26        16.34        14.53 
TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       24.89         6.21        14.99         4.54        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL 
       27.16        23.34        23.34        23.90        22.78        13.97 
TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT 
        6.90        18.84        17.88        17.62        15.09        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A212 
       12.43        15.81        11.08         6.48        19.33        10.19 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       18.87        22.82        20.05        45.76        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       27.35        13.84        11.38        17.92        14.14        19.89 
TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
       16.96         5.88        40.01        41.06        39.88        39.95 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
        7.99        13.84         8.98        96.69        59.01         9.07 
TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR 
       28.93        28.96        25.02        41.06        45.01         1.74 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 
        7.76        14.04         2.43        23.74        13.28         9.47 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A916 
       26.10        18.21        23.24        15.45        23.97        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        18.84        39.95        12.92        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44        14.07        18.28         0.07         0.23 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.66               0.07 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            125.42             191.84 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             19.27              23.34 
[1] "0.7 - 125.4 (19.3)" "0.1 - 191.8 (23.3)"
[1] "hr=" "1.1"
D25V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  13Q GAIN MUTATED                                         8
  13Q GAIN WILD-TYPE                                     387
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  13Q GAIN MUTATED                               1
  13Q GAIN WILD-TYPE                            20
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  13Q GAIN MUTATED                                  20
  13Q GAIN WILD-TYPE                                92
D25V3, multiclass
                                         clus
vv                                        13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                8                387
  MIXED SEROUS AND ENDOMETRIOID                          1                 20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     20                 92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V4, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     9  20
  13Q GAIN WILD-TYPE 132 367
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      9   20
  13Q GAIN WILD-TYPE  132  367
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 9                132
  YES               20                367
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  13Q GAIN MUTATED    19   0   2   3
  13Q GAIN WILD-TYPE 344  23  15  32
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0               19                344
  R1                0                 23
  R2                2                 15
  RX                3                 32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q GAIN MUTATED                                  0     2
  13Q GAIN WILD-TYPE                                4    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  13Q GAIN MUTATED                           8
  13Q GAIN WILD-TYPE                        93
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  13Q GAIN MUTATED                                           0    17
  13Q GAIN WILD-TYPE                                         9   349
D25V6, multiclass
                                           clus
vv                                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    2                 18
  BLACK OR AFRICAN AMERICAN                                8                 93
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  9
  WHITE                                                   17                349
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     0  18
  13Q GAIN WILD-TYPE  14 349
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0   18
  13Q GAIN WILD-TYPE   14  349
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 14
  NOT HISPANIC OR LATINO               18                349
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    28   8
  14Q GAIN WILD-TYPE 429  61
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                36                490 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 8                 61 
$`14Q GAIN MUTATED`
TCGA-A5-A1OH TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A3LP TCGA-AJ-A3EM TCGA-AJ-A3IA 
       36.33         8.02        91.04        14.96        22.26        20.81 
TCGA-AJ-A3NF TCGA-AJ-A3TW TCGA-AP-A3K1 TCGA-AX-A1CC TCGA-AX-A1CR TCGA-AX-A2H4 
       21.21        16.87        21.90        12.43        11.08        30.12 
TCGA-B5-A0JR TCGA-B5-A0K4 TCGA-B5-A1MU TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A26L 
       56.91        17.88        50.89         6.81        35.90        24.13 
TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-D1-A169 TCGA-D1-A1O0 TCGA-D1-A2G5 TCGA-DI-A2QY 
       16.64        67.20        37.32         2.07        41.42       110.10 
TCGA-E6-A1M0 TCGA-EO-A1Y5 TCGA-EO-A22Y TCGA-EO-A3B1 TCGA-EY-A1GC TCGA-EY-A1GW 
       17.06        10.92        51.52        26.96         4.54        11.08 
TCGA-EY-A4KR TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-K6-A3WQ 
       11.38        39.95        59.01         9.07        28.93        14.04 

$`14Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       38.37        36.82        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       19.96        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K4 
       15.95         7.92        11.44         9.60        46.32        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O 
        5.33         5.16         7.33         1.18        14.43        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
        0.39        19.79        29.39         2.40        34.36        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
        1.12         0.76        18.90         1.68         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3NH 
       22.49        17.06        36.99        20.65        15.62        10.19 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.35        15.95        14.76        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       20.78         2.70         0.13        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
       23.31        86.07         8.22        63.91        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       36.89        23.87        12.20        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      117.99       110.37         3.39        63.16        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       31.73        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       55.89        31.30        35.54        46.78        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO 
       30.90        10.42        27.85        16.24        36.13         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D 
       35.34        45.99        66.58        34.98        53.92        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       51.09        27.39        30.02        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CE TCGA-AX-A1CF 
       16.96        13.55        15.25        20.28        20.05        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H2 
       72.56        54.12        67.50        25.12        36.39         4.77 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       71.24        40.80        61.18        81.37        34.32        46.49 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       19.36        26.33        17.75        30.74         2.96        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       64.93         0.23         0.20         0.56        43.82         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
       20.52         1.38         0.30         0.26         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JS TCGA-B5-A0JT 
       18.35        14.47         0.39        80.38        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       30.51        25.91        27.29        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       11.01         4.11         8.71       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
       75.72        54.44        45.90        43.96        40.50        36.82 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV 
       18.41        17.36        16.57       191.84       102.31        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       14.70        11.70        11.87        15.29        12.79       116.25 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 
       96.30        78.81        62.14        33.11        14.27        29.65 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       41.06        34.13        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98        22.06        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       15.45        15.45        14.27         1.81         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       23.70        20.12        11.31        34.98         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       10.16        31.76        24.99        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA 
       61.87        67.99        96.49        30.74        97.41        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       62.79        63.58        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
        0.66        15.72        36.10        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
        0.69        18.67         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
       22.92         1.41        13.22         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 
       18.02        15.06         1.05         3.95         3.52         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV 
       44.88         0.26         4.27         4.11        16.93        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ 
       35.38         9.37        12.39        31.10        23.38        48.36 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
        2.37         6.67        27.32        16.04         7.36        16.80 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       49.15        37.71        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       57.60        51.42        19.40        34.39        26.43        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX 
       17.19        27.16        17.88        22.26        16.34        14.53 
TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       24.89         6.21        14.99        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       23.34        23.34        23.90        22.78        13.97         6.90 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT 
       19.27        18.84        17.88        17.62        15.09        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 
       12.43        15.81         6.48        19.33        12.59        10.19 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       14.40        18.87        22.82        20.05        45.76        31.04 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       29.10        27.35        13.84        17.92        14.14        19.89 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
       14.70        16.96         5.88        40.01        41.06        39.88 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2F4 TCGA-FI-A2F8 
        7.99        13.84         8.98        96.69        28.96        25.02 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KJ-A3U4 
       29.23        41.06        45.01         1.74         7.76         2.43 
TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
       23.74        13.28         9.47        26.10        18.21        23.24 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 
       15.45        23.97        12.92         7.00        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 
       18.84        39.95        12.92        23.64        14.83         4.44 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.07        18.28         0.07         0.23 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              2.07               0.07 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            110.10             191.84 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            21.555             23.425 
[1] "2.1 - 110.1 (21.6)" "0.1 - 191.8 (23.4)"
[1] "hr=" "1.8"
D26V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  14Q GAIN MUTATED                                        14
  14Q GAIN WILD-TYPE                                     381
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  14Q GAIN MUTATED                               2
  14Q GAIN WILD-TYPE                            19
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  14Q GAIN MUTATED                                  20
  14Q GAIN WILD-TYPE                                92
D26V3, multiclass
                                         clus
vv                                        14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               14                381
  MIXED SEROUS AND ENDOMETRIOID                          2                 19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     20                 92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V4, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     3  33
  14Q GAIN WILD-TYPE 138 354
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      3   33
  14Q GAIN WILD-TYPE  138  354
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 3                138
  YES               33                354
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  14Q GAIN MUTATED    24   2   1   5
  14Q GAIN WILD-TYPE 339  21  16  30
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0               24                339
  R1                2                 21
  R2                1                 16
  RX                5                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q GAIN MUTATED                                  0     0
  14Q GAIN WILD-TYPE                                4    20
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  14Q GAIN MUTATED                           3
  14Q GAIN WILD-TYPE                        98
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  14Q GAIN MUTATED                                           1    29
  14Q GAIN WILD-TYPE                                         8   337
D26V6, multiclass
                                           clus
vv                                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    0                 20
  BLACK OR AFRICAN AMERICAN                                3                 98
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   29                337
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     1  27
  14Q GAIN WILD-TYPE  13 340
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1   27
  14Q GAIN WILD-TYPE   13  340
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 13
  NOT HISPANIC OR LATINO               27                340
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED     7   3
  15Q GAIN WILD-TYPE 450  66
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                10                516 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 3                 66 
$`15Q GAIN MUTATED`
TCGA-AJ-A3IA TCGA-AX-A3G1 TCGA-B5-A11I TCGA-BS-A0TE TCGA-D1-A102 TCGA-DI-A1NN 
       20.81        20.52        75.72         4.80         4.44        35.38 
TCGA-E6-A1M0 TCGA-EY-A1GW TCGA-EY-A72D TCGA-PG-A5BC 
       17.06        11.08         5.88        23.24 

$`15Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       38.37        36.82        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       19.96        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK 
       15.95         7.92        11.44        36.33         9.60         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
       91.04        46.32        28.64         5.33         5.16         7.33 
TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       14.96         1.18        14.43        10.26         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG 
       29.39         2.40        34.36        34.16         1.12         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       18.90         1.68         1.64        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH 
       17.06        36.99        20.65        21.21        15.62        10.19 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV 
       15.35        15.95        14.76        16.87        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       12.82        20.78         2.70         0.13        83.67        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D 
        5.95        23.31        86.07         8.22        63.91        57.80 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 
       45.53        36.89        23.87        12.20        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
      125.42       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       60.36        55.89        31.30        35.54        46.78        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        30.90        10.42        27.85        16.24        21.90 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       36.13         0.56        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       53.92        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       35.01        28.54        37.78        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       13.28        19.20        16.96        13.55        15.25        20.28 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       12.43        20.05        76.83        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       25.12        36.39        11.08         4.77        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       40.80        61.18        81.37        34.32        46.49        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       26.33        17.75        30.74         2.96        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G3 
        0.23         0.20         0.56        43.82         0.20         1.38 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.30         0.26         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
        0.39        80.38        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        27.29        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       11.01         4.11         8.71       185.79       113.36        88.34 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q 
       54.44        45.90        43.96        40.50        36.82        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       33.50        27.35        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV 
       17.36        16.57       191.84       102.31        50.89        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       14.70        11.70        11.87        15.29        12.79       116.25 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 
       96.30        78.81        62.14        33.11        14.27        29.65 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       41.06        34.13        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98        22.06        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       15.45        15.45        14.27         1.81         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31         6.81        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
        6.21        10.22        10.16        31.76        24.99        24.13 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       16.64        13.18        10.03         9.86        46.95        23.47 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       85.55        78.21        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       30.74        97.41        67.20        88.34        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        72.72        73.25        59.51        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       49.55        63.16        66.48        16.83        19.79        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I 
       37.32        36.36        37.51        36.79        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02        14.73         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 
       13.22         0.72        18.25        16.87        18.02         2.07 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV 
       44.88         0.26         4.27         4.11        16.93        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ 
        9.37        12.39        31.10       110.10        23.38        48.36 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
        2.37         6.67        27.32        16.04         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       10.92        49.15        37.71        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       46.26        57.60        51.52        51.42        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 
       26.43        35.15        17.19        27.16        17.88        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       22.26        16.34        14.53        24.89         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.90        22.78        13.97         6.90        19.27        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       17.88        17.62        15.09        16.11        12.43        15.81 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 
        6.48        19.33        12.59        10.19        14.40        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 
       22.82        20.05        45.76        31.04        29.10        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       13.84        11.38        17.92        14.14        19.89        14.70 
TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
       16.96        40.01        41.06        39.88        39.95         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       13.84         8.98        96.69        59.01         9.07        28.93 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR 
       28.96        25.02        29.23        41.06        45.01         1.74 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 
        7.76        14.04         2.43        23.74        13.28         9.47 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       26.10        18.21        15.45        23.97        12.92         7.00 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       11.24         6.97        18.84        39.95        12.92        23.64 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83         4.44        14.07        18.28         0.07         0.23 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              4.44               0.07 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             75.72             191.84 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             18.79              23.47 
[1] "4.4 - 75.7 (18.8)"  "0.1 - 191.8 (23.5)"
[1] "hr=" "3.5"
D27V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  15Q GAIN MUTATED                                         7
  15Q GAIN WILD-TYPE                                     388
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  15Q GAIN MUTATED                               0
  15Q GAIN WILD-TYPE                            21
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  15Q GAIN MUTATED                                   3
  15Q GAIN WILD-TYPE                               109
D27V3, multiclass
                                         clus
vv                                        15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                7                388
  MIXED SEROUS AND ENDOMETRIOID                          0                 21
  SEROUS ENDOMETRIAL ADENOCARCINOMA                      3                109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V4, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     1   9
  15Q GAIN WILD-TYPE 140 378
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1    9
  15Q GAIN WILD-TYPE  140  378
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 1                140
  YES                9                378
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  15Q GAIN MUTATED     4   1   1   1
  15Q GAIN WILD-TYPE 359  22  16  34
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0                4                359
  R1                1                 22
  R2                1                 16
  RX                1                 34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q GAIN MUTATED                                  0     1
  15Q GAIN WILD-TYPE                                4    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  15Q GAIN MUTATED                           3
  15Q GAIN WILD-TYPE                        98
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  15Q GAIN MUTATED                                           0     6
  15Q GAIN WILD-TYPE                                         9   360
D27V6, multiclass
                                           clus
vv                                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    1                 19
  BLACK OR AFRICAN AMERICAN                                3                 98
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  9
  WHITE                                                    6                360
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     1   8
  15Q GAIN WILD-TYPE  13 359
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1    8
  15Q GAIN WILD-TYPE   13  359
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 13
  NOT HISPANIC OR LATINO                8                359
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    25   2
  16P GAIN WILD-TYPE 432  67
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                27                499 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 2                 67 
$`16P GAIN MUTATED`
TCGA-A5-A2K2 TCGA-A5-A3LP TCGA-AX-A0IW TCGA-AX-A1C8 TCGA-AX-A3G1 TCGA-B5-A11G 
       91.04        14.96        37.78        13.55        20.52       113.36 
TCGA-B5-A11V TCGA-B5-A1N2 TCGA-BG-A0M8 TCGA-BG-A0VT TCGA-BK-A26L TCGA-BS-A0U9 
       19.56        12.79        36.49        24.39        24.13        67.20 
TCGA-D1-A102 TCGA-D1-A168 TCGA-EO-A1Y7 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC 
        4.44        36.10        49.15        22.26        16.34         4.54 
TCGA-EY-A1GW TCGA-EY-A547 TCGA-EY-A54A TCGA-EY-A72D TCGA-FI-A2D2 TCGA-FI-A2EW 
       11.08        17.92        14.70         5.88        39.95        59.01 
TCGA-PG-A914 TCGA-PG-A915 TCGA-SL-A6J9 
       12.92         7.00         0.07 

$`16P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       38.37        36.82        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       19.96        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK 
       15.95         7.92        11.44        36.33         9.60         8.02 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23M 
       46.32        28.64         5.33         5.16         7.33         1.18 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
       14.43        10.26         0.39        19.79        29.39         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
       34.36        34.16         1.12         0.76        18.90         1.68 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA 
        1.64        14.66        22.49        22.26        17.06        20.81 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ 
       36.99        20.65        21.21        15.62        10.19        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.95        14.76        16.87        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       20.78         2.70         0.13        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
       23.31        86.07         8.22        63.91        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       36.89        23.87        12.20        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      117.99       110.37         3.39        63.16        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       31.73        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       55.89        31.30        35.54        46.78        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
       30.90        10.42        27.85        16.24        21.90        36.13 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       28.54        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       16.96        15.25        20.28        12.43        20.05        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR 
       72.56        54.12        67.50        25.12        36.39        11.08 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
        4.77        30.12        71.24        40.80        61.18        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       34.32        46.49        19.36        26.33        17.75        30.74 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
        2.96        31.13        64.93         0.23         0.20         0.56 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
       43.82         0.20         1.38         0.30         0.26         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR 
        1.18        18.35        14.47         0.39        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       46.75        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        27.29        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E 
       13.74        17.10        17.85        11.01         4.11         8.71 
TCGA-B5-A11F TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      185.79        88.34        75.72        54.44        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       40.50        36.82        32.09        33.50        27.35        16.73 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS 
       19.50        18.41        17.36        16.57       191.84       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        14.40        14.70        11.70        11.87        15.29 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH 
      116.25        96.30        78.81        62.14        33.11        14.27 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       29.65        41.06        34.13        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98        22.06        38.37 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        20.02        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31         6.81        35.90        34.98         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F 
       10.22        10.16        31.76        24.99        16.64        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        23.47        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       97.41        88.34        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI 
       73.25        59.51        62.79        63.58        49.55        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 
        4.87        28.67        23.93        22.55         1.74        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
       32.58         0.66        15.72        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       36.79        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       10.65         0.69        18.67         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
        2.33        22.92         1.41        13.22         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.52        41.42         8.48        44.88         0.26         4.27 
TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        4.11        16.93        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT 
       39.29        36.62        24.30        35.38         9.37        12.39 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       31.10       110.10        23.38        48.36        17.06         2.37 
TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        6.67        27.32        16.04         7.36        16.80        10.92 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       37.71        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       51.52        51.42        19.40        34.39        26.43        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KX TCGA-EO-A3L0 
       17.19        27.16        17.88        26.96        14.53        24.89 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
        6.21        14.99        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       23.34        23.90        22.78        13.97         6.90        19.27 
TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       18.84        17.88        17.62        15.09        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 
       15.81         6.48        19.33        12.59        10.19        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       18.87        22.82        20.05        45.76        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 
       27.35        13.84        11.38        14.14        19.89        16.96 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       40.01        41.06        39.88         7.99        13.84         8.98 
TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 
       96.69         9.07        28.93        28.96        25.02        29.23 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 
       41.06        45.01         1.74         7.76        14.04         2.43 
TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
       23.74        13.28         9.47        26.10        18.21        23.24 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       15.45        23.97        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       12.92        23.64        14.83         4.44        14.07        18.28 
TCGA-SL-A6JA 
        0.23 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.07               0.13 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            113.36             191.84 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             19.56              23.47 
[1] "0.1 - 113.4 (19.6)" "0.1 - 191.8 (23.5)"
[1] "hr=" "1.8"
D28V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  16P GAIN MUTATED                                        15
  16P GAIN WILD-TYPE                                     380
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  16P GAIN MUTATED                               1
  16P GAIN WILD-TYPE                            20
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  16P GAIN MUTATED                                  11
  16P GAIN WILD-TYPE                               101
D28V3, multiclass
                                         clus
vv                                        16P GAIN MUTATED 16P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               15                380
  MIXED SEROUS AND ENDOMETRIOID                          1                 20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     11                101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V4, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     3  24
  16P GAIN WILD-TYPE 138 363
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      3   24
  16P GAIN WILD-TYPE  138  363
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 3                138
  YES               24                363
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16P GAIN MUTATED    17   2   0   4
  16P GAIN WILD-TYPE 346  21  17  31
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               17                346
  R1                2                 21
  R2                0                 17
  RX                4                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P GAIN MUTATED                                  0     0
  16P GAIN WILD-TYPE                                4    20
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  16P GAIN MUTATED                          10
  16P GAIN WILD-TYPE                        91
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16P GAIN MUTATED                                           1    13
  16P GAIN WILD-TYPE                                         8   353
D28V6, multiclass
                                           clus
vv                                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    0                 20
  BLACK OR AFRICAN AMERICAN                               10                 91
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   13                353
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     1  19
  16P GAIN WILD-TYPE  13 348
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   19
  16P GAIN WILD-TYPE   13  348
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 13
  NOT HISPANIC OR LATINO               19                348
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED     9   1
  16Q GAIN WILD-TYPE 448  68
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                10                516 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                 68 
$`16Q GAIN MUTATED`
TCGA-AX-A1C8 TCGA-AX-A2HH TCGA-B5-A0JN TCGA-B5-A11V TCGA-BK-A26L TCGA-BS-A0U9 
       13.55        17.75        80.38        19.56        24.13        67.20 
TCGA-EY-A1GW TCGA-EY-A54A TCGA-FI-A2D2 TCGA-JU-AAVI 
       11.08        14.70        39.95         7.76 

$`16Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       38.37        36.82        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       19.96        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK 
       15.95         7.92        11.44        36.33         9.60         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
       91.04        46.32        28.64         5.33         5.16         7.33 
TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       14.96         1.18        14.43        10.26         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG 
       29.39         2.40        34.36        34.16         1.12         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       18.90         1.68         1.64        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       17.06        20.81        36.99        20.65        21.21        15.62 
TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW 
       10.19        15.35        15.95        14.76        16.87        16.87 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       22.32        12.82        20.78         2.70         0.13        83.67 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
       21.99         5.95        23.31        86.07         8.22        63.91 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       57.80        45.53        36.89        23.87        12.20        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       33.40        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        60.36        55.89        31.30        35.54        46.78 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        30.90        10.42        27.85        16.24 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       21.90        36.13         0.56        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       34.98        53.92        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       60.66        35.01        28.54        37.78        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C9 TCGA-AX-A1CA 
       65.88        13.28        19.20        16.96        15.25        20.28 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       12.43        20.05        76.83        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       25.12        36.39        11.08         4.77        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       40.80        61.18        81.37        34.32        46.49        19.36 
TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       26.33        30.74         2.96        31.13        64.93         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
        0.20         0.56        43.82         0.20        20.52         1.38 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.30         0.26         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
        0.39        56.91        46.75        43.13        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       44.71        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        17.88        13.74        17.10        17.85        11.01 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
        4.11         8.71       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q 
       54.44        45.90        43.96        40.50        36.82        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       33.50        27.35        16.73        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW 
       16.57       191.84       102.31        50.89        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       11.70        11.87        15.29        12.79       116.25        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       78.81        62.14        33.11        14.27        29.65        41.06 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       34.13        34.95        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98        22.06        38.37        36.49        28.27 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        20.02        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31         6.81        35.90        34.98         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F 
       10.22        10.16        31.76        24.99        16.64        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        23.47        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       97.41        88.34        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI 
       73.25        59.51        62.79        63.58        49.55        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       36.36        37.51        36.79        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
       31.07        33.63        10.65         0.69        18.67         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
        0.72        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 
        1.05         3.95         3.52        41.42         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY 
        0.26         4.27         4.11        16.93        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
       27.16        16.31        39.29        36.62        24.30        35.38 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ 
        9.37        12.39        31.10       110.10        23.38        48.36 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       17.06         2.37         6.67        27.32        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
       16.80        10.92        49.15        37.71        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH 
       66.90        46.26        57.60        51.52        51.42        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       34.39        26.43        35.15        17.19        27.16        17.88 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 
       26.96        22.26        16.34        14.53        24.89         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99         4.54        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       23.34        23.90        22.78        13.97         6.90        19.27 
TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       18.84        17.88        17.62        15.09        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 
       15.81         6.48        19.33        12.59        10.19        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       18.87        22.82        20.05        45.76        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       27.35        13.84        11.38        17.92        14.14        19.89 
TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
       16.96         5.88        40.01        41.06        39.88         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       13.84         8.98        96.69        59.01         9.07        28.93 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR 
       28.96        25.02        29.23        41.06        45.01         1.74 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 
       14.04         2.43        23.74        13.28         9.47        26.10 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       18.21        23.24        15.45        23.97        12.92         7.00 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       11.24         6.97        18.84        39.95        12.92        23.64 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83         4.44        14.07        18.28         0.07         0.23 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              7.76               0.07 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             80.38             191.84 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            18.655             23.360 
[1] "7.8 - 80.4 (18.7)"  "0.1 - 191.8 (23.4)"
[1] "hr=" "1.2"
D29V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  16Q GAIN MUTATED                                         5
  16Q GAIN WILD-TYPE                                     390
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  16Q GAIN MUTATED                               1
  16Q GAIN WILD-TYPE                            20
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  16Q GAIN MUTATED                                   4
  16Q GAIN WILD-TYPE                               108
D29V3, multiclass
                                         clus
vv                                        16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                5                390
  MIXED SEROUS AND ENDOMETRIOID                          1                 20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                      4                108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V4, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     1   9
  16Q GAIN WILD-TYPE 140 378
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1    9
  16Q GAIN WILD-TYPE  140  378
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 1                140
  YES                9                378
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16Q GAIN MUTATED     3   3   0   2
  16Q GAIN WILD-TYPE 360  20  17  33
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0                3                360
  R1                3                 20
  R2                0                 17
  RX                2                 33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q GAIN MUTATED                                  0     0
  16Q GAIN WILD-TYPE                                4    20
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  16Q GAIN MUTATED                           4
  16Q GAIN WILD-TYPE                        97
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16Q GAIN MUTATED                                           1     5
  16Q GAIN WILD-TYPE                                         8   361
D29V6, multiclass
                                           clus
vv                                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    0                 20
  BLACK OR AFRICAN AMERICAN                                4                 97
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                    5                361
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     1   7
  16Q GAIN WILD-TYPE  13 360
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1    7
  16Q GAIN WILD-TYPE   13  360
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 13
  NOT HISPANIC OR LATINO                7                360
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED     9   3
  17P GAIN WILD-TYPE 448  66
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                12                514 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                 66 
$`17P GAIN MUTATED`
TCGA-A5-A0R7 TCGA-AJ-A3IA TCGA-AX-A1C4 TCGA-AX-A2HK TCGA-BG-A0M4 TCGA-BK-A0CC 
       17.59        20.81        13.28         2.96        34.98        10.22 
TCGA-D1-A1O0 TCGA-DI-A2QY TCGA-EO-A3B1 TCGA-EY-A1GO TCGA-K6-A3WQ TCGA-SL-A6J9 
        2.07       110.10        26.96        19.27        14.04         0.07 

$`17P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       38.37        36.82        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       19.96        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 
        7.92        11.44        36.33         9.60         8.02        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       46.32        28.64         5.33         5.16         7.33        14.96 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM 
        1.18        14.43        10.26         0.39        19.79        29.39 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI 
        2.40        34.36        34.16         1.12         0.76        18.90 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
        1.68         1.64        14.66        22.49        22.26        17.06 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ 
       36.99        20.65        21.21        15.62        10.19        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.95        14.76        16.87        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       20.78         2.70         0.13        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
       23.31        86.07         8.22        63.91        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       36.89        23.87        12.20        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      117.99       110.37         3.39        63.16        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       31.73        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       55.89        31.30        35.54        46.78        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
       30.90        10.42        27.85        16.24        21.90        36.13 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C5 
       28.54        37.78        43.82        40.11        65.88        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       16.96        13.55        15.25        20.28        12.43        20.05 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       76.83        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       11.08         4.77        30.12        71.24        40.80        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       81.37        34.32        46.49        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
       30.74        31.13        64.93         0.23         0.20         0.56 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 
       43.82         0.20        20.52         1.38         0.30         0.26 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN 
        0.30         1.18        18.35        14.47         0.39        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        46.75        43.13        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB 
       17.88        13.74        17.10        17.85        11.01         4.11 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
        8.71       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R 
       45.90        43.96        40.50        36.82        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW 
       16.57       191.84       102.31        50.89        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       11.70        11.87        15.29        12.79       116.25        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       78.81        62.14        33.11        14.27        29.65        41.06 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       34.13        34.95        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       35.21        22.06        38.37        36.49        28.27        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 
       11.31         6.81        35.90        34.98         6.21        10.16 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
       31.76        24.99        24.13        16.64        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        23.47        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       67.20        88.34        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI 
       73.25        59.51        62.79        63.58        49.55        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       36.36        37.51        36.79        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
       31.07        33.63        10.65         0.69        18.67         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 
        0.72        18.25        16.87        18.02        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        3.95         3.52        41.42         8.48        44.88         0.26 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        4.27         4.11        16.93        89.33        10.92        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO 
       16.31        39.29        36.62        24.30        35.38         9.37 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       12.39        31.10        23.38        48.36        17.06         2.37 
TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        6.67        27.32        16.04         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       49.15        37.71        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       57.60        51.52        51.42        19.40        34.39        26.43 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KW 
       35.15        17.19        27.16        17.88        22.26        16.34 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       14.53        24.89         6.21        14.99         4.54        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK 
       24.36        27.16        23.34        23.34        23.90        22.78 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS 
       13.97         6.90        18.84        17.88        17.62        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        12.43        15.81        11.08         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
       12.59        10.19        14.40        18.87        22.82        20.05 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       45.76        31.04        29.10        27.35        13.84        11.38 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D 
       17.92        14.14        19.89        14.70        16.96         5.88 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
       40.01        41.06        39.88        39.95         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 
        8.98        96.69        59.01         9.07        28.93        28.96 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
       25.02        29.23        41.06        45.01         1.74         7.76 
TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 
        2.43        23.74        13.28         9.47        26.10        18.21 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 
       23.24        15.45        23.97        12.92         7.00        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        18.84        39.95        12.92        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
        4.44        14.07        18.28         0.23 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.07               0.13 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            110.10             191.84 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            15.815             23.470 
[1] "0.1 - 110.1 (15.8)" "0.1 - 191.8 (23.5)"
[1] "hr=" "2.6"
D30V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  17P GAIN MUTATED                                         7
  17P GAIN WILD-TYPE                                     388
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  17P GAIN MUTATED                               0
  17P GAIN WILD-TYPE                            21
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  17P GAIN MUTATED                                   5
  17P GAIN WILD-TYPE                               107
D30V3, multiclass
                                         clus
vv                                        17P GAIN MUTATED 17P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                7                388
  MIXED SEROUS AND ENDOMETRIOID                          0                 21
  SEROUS ENDOMETRIAL ADENOCARCINOMA                      5                107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V4, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     3   9
  17P GAIN WILD-TYPE 138 378
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      3    9
  17P GAIN WILD-TYPE  138  378
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 3                138
  YES                9                378
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17P GAIN MUTATED     7   1   0   3
  17P GAIN WILD-TYPE 356  22  17  32
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0                7                356
  R1                1                 22
  R2                0                 17
  RX                3                 32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P GAIN MUTATED                                  0     0
  17P GAIN WILD-TYPE                                4    20
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  17P GAIN MUTATED                           2
  17P GAIN WILD-TYPE                        99
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17P GAIN MUTATED                                           0     9
  17P GAIN WILD-TYPE                                         9   357
D30V6, multiclass
                                           clus
vv                                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    0                 20
  BLACK OR AFRICAN AMERICAN                                2                 99
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  9
  WHITE                                                    9                357
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     1   9
  17P GAIN WILD-TYPE  13 358
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1    9
  17P GAIN WILD-TYPE   13  358
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 13
  NOT HISPANIC OR LATINO                9                358
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    23   7
  17Q GAIN WILD-TYPE 434  62
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                30                496 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 7                 62 
$`17Q GAIN MUTATED`
TCGA-A5-A0GR TCGA-A5-A0R7 TCGA-AJ-A3IA TCGA-AJ-A3QS TCGA-AX-A1C4 TCGA-AX-A1CF 
       36.82        17.59        20.81        16.87        13.28        76.83 
TCGA-AX-A2H2 TCGA-AX-A2HK TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A1MY TCGA-BG-A0M2 
        4.77         2.96         4.11        75.72        11.87        20.94 
TCGA-BG-A0M4 TCGA-BG-A3PP TCGA-BK-A0CC TCGA-D1-A1O0 TCGA-D1-A3JP TCGA-DI-A1NN 
       34.98         6.81        10.22         2.07        16.93        35.38 
TCGA-EO-A2CH TCGA-EO-A3B1 TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A2ON TCGA-EY-A3L3 
       19.40        26.96        19.27        15.09        20.05        27.35 
TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-PG-A915 TCGA-SL-A6J9 
       11.38        14.70        45.01        14.04         7.00         0.07 

$`17Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       19.59        24.62        29.06        42.35        15.95         7.92 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 
       11.44        36.33         9.60         8.02        91.04        46.32 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M 
       28.64         5.33         5.16         7.33        14.96         1.18 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
       14.43        10.26         0.39        19.79        29.39         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
       34.36        34.16         1.12         0.76        18.90         1.68 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC 
        1.64        14.66        22.49        22.26        17.06        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       20.65        21.21        15.62        10.19        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
       14.76        16.87        22.32        12.82        20.78         2.70 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        0.13        83.67        21.99         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        63.91        57.80        45.53        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       12.20        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        46.78        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       27.85        16.24        21.90        36.13         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       45.99        66.58        34.98        53.92        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        35.01        28.54        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       43.82        40.11        65.88        19.20        16.96        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       15.25        20.28        12.43        20.05        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H5 
       67.50        25.12        36.39        11.08        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       40.80        61.18        81.37        34.32        46.49        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       26.33        17.75        30.74        31.13        64.93         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
        0.20         0.56        43.82         0.20        20.52         1.38 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.30         0.26         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
        0.39        80.38        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        27.29        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J 
       11.01         8.71       185.79       113.36        88.34        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R 
       45.90        43.96        40.50        36.82        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW 
       16.57       191.84       102.31        50.89        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       11.70        15.29        12.79       116.25        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       62.14        33.11        14.27        29.65        41.06        34.13 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M3 TCGA-BG-A0M6 
       34.95        18.61        20.19        19.33        35.21        22.06 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       38.37        36.49        28.27        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       23.47        43.30        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       52.64        52.83        56.58        14.83        12.56        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 
       14.73        14.01        15.45        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 
        9.57        20.02        23.70        20.12        11.31        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
       34.98         6.21        10.16        31.76        24.99        24.13 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       16.64        13.18        10.03         9.86        46.95        23.47 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF 
       96.49        30.74        97.41        67.20        88.34        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       63.58        49.55        63.16        66.48        16.83        19.79 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
        0.69        18.67         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
       22.92         1.41        13.22         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 
       18.02        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KV 
        8.48        44.88         0.26         4.27         4.11        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ 
        9.37        12.39        31.10       110.10        23.38        48.36 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       17.06         2.37         6.67        27.32        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
       16.80        10.92        49.15        37.71        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AS 
       66.90        46.26        57.60        51.52        51.42        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KU 
       26.43        35.15        17.19        27.16        17.88        22.26 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC 
       16.34        14.53        24.89         6.21        14.99         4.54 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR 
       22.78        13.97         6.90        18.84        17.88        17.62 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        12.43        15.81        11.08         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO 
       12.59        10.19        14.40        18.87        22.82        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       31.04        29.10        13.84        17.92        14.14        19.89 
TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
       16.96         5.88        40.01        41.06        39.88        39.95 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
        7.99        13.84         8.98        96.69        59.01         9.07 
TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR 
       28.93        28.96        25.02        29.23        41.06         1.74 
TCGA-JU-AAVI TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 
        7.76         2.43        23.74        13.28         9.47        26.10 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 
       18.21        23.24        15.45        23.97        12.92        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        18.84        39.95        12.92        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
        4.44        14.07        18.28         0.23 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.07               0.13 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             76.83             191.84 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            16.900             23.805 
[1] "0.1 - 76.8 (16.9)"  "0.1 - 191.8 (23.8)"
[1] "hr=" "2.9"
D31V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  17Q GAIN MUTATED                                        13
  17Q GAIN WILD-TYPE                                     382
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  17Q GAIN MUTATED                               0
  17Q GAIN WILD-TYPE                            21
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  17Q GAIN MUTATED                                  17
  17Q GAIN WILD-TYPE                                95
D31V3, multiclass
                                         clus
vv                                        17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               13                382
  MIXED SEROUS AND ENDOMETRIOID                          0                 21
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     17                 95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V4, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     7  23
  17Q GAIN WILD-TYPE 134 364
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      7   23
  17Q GAIN WILD-TYPE  134  364
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 7                134
  YES               23                364
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17Q GAIN MUTATED    18   1   4   3
  17Q GAIN WILD-TYPE 345  22  13  32
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0               18                345
  R1                1                 22
  R2                4                 13
  RX                3                 32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q GAIN MUTATED                                  0     0
  17Q GAIN WILD-TYPE                                4    20
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  17Q GAIN MUTATED                          14
  17Q GAIN WILD-TYPE                        87
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17Q GAIN MUTATED                                           0    14
  17Q GAIN WILD-TYPE                                         9   352
D31V6, multiclass
                                           clus
vv                                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    0                 20
  BLACK OR AFRICAN AMERICAN                               14                 87
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  9
  WHITE                                                   14                352
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     1  23
  17Q GAIN WILD-TYPE  13 344
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      1   23
  17Q GAIN WILD-TYPE   13  344
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 13
  NOT HISPANIC OR LATINO               23                344
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    54  17
  18P GAIN WILD-TYPE 403  52
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                71                455 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                17                 52 
$`18P GAIN MUTATED`
TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A0GE TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A1OG 
       36.69        37.02       105.37        36.82        19.96        11.44 
TCGA-A5-A1OH TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NF 
       36.33        14.43        34.16        22.26        20.81        21.21 
TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A053 TCGA-AP-A0L8 
       10.19        16.87        16.87        20.78         5.95        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A1DQ TCGA-AP-A3K1 
      125.42         3.39        97.71        33.40        46.78        21.90 
TCGA-AP-A5FX TCGA-AX-A1CA TCGA-AX-A2H4 TCGA-AX-A2HC TCGA-AX-A2HK TCGA-AX-A3GI 
       36.13        20.28        30.12        34.32         2.96         0.39 
TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M6 
       17.85        75.72        29.65        34.13        34.95        22.06 
TCGA-BG-A0M8 TCGA-BG-A0VT TCGA-BG-A2AE TCGA-BK-A0CC TCGA-BK-A26L TCGA-BS-A0U9 
       36.49        24.39        23.70        10.22        24.13        67.20 
TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A2G0 TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-D1-A3JP 
       39.48        37.32         3.52        44.88         4.11        16.93 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A2CH 
       35.38         9.37       110.10        48.36        27.32        19.40 
TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EY-A1GR TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A2ON 
       27.16        22.26        17.62        12.59        10.19        20.05 
TCGA-EY-A3L3 TCGA-EY-A72D TCGA-FI-A2CY TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-K6-A3WQ 
       27.35         5.88        41.06        29.23        45.01        14.04 
TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A915 TCGA-QS-A8F1 
        2.43        23.24        23.97         7.00         4.44 

$`18P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA 
       41.06        10.29       106.88       149.56        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
       32.78       112.54        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        60.53        46.55        38.37        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       23.21        68.65        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 
       42.35        15.95         7.92         9.60         8.02        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       46.32        28.64         5.33         5.16         7.33        14.96 
TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
        1.18        10.26         0.39        19.79        29.39         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       34.36         1.12         0.76        18.90         1.68         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG 
       14.66        22.49        17.06        36.99        20.65        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT 
       15.35        15.95        14.76        22.32        12.82         2.70 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        0.13        83.67        21.99        23.31        86.07         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       63.91        57.80        45.53        36.89        23.87        12.20 
TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
       20.91       117.99       110.37        63.16        36.36        31.73 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       83.97        27.12        82.52        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       35.54        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       16.24         0.56        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       53.92        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       35.01        28.54        37.78        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC 
       13.28        19.20        16.96        13.55        15.25        12.43 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       20.05        76.83        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       36.39        11.08         4.77        71.24        40.80        61.18 
TCGA-AX-A2HA TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       81.37        46.49        19.36        26.33        17.75        30.74 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        64.93         0.23         0.20         0.56        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
        0.20        20.52         1.38         0.30         0.26         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
        1.18        18.35        14.47        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        27.29        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.10        11.01         4.11         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
       88.34        54.44        45.90        43.96        40.50        36.82 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU 
       18.41        17.36        16.57       191.84       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 
       14.40        14.70        11.70        11.87        15.29        12.79 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH 
      116.25        96.30        78.81        62.14        33.11        14.27 
TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       41.06        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       34.98        38.37        28.27        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       23.47        43.30        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        26.66        16.34        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.01        15.45        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       20.02        20.12        11.31         6.81        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F 
        6.21        10.16        31.76        24.99        16.64        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        23.47        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       97.41        88.34        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI 
       73.25        59.51        62.79        63.58        49.55        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       21.99        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D 
       32.58         0.66        15.72        36.10        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       36.79        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       10.65         0.69        18.67         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
        2.33        22.92         1.41        13.22         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KV TCGA-DF-A2KY 
       41.42         8.48         0.26         4.27        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT 
       27.16        16.31        39.29        36.62        24.30        12.39 
TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       31.10        23.38        17.06         2.37         6.67        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
        7.36        16.80        10.92        49.15        37.71        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG 
       61.55        66.90        46.26        57.60        51.52        51.42 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 
       34.39        26.43        35.15        17.19        17.88        26.96 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC 
       16.34        14.53        24.89         6.21        14.99         4.54 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ 
       22.78        13.97         6.90        19.27        18.84        17.88 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       15.09        16.11        12.43        15.81        11.08         6.48 
TCGA-EY-A1H0 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP 
       19.33        14.40        18.87        22.82        45.76        31.04 
TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       29.10        13.84        11.38        17.92        14.14        19.89 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
       14.70        16.96        40.01        39.88        39.95         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       13.84         8.98        96.69        59.01         9.07        28.93 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KP-A3VZ 
       28.96        25.02        41.06         1.74         7.76        23.74 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A914 
       13.28         9.47        26.10        18.21        15.45        12.92 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       11.24         6.97        18.84        39.95        12.92        23.64 
TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83        14.07        18.28         0.07         0.23 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.39               0.07 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            125.42             191.84 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             23.70              23.34 
[1] "0.4 - 125.4 (23.7)" "0.1 - 191.8 (23.3)"
[1] "hr=" "2.1"
D32V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  18P GAIN MUTATED                                        21
  18P GAIN WILD-TYPE                                     374
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  18P GAIN MUTATED                               5
  18P GAIN WILD-TYPE                            16
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  18P GAIN MUTATED                                  45
  18P GAIN WILD-TYPE                                67
D32V3, multiclass
                                         clus
vv                                        18P GAIN MUTATED 18P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               21                374
  MIXED SEROUS AND ENDOMETRIOID                          5                 16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     45                 67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V4, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    15  56
  18P GAIN WILD-TYPE 126 331
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     15   56
  18P GAIN WILD-TYPE  126  331
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                15                126
  YES               56                331
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18P GAIN MUTATED    46   1   6   7
  18P GAIN WILD-TYPE 317  22  11  28
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0               46                317
  R1                1                 22
  R2                6                 11
  RX                7                 28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P GAIN MUTATED                                  0     2
  18P GAIN WILD-TYPE                                4    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  18P GAIN MUTATED                          28
  18P GAIN WILD-TYPE                        73
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18P GAIN MUTATED                                           1    36
  18P GAIN WILD-TYPE                                         8   330
D32V6, multiclass
                                           clus
vv                                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    2                 18
  BLACK OR AFRICAN AMERICAN                               28                 73
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   36                330
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     2  50
  18P GAIN WILD-TYPE  12 317
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2   50
  18P GAIN WILD-TYPE   12  317
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 12
  NOT HISPANIC OR LATINO               50                317
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    30  14
  18Q GAIN WILD-TYPE 427  55
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                44                482 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                14                 55 
$`18Q GAIN MUTATED`
TCGA-5B-A90C TCGA-A5-A0GE TCGA-A5-A0R6 TCGA-AJ-A23N TCGA-AJ-A3EM TCGA-AJ-A3IA 
       36.69       105.37        19.96        14.43        22.26        20.81 
TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF 
       21.21        10.19         5.95        48.79       125.42         3.39 
TCGA-AP-A0LO TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A2H4 TCGA-AX-A2HC TCGA-AX-A2HK 
       33.40        21.90        36.13        30.12        34.32         2.96 
TCGA-B5-A11I TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A0VT TCGA-BG-A2AE TCGA-BK-A26L 
       75.72        29.65        34.13        24.39        23.70        24.13 
TCGA-BS-A0U9 TCGA-D1-A15V TCGA-D1-A16I TCGA-D1-A2G0 TCGA-D1-A2G7 TCGA-DI-A1NN 
       67.20        39.48        11.51         3.52        44.88        35.38 
TCGA-DI-A1NO TCGA-EO-A2CH TCGA-EO-A3AZ TCGA-EY-A1GR TCGA-EY-A210 TCGA-EY-A3L3 
        9.37        19.40        27.16        17.62        12.59        27.35 
TCGA-EY-A4KR TCGA-EY-A72D TCGA-FI-A2F9 TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3W3 
       11.38         5.88        29.23        14.04         2.43        26.10 
TCGA-PG-A915 TCGA-QS-A8F1 
        7.00         4.44 

$`18Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       17.85        32.78       112.54        87.32        74.10        57.53 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       65.75        60.53        60.53        46.55        38.37        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 
       28.27        20.81        23.21        68.65        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95         7.92        11.44 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 
       36.33         9.60         8.02        91.04        46.32        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23O 
        5.33         5.16         7.33        14.96         1.18        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
        0.39        19.79        29.39         2.40        34.36        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
        1.12         0.76        18.90         1.68         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       22.49        17.06        36.99        20.65        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.95        14.76        16.87        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
       20.78         2.70         0.13        83.67        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        63.91        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       23.87        12.20        20.91       117.99       110.37        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        83.97        27.12        82.52 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       60.36        55.89        31.30        35.54        46.78        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO 
        6.71        30.90        10.42        27.85        16.24         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D 
       35.34        45.99        66.58        34.98        53.92        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       51.09        27.39        30.02        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       16.96        13.55        15.25        20.28        12.43        20.05 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       76.83        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
       11.08         4.77        71.24        40.80        61.18        81.37 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN 
       46.49        19.36        26.33        17.75        30.74        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       64.93         0.23         0.20         0.56        43.82         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
       20.52         1.38         0.30         0.26         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       18.35        14.47         0.39        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        27.29        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F 
       17.10        17.85        11.01         4.11         8.71       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
      113.36        88.34        54.44        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       36.82        32.09        33.50        27.35        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS 
       19.50        18.41        17.36        16.57       191.84       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        14.40        14.70        11.70        11.87        15.29 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       12.79       116.25        96.30        78.81        62.14        33.11 
TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       14.27        41.06        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98        22.06        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 
       15.45        14.27         1.81         9.57        20.02        20.12 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       11.31         6.81        35.90        34.98         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
       10.16        31.76        24.99        16.64        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        23.47        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ 
       59.51        62.79        63.58        49.55        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        21.99 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       36.79        27.42        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
        0.69        18.67         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
       22.92         1.41        13.22         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G5 
       18.02         2.07        15.06         1.05         3.95        41.42 
TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV 
        8.48         0.26         4.27         4.11        16.93        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
       12.39        31.10       110.10        23.38        48.36        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
        2.37         6.67        27.32        16.04         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       10.92        49.15        37.71        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU 
       46.26        57.60        51.52        51.42        34.39        26.43 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW 
       35.15        17.19        17.88        26.96        22.26        16.34 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       14.53        24.89         6.21        14.99         4.54        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK 
       24.36        27.16        23.34        23.34        23.90        22.78 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GS 
       13.97         6.90        19.27        18.84        17.88        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        12.43        15.81        11.08         6.48        19.33 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       10.19        14.40        18.87        22.82        20.05        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       31.04        29.10        13.84        17.92        14.14        19.89 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
       14.70        16.96        40.01        41.06        39.88        39.95 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
        7.99        13.84         8.98        96.69        59.01         9.07 
TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR 
       28.93        28.96        25.02        41.06        45.01         1.74 
TCGA-JU-AAVI TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A5BC 
        7.76        23.74        13.28         9.47        18.21        23.24 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       15.45        23.97        12.92        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       39.95        12.92        23.64        14.83        14.07        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              2.43               0.07 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            125.42             191.84 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             22.98              23.34 
[1] "2.4 - 125.4 (23.0)" "0.1 - 191.8 (23.3)"
[1] "hr=" "3.1"
D33V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  18Q GAIN MUTATED                                        16
  18Q GAIN WILD-TYPE                                     379
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  18Q GAIN MUTATED                               4
  18Q GAIN WILD-TYPE                            17
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  18Q GAIN MUTATED                                  24
  18Q GAIN WILD-TYPE                                88
D33V3, multiclass
                                         clus
vv                                        18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               16                379
  MIXED SEROUS AND ENDOMETRIOID                          4                 17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     24                 88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V4, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    10  34
  18Q GAIN WILD-TYPE 131 353
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     10   34
  18Q GAIN WILD-TYPE  131  353
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                10                131
  YES               34                353
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18Q GAIN MUTATED    27   0   4   6
  18Q GAIN WILD-TYPE 336  23  13  29
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0               27                336
  R1                0                 23
  R2                4                 13
  RX                6                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q GAIN MUTATED                                  0     1
  18Q GAIN WILD-TYPE                                4    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  18Q GAIN MUTATED                          14
  18Q GAIN WILD-TYPE                        87
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18Q GAIN MUTATED                                           1    25
  18Q GAIN WILD-TYPE                                         8   341
D33V6, multiclass
                                           clus
vv                                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    1                 19
  BLACK OR AFRICAN AMERICAN                               14                 87
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   25                341
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     1  31
  18Q GAIN WILD-TYPE  13 336
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1   31
  18Q GAIN WILD-TYPE   13  336
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 13
  NOT HISPANIC OR LATINO               31                336
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    41  10
  19P GAIN WILD-TYPE 416  59
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                51                475 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                10                 59 
$`19P GAIN MUTATED`
TCGA-AJ-A3BI TCGA-AJ-A3IA TCGA-AJ-A8CW TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF 
       18.90        20.81         0.13        48.79       125.42         3.39 
TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CR 
       97.71        46.78        37.78        16.96        13.55        11.08 
TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A3G1 TCGA-B5-A0JN TCGA-B5-A0K8 
        4.77        40.80        61.18        20.52        80.38        17.85 
TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-BG-A0VT TCGA-BG-A3PP TCGA-BK-A0CC 
       11.87        12.79        29.65        24.39         6.81        10.22 
TCGA-BK-A4ZD TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A16S TCGA-D1-A1NX TCGA-D1-A1O0 
       16.64        49.55        22.55        18.67        18.25         2.07 
TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-EO-A1Y5 
       44.88         4.11         9.37        31.10       110.10        10.92 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GR 
       51.52        51.42        22.26        16.34        23.90        17.62 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A2OQ TCGA-EY-A547 TCGA-FI-A2F9 TCGA-FI-A3PX 
       12.59        10.19        29.10        17.92        29.23        45.01 
TCGA-KP-A3W1 TCGA-PG-A7D5 TCGA-PG-A915 
        9.47        23.97         7.00 

$`19P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       38.37        36.82        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       19.96        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK 
       15.95         7.92        11.44        36.33         9.60         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
       91.04        46.32        28.64         5.33         5.16         7.33 
TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       14.96         1.18        14.43        10.26         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG 
       29.39         2.40        34.36        34.16         1.12         0.76 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
        1.68         1.64        14.66        22.49        22.26        17.06 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ 
       36.99        20.65        21.21        15.62        10.19        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.95        14.76        16.87        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       20.78         2.70        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        63.91        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       23.87        12.20        20.91       117.99       110.37        63.16 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       60.36        55.89        31.30        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
       30.90        10.42        27.85        16.24        21.90        36.13 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       28.54        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       15.25        20.28        12.43        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H4 TCGA-AX-A2H5 
       54.12        67.50        25.12        36.39        30.12        71.24 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       81.37        34.32        46.49        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       30.74         2.96        31.13        64.93         0.23         0.20 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 
        0.56        43.82         0.20         1.38         0.30         0.26 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR 
        0.30         1.18        18.35        14.47         0.39        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       46.75        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        27.29        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F 
       13.74        17.10        11.01         4.11         8.71       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       40.50        36.82        32.09        33.50        27.35        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       191.84 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
      102.31        50.89        14.40        14.70        11.70        15.29 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH 
      116.25        96.30        78.81        62.14        33.11        14.27 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       41.06        34.13        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98        22.06        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        20.02        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 
       20.12        11.31        35.90        34.98         6.21        10.16 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       31.76        24.99        24.13        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       59.51        62.79        63.58        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93         1.74         4.44        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
        0.69         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02        14.73         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 
        1.41        13.22         0.72        16.87        18.02        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA 
        1.05         3.95         3.52        41.42         8.48         0.26 
TCGA-D1-A3DG TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        4.27        16.93        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QT TCGA-E6-A1LX 
       39.29        36.62        24.30        35.38        12.39        23.38 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ 
       48.36        17.06         2.37         6.67        27.32        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
        7.36        16.80        49.15        37.71        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       66.90        46.26        57.60        19.40        34.39        26.43 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KX 
       35.15        17.19        27.16        17.88        26.96        14.53 
TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       24.89         6.21        14.99         4.54        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       27.16        23.34        23.34        22.78        13.97         6.90 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       19.27        18.84        17.88        15.09        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A214 TCGA-EY-A215 
       15.81        11.08         6.48        19.33        14.40        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX 
       22.82        20.05        45.76        31.04        27.35        13.84 
TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D 
       11.38        14.14        19.89        14.70        16.96         5.88 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
       40.01        41.06        39.88        39.95         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 
        8.98        96.69        59.01         9.07        28.93        28.96 
TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 
       25.02        41.06         1.74         7.76        14.04         2.43 
TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       23.74        13.28        26.10        18.21        23.24        15.45 
TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       12.92        11.24         6.97        18.84        39.95        12.92 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       23.64        14.83         4.44        14.07        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.13               0.07 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            125.42             191.84 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             18.90              23.64 
[1] "0.1 - 125.4 (18.9)" "0.1 - 191.8 (23.6)"
[1] "hr=" "1.6"
D34V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  19P GAIN MUTATED                                        20
  19P GAIN WILD-TYPE                                     375
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  19P GAIN MUTATED                               3
  19P GAIN WILD-TYPE                            18
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  19P GAIN MUTATED                                  29
  19P GAIN WILD-TYPE                                83
D34V3, multiclass
                                         clus
vv                                        19P GAIN MUTATED 19P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               20                375
  MIXED SEROUS AND ENDOMETRIOID                          3                 18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     29                 83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V4, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    11  41
  19P GAIN WILD-TYPE 130 346
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     11   41
  19P GAIN WILD-TYPE  130  346
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                11                130
  YES               41                346
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19P GAIN MUTATED    36   3   2   4
  19P GAIN WILD-TYPE 327  20  15  31
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0               36                327
  R1                3                 20
  R2                2                 15
  RX                4                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P GAIN MUTATED                                  0     1
  19P GAIN WILD-TYPE                                4    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  19P GAIN MUTATED                          16
  19P GAIN WILD-TYPE                        85
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19P GAIN MUTATED                                           1    30
  19P GAIN WILD-TYPE                                         8   336
D34V6, multiclass
                                           clus
vv                                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    1                 19
  BLACK OR AFRICAN AMERICAN                               16                 85
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   30                336
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     1  38
  19P GAIN WILD-TYPE  13 329
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1   38
  19P GAIN WILD-TYPE   13  329
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 13
  NOT HISPANIC OR LATINO               38                329
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    42  12
  19Q GAIN WILD-TYPE 415  57
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                54                472 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                12                 57 
$`19Q GAIN MUTATED`
TCGA-A5-A1OG TCGA-A5-A2K3 TCGA-A5-A3LP TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A8CW 
       11.44        46.32        14.96        20.81        10.19         0.13 
TCGA-AP-A0L8 TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 
       48.79        97.71        46.78        28.54        37.78        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A3G1 
       13.55        20.28        11.08         4.77        40.80        20.52 
TCGA-B5-A0JN TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-BG-A0M6 TCGA-BG-A0VT 
       80.38        11.87        12.79        29.65        22.06        24.39 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A16S TCGA-D1-A1NX 
       24.13        16.64        22.55        39.48        18.67        18.25 
TCGA-D1-A1O0 TCGA-D1-A2G7 TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ 
        2.07        44.88         9.37        31.10       110.10        48.36 
TCGA-EO-A1Y5 TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3KU TCGA-EY-A1GR TCGA-EY-A1GS 
       10.92        51.52        51.42        22.26        17.62        15.09 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A2OQ TCGA-EY-A547 TCGA-FI-A2F9 TCGA-FI-A3PX 
       12.59        10.19        29.10        17.92        29.23        45.01 
TCGA-JU-AAVI TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-SL-A6J9 
        7.76         9.47        26.10        23.24        23.97         0.07 

$`19Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       38.37        36.82        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       19.96        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 
       15.95         7.92        36.33         9.60         8.02        91.04 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N 
       28.64         5.33         5.16         7.33         1.18        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
       10.26         0.39        19.79        29.39         2.40        34.36 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       34.16         1.12         0.76        18.90         1.68         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE 
       14.66        22.49        22.26        17.06        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       21.21        15.62        15.35        15.95        14.76        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AP-A051 
       16.87        22.32        12.82        20.78         2.70        83.67 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
       21.99         5.95        23.31        86.07         8.22        63.91 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       57.80        45.53        36.89        23.87        12.20        20.91 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
      125.42       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       31.73        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       55.89        31.30        35.54        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
       10.42        27.85        16.24        21.90        36.13         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D 
       35.34        45.99        66.58        34.98        53.92        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ 
       51.09        27.39        30.02        60.66        35.01        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CC 
       40.11        65.88        13.28        19.20        15.25        12.43 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       20.05        76.83        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       36.39        30.12        71.24        61.18        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       46.49        19.36        26.33        17.75        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        64.93         0.23         0.20         0.56        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.20         1.38         0.30         0.26         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       18.35        14.47         0.39        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        27.29        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.85        11.01         4.11         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       36.82        32.09        33.50        27.35        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS 
       19.50        18.41        17.36        16.57       191.84       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 
       50.89        14.40        14.70        11.70        15.29       116.25 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC 
       96.30        78.81        62.14        33.11        14.27        41.06 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       34.13        34.95        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       35.21        34.98        38.37        36.49        28.27        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       30.81        21.17        20.28        15.42        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        52.64        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 
       13.78        14.73        14.01        15.45        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
        1.81         9.57        20.02        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
        6.81        35.90        34.98         6.21        10.22        10.16 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       31.76        24.99        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        67.20        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       62.79        63.58        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X 
       23.93         1.74         4.44        21.99        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       36.10        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02        14.73         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 
       13.22         0.72        16.87        18.02        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.95         3.52        41.42         8.48         0.26         4.27 
TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        4.11        16.93        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QT TCGA-E6-A1LX 
       39.29        36.62        24.30        35.38        12.39        23.38 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       17.06         2.37         6.67        27.32        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       16.80        49.15        37.71        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       46.26        57.60        19.40        34.39        26.43        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EO-A3KX 
       17.19        27.16        17.88        26.96        16.34        14.53 
TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       24.89         6.21        14.99         4.54        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL 
       27.16        23.34        23.34        23.90        22.78        13.97 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU 
        6.90        19.27        18.84        17.88        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A214 TCGA-EY-A215 
       15.81        11.08         6.48        19.33        14.40        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX 
       22.82        20.05        45.76        31.04        27.35        13.84 
TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D 
       11.38        14.14        19.89        14.70        16.96         5.88 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
       40.01        41.06        39.88        39.95         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 
        8.98        96.69        59.01         9.07        28.93        28.96 
TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       25.02        41.06         1.74        14.04         2.43        23.74 
TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 
       13.28        18.21        15.45        12.92         7.00        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        18.84        39.95        12.92        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
        4.44        14.07        18.28         0.23 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.07               0.20 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            110.10             191.84 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            21.435             23.555 
[1] "0.1 - 110.1 (21.4)" "0.2 - 191.8 (23.6)"
[1] "hr=" "2.1"
D35V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  19Q GAIN MUTATED                                        15
  19Q GAIN WILD-TYPE                                     380
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  19Q GAIN MUTATED                               3
  19Q GAIN WILD-TYPE                            18
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  19Q GAIN MUTATED                                  37
  19Q GAIN WILD-TYPE                                75
D35V3, multiclass
                                         clus
vv                                        19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               15                380
  MIXED SEROUS AND ENDOMETRIOID                          3                 18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     37                 75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V4, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    14  41
  19Q GAIN WILD-TYPE 127 346
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     14   41
  19Q GAIN WILD-TYPE  127  346
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                14                127
  YES               41                346
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19Q GAIN MUTATED    38   3   2   5
  19Q GAIN WILD-TYPE 325  20  15  30
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               38                325
  R1                3                 20
  R2                2                 15
  RX                5                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  0     2
  19Q GAIN WILD-TYPE                                4    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  19Q GAIN MUTATED                          20
  19Q GAIN WILD-TYPE                        81
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19Q GAIN MUTATED                                           0    30
  19Q GAIN WILD-TYPE                                         9   336
D35V6, multiclass
                                           clus
vv                                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    2                 18
  BLACK OR AFRICAN AMERICAN                               20                 81
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  9
  WHITE                                                   30                336
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     0  45
  19Q GAIN WILD-TYPE  14 322
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      0   45
  19Q GAIN WILD-TYPE   14  322
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 14
  NOT HISPANIC OR LATINO               45                322
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    89  21
  20P GAIN WILD-TYPE 368  48
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               110                416 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                21                 48 
$`20P GAIN MUTATED`
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP 
       11.44        36.33        46.32        28.64         7.33        14.96 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QN TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM 
        1.18        14.43         2.40        18.90         1.64        22.26 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A1DO 
       20.81        10.19        57.80       125.42         3.39        31.30 
TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AX-A06B TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 
       46.78        21.90        53.92        28.54        37.78        16.96 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2HK 
       20.28        12.43        11.08         4.77        30.12         2.96 
TCGA-AX-A3FS TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G6 TCGA-AX-A3G7 
        0.23        43.82         0.20         1.38         0.26         0.30 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JT TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A11L 
        0.39        80.38        43.13         4.11        75.72        45.90 
TCGA-B5-A11V TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD 
       19.56       102.31        11.87        12.79       116.25        33.11 
TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0W1 TCGA-BG-A18C 
       29.65        34.13        30.81        24.39        52.83        15.45 
TCGA-BG-A221 TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A56F TCGA-BS-A0TE TCGA-BS-A0U9 
        1.81        10.22        24.13        13.18         4.80        67.20 
TCGA-BS-A0UT TCGA-BS-A0V8 TCGA-D1-A102 TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16J 
       72.72        49.55         4.44        37.32        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-D1-A2G5 TCGA-D1-A3DH 
       31.07        18.67         0.72         2.07        41.42         4.11 
TCGA-DI-A1NN TCGA-DI-A2QT TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       35.38        12.39        27.32        10.92        49.15        37.71 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AV TCGA-EO-A3B1 TCGA-EO-A3KU 
       51.52        51.42        19.40        35.15        26.96        22.26 
TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A214 
       16.34         6.21         6.90        17.62        15.09        14.40 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A54A TCGA-FI-A2CX 
       29.10        27.35        11.38        17.92        14.70        40.01 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ 
       59.01         9.07        28.93        45.01         7.76        14.04 
TCGA-KP-A3VZ TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       23.74         9.47        26.10        23.97        12.92         7.00 
TCGA-QS-A8F1 TCGA-SL-A6J9 
        4.44         0.07 

$`20P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       38.37        36.82        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       19.96        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K5 
       15.95         7.92         9.60         8.02        91.04         5.33 
TCGA-A5-A2K7 TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QO 
        5.16        10.26         0.39        19.79        29.39        34.36 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
       34.16         1.12         0.76         1.68        14.66        22.49 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       17.06        36.99        20.65        21.21        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.95        14.76        16.87        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       20.78         2.70         0.13        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07         8.22        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        12.20        20.91        48.79       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DR 
       25.08        71.67        60.36        55.89        35.54        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX 
        6.71        30.90        10.42        27.85        16.24        36.13 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D 
       46.45        35.34        45.99        66.58        34.98        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ 
       51.09        27.39        30.02        60.66        35.01        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 
       40.11        65.88        13.28        19.20        13.55        15.25 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       20.05        76.83        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       36.39        71.24        40.80        61.18        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN 
       46.49        19.36        26.33        17.75        30.74        31.13 
TCGA-AX-A2IO TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G8 
       64.93         0.20         0.56        20.52         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV 
       18.35        14.47        56.91        46.75        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       44.71        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        17.88        13.74        17.10        17.85        11.01 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11N 
        8.71       185.79       113.36        88.34        54.44        43.96 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       40.50        36.82        32.09        33.50        27.35        16.73 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU 
       19.50        18.41        17.36        16.57       191.84        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB 
       14.40        14.70        11.70        15.29        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       62.14        14.27        41.06        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98        22.06        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       36.49        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.30        43.04        39.32        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU 
       26.66        16.34        34.29        52.64        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 
       12.56        13.78        14.73        14.01        15.45        14.27 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        9.57        20.02        23.70        20.12        11.31         6.81 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       35.90        34.98         6.21        10.16        31.76        24.99 
TCGA-BK-A4ZD TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       16.64        10.03         9.86        46.95        23.47        85.55 
TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
       78.21        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV 
       97.41        88.34        85.84        82.39        81.57        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       59.51        62.79        63.58        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       15.72        36.10        36.36        37.51        36.79        27.42 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1NY 
        2.33        22.92         1.41        13.22        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 
       18.02        15.06         1.05         3.95         3.52         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY 
       44.88         0.26         4.27        16.93        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO 
       27.16        16.31        39.29        36.62        24.30         9.37 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       31.10       110.10        23.38        48.36        17.06         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S 
        6.67        16.04         7.36        16.80        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AY 
       66.90        46.26        57.60        34.39        26.43        17.19 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC 
       27.16        17.88        14.53        24.89        14.99         4.54 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GT 
       22.78        13.97        19.27        18.84        17.88        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       12.43        15.81        11.08         6.48        19.33        12.59 
TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       10.19        18.87        22.82        20.05        45.76        31.04 
TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CY 
       13.84        14.14        19.89        16.96         5.88        41.06 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       39.88        39.95         7.99        13.84         8.98        96.69 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-KJ-A3U4 
       28.96        25.02        29.23        41.06         1.74         2.43 
TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 
       13.28        18.21        23.24        15.45        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI 
       18.84        39.95        12.92        23.64        14.83        14.07 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.07               0.13 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            125.42             191.84 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            19.480             23.785 
[1] "0.1 - 125.4 (19.5)" "0.1 - 191.8 (23.8)"
[1] "hr=" "2"  
D36V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  20P GAIN MUTATED                                        46
  20P GAIN WILD-TYPE                                     349
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  20P GAIN MUTATED                               4
  20P GAIN WILD-TYPE                            17
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  20P GAIN MUTATED                                  60
  20P GAIN WILD-TYPE                                52
D36V3, multiclass
                                         clus
vv                                        20P GAIN MUTATED 20P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               46                349
  MIXED SEROUS AND ENDOMETRIOID                          4                 17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     60                 52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V4, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    16  94
  20P GAIN WILD-TYPE 125 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     16   94
  20P GAIN WILD-TYPE  125  293
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                16                125
  YES               94                293
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20P GAIN MUTATED    66   4   7  10
  20P GAIN WILD-TYPE 297  19  10  25
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0               66                297
  R1                4                 19
  R2                7                 10
  RX               10                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P GAIN MUTATED                                  1     4
  20P GAIN WILD-TYPE                                3    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  20P GAIN MUTATED                          30
  20P GAIN WILD-TYPE                        71
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20P GAIN MUTATED                                           2    64
  20P GAIN WILD-TYPE                                         7   302
D36V6, multiclass
                                           clus
vv                                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  3
  ASIAN                                                    4                 16
  BLACK OR AFRICAN AMERICAN                               30                 71
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                2                  7
  WHITE                                                   64                302
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     2  73
  20P GAIN WILD-TYPE  12 294
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      2   73
  20P GAIN WILD-TYPE   12  294
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 12
  NOT HISPANIC OR LATINO               73                294
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   102  27
  20Q GAIN WILD-TYPE 355  42
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               129                397 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                27                 42 
$`20Q GAIN MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K3 TCGA-A5-A2K4 
       41.06        36.69        11.44        36.33        46.32        28.64 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QN 
        7.33        14.96         1.18        14.43         0.39         2.40 
TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3QS 
       18.90         1.64        22.26        20.81        10.19        16.87 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A1DO 
       63.91        57.80       125.42         3.39        97.71        31.30 
TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AX-A06B TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 
       46.78        21.90        53.92        28.54        37.78        16.96 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2HK 
       20.28        12.43        11.08         4.77        30.12         2.96 
TCGA-AX-A3FS TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 
        0.23        43.82         0.20        20.52         1.38         0.30 
TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JT TCGA-B5-A0K8 
        0.26         0.30         0.39        80.38        43.13        17.85 
TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A11L TCGA-B5-A11V TCGA-B5-A1MR TCGA-B5-A1MS 
        4.11        75.72        45.90        19.56       191.84       102.31 
TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OD 
       11.87        12.79       116.25        33.11        29.65        34.13 
TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0W1 TCGA-BG-A0YV TCGA-BG-A18C 
       36.49        30.81        24.39        52.83        12.56        15.45 
TCGA-BG-A221 TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A56F TCGA-BS-A0TE TCGA-BS-A0U9 
        1.81        10.22        24.13        13.18         4.80        67.20 
TCGA-BS-A0UT TCGA-BS-A0V8 TCGA-D1-A102 TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16J 
       72.72        49.55         4.44        37.32        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-D1-A2G5 TCGA-D1-A3DH 
       31.07        18.67         0.72         2.07        41.42         4.11 
TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A1Y5 
       35.38        12.39       110.10        48.36        27.32        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AV 
       49.15        37.71        51.52        51.42        19.40        35.15 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1GM TCGA-EY-A1GR 
       26.96        22.26        16.34         6.21         6.90        17.62 
TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OQ 
       15.09        11.08         6.48        14.40        20.05        29.10 
TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A54A TCGA-EY-A72D TCGA-FI-A2CX 
       27.35        11.38        17.92        14.70         5.88        40.01 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A3PV TCGA-FI-A3PX TCGA-JU-AAVI 
       59.01         9.07        28.93        41.06        45.01         7.76 
TCGA-K6-A3WQ TCGA-KP-A3VZ TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-PG-A914 
       14.04        23.74         9.47        26.10        23.97        12.92 
TCGA-PG-A915 TCGA-QS-A8F1 TCGA-SL-A6J9 
        7.00         4.44         0.07 

$`20Q GAIN WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
       10.29       106.88       149.56        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       32.78       112.54       105.37        87.32        74.10        57.53 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       65.75        60.53        60.53        46.55        38.37        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        20.81        23.21        68.65        19.96        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       19.59        24.62        29.06        42.35        15.95         7.92 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23O 
        9.60         8.02        91.04         5.33         5.16        10.26 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG 
       19.79        29.39        34.36        34.16         1.12         0.76 
TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE 
        1.68        14.66        22.49        17.06        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW 
       21.21        15.62        15.35        15.95        14.76        16.87 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       22.32        12.82        20.78         2.70         0.13        83.67 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05H 
       21.99         5.95        23.31        86.07         8.22        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD 
       36.89        23.87        12.20        20.91        48.79       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
      110.37        63.16        36.36        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DR 
       25.08        71.67        60.36        55.89        35.54        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX 
        6.71        30.90        10.42        27.85        16.24        36.13 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D 
       46.45        35.34        45.99        66.58        34.98        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ 
       51.09        27.39        30.02        60.66        35.01        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 
       40.11        65.88        13.28        19.20        13.55        15.25 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       20.05        76.83        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       36.39        71.24        40.80        61.18        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN 
       46.49        19.36        26.33        17.75        30.74        31.13 
TCGA-AX-A2IO TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
       64.93         0.20         0.56         1.18        18.35        14.47 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       56.91        46.75        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        27.29        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       13.74        17.10        11.01         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q 
       88.34        54.44        43.96        40.50        36.82        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       33.50        27.35        16.73        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
       16.57        50.89        14.40        14.70        11.70        15.29 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OE 
       96.30        78.81        62.14        14.27        41.06        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       22.06        38.37        28.27        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.30        43.04        39.32        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 
       15.42        26.66        16.34        34.29        52.64        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 
       14.83        13.78        14.73        14.01        15.45        14.27 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        9.57        20.02        23.70        20.12        11.31         6.81 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       35.90        34.98         6.21        10.16        31.76        24.99 
TCGA-BK-A4ZD TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       16.64        10.03         9.86        46.95        23.47        85.55 
TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
       78.21        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV 
       97.41        88.34        85.84        82.39        81.57        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       59.51        62.79        63.58        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       15.72        36.10        36.36        37.51        36.79        27.42 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1NY 
        2.33        22.92         1.41        13.22        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 
       18.02        15.06         1.05         3.95         3.52         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY 
       44.88         0.26         4.27        16.93        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO 
       27.16        16.31        39.29        36.62        24.30         9.37 
TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       31.10        23.38        17.06         2.37         6.67        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
        7.36        16.80        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       57.60        34.39        26.43        17.19        27.16        17.88 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       14.53        24.89        14.99         4.54        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL 
       27.16        23.34        23.34        23.90        22.78        13.97 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       19.27        18.84        17.88        16.11        12.43        15.81 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO 
       19.33        12.59        10.19        18.87        22.82        45.76 
TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CY 
       31.04        13.84        14.14        19.89        16.96        41.06 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       39.88        39.95         7.99        13.84         8.98        96.69 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-KP-A3W0 
       28.96        25.02        29.23         1.74         2.43        13.28 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       18.21        23.24        15.45        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       39.95        12.92        23.64        14.83        14.07        18.28 
TCGA-SL-A6JA 
        0.23 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.07               0.13 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            191.84             185.79 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             20.05              23.87 
[1] "0.1 - 191.8 (20.1)" "0.1 - 185.8 (23.9)"
[1] "hr=" "2.2"
D37V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  20Q GAIN MUTATED                                        56
  20Q GAIN WILD-TYPE                                     339
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  20Q GAIN MUTATED                               4
  20Q GAIN WILD-TYPE                            17
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  20Q GAIN MUTATED                                  70
  20Q GAIN WILD-TYPE                                42
D37V3, multiclass
                                         clus
vv                                        20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               56                339
  MIXED SEROUS AND ENDOMETRIOID                          4                 17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     70                 42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V4, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    20 110
  20Q GAIN WILD-TYPE 121 277
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     20  110
  20Q GAIN WILD-TYPE  121  277
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                20                121
  YES              110                277
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20Q GAIN MUTATED    76   5   9  11
  20Q GAIN WILD-TYPE 287  18   8  24
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0               76                287
  R1                5                 18
  R2                9                  8
  RX               11                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q GAIN MUTATED                                  1     4
  20Q GAIN WILD-TYPE                                3    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  20Q GAIN MUTATED                          38
  20Q GAIN WILD-TYPE                        63
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20Q GAIN MUTATED                                           3    75
  20Q GAIN WILD-TYPE                                         6   291
D37V6, multiclass
                                           clus
vv                                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  3
  ASIAN                                                    4                 16
  BLACK OR AFRICAN AMERICAN                               38                 63
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                3                  6
  WHITE                                                   75                291
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     4  87
  20Q GAIN WILD-TYPE  10 280
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      4   87
  20Q GAIN WILD-TYPE   10  280
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 10
  NOT HISPANIC OR LATINO               87                280
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    29   9
  21Q GAIN WILD-TYPE 428  60
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                38                488 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 9                 60 
$`21Q GAIN MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0R6 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A3BD 
       37.02        19.96         7.33        14.96        14.43        34.16 
TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3TW TCGA-AP-A1DQ 
       22.26        20.81        21.21        10.19        16.87        46.78 
TCGA-AX-A0IW TCGA-AX-A1C4 TCGA-AX-A2HK TCGA-AX-A3FW TCGA-AX-A3G1 TCGA-B5-A1MY 
       37.78        13.28         2.96         0.56        20.52        11.87 
TCGA-B5-A5OD TCGA-BS-A0U9 TCGA-D1-A2G5 TCGA-D1-A3DH TCGA-DI-A2QY TCGA-E6-A1LZ 
       34.13        67.20        41.42         4.11       110.10        48.36 
TCGA-EO-A22Y TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1GS TCGA-EY-A2ON TCGA-EY-A3L3 
       51.52        27.16        26.96        15.09        20.05        27.35 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F9 TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-PG-A914 
       59.01         9.07        29.23        26.10        23.97        12.92 
TCGA-QS-A8F1 TCGA-SL-A6J9 
        4.44         0.07 

$`21Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88       149.56        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 
       36.82        28.27        20.81        23.21        68.65        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       19.59        24.62        29.06        42.35        15.95         7.92 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 
       11.44        36.33         9.60         8.02        91.04        46.32 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK 
       28.64         5.33         5.16         1.18        10.26         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG 
       19.79        29.39         2.40        34.36         1.12         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 
       18.90         1.68         1.64        14.66        22.49        17.06 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       36.99        20.65        15.62        15.35        15.95        14.76 
TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW 
       16.87        22.32        12.82        20.78         2.70         0.13 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       83.67        21.99         5.95        23.31        86.07         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       63.91        57.80        45.53        36.89        23.87        12.20 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        55.89        31.30        35.54 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        30.90        10.42        27.85        16.24 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       21.90        36.13         0.56        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       34.98        53.92        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        35.01        28.54        43.82        40.11        65.88 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       19.20        16.96        13.55        15.25        20.28        12.43 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       20.05        76.83        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       36.39        11.08         4.77        30.12        71.24        40.80 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       61.18        81.37        34.32        46.49        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       17.75        30.74        31.13        64.93         0.23         0.20 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
       43.82         0.20         1.38         0.30         0.26         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR 
        1.18        18.35        14.47         0.39        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       46.75        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        27.29        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E 
       13.74        17.10        17.85        11.01         4.11         8.71 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L 
      185.79       113.36        88.34        75.72        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       43.96        40.50        36.82        32.09        33.50        27.35 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
      191.84       102.31        50.89        14.40        14.70        11.70 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       15.29        12.79       116.25        96.30        78.81        62.14 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW 
       33.11        14.27        29.65        41.06        34.95        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 
       20.19        19.33        20.94        35.21        34.98        22.06 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       38.37        36.49        28.27        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       23.47        43.30        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       52.64        52.83        56.58        14.83        12.56        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 
       14.73        14.01        15.45        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        9.57        20.02        23.70        20.12        11.31         6.81 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       35.90        34.98         6.21        10.22        10.16        31.76 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       24.99        24.13        16.64        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA 
       61.87        67.99        96.49        30.74        97.41        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       62.79        63.58        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       36.79        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       10.65         0.69        18.67         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
        2.33        22.92         1.41        13.22         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JP 
        3.52         8.48        44.88         0.26         4.27        16.93 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX 
       24.30        35.38         9.37        12.39        31.10        23.38 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       17.06         2.37         6.67        27.32        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
       16.80        10.92        49.15        37.71        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       66.90        46.26        57.60        51.42        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KW 
       26.43        35.15        17.19        17.88        22.26        16.34 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       14.53        24.89         6.21        14.99         4.54        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK 
       24.36        27.16        23.34        23.34        23.90        22.78 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR 
       13.97         6.90        19.27        18.84        17.88        17.62 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        12.43        15.81        11.08         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO 
       12.59        10.19        14.40        18.87        22.82        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 
       31.04        29.10        13.84        11.38        17.92        14.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY 
       19.89        14.70        16.96         5.88        40.01        41.06 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       39.88        39.95         7.99        13.84         8.98        96.69 
TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR 
       28.93        28.96        25.02        41.06        45.01         1.74 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 
        7.76        14.04         2.43        23.74        13.28         9.47 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 
       18.21        23.24        15.45         7.00        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI 
       18.84        39.95        12.92        23.64        14.83        14.07 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.07               0.13 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            110.10             191.84 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            21.010             23.425 
[1] "0.1 - 110.1 (21.0)" "0.1 - 191.8 (23.4)"
[1] "hr=" "2.2"
D38V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  21Q GAIN MUTATED                                        12
  21Q GAIN WILD-TYPE                                     383
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  21Q GAIN MUTATED                               1
  21Q GAIN WILD-TYPE                            20
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  21Q GAIN MUTATED                                  25
  21Q GAIN WILD-TYPE                                87
D38V3, multiclass
                                         clus
vv                                        21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               12                383
  MIXED SEROUS AND ENDOMETRIOID                          1                 20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     25                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V4, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     7  31
  21Q GAIN WILD-TYPE 134 356
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      7   31
  21Q GAIN WILD-TYPE  134  356
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 7                134
  YES               31                356
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  21Q GAIN MUTATED    26   1   3   3
  21Q GAIN WILD-TYPE 337  22  14  32
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0               26                337
  R1                1                 22
  R2                3                 14
  RX                3                 32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q GAIN MUTATED                                  0     0
  21Q GAIN WILD-TYPE                                4    20
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  21Q GAIN MUTATED                          12
  21Q GAIN WILD-TYPE                        89
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  21Q GAIN MUTATED                                           1    22
  21Q GAIN WILD-TYPE                                         8   344
D38V6, multiclass
                                           clus
vv                                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    0                 20
  BLACK OR AFRICAN AMERICAN                               12                 89
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   22                344
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     0  27
  21Q GAIN WILD-TYPE  14 340
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   27
  21Q GAIN WILD-TYPE   14  340
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 14
  NOT HISPANIC OR LATINO               27                340
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    23   7
  22Q GAIN WILD-TYPE 434  62
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                30                496 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 7                 62 
$`22Q GAIN MUTATED`
TCGA-A5-A0G5 TCGA-A5-A2K4 TCGA-AP-A05A TCGA-AP-A0LI TCGA-AP-A3K1 TCGA-AX-A1CF 
       37.02        28.64        63.91        97.71        21.90        76.83 
TCGA-AX-A2H2 TCGA-AX-A3GI TCGA-B5-A0K8 TCGA-B5-A1MR TCGA-B5-A3S1 TCGA-BK-A26L 
        4.77         0.39        17.85       191.84        29.65        24.13 
TCGA-D1-A1O0 TCGA-D1-A3JP TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A2CH TCGA-EY-A1GO 
        2.07        16.93        10.92        37.71        19.40        19.27 
TCGA-EY-A1GS TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2CX 
       15.09        27.35        13.84        11.38        14.70        40.01 
TCGA-FI-A2CY TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-KP-A3W1 
       41.06        96.69        59.01         9.07        28.93         9.47 

$`22Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88       149.56        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       36.82        28.27        20.81        23.21        68.65        19.96 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 
        7.92        11.44        36.33         9.60         8.02        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M 
       46.32         5.33         5.16         7.33        14.96         1.18 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
       14.43        10.26         0.39        19.79        29.39         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
       34.36        34.16         1.12         0.76        18.90         1.68 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA 
        1.64        14.66        22.49        22.26        17.06        20.81 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ 
       36.99        20.65        21.21        15.62        10.19        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.95        14.76        16.87        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       20.78         2.70         0.13        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07         8.22        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       23.87        12.20        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37         3.39        63.16        36.36        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        46.78        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       27.85        16.24        36.13         0.56        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       66.58        34.98        53.92        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        35.01        28.54        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        65.88        13.28        19.20        16.96        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       15.25        20.28        12.43        20.05        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H5 
       67.50        25.12        36.39        11.08        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       40.80        61.18        81.37        34.32        46.49        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       26.33        17.75        30.74         2.96        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
        0.23         0.20         0.56        43.82         0.20        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        1.38         0.30         0.26         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       14.47        80.38        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       25.91        27.29        17.88        13.74        17.10        11.01 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
        4.11         8.71       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q 
       54.44        45.90        43.96        40.50        36.82        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       33.50        27.35        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW 
       17.36        16.57       102.31        50.89        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       11.70        11.87        15.29        12.79       116.25        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD 
       78.81        62.14        33.11        14.27        41.06        34.13 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       34.98        22.06        38.37        36.49        28.27        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       11.31         6.81        35.90        34.98         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
       10.16        31.76        24.99        16.64        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        23.47        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       67.20        88.34        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI 
       73.25        59.51        62.79        63.58        49.55        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       36.36        37.51        36.79        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
       31.07        33.63        10.65         0.69        18.67         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 
        0.72        18.25        16.87        18.02        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        3.95         3.52        41.42         8.48        44.88         0.26 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        4.27         4.11        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT 
       39.29        36.62        24.30        35.38         9.37        12.39 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       31.10       110.10        23.38        48.36        17.06         2.37 
TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 
        6.67        27.32        16.04         7.36        16.80        49.15 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       51.42        34.39        26.43        35.15        17.19        27.16 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       17.88        26.96        22.26        16.34        14.53        24.89 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
        6.21        14.99         4.54        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       23.34        23.34        23.90        22.78        13.97         6.90 
TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       18.84        17.88        17.62        16.11        12.43        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 
       11.08         6.48        19.33        12.59        10.19        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       18.87        22.82        20.05        45.76        31.04        29.10 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2D0 
       17.92        14.14        19.89        16.96         5.88        39.88 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2F4 TCGA-FI-A2F8 
       39.95         7.99        13.84         8.98        28.96        25.02 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ 
       29.23        41.06        45.01         1.74         7.76        14.04 
TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
        2.43        23.74        13.28        26.10        18.21        23.24 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 
       15.45        23.97        12.92         7.00        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 
       18.84        39.95        12.92        23.64        14.83         4.44 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.07        18.28         0.07         0.23 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.39               0.07 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            191.84             185.79 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            23.015             23.340 
[1] "0.4 - 191.8 (23.0)" "0.1 - 185.8 (23.3)"
[1] "hr=" "1.8"
D39V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  22Q GAIN MUTATED                                         7
  22Q GAIN WILD-TYPE                                     388
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  22Q GAIN MUTATED                               1
  22Q GAIN WILD-TYPE                            20
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  22Q GAIN MUTATED                                  23
  22Q GAIN WILD-TYPE                                89
D39V3, multiclass
                                         clus
vv                                        22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                7                388
  MIXED SEROUS AND ENDOMETRIOID                          1                 20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     23                 89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V4, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     7  24
  22Q GAIN WILD-TYPE 134 363
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      7   24
  22Q GAIN WILD-TYPE  134  363
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 7                134
  YES               24                363
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  22Q GAIN MUTATED    19   1   4   3
  22Q GAIN WILD-TYPE 344  22  13  32
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0               19                344
  R1                1                 22
  R2                4                 13
  RX                3                 32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q GAIN MUTATED                                  0     0
  22Q GAIN WILD-TYPE                                4    20
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  22Q GAIN MUTATED                          10
  22Q GAIN WILD-TYPE                        91
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  22Q GAIN MUTATED                                           0    16
  22Q GAIN WILD-TYPE                                         9   350
D39V6, multiclass
                                           clus
vv                                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    0                 20
  BLACK OR AFRICAN AMERICAN                               10                 91
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  9
  WHITE                                                   16                350
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     0  19
  22Q GAIN WILD-TYPE  14 348
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0   19
  22Q GAIN WILD-TYPE   14  348
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 14
  NOT HISPANIC OR LATINO               19                348
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    54  10
  XP GAIN WILD-TYPE 403  59
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               64               462 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               10                59 
$`XP GAIN MUTATED`
TCGA-A5-A0GV TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NG TCGA-AJ-A3TW TCGA-AJ-A8CW 
       20.81        22.26        20.81        15.62        16.87         0.13 
TCGA-AP-A0LF TCGA-AP-A0LO TCGA-AP-A1DO TCGA-AP-A1E4 TCGA-AX-A05W TCGA-AX-A0IW 
        3.39        33.40        31.30        16.24        68.35        37.78 
TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HH TCGA-B5-A0JR TCGA-B5-A0JT 
       30.12        40.80        81.37        17.75        56.91        43.13 
TCGA-B5-A0K4 TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A5OD TCGA-BG-A0M0 TCGA-BG-A0M2 
       17.88        33.50        27.35        34.13        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0MS TCGA-BG-A0RY TCGA-BG-A0W1 TCGA-BK-A0C9 
       35.21        34.98        30.81        15.42        52.83        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L TCGA-BS-A0TE TCGA-BS-A0TI TCGA-BS-A0UT 
       10.22        10.16        24.13         4.80        61.87        72.72 
TCGA-BS-A0V8 TCGA-D1-A102 TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A17R TCGA-D1-A2G5 
       49.55         4.44         0.66        36.10        11.15        41.42 
TCGA-D1-A2G6 TCGA-E6-A1M0 TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A22Y TCGA-EO-A3AS 
        8.48        17.06        27.32        10.92        51.52        34.39 
TCGA-EO-A3B1 TCGA-EY-A1G7 TCGA-EY-A1GH TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GX 
       26.96         6.21        23.34        17.88        15.09         6.48 
TCGA-EY-A1H0 TCGA-EY-A212 TCGA-FI-A2D4 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-K6-A3WQ 
       19.33        10.19         7.99        59.01         9.07        14.04 
TCGA-KP-A3VZ TCGA-KP-A3W1 TCGA-QS-A744 TCGA-SL-A6J9 
       23.74         9.47        14.83         0.07 

$`XP GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        36.82        28.27        23.21        68.65        19.96 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 
        7.92        11.44        36.33         9.60         8.02        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       46.32        28.64         5.33         5.16         7.33        14.96 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM 
        1.18        14.43        10.26         0.39        19.79        29.39 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI 
        2.40        34.36        34.16         1.12         0.76        18.90 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC 
        1.68         1.64        14.66        22.49        17.06        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65        21.21        10.19        15.35        15.95        14.76 
TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AP-A051 
       16.87        22.32        12.82        20.78         2.70        83.67 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
       21.99         5.95        23.31        86.07         8.22        63.91 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       57.80        45.53        36.89        23.87        12.20        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP 
       97.71        31.73        83.97        27.12        82.52        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       55.89        35.54        46.78        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       10.42        27.85        21.90        36.13         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       19.82        29.69        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       66.58        34.98        53.92        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        35.01        28.54        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       65.88        13.28        19.20        16.96        13.55        15.25 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       20.28        12.43        20.05        76.83        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 
       67.50        25.12        36.39        11.08         4.77        71.24 
TCGA-AX-A2H8 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HJ 
       61.18        34.32        46.49        19.36        26.33        30.74 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
        2.96        31.13        64.93         0.23         0.20         0.56 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 
       43.82         0.20        20.52         1.38         0.30         0.26 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN 
        0.30         1.18        18.35        14.47         0.39        80.38 
TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       46.75        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 
       28.34        30.51        25.91        27.29        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.85        11.01         4.11         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       36.82        32.09        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV 
       17.36        16.57       191.84       102.31        50.89        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       14.70        11.70        11.87        15.29        12.79       116.25 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 
       96.30        78.81        62.14        33.11        14.27        29.65 
TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M6 TCGA-BG-A0M7 
       41.06        34.95        18.61        20.19        22.06        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       36.49        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VT 
       43.30        43.04        39.32        21.17        20.28        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU 
       26.66        16.34        34.29        52.64        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C 
       11.31         6.81        34.98         6.21        31.76        24.99 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       16.64        13.18        10.03         9.86        46.95        23.47 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
       85.55        78.21        77.95        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        67.20        88.34        85.84        82.39        81.57 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ 
       73.25        59.51        62.79        63.58        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A167 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       15.72        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       18.67         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02        14.73         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.51         1.78        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 
       13.22         0.72        18.25        16.87        18.02         2.07 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G7 TCGA-D1-A3DA 
       15.06         1.05         3.95         3.52        44.88         0.26 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        4.27         4.11        16.93        89.33        10.92        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO 
       16.31        39.29        36.62        24.30        35.38         9.37 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A2P8 
       12.39        31.10       110.10        23.38        48.36         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 
        6.67        16.04         7.36        16.80        49.15        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG 
       61.74        61.55        66.90        46.26        57.60        51.42 
TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       19.40        26.43        35.15        17.19        27.16        17.88 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC 
       22.26        16.34        14.53        24.89        14.99         4.54 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK 
       53.88        24.36        27.16        23.34        23.90        22.78 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GT 
       13.97         6.90        19.27        18.84        17.62        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A215 
       12.43        15.81        11.08        12.59        14.40        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 
       22.82        20.05        45.76        31.04        29.10        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       13.84        11.38        17.92        14.14        19.89        14.70 
TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
       16.96         5.88        40.01        41.06        39.88        39.95 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 
       13.84         8.98        96.69        28.93        28.96        25.02 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KJ-A3U4 
       29.23        41.06        45.01         1.74         7.76         2.43 
TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 
       13.28        26.10        18.21        23.24        15.45        23.97 
TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       12.92         7.00        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       12.92        23.64         4.44        14.07        18.28         0.23 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.07              0.20 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            81.37            191.84 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           20.875            23.470 
[1] "0.1 - 81.4 (20.9)"  "0.2 - 191.8 (23.5)"
[1] "hr=" "1.5"
D40V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  XP GAIN MUTATED                                        46
  XP GAIN WILD-TYPE                                     349
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  XP GAIN MUTATED                               1
  XP GAIN WILD-TYPE                            20
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  XP GAIN MUTATED                                  17
  XP GAIN WILD-TYPE                                95
D40V3, multiclass
                                         clus
vv                                        XP GAIN MUTATED XP GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              46               349
  MIXED SEROUS AND ENDOMETRIOID                         1                20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    17                95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V4, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    13  51
  XP GAIN WILD-TYPE 128 336
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     13   51
  XP GAIN WILD-TYPE  128  336
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               13               128
  YES              51               336
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XP GAIN MUTATED    44   2   5   5
  XP GAIN WILD-TYPE 319  21  12  30
D40V5, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  R0              44               319
  R1               2                21
  R2               5                12
  RX               5                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP GAIN MUTATED                                  0     2
  XP GAIN WILD-TYPE                                4    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  XP GAIN MUTATED                          10
  XP GAIN WILD-TYPE                        91
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XP GAIN MUTATED                                           1    46
  XP GAIN WILD-TYPE                                         8   320
D40V6, multiclass
                                           clus
vv                                          XP GAIN MUTATED XP GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   2                18
  BLACK OR AFRICAN AMERICAN                              10                91
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 8
  WHITE                                                  46               320
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     1  48
  XP GAIN WILD-TYPE  13 319
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      1   48
  XP GAIN WILD-TYPE   13  319
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                13
  NOT HISPANIC OR LATINO              48               319
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    49  14
  XQ GAIN WILD-TYPE 408  55
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               63               463 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               14                55 
$`XQ GAIN MUTATED`
TCGA-A5-A0GV TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A3EM TCGA-AJ-A3NG TCGA-AJ-A3TW 
       20.81        14.96        14.43        22.26        15.62        16.87 
TCGA-AJ-A8CW TCGA-AP-A0L8 TCGA-AP-A0LO TCGA-AP-A1DO TCGA-AP-A1E4 TCGA-AP-A5FX 
        0.13        48.79        33.40        31.30        16.24        36.13 
TCGA-AX-A05W TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HH TCGA-B5-A0JR 
       68.35        30.12        40.80        81.37        17.75        56.91 
TCGA-B5-A0JT TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A5OD TCGA-BG-A0M0 TCGA-BG-A0M2 
       43.13        33.50        27.35        34.13        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0RY TCGA-BG-A0W1 
       35.21        34.98        22.06        30.81        15.42        52.83 
TCGA-BK-A0C9 TCGA-BK-A0CC TCGA-BK-A26L TCGA-BS-A0TE TCGA-BS-A0TI TCGA-BS-A0UT 
       35.90        10.22        24.13         4.80        61.87        72.72 
TCGA-BS-A0V8 TCGA-D1-A102 TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A17R TCGA-D1-A2G5 
       49.55         4.44         0.66        36.10        11.15        41.42 
TCGA-D1-A2G6 TCGA-E6-A1M0 TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A22Y TCGA-EO-A2CH 
        8.48        17.06        27.32        10.92        51.52        19.40 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1G7 TCGA-EY-A1GH TCGA-EY-A1GQ TCGA-EY-A1GX 
       26.96        22.26         6.21        23.34        17.88         6.48 
TCGA-EY-A1H0 TCGA-EY-A3L3 TCGA-EY-A547 TCGA-FI-A2D4 TCGA-K6-A3WQ TCGA-KP-A3VZ 
       19.33        27.35        17.92         7.99        14.04        23.74 
TCGA-KP-A3W1 TCGA-QS-A744 TCGA-SL-A6J9 
        9.47        14.83         0.07 

$`XQ GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        36.82        28.27        23.21        68.65        19.96 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 
        7.92        11.44        36.33         9.60         8.02        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23M 
       46.32        28.64         5.33         5.16         7.33         1.18 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
       10.26         0.39        19.79        29.39         2.40        34.36 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       34.16         1.12         0.76        18.90         1.68         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE 
       14.66        22.49        17.06        20.81        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       21.21        10.19        15.35        15.95        14.76        16.87 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AP-A051 TCGA-AP-A052 
       22.32        12.82        20.78         2.70        83.67        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D 
        5.95        23.31        86.07         8.22        63.91        57.80 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 
       45.53        36.89        23.87        12.20        20.91       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      117.99       110.37         3.39        63.16        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ 
       31.73        83.97        27.12        82.52        61.64        80.78 
TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        46.78        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       27.85        21.90         0.56        13.58        19.82        29.69 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       53.92        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       35.01        28.54        37.78        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       13.28        19.20        16.96        13.55        15.25        20.28 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       12.43        20.05        76.83        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H8 
       25.12        36.39        11.08         4.77        71.24        61.18 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK 
       34.32        46.49        19.36        26.33        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        64.93         0.23         0.20         0.56        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
        0.20        20.52         1.38         0.30         0.26         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JS 
        1.18        18.35        14.47         0.39        80.38        46.75 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        27.29        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.85        11.01         4.11         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       36.82        32.09        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV 
       17.36        16.57       191.84       102.31        50.89        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       14.70        11.70        11.87        15.29        12.79       116.25 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 
       96.30        78.81        62.14        33.11        14.27        29.65 
TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M7 TCGA-BG-A0M8 
       41.06        34.95        18.61        20.19        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VT TCGA-BG-A0VV 
       43.04        39.32        21.17        20.28        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       16.34        34.29        52.64        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 
       13.78        14.73        14.01        15.45        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
        1.81         9.57        20.02        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
        6.81        34.98         6.21        10.16        31.76        24.99 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       16.64        13.18        10.03         9.86        46.95        23.47 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
       85.55        78.21        77.95        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        67.20        88.34        85.84        82.39        81.57 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ 
       73.25        59.51        62.79        63.58        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A167 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       15.72        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       18.67         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02        14.73         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.51         1.78        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 
       13.22         0.72        18.25        16.87        18.02         2.07 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G7 TCGA-D1-A3DA 
       15.06         1.05         3.95         3.52        44.88         0.26 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        4.27         4.11        16.93        89.33        10.92        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO 
       16.31        39.29        36.62        24.30        35.38         9.37 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A2P8 
       12.39        31.10       110.10        23.38        48.36         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 
        6.67        16.04         7.36        16.80        49.15        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG 
       61.74        61.55        66.90        46.26        57.60        51.42 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       34.39        26.43        35.15        17.19        27.16        17.88 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       16.34        14.53        24.89        14.99         4.54        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL 
       24.36        27.16        23.34        23.90        22.78        13.97 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT 
        6.90        19.27        18.84        17.62        15.09        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 
       12.43        15.81        11.08        12.59        10.19        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       18.87        22.82        20.05        45.76        31.04        29.10 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
       13.84        11.38        14.14        19.89        14.70        16.96 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D5 
        5.88        40.01        41.06        39.88        39.95        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 
        8.98        96.69        59.01         9.07        28.93        28.96 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
       25.02        29.23        41.06        45.01         1.74         7.76 
TCGA-KJ-A3U4 TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
        2.43        13.28        26.10        18.21        23.24        15.45 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       23.97        12.92         7.00        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       39.95        12.92        23.64         4.44        14.07        18.28 
TCGA-SL-A6JA 
        0.23 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.07              0.20 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            81.37            191.84 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            22.26             23.47 
[1] "0.1 - 81.4 (22.3)"  "0.2 - 191.8 (23.5)"
[1] "hr=" "2.2"
D41V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  XQ GAIN MUTATED                                        43
  XQ GAIN WILD-TYPE                                     352
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  XQ GAIN MUTATED                               2
  XQ GAIN WILD-TYPE                            19
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  XQ GAIN MUTATED                                  18
  XQ GAIN WILD-TYPE                                94
D41V3, multiclass
                                         clus
vv                                        XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              43               352
  MIXED SEROUS AND ENDOMETRIOID                         2                19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    18                94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V4, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    14  49
  XQ GAIN WILD-TYPE 127 338
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     14   49
  XQ GAIN WILD-TYPE  127  338
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               14               127
  YES              49               338
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XQ GAIN MUTATED    44   2   5   6
  XQ GAIN WILD-TYPE 319  21  12  29
D41V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              44               319
  R1               2                21
  R2               5                12
  RX               6                29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ GAIN MUTATED                                  0     2
  XQ GAIN WILD-TYPE                                4    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  XQ GAIN MUTATED                          12
  XQ GAIN WILD-TYPE                        89
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XQ GAIN MUTATED                                           1    43
  XQ GAIN WILD-TYPE                                         8   323
D41V6, multiclass
                                           clus
vv                                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   2                18
  BLACK OR AFRICAN AMERICAN                              12                89
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 8
  WHITE                                                  43               323
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     1  45
  XQ GAIN WILD-TYPE  13 322
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1   45
  XQ GAIN WILD-TYPE   13  322
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                13
  NOT HISPANIC OR LATINO              45               322
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    20   5
  1P LOSS WILD-TYPE 437  64
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               25               501 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                5                64 
$`1P LOSS MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0GN TCGA-A5-A1OH TCGA-A5-A2K3 TCGA-AJ-A23M TCGA-AP-A0L8 
      149.56        60.53        36.33        46.32         1.18        48.79 
TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A1CR 
        3.39        97.71        13.55        20.28        76.83        11.08 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-B5-A11P TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1GO 
        4.77        30.12        36.82        27.16        26.96        19.27 
TCGA-EY-A1GP TCGA-EY-A2OO TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PX TCGA-PG-A915 
       18.84        45.76        28.93        25.02        45.01         7.00 
TCGA-QS-A8F1 
        4.44 

$`1P LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       57.53        65.75        60.53        46.55        38.37        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        20.81        23.21        68.65        19.96        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       19.59        24.62        29.06        42.35        15.95         7.92 
TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A2K5 
       11.44         9.60         8.02        91.04        28.64         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
        5.16         7.33        14.96        14.43        10.26         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF 
       19.79        29.39         2.40        34.36        34.16         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76        18.90         1.68         1.64        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.26        17.06        20.81        36.99        20.65        21.21 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       15.62        10.19        15.35        15.95        14.76        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW 
       16.87        22.32        12.82        20.78         2.70         0.13 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       83.67        21.99         5.95        23.31        86.07         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       63.91        57.80        45.53        36.89        23.87        12.20 
TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       20.91       125.42       117.99       110.37        63.16        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       31.73        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       55.89        31.30        35.54        46.78        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
       30.90        10.42        27.85        16.24        21.90        36.13 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       28.54        37.78        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI 
       19.20        16.96        15.25        12.43        20.05        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2H7 
       54.12        67.50        25.12        36.39        71.24        40.80 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       61.18        81.37        34.32        46.49        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       17.75        30.74         2.96        31.13        64.93         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
        0.20         0.56        43.82         0.20        20.52         1.38 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.30         0.26         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
        0.39        80.38        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        27.29        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       11.01         4.11         8.71       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       75.72        54.44        45.90        43.96        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       33.50        27.35        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV 
       17.36        16.57       191.84       102.31        50.89        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       14.70        11.70        11.87        15.29        12.79       116.25 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 
       96.30        78.81        62.14        33.11        14.27        29.65 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       41.06        34.13        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98        22.06        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       15.45        15.45        14.27         1.81         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31         6.81        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
        6.21        10.22        10.16        31.76        24.99        24.13 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       16.64        13.18        10.03         9.86        46.95        23.47 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF 
       96.49        30.74        97.41        67.20        88.34        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       63.58        49.55        63.16        66.48        16.83        19.79 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
        0.69        18.67         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
       22.92         1.41        13.22         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       18.02         2.07        15.06         1.05         3.95         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
       41.42         8.48        44.88         0.26         4.27         4.11 
TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
       16.93        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU 
       36.62        24.30        35.38         9.37        12.39        31.10 
TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
      110.10        23.38        48.36        17.06         2.37         6.67 
TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       27.32        16.04         7.36        16.80        10.92        49.15 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       37.71        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       51.52        51.42        19.40        34.39        26.43        35.15 
TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       17.19        17.88        22.26        16.34        14.53        24.89 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
        6.21        14.99         4.54        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       23.34        23.34        23.90        22.78        13.97         6.90 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       17.88        17.62        15.09        16.11        12.43        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 
       11.08         6.48        19.33        12.59        10.19        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 
       18.87        22.82        20.05        31.04        29.10        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       13.84        11.38        17.92        14.14        19.89        14.70 
TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
       16.96         5.88        40.01        41.06        39.88        39.95 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
        7.99        13.84         8.98        96.69        59.01         9.07 
TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ 
       28.96        29.23        41.06         1.74         7.76        14.04 
TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 
        2.43        23.74        13.28         9.47        26.10        18.21 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 
       23.24        15.45        23.97        12.92        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI 
       18.84        39.95        12.92        23.64        14.83        14.07 
TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       18.28         0.07         0.23 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             1.18              0.07 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           149.56            191.84 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            27.16             23.24 
[1] "1.2 - 149.6 (27.2)" "0.1 - 191.8 (23.2)"
[1] "hr=" "1.4"
D42V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  1P LOSS MUTATED                                         6
  1P LOSS WILD-TYPE                                     389
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  1P LOSS MUTATED                               3
  1P LOSS WILD-TYPE                            18
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  1P LOSS MUTATED                                  16
  1P LOSS WILD-TYPE                                96
D42V3, multiclass
                                         clus
vv                                        1P LOSS MUTATED 1P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               6               389
  MIXED SEROUS AND ENDOMETRIOID                         3                18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    16                96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V4, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     6  19
  1P LOSS WILD-TYPE 135 368
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      6   19
  1P LOSS WILD-TYPE  135  368
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                6               135
  YES              19               368
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1P LOSS MUTATED    15   3   4   0
  1P LOSS WILD-TYPE 348  20  13  35
D42V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              15               348
  R1               3                20
  R2               4                13
  RX               0                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P LOSS MUTATED                                  0     1
  1P LOSS WILD-TYPE                                4    19
                   vv
clus                BLACK OR AFRICAN AMERICAN
  1P LOSS MUTATED                           7
  1P LOSS WILD-TYPE                        94
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1P LOSS MUTATED                                           0    15
  1P LOSS WILD-TYPE                                         9   351
D42V6, multiclass
                                           clus
vv                                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   1                19
  BLACK OR AFRICAN AMERICAN                               7                94
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 9
  WHITE                                                  15               351
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     0  18
  1P LOSS WILD-TYPE  14 349
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0   18
  1P LOSS WILD-TYPE   14  349
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                14
  NOT HISPANIC OR LATINO              18               349
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    10   4
  1Q LOSS WILD-TYPE 447  65
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               14               512 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                4                65 
$`1Q LOSS MUTATED`
TCGA-A5-A0G2 TCGA-AJ-A23M TCGA-AP-A0L8 TCGA-AP-A0LF TCGA-AX-A1CF TCGA-AX-A1CR 
      149.56         1.18        48.79         3.39        76.83        11.08 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1GP TCGA-FI-A2EY 
        4.77        30.12        27.16        26.96        18.84        28.93 
TCGA-FI-A2F8 TCGA-PG-A915 
       25.02         7.00 

$`1Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       36.82        28.27        20.81        23.21        68.65        19.96 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 
        7.92        11.44        36.33         9.60         8.02        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       46.32        28.64         5.33         5.16         7.33        14.96 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
       14.43        10.26         0.39        19.79        29.39         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
       34.36        34.16         1.12         0.76        18.90         1.68 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA 
        1.64        14.66        22.49        22.26        17.06        20.81 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ 
       36.99        20.65        21.21        15.62        10.19        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.95        14.76        16.87        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       20.78         2.70         0.13        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
       23.31        86.07         8.22        63.91        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        12.20        20.91       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        63.16        36.36        97.71        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        46.78        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       27.85        16.24        21.90        36.13         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       45.99        66.58        34.98        53.92        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        35.01        28.54        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        65.88        13.28        19.20        16.96 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI 
       13.55        15.25        20.28        12.43        20.05        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2H7 
       54.12        67.50        25.12        36.39        71.24        40.80 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       61.18        81.37        34.32        46.49        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       17.75        30.74         2.96        31.13        64.93         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
        0.20         0.56        43.82         0.20        20.52         1.38 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.30         0.26         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
        0.39        80.38        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        27.29        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       11.01         4.11         8.71       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
       75.72        54.44        45.90        43.96        40.50        36.82 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU 
       18.41        17.36        16.57       191.84       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 
       14.40        14.70        11.70        11.87        15.29        12.79 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH 
      116.25        96.30        78.81        62.14        33.11        14.27 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       29.65        41.06        34.13        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98        22.06        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       36.49        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       43.30        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.01        15.45        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 
       20.02        23.70        20.12        11.31         6.81        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       34.98         6.21        10.22        10.16        31.76        24.99 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.13        16.64        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        67.20        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       62.79        63.58        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       36.79        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       10.65         0.69        18.67         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
        2.33        22.92         1.41        13.22         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.52        41.42         8.48        44.88         0.26         4.27 
TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        4.11        16.93        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT 
       39.29        36.62        24.30        35.38         9.37        12.39 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       31.10       110.10        23.38        48.36        17.06         2.37 
TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        6.67        27.32        16.04         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       49.15        37.71        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       57.60        51.52        51.42        19.40        34.39        26.43 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX 
       35.15        17.19        17.88        22.26        16.34        14.53 
TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       24.89         6.21        14.99         4.54        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL 
       27.16        23.34        23.34        23.90        22.78        13.97 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT 
        6.90        19.27        17.88        17.62        15.09        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       12.43        15.81        11.08         6.48        19.33        12.59 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       10.19        14.40        18.87        22.82        20.05        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 
       31.04        29.10        27.35        13.84        11.38        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX 
       14.14        19.89        14.70        16.96         5.88        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       41.06        39.88        39.95         7.99        13.84         8.98 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-FI-A3PV 
       96.69        59.01         9.07        28.96        29.23        41.06 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       45.01         1.74         7.76        14.04         2.43        23.74 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       13.28         9.47        26.10        18.21        23.24        15.45 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       23.97        12.92        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       12.92        23.64        14.83         4.44        14.07        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             1.18              0.07 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           149.56            191.84 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           25.990            23.325 
[1] "1.2 - 149.6 (26.0)" "0.1 - 191.8 (23.3)"
[1] "hr=" "2.1"
D43V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  1Q LOSS MUTATED                                         3
  1Q LOSS WILD-TYPE                                     392
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  1Q LOSS MUTATED                               2
  1Q LOSS WILD-TYPE                            19
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  1Q LOSS MUTATED                                   9
  1Q LOSS WILD-TYPE                               103
D43V3, multiclass
                                         clus
vv                                        1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               3               392
  MIXED SEROUS AND ENDOMETRIOID                         2                19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     9               103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V4, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     2  12
  1Q LOSS WILD-TYPE 139 375
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2   12
  1Q LOSS WILD-TYPE  139  375
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                2               139
  YES              12               375
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1Q LOSS MUTATED     9   1   3   0
  1Q LOSS WILD-TYPE 354  22  14  35
D43V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0               9               354
  R1               1                22
  R2               3                14
  RX               0                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q LOSS MUTATED                                  0     1
  1Q LOSS WILD-TYPE                                4    19
                   vv
clus                BLACK OR AFRICAN AMERICAN
  1Q LOSS MUTATED                           4
  1Q LOSS WILD-TYPE                        97
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1Q LOSS MUTATED                                           0     7
  1Q LOSS WILD-TYPE                                         9   359
D43V6, multiclass
                                           clus
vv                                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   1                19
  BLACK OR AFRICAN AMERICAN                               4                97
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 9
  WHITE                                                   7               359
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0  10
  1Q LOSS WILD-TYPE  14 357
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0   10
  1Q LOSS WILD-TYPE   14  357
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                14
  NOT HISPANIC OR LATINO              10               357
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED     8   3
  2P LOSS WILD-TYPE 449  66
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               11               515 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                3                66 
$`2P LOSS MUTATED`
TCGA-AJ-A3BD TCGA-AJ-A3EM TCGA-AW-A1PO TCGA-AX-A2H4 TCGA-BG-A18C TCGA-BS-A0U9 
       34.16        22.26         0.56        30.12        15.45        67.20 
TCGA-D1-A1O0 TCGA-EY-A1GW TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-PG-A915 
        2.07        11.08        29.23        41.06         7.00 

$`2P LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       38.37        36.82        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       19.96        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK 
       15.95         7.92        11.44        36.33         9.60         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
       91.04        46.32        28.64         5.33         5.16         7.33 
TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       14.96         1.18        14.43        10.26         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI 
       29.39         2.40        34.36         1.12         0.76        18.90 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3IA 
        1.68         1.64        14.66        22.49        17.06        20.81 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ 
       36.99        20.65        21.21        15.62        10.19        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.95        14.76        16.87        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       20.78         2.70         0.13        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
       23.31        86.07         8.22        63.91        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       36.89        23.87        12.20        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      117.99       110.37         3.39        63.16        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       31.73        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       55.89        31.30        35.54        46.78        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
       30.90        10.42        27.85        16.24        21.90        36.13 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D 
       35.34        45.99        66.58        34.98        53.92        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       51.09        27.39        30.02        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       16.96        13.55        15.25        20.28        12.43        20.05 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       76.83        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
       11.08         4.77        71.24        40.80        61.18        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       34.32        46.49        19.36        26.33        17.75        30.74 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
        2.96        31.13        64.93         0.23         0.20         0.56 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 
       43.82         0.20        20.52         1.38         0.30         0.26 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN 
        0.30         1.18        18.35        14.47         0.39        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        46.75        43.13        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB 
       17.88        13.74        17.10        17.85        11.01         4.11 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
        8.71       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R 
       45.90        43.96        40.50        36.82        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW 
       16.57       191.84       102.31        50.89        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       11.70        11.87        15.29        12.79       116.25        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       78.81        62.14        33.11        14.27        29.65        41.06 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       34.13        34.95        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98        22.06        38.37        36.49        28.27 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       11.31         6.81        35.90        34.98         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F 
       10.16        31.76        24.99        24.13        16.64        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        23.47        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       97.41        88.34        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI 
       73.25        59.51        62.79        63.58        49.55        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       36.36        37.51        36.79        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
       31.07        33.63        10.65         0.69        18.67         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 
        0.72        18.25        16.87        18.02        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        3.95         3.52        41.42         8.48        44.88         0.26 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        4.27         4.11        16.93        89.33        10.92        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO 
       16.31        39.29        36.62        24.30        35.38         9.37 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
       12.39        31.10       110.10        23.38        48.36        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
        2.37         6.67        27.32        16.04         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       10.92        49.15        37.71        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       46.26        57.60        51.52        51.42        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 
       26.43        35.15        17.19        27.16        17.88        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       22.26        16.34        14.53        24.89         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.90        22.78        13.97         6.90        19.27        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       17.88        17.62        15.09        16.11        12.43        15.81 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 
        6.48        19.33        12.59        10.19        14.40        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 
       22.82        20.05        45.76        31.04        29.10        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       13.84        11.38        17.92        14.14        19.89        14.70 
TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
       16.96         5.88        40.01        41.06        39.88        39.95 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
        7.99        13.84         8.98        96.69        59.01         9.07 
TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
       28.93        28.96        25.02        45.01         1.74         7.76 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 
       14.04         2.43        23.74        13.28         9.47        26.10 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 
       18.21        23.24        15.45        23.97        12.92        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        18.84        39.95        12.92        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44        14.07        18.28         0.07         0.23 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.56              0.07 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            67.20            191.84 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            22.26             23.34 
[1] "0.6 - 67.2 (22.3)"  "0.1 - 191.8 (23.3)"
[1] "hr=" "2.7"
D44V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  2P LOSS MUTATED                                         7
  2P LOSS WILD-TYPE                                     388
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  2P LOSS MUTATED                               0
  2P LOSS WILD-TYPE                            21
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  2P LOSS MUTATED                                   4
  2P LOSS WILD-TYPE                               108
D44V3, multiclass
                                         clus
vv                                        2P LOSS MUTATED 2P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               7               388
  MIXED SEROUS AND ENDOMETRIOID                         0                21
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     4               108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V4, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     1  10
  2P LOSS WILD-TYPE 140 377
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      1   10
  2P LOSS WILD-TYPE  140  377
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                1               140
  YES              10               377
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2P LOSS MUTATED     7   1   1   2
  2P LOSS WILD-TYPE 356  22  16  33
D44V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0               7               356
  R1               1                22
  R2               1                16
  RX               2                33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P LOSS MUTATED                                  0     0
  2P LOSS WILD-TYPE                                4    20
                   vv
clus                BLACK OR AFRICAN AMERICAN
  2P LOSS MUTATED                           2
  2P LOSS WILD-TYPE                        99
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2P LOSS MUTATED                                           1     8
  2P LOSS WILD-TYPE                                         8   358
D44V6, multiclass
                                           clus
vv                                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   0                20
  BLACK OR AFRICAN AMERICAN                               2                99
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 8
  WHITE                                                   8               358
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     1   9
  2P LOSS WILD-TYPE  13 358
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      1    9
  2P LOSS WILD-TYPE   13  358
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                13
  NOT HISPANIC OR LATINO               9               358
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    12   5
  2Q LOSS WILD-TYPE 445  64
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               17               509 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                5                64 
$`2Q LOSS MUTATED`
TCGA-AJ-A3BD TCGA-AJ-A3EM TCGA-AJ-A3QS TCGA-AP-A0L8 TCGA-AW-A1PO TCGA-AX-A2H4 
       34.16        22.26        16.87        48.79         0.56        30.12 
TCGA-AX-A3G1 TCGA-BG-A18C TCGA-BS-A0U9 TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-EY-A1GC 
       20.52        15.45        67.20         2.07         4.27         4.54 
TCGA-EY-A1GW TCGA-EY-A2OQ TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-PG-A915 
       11.08        29.10        29.23        41.06         7.00 

$`2Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       38.37        36.82        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       19.96        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK 
       15.95         7.92        11.44        36.33         9.60         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
       91.04        46.32        28.64         5.33         5.16         7.33 
TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       14.96         1.18        14.43        10.26         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI 
       29.39         2.40        34.36         1.12         0.76        18.90 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3IA 
        1.68         1.64        14.66        22.49        17.06        20.81 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ 
       36.99        20.65        21.21        15.62        10.19        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.95        14.76        16.87        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        2.70         0.13        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        63.91        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        12.20        20.91       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        46.78        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T 
       27.85        16.24        21.90        36.13        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       66.58        34.98        53.92        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        35.01        28.54        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        65.88        13.28        19.20        16.96        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       15.25        20.28        12.43        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 
       54.12        67.50        25.12        36.39        11.08         4.77 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       71.24        40.80        61.18        81.37        34.32        46.49 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       19.36        26.33        17.75        30.74         2.96        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       64.93         0.23         0.20         0.56        43.82         0.20 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        1.38         0.30         0.26         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       14.47         0.39        80.38        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        27.29        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.85        11.01         4.11         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       36.82        32.09        33.50        27.35        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS 
       19.50        18.41        17.36        16.57       191.84       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        14.40        14.70        11.70        11.87        15.29 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       12.79       116.25        96.30        78.81        62.14        33.11 
TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW 
       14.27        29.65        41.06        34.13        34.95        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 
       20.19        19.33        20.94        35.21        34.98        22.06 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       38.37        36.49        28.27        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       23.47        43.30        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       52.64        52.83        56.58        14.83        12.56        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.73        14.01        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 
       20.02        23.70        20.12        11.31         6.81        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       34.98         6.21        10.22        10.16        31.76        24.99 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.13        16.64        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        30.74        97.41        88.34        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       63.58        49.55        63.16        66.48        16.83        19.79 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
        0.69        18.67         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
       22.92         1.41        13.22         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 
       18.02        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV 
        8.48        44.88         0.26         4.11        16.93        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX 
       35.38         9.37        12.39        31.10       110.10        23.38 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ 
       48.36        17.06         2.37         6.67        27.32        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
        7.36        16.80        10.92        49.15        37.71        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG 
       61.55        66.90        46.26        57.60        51.52        51.42 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       19.40        34.39        26.43        35.15        17.19        27.16 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       17.88        26.96        22.26        16.34        14.53        24.89 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
        6.21        14.99        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       23.34        23.90        22.78        13.97         6.90        19.27 
TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       18.84        17.88        17.62        15.09        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 
       15.81         6.48        19.33        12.59        10.19        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 
       18.87        22.82        20.05        45.76        31.04        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       13.84        11.38        17.92        14.14        19.89        14.70 
TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
       16.96         5.88        40.01        41.06        39.88        39.95 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
        7.99        13.84         8.98        96.69        59.01         9.07 
TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
       28.93        28.96        25.02        45.01         1.74         7.76 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 
       14.04         2.43        23.74        13.28         9.47        26.10 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 
       18.21        23.24        15.45        23.97        12.92        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        18.84        39.95        12.92        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44        14.07        18.28         0.07         0.23 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.56              0.07 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            67.20            191.84 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            20.52             23.38 
[1] "0.6 - 67.2 (20.5)"  "0.1 - 191.8 (23.4)"
[1] "hr=" "3.1"
D45V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  2Q LOSS MUTATED                                        11
  2Q LOSS WILD-TYPE                                     384
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  2Q LOSS MUTATED                               0
  2Q LOSS WILD-TYPE                            21
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  2Q LOSS MUTATED                                   6
  2Q LOSS WILD-TYPE                               106
D45V3, multiclass
                                         clus
vv                                        2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              11               384
  MIXED SEROUS AND ENDOMETRIOID                         0                21
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     6               106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V4, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     2  15
  2Q LOSS WILD-TYPE 139 372
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2   15
  2Q LOSS WILD-TYPE  139  372
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                2               139
  YES              15               372
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2Q LOSS MUTATED    12   1   1   2
  2Q LOSS WILD-TYPE 351  22  16  33
D45V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0              12               351
  R1               1                22
  R2               1                16
  RX               2                33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q LOSS MUTATED                                  0     0
  2Q LOSS WILD-TYPE                                4    20
                   vv
clus                BLACK OR AFRICAN AMERICAN
  2Q LOSS MUTATED                           4
  2Q LOSS WILD-TYPE                        97
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2Q LOSS MUTATED                                           1    12
  2Q LOSS WILD-TYPE                                         8   354
D45V6, multiclass
                                           clus
vv                                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   0                20
  BLACK OR AFRICAN AMERICAN                               4                97
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 8
  WHITE                                                  12               354
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     1  14
  2Q LOSS WILD-TYPE  13 353
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      1   14
  2Q LOSS WILD-TYPE   13  353
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                13
  NOT HISPANIC OR LATINO              14               353
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    41   9
  3P LOSS WILD-TYPE 416  60
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               50               476 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                9                60 
$`3P LOSS MUTATED`
TCGA-2E-A9G8 TCGA-A5-A1OG TCGA-A5-A2K3 TCGA-AJ-A23M TCGA-AJ-A3BF TCGA-AJ-A3EJ 
       41.06        11.44        46.32         1.18         1.12         1.64 
TCGA-AJ-A3TW TCGA-AP-A052 TCGA-AP-A05D TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DQ 
       16.87        21.99        57.80       125.42        97.71        46.78 
TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 
       21.90         0.56        37.78        36.39        11.08        61.18 
TCGA-AX-A2HK TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K3 TCGA-B5-A0KB 
        2.96         0.30         0.39        80.38        27.29         4.11 
TCGA-B5-A11I TCGA-BG-A0M6 TCGA-BG-A0YV TCGA-BG-A18C TCGA-BK-A4ZD TCGA-BS-A0TI 
       75.72        22.06        12.56        15.45        16.64        61.87 
TCGA-D1-A0ZZ TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-DI-A1NN 
       22.55        31.07        18.67         0.72         2.07        35.38 
TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GV TCGA-EY-A2OQ 
       16.34        23.90        19.27        18.84        15.81        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2EY TCGA-KP-A3W3 
       27.35        13.84        14.70        39.95        28.93        26.10 
TCGA-KP-A3W4 TCGA-SL-A6J9 
       18.21         0.07 

$`3P LOSS WILD-TYPE`
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       36.69        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       36.82        28.27        20.81        23.21        68.65        19.96 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K4 
        7.92        36.33         9.60         8.02        91.04        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O 
        5.33         5.16         7.33        14.96        14.43        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
        0.39        19.79        29.39         2.40        34.36        34.16 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
        0.76        18.90         1.68        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       17.06        20.81        36.99        20.65        21.21        15.62 
TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DV 
       10.19        15.35        15.95        14.76        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A053 
       12.82        20.78         2.70         0.13        83.67         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07         8.22        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        12.20        20.91        48.79       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
        3.39        63.16        36.36        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        55.89        31.30        35.54 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        30.90        10.42        27.85        16.24 
TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       36.13        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       28.54        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       16.96        13.55        15.25        20.28        12.43        20.05 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 
       76.83        72.56        54.12        67.50        25.12         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       30.12        71.24        40.80        81.37        34.32        46.49 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO 
       19.36        26.33        17.75        30.74        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
        0.23         0.20         0.56        43.82         0.20        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        1.38         0.26         0.30         1.18        18.35        14.47 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        46.75        43.13        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 
       32.55        28.64        28.34        30.51        25.91        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       13.74        17.10        17.85        11.01         8.71       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
      113.36        88.34        54.44        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       36.82        32.09        33.50        27.35        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS 
       19.50        18.41        17.36        16.57       191.84       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        14.40        14.70        11.70        11.87        15.29 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       12.79       116.25        96.30        78.81        62.14        33.11 
TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW 
       14.27        29.65        41.06        34.13        34.95        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        34.98        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       36.49        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       43.30        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        20.02        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31         6.81        35.90        34.98         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F 
       10.22        10.16        31.76        24.99        24.13        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        23.47        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
        4.80        77.95        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       67.20        88.34        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI 
       73.25        59.51        62.79        63.58        49.55        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
        4.87        28.67        23.93         1.74         4.44        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16O 
       37.51        36.79        27.42        11.51        29.92        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
       22.92         1.41        13.22        18.25        16.87        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV 
       44.88         0.26         4.27         4.11        16.93        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ 
        9.37        12.39        31.10       110.10        23.38        48.36 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       17.06         2.37         6.67        27.32        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
       16.80        10.92        49.15        37.71        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH 
       66.90        46.26        57.60        51.52        51.42        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       34.39        26.43        35.15        17.19        27.16        17.88 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       26.96        22.26        14.53        24.89         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS 
       22.78        13.97         6.90        17.88        17.62        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       16.11        12.43        11.08         6.48        19.33        12.59 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       10.19        14.40        18.87        22.82        20.05        45.76 
TCGA-EY-A2OP TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 
       31.04        11.38        17.92        14.14        19.89        16.96 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 
        5.88        40.01        41.06        39.88         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F8 
        8.98        96.69        59.01         9.07        28.96        25.02 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ 
       29.23        41.06        45.01         1.74         7.76        14.04 
TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-PG-A5BC TCGA-PG-A6IB 
        2.43        23.74        13.28         9.47        23.24        15.45 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       23.97        12.92         7.00        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       39.95        12.92        23.64        14.83         4.44        14.07 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.07              0.13 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           125.42            191.84 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           20.585            23.555 
[1] "0.1 - 125.4 (20.6)" "0.1 - 191.8 (23.6)"
[1] "hr=" "1.6"
D46V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  3P LOSS MUTATED                                        18
  3P LOSS WILD-TYPE                                     377
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  3P LOSS MUTATED                               6
  3P LOSS WILD-TYPE                            15
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  3P LOSS MUTATED                                  26
  3P LOSS WILD-TYPE                                86
D46V3, multiclass
                                         clus
vv                                        3P LOSS MUTATED 3P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              18               377
  MIXED SEROUS AND ENDOMETRIOID                         6                15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    26                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V4, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    11  39
  3P LOSS WILD-TYPE 130 348
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     11   39
  3P LOSS WILD-TYPE  130  348
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               11               130
  YES              39               348
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3P LOSS MUTATED    36   2   2   3
  3P LOSS WILD-TYPE 327  21  15  32
D46V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0              36               327
  R1               2                21
  R2               2                15
  RX               3                32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  0     1
  3P LOSS WILD-TYPE                                4    19
                   vv
clus                BLACK OR AFRICAN AMERICAN
  3P LOSS MUTATED                          14
  3P LOSS WILD-TYPE                        87
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3P LOSS MUTATED                                           1    33
  3P LOSS WILD-TYPE                                         8   333
D46V6, multiclass
                                           clus
vv                                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   1                19
  BLACK OR AFRICAN AMERICAN                              14                87
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 8
  WHITE                                                  33               333
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     0  38
  3P LOSS WILD-TYPE  14 329
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0   38
  3P LOSS WILD-TYPE   14  329
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                14
  NOT HISPANIC OR LATINO              38               329
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    26   4
  3Q LOSS WILD-TYPE 431  65
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               30               496 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4                65 
$`3Q LOSS MUTATED`
TCGA-2E-A9G8 TCGA-A5-A2K3 TCGA-AJ-A23M TCGA-AJ-A3BF TCGA-AJ-A3TW TCGA-AP-A052 
       41.06        46.32         1.18         1.12        16.87        21.99 
TCGA-AP-A05D TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AX-A0IW 
       57.80       125.42        97.71        46.78        21.90        37.78 
TCGA-AX-A2H8 TCGA-AX-A2HK TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K8 
       61.18         2.96         0.30         0.39        80.38        17.85 
TCGA-B5-A0KB TCGA-BK-A4ZD TCGA-D1-A16S TCGA-D1-A1O0 TCGA-EO-A3AZ TCGA-EY-A1GJ 
        4.11        16.64        18.67         2.07        27.16        23.90 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A54A TCGA-FI-A2D2 
       19.27        18.84        29.10        27.35        14.70        39.95 

$`3Q LOSS WILD-TYPE`
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       36.69        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       36.82        28.27        20.81        23.21        68.65        19.96 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 
        7.92        11.44        36.33         9.60         8.02        91.04 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N 
       28.64         5.33         5.16         7.33        14.96        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
       10.26         0.39        19.79        29.39         2.40        34.36 
TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
       34.16         0.76        18.90         1.68         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE 
       22.49        22.26        17.06        20.81        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       21.21        15.62        10.19        15.35        15.95        14.76 
TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW 
       16.87        22.32        12.82        20.78         2.70         0.13 
TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
       83.67         5.95        23.31        86.07         8.22        63.91 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 
       45.53        36.89        23.87        12.20        20.91        48.79 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
      117.99       110.37         3.39        63.16        36.36        31.73 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       83.97        27.12        82.52        33.40        61.64        80.78 
TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       31.30        35.54        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       27.85        16.24        36.13         0.56        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       66.58        34.98        53.92        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        35.01        28.54        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       65.88        13.28        19.20        16.96        13.55        15.25 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       20.28        12.43        20.05        76.83        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 
       67.50        25.12        36.39        11.08         4.77        30.12 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       71.24        40.80        81.37        34.32        46.49        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       26.33        17.75        30.74        31.13        64.93         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
        0.20         0.56        43.82         0.20        20.52         1.38 
TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR 
        0.26         0.30         1.18        18.35        14.47        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       46.75        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        27.29        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       13.74        17.10        11.01         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       36.82        32.09        33.50        27.35        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS 
       19.50        18.41        17.36        16.57       191.84       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        14.40        14.70        11.70        11.87        15.29 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       12.79       116.25        96.30        78.81        62.14        33.11 
TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW 
       14.27        29.65        41.06        34.13        34.95        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 
       20.19        19.33        20.94        35.21        34.98        22.06 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       38.37        36.49        28.27        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       23.47        43.30        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       52.64        52.83        56.58        14.83        12.56        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 
       14.73        14.01        15.45        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        9.57        20.02        23.70        20.12        11.31         6.81 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       35.90        34.98         6.21        10.22        10.16        31.76 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.99        24.13        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        67.20        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       62.79        63.58        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       36.79        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
       22.92         1.41        13.22         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 
       18.02        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP 
        8.48        44.88         0.26         4.27         4.11        16.93 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY 
       24.30        35.38         9.37        12.39        31.10       110.10 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 
       23.38        48.36        17.06         2.37         6.67        27.32 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       16.04         7.36        16.80        10.92        49.15        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       51.42        19.40        34.39        26.43        35.15        17.19 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       17.88        26.96        22.26        16.34        14.53        24.89 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
        6.21        14.99         4.54        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GQ 
       23.34        23.34        22.78        13.97         6.90        17.88 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       17.62        15.09        16.11        12.43        15.81        11.08 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 
        6.48        19.33        12.59        10.19        14.40        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A4KR 
       22.82        20.05        45.76        31.04        13.84        11.38 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX 
       17.92        14.14        19.89        16.96         5.88        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       41.06        39.88         7.99        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 
       59.01         9.07        28.93        28.96        25.02        29.23 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 
       41.06        45.01         1.74         7.76        14.04         2.43 
TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
       23.74        13.28         9.47        26.10        18.21        23.24 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 
       15.45        23.97        12.92         7.00        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 
       18.84        39.95        12.92        23.64        14.83         4.44 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.07        18.28         0.07         0.23 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.30              0.07 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           125.42            191.84 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           21.945            23.360 
[1] "0.3 - 125.4 (21.9)" "0.1 - 191.8 (23.4)"
[1] "hr=" "1"  
D47V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  3Q LOSS MUTATED                                        11
  3Q LOSS WILD-TYPE                                     384
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  3Q LOSS MUTATED                               2
  3Q LOSS WILD-TYPE                            19
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  3Q LOSS MUTATED                                  17
  3Q LOSS WILD-TYPE                                95
D47V3, multiclass
                                         clus
vv                                        3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              11               384
  MIXED SEROUS AND ENDOMETRIOID                         2                19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    17                95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V4, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     5  25
  3Q LOSS WILD-TYPE 136 362
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      5   25
  3Q LOSS WILD-TYPE  136  362
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                5               136
  YES              25               362
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3Q LOSS MUTATED    21   0   2   1
  3Q LOSS WILD-TYPE 342  23  15  34
D47V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0              21               342
  R1               0                23
  R2               2                15
  RX               1                34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  0     0
  3Q LOSS WILD-TYPE                                4    20
                   vv
clus                BLACK OR AFRICAN AMERICAN
  3Q LOSS MUTATED                          11
  3Q LOSS WILD-TYPE                        90
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3Q LOSS MUTATED                                           1    17
  3Q LOSS WILD-TYPE                                         8   349
D47V6, multiclass
                                           clus
vv                                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   0                20
  BLACK OR AFRICAN AMERICAN                              11                90
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 8
  WHITE                                                  17               349
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0  19
  3Q LOSS WILD-TYPE  14 348
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0   19
  3Q LOSS WILD-TYPE   14  348
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                14
  NOT HISPANIC OR LATINO              19               348
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    77  22
  4P LOSS WILD-TYPE 380  47
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               99               427 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               22                47 
$`4P LOSS MUTATED`
TCGA-5B-A90C TCGA-A5-A0G2 TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A1OH 
       36.69       149.56        60.53        36.82        19.96        36.33 
TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A2QK 
       91.04        28.64         7.33        14.96         1.18         0.39 
TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3EJ TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3QS 
       29.39        34.16         1.64        21.21        10.19        16.87 
TCGA-AJ-A3TW TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A0L9 TCGA-AP-A0LF 
       16.87         5.95        57.80        45.53       125.42         3.39 
TCGA-AP-A0LO TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A06B TCGA-AX-A0IW 
       33.40        21.90        36.13         0.56        53.92        37.78 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 
       20.28        12.43        76.83        11.08         4.77        30.12 
TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3G1 
       61.18        19.36         2.96        64.93         0.23        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-B5-A0JX TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A11P 
        1.38         0.30        44.71        17.85        75.72        36.82 
TCGA-B5-A1MY TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M8 TCGA-BG-A0YV 
       11.87        29.65        34.13        34.95        36.49        12.56 
TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A26L TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A15V 
        6.81        10.22        24.13        67.20        49.55        39.48 
TCGA-D1-A169 TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A179 TCGA-D1-A1NW 
       37.32         0.69        18.67         3.95        14.73         0.72 
TCGA-D1-A1O0 TCGA-D1-A3JP TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY TCGA-EO-A3AZ 
        2.07        16.93        35.38        12.39       110.10        27.16 
TCGA-EO-A3KU TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A212 
       22.26         4.54        19.27        18.84        17.62        10.19 
TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-FI-A2EX 
       14.40        20.05        45.76        27.35        13.84         9.07 
TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ 
       28.93        25.02        41.06        45.01         7.76        14.04 
TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
       23.74        13.28         9.47        26.10        18.21        23.24 
TCGA-PG-A7D5 TCGA-PG-A915 TCGA-QS-A8F1 
       23.97         7.00         4.44 

$`4P LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
       41.06        10.29       106.88        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       32.78       112.54       105.37        87.32        74.10        57.53 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        38.37        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       23.21        68.65        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A1OK 
       42.35        15.95         7.92        11.44         9.60         8.02 
TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL 
       46.32         5.33         5.16        14.43        10.26        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
        2.40        34.36         1.12         0.76        18.90         1.68 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC 
       14.66        22.49        22.26        17.06        20.81        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV 
       20.65        15.62        15.35        15.95        14.76        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       12.82        20.78         2.70         0.13        83.67        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N 
       23.31        86.07         8.22        63.91        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       12.20        20.91        48.79       117.99       110.37        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        83.97        27.12        82.52 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       60.36        55.89        31.30        35.54        46.78        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AX-A05S 
        6.71        30.90        10.42        27.85        16.24        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       45.99        66.58        34.98        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        35.01        28.54        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       65.88        13.28        19.20        16.96        13.55        15.25 
TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       20.05        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG 
       71.24        40.80        81.37        34.32        46.49        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       17.75        30.74        31.13         0.20         0.56        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.20         0.26         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
        0.39        80.38        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       40.67        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB 
       27.29        17.88        13.74        17.10        11.01         4.11 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
        8.71       185.79       113.36        88.34        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       43.96        40.50        32.09        33.50        27.35        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       191.84 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
      102.31        50.89        14.40        14.70        11.70        15.29 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       12.79       116.25        96.30        78.81        62.14        33.11 
TCGA-B5-A3FH TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       14.27        41.06        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       35.21        34.98        22.06        38.37        28.27        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 
       13.78        14.73        14.01        15.45        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
        1.81         9.57        20.02        23.70        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       35.90        34.98         6.21        10.16        31.76        24.99 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       16.64        13.18        10.03         9.86        46.95        23.47 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       96.49        30.74        97.41        88.34        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        72.72        73.25        59.51        62.79        63.58 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.16        66.48        16.83        19.79        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        4.44        21.99        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B 
       29.33        32.58         0.66        15.72        36.10        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       37.51        36.79        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       33.63        10.65         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 
       13.22        18.25        16.87        18.02        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        3.95         3.52        41.42         8.48        44.88         0.26 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        4.27         4.11        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A1LX 
       39.29        36.62        24.30         9.37        31.10        23.38 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ 
       48.36        17.06         2.37         6.67        27.32        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
        7.36        16.80        10.92        49.15        37.71        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG 
       61.55        66.90        46.26        57.60        51.52        51.42 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 
       19.40        34.39        26.43        35.15        17.19        17.88 
TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       26.96        16.34        14.53        24.89         6.21        14.99 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT 
       22.78        13.97         6.90        17.88        15.09        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       12.43        15.81        11.08         6.48        19.33        12.59 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A547 
       18.87        22.82        31.04        29.10        11.38        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX 
       14.14        19.89        14.70        16.96         5.88        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       41.06        39.88        39.95         7.99        13.84         8.98 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-KJ-A3U4 
       96.69        59.01        28.96        29.23         1.74         2.43 
TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       15.45        12.92        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       12.92        23.64        14.83        14.07        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.23              0.07 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           149.56            191.84 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            20.28             23.70 
[1] "0.2 - 149.6 (20.3)" "0.1 - 191.8 (23.7)"
[1] "hr=" "2.3"
D48V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  4P LOSS MUTATED                                        31
  4P LOSS WILD-TYPE                                     364
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  4P LOSS MUTATED                               6
  4P LOSS WILD-TYPE                            15
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  4P LOSS MUTATED                                  63
  4P LOSS WILD-TYPE                                49
D48V3, multiclass
                                         clus
vv                                        4P LOSS MUTATED 4P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              31               364
  MIXED SEROUS AND ENDOMETRIOID                         6                15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    63                49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V4, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    18  82
  4P LOSS WILD-TYPE 123 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     18   82
  4P LOSS WILD-TYPE  123  305
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               18               123
  YES              82               305
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4P LOSS MUTATED    64   5   5   7
  4P LOSS WILD-TYPE 299  18  12  28
D48V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0              64               299
  R1               5                18
  R2               5                12
  RX               7                28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P LOSS MUTATED                                  1     1
  4P LOSS WILD-TYPE                                3    19
                   vv
clus                BLACK OR AFRICAN AMERICAN
  4P LOSS MUTATED                          21
  4P LOSS WILD-TYPE                        80
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4P LOSS MUTATED                                           3    69
  4P LOSS WILD-TYPE                                         6   297
D48V6, multiclass
                                           clus
vv                                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 3
  ASIAN                                                   1                19
  BLACK OR AFRICAN AMERICAN                              21                80
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               3                 6
  WHITE                                                  69               297
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     4  72
  4P LOSS WILD-TYPE  10 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      4   72
  4P LOSS WILD-TYPE   10  295
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                10
  NOT HISPANIC OR LATINO              72               295
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    78  22
  4Q LOSS WILD-TYPE 379  47
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              100               426 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               22                47 
$`4Q LOSS MUTATED`
TCGA-5B-A90C TCGA-A5-A0G2 TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 
       36.69       149.56        65.75        60.53        36.82        19.96 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M 
       11.44        36.33        91.04        28.64         7.33         1.18 
TCGA-AJ-A23N TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3EJ TCGA-AJ-A3NF TCGA-AJ-A3NH 
       14.43        29.39        34.16         1.64        21.21        10.19 
TCGA-AJ-A3QS TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LI 
       16.87        57.80        45.53       125.42         3.39        97.71 
TCGA-AP-A0LO TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1CA 
       33.40        21.90        36.13         0.56        37.78        20.28 
TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H8 
       12.43        76.83        11.08         4.77        30.12        61.18 
TCGA-AX-A2HF TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3G1 TCGA-AX-A3G4 
       19.36         2.96        64.93         0.23        20.52         0.30 
TCGA-B5-A0JN TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A1N2 
       80.38        75.72        36.82        50.89        11.87        12.79 
TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M8 TCGA-BG-A0YV 
       33.11        29.65        34.13        34.95        36.49        12.56 
TCGA-BG-A3PP TCGA-BK-A26L TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A15V TCGA-D1-A169 
        6.81        24.13        67.20        49.55        39.48        37.32 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A179 TCGA-D1-A1NW TCGA-D1-A1O0 
        0.69        18.67         3.95        14.73         0.72         2.07 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DI-A1NN TCGA-DI-A1NO TCGA-EO-A3AZ 
        4.27         4.11        16.93        35.38         9.37        27.16 
TCGA-EO-A3KU TCGA-EY-A1GC TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR 
       22.26         4.54         6.90        19.27        18.84        17.62 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2OO TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-FI-A2EX 
       10.19        14.40        45.76        27.35        13.84         9.07 
TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ 
       28.93        25.02        41.06        45.01         7.76        14.04 
TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
        2.43        23.74        13.28        26.10        18.21        23.24 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A8F1 
       23.97        12.92         7.00         4.44 

$`4Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
       41.06        10.29       106.88        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       32.78       112.54       105.37        87.32        74.10        57.53 
TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       60.53        46.55        38.37        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       68.65        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K5 
       15.95         7.92         9.60         8.02        46.32         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
        5.16        14.96        10.26         0.39        19.79         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK 
       34.36         1.12         0.76        18.90         1.68        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE 
       22.49        22.26        17.06        20.81        36.99        20.65 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DV 
       15.62        15.35        15.95        14.76        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       12.82        20.78         2.70         0.13        83.67        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J 
        5.95        23.31        86.07         8.22        63.91        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        12.20        20.91        48.79       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       63.16        36.36        31.73        83.97        27.12        82.52 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       60.36        55.89        31.30        35.54        46.78        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AX-A05S 
        6.71        30.90        10.42        27.85        16.24        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       45.99        66.58        34.98        53.92        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ 
       27.39        30.02        60.66        35.01        28.54        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        65.88        13.28        19.20        16.96        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       15.25        20.05        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       36.39        71.24        40.80        81.37        34.32        46.49 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FT TCGA-AX-A3FW 
       26.33        17.75        30.74        31.13         0.20         0.56 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
       43.82         0.20         1.38         0.26         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       18.35        14.47         0.39        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        27.29        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.85        11.01         4.11         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       88.34        54.44        45.90        43.96        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       33.50        27.35        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV TCGA-B5-A1MW 
       17.36        16.57       191.84       102.31        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       11.70        15.29       116.25        96.30        78.81        62.14 
TCGA-B5-A3FH TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       14.27        41.06        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       35.21        34.98        22.06        38.37        28.27        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 
       13.78        14.73        14.01        15.45        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
        1.81         9.57        20.02        23.70        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       35.90        34.98         6.21        10.22        10.16        31.76 
TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.99        16.64        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        30.74        97.41        88.34        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        62.79 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        63.16        66.48        16.83        19.79        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74         4.44        21.99        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       36.36        37.51        36.79        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       31.07        33.63        10.65         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
        6.64        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 
        1.41        13.22        18.25        16.87        18.02        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 
        1.05         3.95         3.52        41.42         8.48        44.88 
TCGA-D1-A3DA TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
        0.26        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX 
       36.62        24.30        12.39        31.10       110.10        23.38 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ 
       48.36        17.06         2.37         6.67        27.32        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
        7.36        16.80        10.92        49.15        37.71        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG 
       61.55        66.90        46.26        57.60        51.52        51.42 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 
       19.40        34.39        26.43        35.15        17.19        17.88 
TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       26.96        16.34        14.53        24.89         6.21        14.99 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       22.78        13.97        17.88        15.09        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A215 
       15.81        11.08         6.48        19.33        12.59        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A547 
       22.82        20.05        31.04        29.10        11.38        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX 
       14.14        19.89        14.70        16.96         5.88        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       41.06        39.88        39.95         7.99        13.84         8.98 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-KP-A3W1 
       96.69        59.01        28.96        29.23         1.74         9.47 
TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       15.45        11.24         6.97        18.84        39.95        12.92 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       23.64        14.83        14.07        18.28         0.07         0.23 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.23              0.07 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           149.56            191.84 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           20.865            23.555 
[1] "0.2 - 149.6 (20.9)" "0.1 - 191.8 (23.6)"
[1] "hr=" "2.2"
D49V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  4Q LOSS MUTATED                                        32
  4Q LOSS WILD-TYPE                                     363
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  4Q LOSS MUTATED                               7
  4Q LOSS WILD-TYPE                            14
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  4Q LOSS MUTATED                                  62
  4Q LOSS WILD-TYPE                                50
D49V3, multiclass
                                         clus
vv                                        4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              32               363
  MIXED SEROUS AND ENDOMETRIOID                         7                14
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    62                50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V4, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    18  83
  4Q LOSS WILD-TYPE 123 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     18   83
  4Q LOSS WILD-TYPE  123  304
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               18               123
  YES              83               304
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4Q LOSS MUTATED    65   5   5   6
  4Q LOSS WILD-TYPE 298  18  12  29
D49V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0              65               298
  R1               5                18
  R2               5                12
  RX               6                29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q LOSS MUTATED                                  0     2
  4Q LOSS WILD-TYPE                                4    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  4Q LOSS MUTATED                          26
  4Q LOSS WILD-TYPE                        75
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4Q LOSS MUTATED                                           3    66
  4Q LOSS WILD-TYPE                                         6   300
D49V6, multiclass
                                           clus
vv                                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   2                18
  BLACK OR AFRICAN AMERICAN                              26                75
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               3                 6
  WHITE                                                  66               300
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     2  72
  4Q LOSS WILD-TYPE  12 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      2   72
  4Q LOSS WILD-TYPE   12  295
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                12
  NOT HISPANIC OR LATINO              72               295
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    42  12
  5P LOSS WILD-TYPE 415  57
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               54               472 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               12                57 
$`5P LOSS MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A2QM 
      149.56        19.96        17.59         7.33         1.18        29.39 
TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3QS TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 
        1.64        22.26        16.87        45.53        48.79       125.42 
TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A3K1 TCGA-AX-A06B TCGA-AX-A2H4 
        3.39        97.71        33.40        21.90        53.92        30.12 
TCGA-AX-A2HF TCGA-AX-A3FZ TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A1N2 
       19.36         0.20        17.85         4.11        75.72        12.79 
TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BG-A0M8 TCGA-BG-A3PP TCGA-BK-A0CC 
       33.11        29.65        34.95        36.49         6.81        10.22 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-D1-A15V TCGA-D1-A16I TCGA-D1-A16S 
       24.13        16.64        67.20        39.48        11.51        18.67 
TCGA-D1-A16V TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A3JP TCGA-EO-A2CG TCGA-EO-A3KU 
        3.95        14.73        13.22        16.93        51.42        22.26 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A212 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-FI-A3PV 
       19.27        18.84        10.19        13.84        11.38        41.06 
TCGA-FI-A3PX TCGA-KJ-A3U4 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A914 TCGA-QS-A8F1 
       45.01         2.43         9.47        26.10        12.92         4.44 

$`5P LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 
       36.82        28.27        20.81        23.21        68.65        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95         7.92        11.44 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 
       36.33         9.60         8.02        91.04        46.32        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
        5.33         5.16        14.96        14.43        10.26         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG 
       19.79         2.40        34.36        34.16         1.12         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3IA 
       18.90         1.68        14.66        22.49        17.06        20.81 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ 
       36.99        20.65        21.21        15.62        10.19        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.95        14.76        16.87        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        2.70         0.13        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N 
       86.07         8.22        63.91        57.80        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       12.20        20.91       117.99       110.37        63.16        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ 
       31.73        83.97        27.12        82.52        61.64        80.78 
TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        46.78        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       10.42        27.85        16.24        36.13         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       45.99        66.58        34.98        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        35.01        28.54        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        65.88        13.28        19.20        16.96        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       15.25        20.28        12.43        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 
       54.12        67.50        25.12        36.39        11.08         4.77 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       71.24        40.80        61.18        81.37        34.32        46.49 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       26.33        17.75        30.74         2.96        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G3 
        0.23         0.20         0.56        43.82        20.52         1.38 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.30         0.26         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
        0.39        80.38        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       25.91        27.29        17.88        13.74        17.10        11.01 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
        8.71       185.79       113.36        88.34        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       43.96        40.50        36.82        32.09        33.50        27.35 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
      191.84       102.31        50.89        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       11.87        15.29       116.25        96.30        78.81        62.14 
TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       14.27        41.06        34.13        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 
       20.94        35.21        34.98        22.06        38.37        28.27 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        20.02        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 
       20.12        11.31        35.90        34.98         6.21        10.16 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       31.76        24.99        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        30.74        97.41        88.34        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       63.58        49.55        63.16        66.48        16.83        19.79 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74         4.44        21.99        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       36.10        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X 
       29.92        31.07        33.63        10.65         0.69         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
       17.49        19.53         6.64        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
        2.33        22.92         1.41         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       18.02         2.07        15.06         1.05         3.95         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
       41.42         8.48        44.88         0.26         4.27         4.11 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY 
       24.30        35.38         9.37        12.39        31.10       110.10 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 
       23.38        48.36        17.06         2.37         6.67        27.32 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       16.04         7.36        16.80        10.92        49.15        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       19.40        34.39        26.43        35.15        17.19        27.16 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 
       17.88        26.96        16.34        14.53        24.89         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99         4.54        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GQ 
       23.34        23.90        22.78        13.97         6.90        17.88 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       17.62        15.09        16.11        12.43        15.81        11.08 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM 
        6.48        19.33        12.59        14.40        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A547 
       20.05        45.76        31.04        29.10        27.35        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX 
       14.14        19.89        14.70        16.96         5.88        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       41.06        39.88        39.95         7.99        13.84         8.98 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 
       96.69        59.01         9.07        28.93        28.96        25.02 
TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3VZ TCGA-KP-A3W0 
       29.23         1.74         7.76        14.04        23.74        13.28 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A915 TCGA-PG-A916 
       18.21        23.24        15.45        23.97         7.00        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        18.84        39.95        12.92        23.64        14.83 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.07        18.28         0.07         0.23 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.20              0.07 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           149.56            191.84 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           19.055            23.720 
[1] "0.2 - 149.6 (19.1)" "0.1 - 191.8 (23.7)"
[1] "hr=" "2"  
D50V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  5P LOSS MUTATED                                        16
  5P LOSS WILD-TYPE                                     379
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  5P LOSS MUTATED                               1
  5P LOSS WILD-TYPE                            20
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  5P LOSS MUTATED                                  37
  5P LOSS WILD-TYPE                                75
D50V3, multiclass
                                         clus
vv                                        5P LOSS MUTATED 5P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              16               379
  MIXED SEROUS AND ENDOMETRIOID                         1                20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    37                75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V4, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    18  36
  5P LOSS WILD-TYPE 123 351
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     18   36
  5P LOSS WILD-TYPE  123  351
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               18               123
  YES              36               351
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5P LOSS MUTATED    35   0   3   5
  5P LOSS WILD-TYPE 328  23  14  30
D50V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0              35               328
  R1               0                23
  R2               3                14
  RX               5                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P LOSS MUTATED                                  0     2
  5P LOSS WILD-TYPE                                4    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  5P LOSS MUTATED                          15
  5P LOSS WILD-TYPE                        86
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5P LOSS MUTATED                                           1    33
  5P LOSS WILD-TYPE                                         8   333
D50V6, multiclass
                                           clus
vv                                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   2                18
  BLACK OR AFRICAN AMERICAN                              15                86
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 8
  WHITE                                                  33               333
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     3  35
  5P LOSS WILD-TYPE  11 332
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      3   35
  5P LOSS WILD-TYPE   11  332
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                11
  NOT HISPANIC OR LATINO              35               332
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    56  17
  5Q LOSS WILD-TYPE 401  52
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               73               453 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               17                52 
$`5Q LOSS MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A1OH TCGA-A5-A3LO TCGA-AJ-A23M 
      149.56        19.96        17.59        36.33         7.33         1.18 
TCGA-AJ-A2QM TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3QS 
       29.39         1.64        22.26        20.81        10.19        16.87 
TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AX-A06B 
       45.53        48.79       125.42        97.71        33.40        53.92 
TCGA-AX-A0IW TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2HF 
       37.78        20.28        76.83         4.77        30.12        19.36 
TCGA-AX-A3FZ TCGA-AX-A3G6 TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A1MU 
        0.20         0.26        17.85         4.11        75.72        50.89 
TCGA-B5-A1N2 TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M6 
       12.79        33.11        29.65        34.13        34.95        22.06 
TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L 
       36.49        12.56         6.81        10.22        10.16        24.13 
TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A16I TCGA-D1-A16S 
       16.64        67.20        22.55        39.48        11.51        18.67 
TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A3JP TCGA-DI-A1NO TCGA-DI-A2QY TCGA-EO-A2CG 
       14.73        13.22        16.93         9.37       110.10        51.42 
TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GW TCGA-EY-A212 
       27.16        22.26        19.27        18.84        11.08        10.19 
TCGA-EY-A214 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-FI-A2D2 TCGA-FI-A2F8 TCGA-FI-A3PV 
       14.40        13.84        11.38        39.95        25.02        41.06 
TCGA-FI-A3PX TCGA-KJ-A3U4 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A914 TCGA-PG-A915 
       45.01         2.43         9.47        26.10        12.92         7.00 
TCGA-QS-A8F1 
        4.44 

$`5Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 
       36.82        28.27        20.81        23.21        68.65        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95         7.92        11.44 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
        9.60         8.02        91.04        46.32        28.64         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
        5.16        14.96        14.43        10.26         0.39        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI 
        2.40        34.36        34.16         1.12         0.76        18.90 
TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE 
        1.68        14.66        22.49        17.06        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW 
       21.21        15.62        15.35        15.95        14.76        16.87 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       22.32        12.82        20.78         2.70         0.13        83.67 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
       21.99         5.95        23.31        86.07         8.22        63.91 
TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD 
       57.80        36.89        23.87        12.20        20.91       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37         3.39        63.16        36.36        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       27.12        82.52        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        55.89        31.30        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       46.78        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       16.24        21.90        36.13         0.56        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       66.58        34.98        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        35.01        28.54        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC 
       13.28        19.20        16.96        13.55        15.25        12.43 
TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       20.05        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A1CR TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       11.08        71.24        40.80        61.18        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       46.49        26.33        17.75        30.74         2.96        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 
       64.93         0.23         0.20         0.56        43.82        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        1.38         0.30         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
        0.39        80.38        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       25.91        27.29        17.88        13.74        17.10        11.01 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
        8.71       185.79       113.36        88.34        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       43.96        40.50        36.82        32.09        33.50        27.35 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      191.84       102.31        14.40        14.70        11.70        11.87 
TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH 
       15.29       116.25        96.30        78.81        62.14        14.27 
TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       41.06        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       34.98        38.37        28.27        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       23.47        43.30        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.01        15.45        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA 
       20.02        23.70        20.12        11.31        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
        6.21        31.76        24.99        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA 
       61.87        67.99        96.49        30.74        97.41        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       62.79        63.58        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X 
       23.93         1.74         4.44        21.99        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       36.10        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V 
       29.92        31.07        33.63        10.65         0.69         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NW TCGA-D1-A1NX 
       24.30         2.33        22.92         1.41         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.52        41.42         8.48        44.88         0.26         4.27 
TCGA-D1-A3DH TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
        4.11        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX 
       36.62        24.30        35.38        12.39        31.10        23.38 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ 
       48.36        17.06         2.37         6.67        27.32        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
        7.36        16.80        10.92        49.15        37.71        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH 
       61.55        66.90        46.26        57.60        51.52        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 
       34.39        26.43        35.15        17.19        17.88        26.96 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC 
       16.34        14.53        24.89         6.21        14.99         4.54 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS 
       22.78        13.97         6.90        17.88        17.62        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       16.11        12.43        15.81         6.48        19.33        12.59 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       18.87        22.82        20.05        45.76        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
       27.35        17.92        14.14        19.89        14.70        16.96 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 
        5.88        40.01        41.06        39.88         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 
        8.98        96.69        59.01         9.07        28.93        28.96 
TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3VZ TCGA-KP-A3W0 
       29.23         1.74         7.76        14.04        23.74        13.28 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A916 TCGA-PG-A917 
       18.21        23.24        15.45        23.97        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI 
       18.84        39.95        12.92        23.64        14.83        14.07 
TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       18.28         0.07         0.23 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.20              0.07 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           149.56            191.84 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            19.96             23.74 
[1] "0.2 - 149.6 (20.0)" "0.1 - 191.8 (23.7)"
[1] "hr=" "2.1"
D51V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  5Q LOSS MUTATED                                        19
  5Q LOSS WILD-TYPE                                     376
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  5Q LOSS MUTATED                               4
  5Q LOSS WILD-TYPE                            17
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  5Q LOSS MUTATED                                  50
  5Q LOSS WILD-TYPE                                62
D51V3, multiclass
                                         clus
vv                                        5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              19               376
  MIXED SEROUS AND ENDOMETRIOID                         4                17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    50                62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V4, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    21  52
  5Q LOSS WILD-TYPE 120 335
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     21   52
  5Q LOSS WILD-TYPE  120  335
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               21               120
  YES              52               335
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5Q LOSS MUTATED    48   2   3   6
  5Q LOSS WILD-TYPE 315  21  14  29
D51V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0              48               315
  R1               2                21
  R2               3                14
  RX               6                29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q LOSS MUTATED                                  0     2
  5Q LOSS WILD-TYPE                                4    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  5Q LOSS MUTATED                          20
  5Q LOSS WILD-TYPE                        81
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5Q LOSS MUTATED                                           1    46
  5Q LOSS WILD-TYPE                                         8   320
D51V6, multiclass
                                           clus
vv                                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   2                18
  BLACK OR AFRICAN AMERICAN                              20                81
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 8
  WHITE                                                  46               320
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     4  48
  5Q LOSS WILD-TYPE  10 319
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      4   48
  5Q LOSS WILD-TYPE   10  319
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                10
  NOT HISPANIC OR LATINO              48               319
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    13   3
  6P LOSS WILD-TYPE 444  66
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               16               510 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                3                66 
$`6P LOSS MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AP-A05J 
      149.56        60.53        19.96        10.19        57.80        36.89 
TCGA-AP-A0L9 TCGA-AX-A1C7 TCGA-AX-A2H4 TCGA-B5-A11P TCGA-BG-A3PP TCGA-E6-A8L9 
      125.42        16.96        30.12        36.82         6.81        27.32 
TCGA-EY-A2OQ TCGA-FI-A2D2 TCGA-FI-A3PV TCGA-KJ-A3U4 
       29.10        39.95        41.06         2.43 

$`6P LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       57.53        65.75        60.53        46.55        38.37        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 
       28.27        20.81        23.21        68.65        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95         7.92        11.44 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 
       36.33         9.60         8.02        91.04        46.32        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N 
        5.33         5.16         7.33        14.96         1.18        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
       10.26         0.39        19.79        29.39         2.40        34.36 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       34.16         1.12         0.76        18.90         1.68         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC 
       14.66        22.49        22.26        17.06        20.81        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65        21.21        15.62        15.35        15.95        14.76 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
       16.87        16.87        22.32        12.82        20.78         2.70 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        0.13        83.67        21.99         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
        8.22        63.91        45.53        23.87        12.20        20.91 
TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       60.36        55.89        31.30        35.54        46.78        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        30.90        10.42        27.85        16.24        21.90 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       36.13         0.56        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       53.92        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       35.01        28.54        37.78        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       13.28        19.20        13.55        15.25        20.28        12.43 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       20.05        76.83        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       36.39        11.08         4.77        71.24        40.80        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       81.37        34.32        46.49        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       30.74         2.96        31.13        64.93         0.23         0.20 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 
        0.56        43.82         0.20        20.52         1.38         0.30 
TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
        0.26         0.30         1.18        18.35        14.47         0.39 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       80.38        56.91        46.75        43.13        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       44.71        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        17.88        13.74        17.10        17.85        11.01 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
        4.11         8.71       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        45.90        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW 
       16.57       191.84       102.31        50.89        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       11.70        11.87        15.29        12.79       116.25        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       78.81        62.14        33.11        14.27        29.65        41.06 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       34.13        34.95        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98        22.06        38.37        36.49        28.27 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        20.02        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       20.12        11.31        35.90        34.98         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F 
       10.16        31.76        24.99        24.13        16.64        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        23.47        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        67.20        88.34        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       72.72        73.25        59.51        62.79        63.58        49.55 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.16        66.48        16.83        19.79        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        4.44        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I 
       37.32        36.36        37.51        36.79        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02        14.73         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 
       13.22         0.72        18.25        16.87        18.02         2.07 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV 
       44.88         0.26         4.27         4.11        16.93        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX 
       35.38         9.37        12.39        31.10       110.10        23.38 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       48.36        17.06         2.37         6.67        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
       16.80        10.92        49.15        37.71        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH 
       66.90        46.26        57.60        51.52        51.42        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       34.39        26.43        35.15        17.19        27.16        17.88 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 
       26.96        22.26        16.34        14.53        24.89         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99         4.54        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       23.34        23.90        22.78        13.97         6.90        19.27 
TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       18.84        17.88        17.62        15.09        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 
       15.81        11.08         6.48        19.33        12.59        10.19 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       14.40        18.87        22.82        20.05        45.76        31.04 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       27.35        13.84        11.38        17.92        14.14        19.89 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
       14.70        16.96         5.88        40.01        41.06        39.88 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
        7.99        13.84         8.98        96.69        59.01         9.07 
TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR 
       28.93        28.96        25.02        29.23        45.01         1.74 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 
        7.76        14.04        23.74        13.28         9.47        26.10 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       18.21        23.24        15.45        23.97        12.92         7.00 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       11.24         6.97        18.84        39.95        12.92        23.64 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83         4.44        14.07        18.28         0.07         0.23 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             2.43              0.07 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           149.56            191.84 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           33.470            23.225 
[1] "2.4 - 149.6 (33.5)" "0.1 - 191.8 (23.2)"
[1] "hr=" "1.1"
D52V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  6P LOSS MUTATED                                         4
  6P LOSS WILD-TYPE                                     391
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  6P LOSS MUTATED                               1
  6P LOSS WILD-TYPE                            20
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  6P LOSS MUTATED                                  12
  6P LOSS WILD-TYPE                               100
D52V3, multiclass
                                         clus
vv                                        6P LOSS MUTATED 6P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               4               391
  MIXED SEROUS AND ENDOMETRIOID                         1                20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    12               100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V4, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     5  12
  6P LOSS WILD-TYPE 136 375
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      5   12
  6P LOSS WILD-TYPE  136  375
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                5               136
  YES              12               375
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6P LOSS MUTATED    14   0   1   0
  6P LOSS WILD-TYPE 349  23  16  35
D52V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              14               349
  R1               0                23
  R2               1                16
  RX               0                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P LOSS MUTATED                                  0     1
  6P LOSS WILD-TYPE                                4    19
                   vv
clus                BLACK OR AFRICAN AMERICAN
  6P LOSS MUTATED                           2
  6P LOSS WILD-TYPE                        99
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6P LOSS MUTATED                                           0    13
  6P LOSS WILD-TYPE                                         9   353
D52V6, multiclass
                                           clus
vv                                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   1                19
  BLACK OR AFRICAN AMERICAN                               2                99
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 9
  WHITE                                                  13               353
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     1  11
  6P LOSS WILD-TYPE  13 356
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1   11
  6P LOSS WILD-TYPE   13  356
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                13
  NOT HISPANIC OR LATINO              11               356
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    19   5
  6Q LOSS WILD-TYPE 438  64
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               24               502 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                5                64 
$`6Q LOSS MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-AJ-A3BF TCGA-AJ-A3IA TCGA-AJ-A3NH 
      149.56        60.53        19.96         1.12        20.81        10.19 
TCGA-AJ-A3QS TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A0L9 TCGA-AW-A1PO TCGA-AX-A1C7 
       16.87        57.80        36.89       125.42         0.56        16.96 
TCGA-AX-A2H4 TCGA-B5-A11P TCGA-B5-A1MY TCGA-BG-A3PP TCGA-D1-A16I TCGA-E6-A8L9 
       30.12        36.82        11.87         6.81        11.51        27.32 
TCGA-EO-A3B1 TCGA-EY-A2OQ TCGA-FI-A2D2 TCGA-FI-A3PV TCGA-KJ-A3U4 TCGA-PG-A7D5 
       26.96        29.10        39.95        41.06         2.43        23.97 

$`6Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       57.53        65.75        60.53        46.55        38.37        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 
       28.27        20.81        23.21        68.65        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95         7.92        11.44 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 
       36.33         9.60         8.02        91.04        46.32        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N 
        5.33         5.16         7.33        14.96         1.18        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
       10.26         0.39        19.79        29.39         2.40        34.36 
TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
       34.16         0.76        18.90         1.68         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.49        22.26        17.06        36.99        20.65        21.21 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DV 
       15.62        15.35        15.95        14.76        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       12.82        20.78         2.70         0.13        83.67        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
        5.95        23.31        86.07         8.22        63.91        45.53 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        12.20        20.91        48.79       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        46.78        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T 
       27.85        16.24        21.90        36.13        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       66.58        34.98        53.92        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        35.01        28.54        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 
       40.11        65.88        13.28        19.20        13.55        15.25 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       20.28        12.43        20.05        76.83        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 
       67.50        25.12        36.39        11.08         4.77        71.24 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       40.80        61.18        81.37        34.32        46.49        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       26.33        17.75        30.74         2.96        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
        0.23         0.20         0.56        43.82         0.20        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        1.38         0.30         0.26         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       14.47         0.39        80.38        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        27.29        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.85        11.01         4.11         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        45.90        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU 
       18.41        17.36        16.57       191.84       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       14.40        14.70        11.70        15.29        12.79       116.25 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 
       96.30        78.81        62.14        33.11        14.27        29.65 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       41.06        34.13        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98        22.06        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       15.45        15.45        14.27         1.81         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       23.70        20.12        11.31        35.90        34.98         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD 
       10.22        10.16        31.76        24.99        24.13        16.64 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        23.47        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       30.74        97.41        67.20        88.34        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        72.72        73.25        59.51        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       49.55        63.16        66.48        16.83        19.79        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       36.10        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02        14.73         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 
       13.22         0.72        18.25        16.87        18.02         2.07 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV 
       44.88         0.26         4.27         4.11        16.93        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX 
       35.38         9.37        12.39        31.10       110.10        23.38 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       48.36        17.06         2.37         6.67        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
       16.80        10.92        49.15        37.71        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH 
       66.90        46.26        57.60        51.52        51.42        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       34.39        26.43        35.15        17.19        27.16        17.88 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       22.26        16.34        14.53        24.89         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.90        22.78        13.97         6.90        19.27        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       17.88        17.62        15.09        16.11        12.43        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 
       11.08         6.48        19.33        12.59        10.19        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 
       18.87        22.82        20.05        45.76        31.04        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       13.84        11.38        17.92        14.14        19.89        14.70 
TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
       16.96         5.88        40.01        41.06        39.88         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       13.84         8.98        96.69        59.01         9.07        28.93 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
       28.96        25.02        29.23        45.01         1.74         7.76 
TCGA-K6-A3WQ TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 
       14.04        23.74        13.28         9.47        26.10        18.21 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 
       23.24        15.45        12.92         7.00        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 
       18.84        39.95        12.92        23.64        14.83         4.44 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.07        18.28         0.07         0.23 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.56              0.07 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           149.56            191.84 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           25.465            23.325 
[1] "0.6 - 149.6 (25.5)" "0.1 - 191.8 (23.3)"
[1] "hr=" "1.4"
D53V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  6Q LOSS MUTATED                                         5
  6Q LOSS WILD-TYPE                                     390
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  6Q LOSS MUTATED                               1
  6Q LOSS WILD-TYPE                            20
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  6Q LOSS MUTATED                                  19
  6Q LOSS WILD-TYPE                                93
D53V3, multiclass
                                         clus
vv                                        6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               5               390
  MIXED SEROUS AND ENDOMETRIOID                         1                20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    19                93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V4, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     7  18
  6Q LOSS WILD-TYPE 134 369
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      7   18
  6Q LOSS WILD-TYPE  134  369
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO                7               134
  YES              18               369
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6Q LOSS MUTATED    21   0   1   0
  6Q LOSS WILD-TYPE 342  23  16  35
D53V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              21               342
  R1               0                23
  R2               1                16
  RX               0                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q LOSS MUTATED                                  0     1
  6Q LOSS WILD-TYPE                                4    19
                   vv
clus                BLACK OR AFRICAN AMERICAN
  6Q LOSS MUTATED                           5
  6Q LOSS WILD-TYPE                        96
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6Q LOSS MUTATED                                           0    17
  6Q LOSS WILD-TYPE                                         9   349
D53V6, multiclass
                                           clus
vv                                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   1                19
  BLACK OR AFRICAN AMERICAN                               5                96
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 9
  WHITE                                                  17               349
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     1  17
  6Q LOSS WILD-TYPE  13 350
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      1   17
  6Q LOSS WILD-TYPE   13  350
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                13
  NOT HISPANIC OR LATINO              17               350
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    33  10
  7P LOSS WILD-TYPE 424  59
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               43               483 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               10                59 
$`7P LOSS MUTATED`
TCGA-A5-A0R6 TCGA-AJ-A23M TCGA-AP-A054 TCGA-AP-A0L8 TCGA-AP-A1DQ TCGA-AX-A06B 
       19.96         1.18        23.31        48.79        46.78        53.92 
TCGA-AX-A1CA TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IO 
       20.28        11.08         4.77        30.74         2.96        64.93 
TCGA-B5-A0JN TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I TCGA-BG-A3PP TCGA-BK-A0CC 
       80.38        17.85         4.11        75.72         6.81        10.22 
TCGA-BS-A0U9 TCGA-D1-A16V TCGA-D1-A1O0 TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DI-A1NN 
       67.20         3.95         2.07        44.88         4.11        35.38 
TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EC-A1NJ TCGA-EO-A1Y8 TCGA-EO-A2CH TCGA-EO-A3KU 
      110.10        48.36        16.04        37.71        19.40        22.26 
TCGA-EY-A1GC TCGA-EY-A212 TCGA-EY-A2OO TCGA-EY-A547 TCGA-FI-A2EW TCGA-FI-A2F8 
        4.54        10.19        45.76        17.92        59.01        25.02 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-PG-A5BC TCGA-PG-A7D5 
       29.23        41.06        23.74        13.28        23.24        23.97 
TCGA-PG-A915 
        7.00 

$`7P LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       38.37        36.82        28.27        20.81        23.21        68.65 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 
        7.92        11.44        36.33         9.60         8.02        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       46.32        28.64         5.33         5.16         7.33        14.96 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
       14.43        10.26         0.39        19.79        29.39         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
       34.36        34.16         1.12         0.76        18.90         1.68 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA 
        1.64        14.66        22.49        22.26        17.06        20.81 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ 
       36.99        20.65        21.21        15.62        10.19        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.95        14.76        16.87        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       20.78         2.70         0.13        83.67        21.99         5.95 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        63.91        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        12.20        20.91       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       35.54        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       16.24        21.90        36.13         0.56        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       66.58        34.98        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       60.66        35.01        28.54        37.78        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       65.88        13.28        19.20        16.96        13.55        15.25 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       12.43        20.05        76.83        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       25.12        36.39        30.12        71.24        40.80        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       81.37        34.32        46.49        19.36        26.33        17.75 
TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       31.13         0.23         0.20         0.56        43.82         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
       20.52         1.38         0.30         0.26         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       18.35        14.47         0.39        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        27.29        17.88        13.74        17.10 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J 
       11.01         8.71       185.79       113.36        88.34        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R 
       45.90        43.96        40.50        36.82        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW 
       16.57       191.84       102.31        50.89        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       11.70        11.87        15.29        12.79       116.25        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       78.81        62.14        33.11        14.27        29.65        41.06 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       34.13        34.95        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98        22.06        38.37        36.49        28.27 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        20.02        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 
       20.12        11.31        35.90        34.98         6.21        10.16 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
       31.76        24.99        24.13        16.64        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        23.47        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ 
       59.51        62.79        63.58        49.55        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       37.51        36.79        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69        18.67         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
        2.33        22.92         1.41        13.22         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       16.87        18.02        15.06         1.05         3.95         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JP TCGA-DF-A2KV 
       41.42         8.48         0.26         4.27        16.93        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 
        9.37        12.39        31.10        23.38        17.06         2.37 
TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
        6.67        27.32         7.36        16.80        10.92        49.15 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       51.42        34.39        26.43        35.15        17.19        27.16 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 
       17.88        26.96        16.34        14.53        24.89         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       14.99        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.90        22.78        13.97         6.90        19.27        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       17.88        17.62        15.09        16.11        12.43        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A215 
       11.08         6.48        19.33        12.59        14.40        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX 
       22.82        20.05        31.04        29.10        27.35        13.84 
TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D 
       11.38        14.14        19.89        14.70        16.96         5.88 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
       40.01        41.06        39.88        39.95         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A3PX 
        8.98        96.69         9.07        28.93        28.96        45.01 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3W1 TCGA-KP-A3W3 
        1.74         7.76        14.04         2.43         9.47        26.10 
TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       18.21        15.45        12.92        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       39.95        12.92        23.64        14.83         4.44        14.07 
TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       18.28         0.07         0.23 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             1.18              0.07 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           110.10            191.84 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            23.24             23.38 
[1] "1.2 - 110.1 (23.2)" "0.1 - 191.8 (23.4)"
[1] "hr=" "2"  
D54V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  7P LOSS MUTATED                                        14
  7P LOSS WILD-TYPE                                     381
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  7P LOSS MUTATED                               2
  7P LOSS WILD-TYPE                            19
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  7P LOSS MUTATED                                  27
  7P LOSS WILD-TYPE                                85
D54V3, multiclass
                                         clus
vv                                        7P LOSS MUTATED 7P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              14               381
  MIXED SEROUS AND ENDOMETRIOID                         2                19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    27                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V4, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    10  33
  7P LOSS WILD-TYPE 131 354
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     10   33
  7P LOSS WILD-TYPE  131  354
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO               10               131
  YES              33               354
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7P LOSS MUTATED    28   4   1   4
  7P LOSS WILD-TYPE 335  19  16  31
D54V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  R0              28               335
  R1               4                19
  R2               1                16
  RX               4                31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P LOSS MUTATED                                  0     1
  7P LOSS WILD-TYPE                                4    19
                   vv
clus                BLACK OR AFRICAN AMERICAN
  7P LOSS MUTATED                          14
  7P LOSS WILD-TYPE                        87
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7P LOSS MUTATED                                           1    22
  7P LOSS WILD-TYPE                                         8   344
D54V6, multiclass
                                           clus
vv                                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   1                19
  BLACK OR AFRICAN AMERICAN                              14                87
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 8
  WHITE                                                  22               344
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     1  27
  7P LOSS WILD-TYPE  13 340
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1   27
  7P LOSS WILD-TYPE   13  340
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                13
  NOT HISPANIC OR LATINO              27               340
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED    34   7
  7Q LOSS WILD-TYPE 423  62
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               41               485 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                7                62 
$`7Q LOSS MUTATED`
TCGA-A5-A0R6 TCGA-A5-A2K2 TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AX-A1CA TCGA-AX-A1CR 
       19.96        91.04         1.18        34.16        20.28        11.08 
TCGA-AX-A2HK TCGA-B5-A0JN TCGA-B5-A0K8 TCGA-B5-A11I TCGA-BG-A0M6 TCGA-BG-A0YV 
        2.96        80.38        17.85        75.72        22.06        12.56 
TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L TCGA-BS-A0U9 TCGA-D1-A15V 
        6.81        10.22        10.16        24.13        67.20        39.48 
TCGA-D1-A16S TCGA-D1-A1O0 TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A2QY 
       18.67         2.07        44.88         4.11        35.38       110.10 
TCGA-E6-A1LZ TCGA-EO-A2CH TCGA-EO-A3KU TCGA-EY-A1GC TCGA-EY-A212 TCGA-EY-A2ON 
       48.36        19.40        22.26         4.54        10.19        20.05 
TCGA-EY-A2OO TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV 
       45.76        96.69        59.01        25.02        29.23        41.06 
TCGA-FI-A3PX TCGA-KP-A3W0 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A915 
       45.01        13.28        23.24        23.97         7.00 

$`7Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       38.37        36.82        28.27        20.81        23.21        68.65 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 
        7.92        11.44        36.33         9.60         8.02        46.32 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N 
       28.64         5.33         5.16         7.33        14.96        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
       10.26         0.39        19.79        29.39         2.40        34.36 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
        1.12         0.76        18.90         1.68         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE 
       22.49        22.26        17.06        20.81        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       21.21        15.62        10.19        15.35        15.95        14.76 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
       16.87        16.87        22.32        12.82        20.78         2.70 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        0.13        83.67        21.99         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        63.91        57.80        45.53        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       12.20        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        46.78        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       27.85        16.24        21.90        36.13         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       45.99        66.58        34.98        53.92        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        35.01        28.54        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        65.88        13.28        19.20        16.96 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       13.55        15.25        12.43        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H2 TCGA-AX-A2H4 
       54.12        67.50        25.12        36.39         4.77        30.12 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       71.24        40.80        61.18        81.37        34.32        46.49 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO 
       19.36        26.33        17.75        30.74        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
        0.23         0.20         0.56        43.82         0.20        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        1.38         0.30         0.26         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       14.47         0.39        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       25.91        27.29        17.88        13.74        17.10        11.01 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J 
        4.11         8.71       185.79       113.36        88.34        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R 
       45.90        43.96        40.50        36.82        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW 
       16.57       191.84       102.31        50.89        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       11.70        11.87        15.29        12.79       116.25        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       78.81        62.14        33.11        14.27        29.65        41.06 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       34.13        34.95        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       35.21        34.98        38.37        36.49        28.27        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 
       13.78        14.73        14.01        15.45        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
        1.81         9.57        20.02        23.70        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD 
       35.90        34.98         6.21        31.76        24.99        16.64 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        23.47        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41        88.34        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       72.72        73.25        59.51        62.79        63.58        49.55 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.16        66.48        16.83        19.79        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        4.44        21.99        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       36.36        37.51        36.79        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X 
       31.07        33.63        10.65         0.69         3.95         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
       17.49        19.53         6.64        30.15        18.02        14.73 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW 
       24.30         2.33        22.92         1.41        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       18.25        16.87        18.02        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JP 
        3.52        41.42         8.48         0.26         4.27        16.93 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 
       24.30         9.37        12.39        31.10        23.38        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
        2.37         6.67        27.32        16.04         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       10.92        49.15        37.71        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU 
       46.26        57.60        51.52        51.42        34.39        26.43 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KW 
       35.15        17.19        27.16        17.88        26.96        16.34 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       14.53        24.89         6.21        14.99        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL 
       27.16        23.34        23.34        23.90        22.78        13.97 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS 
        6.90        19.27        18.84        17.88        17.62        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        12.43        15.81        11.08         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A2OQ 
       12.59        14.40        18.87        22.82        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       27.35        13.84        11.38        17.92        14.14        19.89 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
       14.70        16.96         5.88        40.01        41.06        39.88 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EX TCGA-FI-A2EY 
       39.95         7.99        13.84         8.98         9.07        28.93 
TCGA-FI-A2F4 TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       28.96         1.74         7.76        14.04         2.43        23.74 
TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 
        9.47        26.10        18.21        15.45        12.92        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        18.84        39.95        12.92        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44        14.07        18.28         0.07         0.23 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             1.18              0.07 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           110.10            191.84 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            22.26             23.38 
[1] "1.2 - 110.1 (22.3)" "0.1 - 191.8 (23.4)"
[1] "hr=" "1.3"
D55V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  7Q LOSS MUTATED                                         8
  7Q LOSS WILD-TYPE                                     387
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  7Q LOSS MUTATED                               2
  7Q LOSS WILD-TYPE                            19
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  7Q LOSS MUTATED                                  31
  7Q LOSS WILD-TYPE                                81
D55V3, multiclass
                                         clus
vv                                        7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               8               387
  MIXED SEROUS AND ENDOMETRIOID                         2                19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    31                81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V4, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     9  32
  7Q LOSS WILD-TYPE 132 355
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      9   32
  7Q LOSS WILD-TYPE  132  355
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                9               132
  YES              32               355
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7Q LOSS MUTATED    28   2   2   4
  7Q LOSS WILD-TYPE 335  21  15  31
D55V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0              28               335
  R1               2                21
  R2               2                15
  RX               4                31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q LOSS MUTATED                                  0     0
  7Q LOSS WILD-TYPE                                4    20
                   vv
clus                BLACK OR AFRICAN AMERICAN
  7Q LOSS MUTATED                          11
  7Q LOSS WILD-TYPE                        90
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7Q LOSS MUTATED                                           1    24
  7Q LOSS WILD-TYPE                                         8   342
D55V6, multiclass
                                           clus
vv                                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   0                20
  BLACK OR AFRICAN AMERICAN                              11                90
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 8
  WHITE                                                  24               342
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1  30
  7Q LOSS WILD-TYPE  13 337
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   30
  7Q LOSS WILD-TYPE   13  337
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                13
  NOT HISPANIC OR LATINO              30               337
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    65  13
  8P LOSS WILD-TYPE 392  56
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               78               448 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               13                56 
$`8P LOSS MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A1OH TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-AJ-A23M 
       41.06        36.69        36.33        46.32        28.64         1.18 
TCGA-AJ-A3NF TCGA-AJ-A3TW TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 
       21.21        16.87        57.80        45.53        36.89        48.79 
TCGA-AP-A0LF TCGA-AP-A1DQ TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 
        3.39        46.78         0.56        37.78        16.96        13.55 
TCGA-AX-A1CC TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-AX-A3G3 
       12.43        25.12        36.39        71.24        19.36         1.38 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A1MS 
        0.39        80.38        17.85         4.11        75.72       102.31 
TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A0M6 TCGA-BG-A0M8 
       11.87        12.79        29.65        34.13        22.06        36.49 
TCGA-BG-A0MT TCGA-BG-A0YU TCGA-BG-A3PP TCGA-BK-A139 TCGA-BK-A26L TCGA-D1-A0ZP 
       21.17        14.83         6.81        10.16        24.13        29.95 
TCGA-D1-A0ZZ TCGA-D1-A16G TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A2G7 TCGA-D1-A3DH 
       22.55        27.42        13.22         0.72        44.88         4.11 
TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY TCGA-EO-A1Y7 TCGA-EO-A2CG TCGA-EO-A3KU 
       35.38        12.39       110.10        49.15        51.42        22.26 
TCGA-EY-A1GJ TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A3L3 
       23.90        15.09        15.81        10.19        14.40        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EW 
       13.84        11.38        17.92        39.95        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
        9.07        28.93        41.06        45.01         1.74         7.76 
TCGA-KP-A3VZ TCGA-KP-A3W1 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       23.74         9.47        23.24        23.97        12.92         7.00 

$`8P LOSS WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
       10.29       106.88       149.56        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       32.78       112.54       105.37        87.32        74.10        57.53 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       65.75        60.53        60.53        46.55        38.37        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        20.81        23.21        68.65        19.96        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       19.59        24.62        29.06        42.35        15.95         7.92 
TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K5 TCGA-A5-A2K7 
       11.44         9.60         8.02        91.04         5.33         5.16 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
        7.33        14.96        14.43        10.26         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG 
       29.39         2.40        34.36        34.16         1.12         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       18.90         1.68         1.64        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3NH 
       17.06        20.81        36.99        20.65        15.62        10.19 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.35        15.95        14.76        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       20.78         2.70         0.13        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05N TCGA-AP-A05O 
       23.31        86.07         8.22        63.91        23.87        12.20 
TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       20.91       125.42       117.99       110.37        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       60.36        55.89        31.30        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
       30.90        10.42        27.85        16.24        21.90        36.13 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D 
       35.34        45.99        66.58        34.98        53.92        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       51.09        27.39        30.02        60.66        35.01        28.54 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 
       43.82        40.11        65.88        13.28        19.20        15.25 
TCGA-AX-A1CA TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       20.28        20.05        76.83        72.56        54.12        67.50 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
       11.08         4.77        30.12        40.80        61.18        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       34.32        46.49        26.33        17.75        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        64.93         0.23         0.20         0.56        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.20        20.52         0.30         0.26         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       18.35        14.47        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       25.91        27.29        17.88        13.74        17.10        11.01 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
        8.71       185.79       113.36        88.34        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       43.96        40.50        36.82        32.09        33.50        27.35 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
      191.84        50.89        14.40        14.70        11.70        15.29 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH 
      116.25        96.30        78.81        62.14        33.11        14.27 
TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       41.06        34.95        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       35.21        34.98        38.37        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        12.56        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.01        15.45        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA 
       20.02        23.70        20.12        11.31        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F 
        6.21        10.22        31.76        24.99        16.64        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        23.47        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        67.20        88.34        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       72.72        73.25        59.51        62.79        63.58        49.55 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       63.16        66.48        16.83        19.79         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
        4.87        28.67        23.93         1.74         4.44        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       37.51        36.79        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       10.65         0.69        18.67         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
        2.33        22.92         1.41        18.25        16.87        18.02 
TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 
        2.07        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY 
        8.48         0.26         4.27        16.93        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO 
       27.16        16.31        39.29        36.62        24.30         9.37 
TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       31.10        23.38        48.36        17.06         2.37         6.67 
TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       27.32        16.04         7.36        16.80        10.92        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       19.40        34.39        26.43        35.15        17.19        27.16 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 
       17.88        26.96        16.34        14.53        24.89         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99         4.54        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.34        22.78        13.97         6.90        19.27        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A1GX 
       17.88        17.62        16.11        12.43        11.08         6.48 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       19.33        12.59        18.87        22.82        20.05        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
       31.04        29.10        14.14        19.89        14.70        16.96 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 
        5.88        40.01        41.06        39.88         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-K6-A3WQ TCGA-KJ-A3U4 
        8.98        28.96        25.02        29.23        14.04         2.43 
TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 
       13.28        26.10        18.21        15.45        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 
       18.84        39.95        12.92        23.64        14.83         4.44 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.07        18.28         0.07         0.23 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.39              0.07 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           110.10            191.84 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           22.895            23.360 
[1] "0.4 - 110.1 (22.9)" "0.1 - 191.8 (23.4)"
[1] "hr=" "1.4"
D56V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  8P LOSS MUTATED                                        17
  8P LOSS WILD-TYPE                                     378
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  8P LOSS MUTATED                               4
  8P LOSS WILD-TYPE                            17
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  8P LOSS MUTATED                                  57
  8P LOSS WILD-TYPE                                55
D56V3, multiclass
                                         clus
vv                                        8P LOSS MUTATED 8P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              17               378
  MIXED SEROUS AND ENDOMETRIOID                         4                17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    57                55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V4, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    19  59
  8P LOSS WILD-TYPE 122 328
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     19   59
  8P LOSS WILD-TYPE  122  328
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO               19               122
  YES              59               328
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8P LOSS MUTATED    50   4   3   8
  8P LOSS WILD-TYPE 313  19  14  27
D56V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0              50               313
  R1               4                19
  R2               3                14
  RX               8                27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P LOSS MUTATED                                  1     1
  8P LOSS WILD-TYPE                                3    19
                   vv
clus                BLACK OR AFRICAN AMERICAN
  8P LOSS MUTATED                          24
  8P LOSS WILD-TYPE                        77
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8P LOSS MUTATED                                           0    48
  8P LOSS WILD-TYPE                                         9   318
D56V6, multiclass
                                           clus
vv                                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 3
  ASIAN                                                   1                19
  BLACK OR AFRICAN AMERICAN                              24                77
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 9
  WHITE                                                  48               318
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     1  55
  8P LOSS WILD-TYPE  13 312
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1   55
  8P LOSS WILD-TYPE   13  312
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                13
  NOT HISPANIC OR LATINO              55               312
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    22   2
  8Q LOSS WILD-TYPE 435  67
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               24               502 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                67 
$`8Q LOSS MUTATED`
TCGA-A5-A2K3 TCGA-AJ-A23M TCGA-AP-A05D TCGA-AX-A1C7 TCGA-AX-A2H5 TCGA-AX-A2HF 
       46.32         1.18        57.80        16.96        71.24        19.36 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0KB TCGA-B5-A3S1 TCGA-BG-A0YU TCGA-BG-A3PP 
        0.39        80.38         4.11        29.65        14.83         6.81 
TCGA-BK-A26L TCGA-DI-A1NN TCGA-DI-A2QT TCGA-EO-A3KU TCGA-EY-A3L3 TCGA-EY-A3QX 
       24.13        35.38        12.39        22.26        27.35        13.84 
TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A3PX TCGA-KP-A3VZ TCGA-PG-A7D5 
       39.95        96.69        28.93        45.01        23.74        23.97 

$`8Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       38.37        36.82        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       19.96        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK 
       15.95         7.92        11.44        36.33         9.60         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       91.04        28.64         5.33         5.16         7.33        14.96 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
       14.43        10.26         0.39        19.79        29.39         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
       34.36        34.16         1.12         0.76        18.90         1.68 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA 
        1.64        14.66        22.49        22.26        17.06        20.81 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ 
       36.99        20.65        21.21        15.62        10.19        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.95        14.76        16.87        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       20.78         2.70         0.13        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07         8.22        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       23.87        12.20        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      110.37         3.39        63.16        36.36        97.71        31.73 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       83.97        27.12        82.52        33.40        61.64        80.78 
TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        46.78        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
       10.42        27.85        16.24        21.90        36.13         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D 
       35.34        45.99        66.58        34.98        53.92        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       51.09        27.39        30.02        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       13.55        15.25        20.28        12.43        20.05        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR 
       72.56        54.12        67.50        25.12        36.39        11.08 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
        4.77        30.12        40.80        61.18        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       46.49        26.33        17.75        30.74         2.96        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       64.93         0.23         0.20         0.56        43.82         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
       20.52         1.38         0.30         0.26         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       18.35        14.47        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        27.29        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       11.01         8.71       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q 
       54.44        45.90        43.96        40.50        36.82        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       33.50        27.35        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV 
       17.36        16.57       191.84       102.31        50.89        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       14.70        11.70        11.87        15.29        12.79       116.25 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC 
       96.30        78.81        62.14        33.11        14.27        41.06 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       34.13        34.95        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98        22.06        38.37        36.49        28.27 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        52.64        52.83        56.58 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       11.31        35.90        34.98         6.21        10.22        10.16 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       31.76        24.99        16.64        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ 
       59.51        62.79        63.58        49.55        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       37.51        36.79        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X 
       33.63        10.65         0.69        18.67         3.95         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
       17.49        19.53         6.64        30.15        18.02        14.73 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW 
       24.30         2.33        22.92         1.41        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
       18.25        16.87        18.02         2.07        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        3.95         3.52        41.42         8.48        44.88         0.26 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        4.27         4.11        16.93        89.33        10.92        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QU 
       16.31        39.29        36.62        24.30         9.37        31.10 
TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
      110.10        23.38        48.36        17.06         2.37         6.67 
TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       27.32        16.04         7.36        16.80        10.92        49.15 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       37.71        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       51.52        51.42        19.40        34.39        26.43        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EO-A3KX 
       17.19        27.16        17.88        26.96        16.34        14.53 
TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       24.89         6.21        14.99         4.54        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL 
       27.16        23.34        23.34        23.90        22.78        13.97 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS 
        6.90        19.27        18.84        17.88        17.62        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        12.43        15.81        11.08         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
       12.59        10.19        14.40        18.87        22.82        20.05 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 
       45.76        31.04        29.10        11.38        17.92        14.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY 
       19.89        14.70        16.96         5.88        40.01        41.06 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EX 
       39.88         7.99        13.84         8.98        59.01         9.07 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI 
       28.96        25.02        29.23        41.06         1.74         7.76 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 
       14.04         2.43        13.28         9.47        26.10        18.21 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 
       23.24        15.45        12.92         7.00        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 
       18.84        39.95        12.92        23.64        14.83         4.44 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.07        18.28         0.07         0.23 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.39              0.07 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            96.69            191.84 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           24.050            23.275 
[1] "0.4 - 96.7 (24.0)"  "0.1 - 191.8 (23.3)"
[1] "hr=" "1.5"
D57V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  8Q LOSS MUTATED                                         2
  8Q LOSS WILD-TYPE                                     393
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  8Q LOSS MUTATED                               1
  8Q LOSS WILD-TYPE                            20
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  8Q LOSS MUTATED                                  21
  8Q LOSS WILD-TYPE                                91
D57V3, multiclass
                                         clus
vv                                        8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               2               393
  MIXED SEROUS AND ENDOMETRIOID                         1                20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    21                91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V4, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     5  19
  8Q LOSS WILD-TYPE 136 368
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      5   19
  8Q LOSS WILD-TYPE  136  368
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                5               136
  YES              19               368
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8Q LOSS MUTATED    14   1   1   3
  8Q LOSS WILD-TYPE 349  22  16  32
D57V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              14               349
  R1               1                22
  R2               1                16
  RX               3                32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  1     0
  8Q LOSS WILD-TYPE                                3    20
                   vv
clus                BLACK OR AFRICAN AMERICAN
  8Q LOSS MUTATED                           6
  8Q LOSS WILD-TYPE                        95
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8Q LOSS MUTATED                                           0    15
  8Q LOSS WILD-TYPE                                         9   351
D57V6, multiclass
                                           clus
vv                                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 3
  ASIAN                                                   0                20
  BLACK OR AFRICAN AMERICAN                               6                95
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 9
  WHITE                                                  15               351
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     1  17
  8Q LOSS WILD-TYPE  13 350
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1   17
  8Q LOSS WILD-TYPE   13  350
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                13
  NOT HISPANIC OR LATINO              17               350
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    76  25
  9P LOSS WILD-TYPE 381  44
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              101               425 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               25                44 
$`9P LOSS MUTATED`
TCGA-5B-A90C TCGA-A5-A0G2 TCGA-A5-A0GG TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A0R7 
       36.69       149.56        87.32        36.82        19.96        17.59 
TCGA-A5-A0VP TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N 
       42.35        91.04        28.64         7.33         1.18        14.43 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3I9 
       34.16         1.12        18.90         1.64        22.26        17.06 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A05D 
       20.81        10.19        20.78        21.99         5.95        57.80 
TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 
       45.53        48.79       125.42        97.71        46.78        21.90 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CF 
       36.13         0.56        37.78        16.96        13.55        76.83 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G4 
       36.39        11.08        30.12        43.82        20.52         0.30 
TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11P TCGA-B5-A1MS 
        0.26         0.39        17.85         4.11        36.82       102.31 
TCGA-B5-A1MY TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BG-A0M6 
       11.87       116.25        33.11        29.65        34.95        22.06 
TCGA-BG-A0M8 TCGA-BG-A18C TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD 
       36.49        15.45        10.22        10.16        24.13        16.64 
TCGA-BS-A0TI TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16N 
       61.87        49.55        22.55        39.48        37.32        31.07 
TCGA-D1-A16S TCGA-D1-A1NU TCGA-D1-A1O0 TCGA-D1-A3JP TCGA-DI-A1NN TCGA-DI-A2QT 
       18.67        13.22         2.07        16.93        35.38        12.39 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-EO-A1Y7 TCGA-EO-A2CG TCGA-EO-A3AZ TCGA-EO-A3B1 
       31.10       110.10        49.15        51.42        27.16        26.96 
TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A212 
       16.34         4.54        19.27        15.09        15.81        10.19 
TCGA-EY-A214 TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EX TCGA-FI-A2EY 
       14.40        14.70        41.06        39.95         9.07        28.93 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3VZ 
       25.02        29.23        41.06         7.76        14.04        23.74 
TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-QS-A8F1 
        9.47        26.10        18.21        23.24         4.44 

$`9P LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
       41.06        10.29       106.88        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
       32.78       112.54       105.37        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        60.53        46.55        38.37        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VQ 
       23.21        68.65        19.59        24.62        29.06        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 
        7.92        11.44        36.33         9.60         8.02        46.32 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
        5.33         5.16        14.96        10.26         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK 
       29.39         2.40        34.36         0.76         1.68        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       22.49        36.99        20.65        21.21        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.95        14.76        16.87        16.87        22.32        12.82 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        2.70         0.13        83.67        23.31        86.07         8.22 
TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD 
       63.91        36.89        23.87        12.20        20.91       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37         3.39        63.16        36.36        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       35.54        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       16.24        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       28.54        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       15.25        20.28        12.43        20.05        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       67.50        25.12         4.77        71.24        40.80        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       81.37        34.32        46.49        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       30.74         2.96        31.13        64.93         0.23         0.20 
TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.56         0.20         1.38         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       14.47        80.38        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       25.91        27.29        17.88        13.74        17.10        11.01 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
        8.71       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       45.90        43.96        40.50        32.09        33.50        27.35 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
      191.84        50.89        14.40        14.70        11.70        15.29 
TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC 
       12.79        96.30        78.81        62.14        14.27        41.06 
TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.13        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       34.98        38.37        28.27        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       23.47        43.30        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       52.64        52.83        56.58        14.83        12.56        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.73        14.01        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 
       20.02        23.70        20.12        11.31         6.81        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 
       34.98         6.21        31.76        24.99        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        23.47        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       77.95        67.99        96.49        30.74        97.41        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       59.51        62.79        63.58        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X 
       23.93         1.74         4.44        21.99        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I 
       36.10        36.36        37.51        36.79        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X 
       29.92        33.63        10.65         0.69         3.95         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
       17.49        19.53         6.64        30.15        18.02        14.73 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NW TCGA-D1-A1NX 
       24.30         2.33        22.92         1.41         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       16.87        18.02        15.06         1.05         3.95         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
       41.42         8.48        44.88         0.26         4.27         4.11 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       24.30         9.37        23.38        48.36        17.06         2.37 
TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        6.67        27.32        16.04         7.36        16.80        10.92 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       37.71        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       51.52        19.40        34.39        26.43        35.15        17.19 
TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       17.88        22.26        14.53        24.89         6.21        14.99 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR 
       22.78        13.97         6.90        18.84        17.88        17.62 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       16.11        12.43        11.08         6.48        19.33        12.59 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       18.87        22.82        20.05        45.76        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       27.35        13.84        11.38        17.92        14.14        19.89 
TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 
       16.96         5.88        40.01        39.88         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-FI-A3PX TCGA-H5-A2HR 
        8.98        96.69        59.01        28.96        45.01         1.74 
TCGA-KJ-A3U4 TCGA-KP-A3W0 TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
        2.43        13.28        15.45        23.97        12.92         7.00 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       11.24         6.97        18.84        39.95        12.92        23.64 
TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83        14.07        18.28         0.07         0.23 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.26              0.07 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           149.56            191.84 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            22.26             23.47 
[1] "0.3 - 149.6 (22.3)" "0.1 - 191.8 (23.5)"
[1] "hr=" "2.3"
D58V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  9P LOSS MUTATED                                        35
  9P LOSS WILD-TYPE                                     360
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  9P LOSS MUTATED                               8
  9P LOSS WILD-TYPE                            13
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  9P LOSS MUTATED                                  58
  9P LOSS WILD-TYPE                                54
D58V3, multiclass
                                         clus
vv                                        9P LOSS MUTATED 9P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              35               360
  MIXED SEROUS AND ENDOMETRIOID                         8                13
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    58                54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V4, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    24  77
  9P LOSS WILD-TYPE 117 310
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     24   77
  9P LOSS WILD-TYPE  117  310
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               24               117
  YES              77               310
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9P LOSS MUTATED    62   5   7   9
  9P LOSS WILD-TYPE 301  18  10  26
D58V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0              62               301
  R1               5                18
  R2               7                10
  RX               9                26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P LOSS MUTATED                                  1     2
  9P LOSS WILD-TYPE                                3    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  9P LOSS MUTATED                          23
  9P LOSS WILD-TYPE                        78
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9P LOSS MUTATED                                           2    67
  9P LOSS WILD-TYPE                                         7   299
D58V6, multiclass
                                           clus
vv                                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 3
  ASIAN                                                   2                18
  BLACK OR AFRICAN AMERICAN                              23                78
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               2                 7
  WHITE                                                  67               299
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     2  72
  9P LOSS WILD-TYPE  12 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      2   72
  9P LOSS WILD-TYPE   12  295
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                12
  NOT HISPANIC OR LATINO              72               295
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    93  27
  9Q LOSS WILD-TYPE 364  42
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              120               406 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               27                42 
$`9Q LOSS MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0GG TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A0R7 
       41.06        36.69        87.32        36.82        19.96        17.59 
TCGA-A5-A0VP TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A2QK 
       42.35        91.04        28.64         7.33         1.18         0.39 
TCGA-AJ-A2QN TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM 
        2.40        34.16         1.12        18.90         1.64        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A053 
       17.06        20.81        10.19        20.78        21.99         5.95 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A3K1 
       57.80        45.53        48.79       125.42        97.71        21.90 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A06B TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CF 
       36.13         0.56        53.92        37.78        16.96        76.83 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A2HK 
       36.39        11.08        30.12        61.18        19.36         2.96 
TCGA-AX-A3FS TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3GI 
        0.23        43.82        20.52         0.30         0.26         0.39 
TCGA-B5-A0JN TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS 
       80.38        17.85         4.11        75.72        36.82       102.31 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OE 
       50.89        11.87       116.25        33.11        29.65        34.95 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-BG-A18C TCGA-BG-A221 TCGA-BK-A0CC 
       22.06        36.49        12.56        15.45         1.81        10.22 
TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0V8 TCGA-D1-A0ZQ 
       10.16        24.13        16.64        61.87        49.55         8.55 
TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A16V 
       22.55        39.48        37.32        31.07        18.67         3.95 
TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1O0 TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-D1-A3JP 
       28.08        13.22         2.07        44.88         4.11        16.93 
TCGA-DI-A1NN TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       35.38        31.10       110.10        48.36        49.15        37.71 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1GC 
       51.42        19.40        27.16        26.96        16.34         4.54 
TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 
       19.27        15.09        15.81        12.59        10.19        14.40 
TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EX TCGA-FI-A2EY 
       20.05        29.10        41.06        39.95         9.07        28.93 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ 
       25.02        29.23        41.06        45.01         7.76        14.04 
TCGA-KP-A3VZ TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-QS-A8F1 
       23.74         9.47        26.10        18.21        23.24         4.44 

$`9Q LOSS WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
       10.29       106.88       149.56        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
       32.78       112.54       105.37        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        60.53        46.55        38.37        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VQ 
       23.21        68.65        19.59        24.62        29.06        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 
        7.92        11.44        36.33         9.60         8.02        46.32 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL 
        5.33         5.16        14.96        14.43        10.26        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
       29.39        34.36         0.76         1.68        14.66        22.49 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       36.99        20.65        21.21        15.62        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT 
       14.76        16.87        16.87        22.32        12.82         2.70 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
        0.13        83.67        23.31        86.07         8.22        63.91 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE 
       36.89        23.87        12.20        20.91       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
        3.39        63.16        36.36        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        55.89        31.30        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       46.78        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       16.24        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D 
       46.45        35.34        45.99        66.58        34.98        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       51.09        27.39        30.02        60.66        35.01        28.54 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 
       43.82        40.11        65.88        13.28        19.20        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       15.25        20.28        12.43        20.05        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA 
       67.50        25.12         4.77        71.24        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN 
       34.32        46.49        26.33        17.75        30.74        31.13 
TCGA-AX-A2IO TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G7 
       64.93         0.20         0.56         0.20         1.38         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        1.18        18.35        14.47        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        27.29        17.88        13.74        17.10 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J 
       11.01         8.71       185.79       113.36        88.34        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       45.90        43.96        40.50        32.09        33.50        27.35 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 
      191.84        14.40        14.70        11.70        15.29        12.79 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD 
       96.30        78.81        62.14        14.27        41.06        34.13 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        34.98 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       43.30        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       15.45        14.27         9.57        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B 
       11.31         6.81        35.90        34.98         6.21        31.76 
TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       24.99        13.18        10.03         9.86        46.95        23.47 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 
       85.55        78.21         4.80        77.95        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       30.74        97.41        67.20        88.34        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        72.72        73.25        59.51        62.79        63.58 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZR 
       63.16        66.48        16.83        19.79        29.95         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
        4.87        28.67        23.93         1.74         4.44        21.99 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
        0.66        15.72        36.10        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       27.42        11.51        29.92        33.63        10.65         0.69 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.01        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NW TCGA-D1-A1NX 
       24.30         2.33        22.92         1.41         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       16.87        18.02        15.06         1.05         3.95         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KV TCGA-DF-A2KY 
       41.42         8.48         0.26         4.27        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO 
       27.16        16.31        39.29        36.62        24.30         9.37 
TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 
       12.39        23.38        17.06         2.37         6.67        27.32 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A22R TCGA-EO-A22S 
       16.04         7.36        16.80        10.92        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3AU 
       66.90        46.26        57.60        51.52        34.39        26.43 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KX TCGA-EO-A3L0 
       35.15        17.19        17.88        22.26        14.53        24.89 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
        6.21        14.99        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP 
       23.34        23.90        22.78        13.97         6.90        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A1GX 
       17.88        17.62        16.11        12.43        11.08         6.48 
TCGA-EY-A1H0 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 
       19.33        18.87        22.82        45.76        31.04        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       13.84        11.38        17.92        14.14        19.89        14.70 
TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 
       16.96         5.88        40.01        39.88         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-H5-A2HR TCGA-KJ-A3U4 
        8.98        96.69        59.01        28.96         1.74         2.43 
TCGA-KP-A3W0 TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 
       13.28        15.45        23.97        12.92         7.00        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        18.84        39.95        12.92        23.64        14.83 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.07        18.28         0.07         0.23 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.23              0.07 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           125.42            191.84 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           22.405            23.425 
[1] "0.2 - 125.4 (22.4)" "0.1 - 191.8 (23.4)"
[1] "hr=" "2.2"
D59V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  9Q LOSS MUTATED                                        48
  9Q LOSS WILD-TYPE                                     347
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  9Q LOSS MUTATED                               9
  9Q LOSS WILD-TYPE                            12
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  9Q LOSS MUTATED                                  63
  9Q LOSS WILD-TYPE                                49
D59V3, multiclass
                                         clus
vv                                        9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              48               347
  MIXED SEROUS AND ENDOMETRIOID                         9                12
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    63                49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V4, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    27  93
  9Q LOSS WILD-TYPE 114 294
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     27   93
  9Q LOSS WILD-TYPE  114  294
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               27               114
  YES              93               294
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9Q LOSS MUTATED    77   4   7   9
  9Q LOSS WILD-TYPE 286  19  10  26
D59V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              77               286
  R1               4                19
  R2               7                10
  RX               9                26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q LOSS MUTATED                                  0     1
  9Q LOSS WILD-TYPE                                4    19
                   vv
clus                BLACK OR AFRICAN AMERICAN
  9Q LOSS MUTATED                          28
  9Q LOSS WILD-TYPE                        73
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9Q LOSS MUTATED                                           2    81
  9Q LOSS WILD-TYPE                                         7   285
D59V6, multiclass
                                           clus
vv                                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   1                19
  BLACK OR AFRICAN AMERICAN                              28                73
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               2                 7
  WHITE                                                  81               285
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     2  86
  9Q LOSS WILD-TYPE  12 281
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      2   86
  9Q LOSS WILD-TYPE   12  281
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                12
  NOT HISPANIC OR LATINO              86               281
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    32  10
  10P LOSS WILD-TYPE 425  59
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                42                484 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                10                 59 
$`10P LOSS MUTATED`
TCGA-A5-A1OH TCGA-AJ-A3BF TCGA-AJ-A3NF TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A0L9 
       36.33         1.12        21.21        21.99        45.53       125.42 
TCGA-AP-A0LI TCGA-AP-A5FX TCGA-AX-A06B TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 
       97.71        36.13        53.92        36.39        11.08         4.77 
TCGA-AX-A2HK TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0KB TCGA-BG-A0M8 
        2.96        20.52         0.30         0.39         4.11        36.49 
TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A26L TCGA-BS-A0U9 TCGA-D1-A16I TCGA-D1-A3JP 
       15.45         6.81        24.13        67.20        11.51        16.93 
TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A3AZ TCGA-EO-A3KW TCGA-EY-A1GR 
       35.38        48.36        27.32        27.16        16.34        17.62 
TCGA-EY-A1GS TCGA-EY-A2OQ TCGA-FI-A2D2 TCGA-FI-A2EY TCGA-FI-A3PV TCGA-FI-A3PX 
       15.09        29.10        39.95        28.93        41.06        45.01 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3VZ TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A915 
        7.76        14.04        23.74        26.10        18.21         7.00 

$`10P LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       38.37        36.82        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       19.96        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 
       15.95         7.92        11.44         9.60         8.02        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       46.32        28.64         5.33         5.16         7.33        14.96 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM 
        1.18        14.43        10.26         0.39        19.79        29.39 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
        2.40        34.36        34.16         0.76        18.90         1.68 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA 
        1.64        14.66        22.49        22.26        17.06        20.81 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       36.99        20.65        15.62        10.19        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       14.76        16.87        16.87        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        2.70         0.13        83.67         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
        8.22        63.91        57.80        36.89        23.87        12.20 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       20.91        48.79       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       60.36        55.89        31.30        35.54        46.78        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        30.90        10.42        27.85        16.24        21.90 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D 
       46.45        35.34        45.99        66.58        34.98        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       51.09        27.39        30.02        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       16.96        13.55        15.25        20.28        12.43        20.05 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H4 
       76.83        72.56        54.12        67.50        25.12        30.12 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       71.24        40.80        61.18        81.37        34.32        46.49 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO 
       19.36        26.33        17.75        30.74        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G3 
        0.23         0.20         0.56        43.82         0.20         1.38 
TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN 
        0.26         0.30         1.18        18.35        14.47        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        46.75        43.13        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       17.88        13.74        17.10        17.85        11.01         8.71 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L 
      185.79       113.36        88.34        75.72        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       43.96        40.50        36.82        32.09        33.50        27.35 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
      191.84       102.31        50.89        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       11.87        15.29        12.79       116.25        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       62.14        33.11        14.27        29.65        41.06        34.13 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       34.98        22.06        38.37        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        52.64        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 
       13.78        14.73        14.01        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 
        9.57        20.02        23.70        20.12        11.31        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       34.98         6.21        10.22        10.16        31.76        24.99 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       16.64        13.18        10.03         9.86        46.95        23.47 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       96.49        30.74        97.41        88.34        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        72.72        73.25        59.51        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       49.55        63.16        66.48        16.83        19.79        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       36.10        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02        14.73         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 
       13.22         0.72        18.25        16.87        18.02         2.07 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KV TCGA-DF-A2KY 
       44.88         0.26         4.27         4.11        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO 
       27.16        16.31        39.29        36.62        24.30         9.37 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 
       12.39        31.10       110.10        23.38        17.06         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
        6.67        16.04         7.36        16.80        10.92        49.15 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       37.71        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       51.52        51.42        19.40        34.39        26.43        35.15 
TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KX TCGA-EO-A3L0 
       17.19        17.88        26.96        22.26        14.53        24.89 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
        6.21        14.99         4.54        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       23.34        23.34        23.90        22.78        13.97         6.90 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       19.27        18.84        17.88        16.11        12.43        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 
       11.08         6.48        19.33        12.59        10.19        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 
       18.87        22.82        20.05        45.76        31.04        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       13.84        11.38        17.92        14.14        19.89        14.70 
TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
       16.96         5.88        40.01        41.06        39.88         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 
       13.84         8.98        96.69        59.01         9.07        28.96 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-KP-A3W0 TCGA-KP-A3W1 
       25.02        29.23         1.74         2.43        13.28         9.47 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 
       23.24        15.45        23.97        12.92        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 
       18.84        39.95        12.92        23.64        14.83         4.44 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.07        18.28         0.07         0.23 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.30               0.07 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            125.42             191.84 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            22.865             23.340 
[1] "0.3 - 125.4 (22.9)" "0.1 - 191.8 (23.3)"
[1] "hr=" "2.1"
D60V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  10P LOSS MUTATED                                         9
  10P LOSS WILD-TYPE                                     386
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  10P LOSS MUTATED                               4
  10P LOSS WILD-TYPE                            17
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  10P LOSS MUTATED                                  29
  10P LOSS WILD-TYPE                                83
D60V3, multiclass
                                         clus
vv                                        10P LOSS MUTATED 10P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                9                386
  MIXED SEROUS AND ENDOMETRIOID                          4                 17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     29                 83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V4, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     7  35
  10P LOSS WILD-TYPE 134 352
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      7   35
  10P LOSS WILD-TYPE  134  352
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 7                134
  YES               35                352
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10P LOSS MUTATED    27   2   3   5
  10P LOSS WILD-TYPE 336  21  14  30
D60V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               27                336
  R1                2                 21
  R2                3                 14
  RX                5                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P LOSS MUTATED                                  0     0
  10P LOSS WILD-TYPE                                4    20
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  10P LOSS MUTATED                          13
  10P LOSS WILD-TYPE                        88
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10P LOSS MUTATED                                           2    25
  10P LOSS WILD-TYPE                                         7   341
D60V6, multiclass
                                           clus
vv                                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    0                 20
  BLACK OR AFRICAN AMERICAN                               13                 88
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                2                  7
  WHITE                                                   25                341
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     0  32
  10P LOSS WILD-TYPE  14 335
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      0   32
  10P LOSS WILD-TYPE   14  335
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 14
  NOT HISPANIC OR LATINO               32                335
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    30   9
  10Q LOSS WILD-TYPE 427  60
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                39                487 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 9                 60 
$`10Q LOSS MUTATED`
TCGA-A5-A1OH TCGA-AJ-A3BF TCGA-AJ-A3TW TCGA-AP-A05H TCGA-AP-A0L9 TCGA-AP-A0LI 
       36.33         1.12        16.87        45.53       125.42        97.71 
TCGA-AP-A5FX TCGA-AX-A06B TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2HK TCGA-AX-A3G1 
       36.13        53.92        11.08         4.77         2.96        20.52 
TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0KB TCGA-B5-A1MS TCGA-B5-A3FD TCGA-BG-A0M8 
        0.30         0.39         4.11       102.31        33.11        36.49 
TCGA-BG-A18C TCGA-BG-A3PP TCGA-BS-A0U9 TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A17K 
       15.45         6.81        67.20        11.51        29.92        28.08 
TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DI-A1NN TCGA-EO-A3AZ TCGA-EO-A3KW TCGA-EY-A1GR 
        4.11        16.93        35.38        27.16        16.34        17.62 
TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A3PV TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ 
       39.95        96.69        41.06        45.01         7.76        14.04 
TCGA-KJ-A3U4 TCGA-KP-A3W3 TCGA-KP-A3W4 
        2.43        26.10        18.21 

$`10Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       38.37        36.82        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       19.96        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 
       15.95         7.92        11.44         9.60         8.02        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       46.32        28.64         5.33         5.16         7.33        14.96 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM 
        1.18        14.43        10.26         0.39        19.79        29.39 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
        2.40        34.36        34.16         0.76        18.90         1.68 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA 
        1.64        14.66        22.49        22.26        17.06        20.81 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ 
       36.99        20.65        21.21        15.62        10.19        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.95        14.76        16.87        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        2.70         0.13        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N 
       86.07         8.22        63.91        57.80        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       12.20        20.91        48.79       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       63.16        36.36        31.73        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       33.40        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        60.36        55.89        31.30        35.54        46.78 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        30.90        10.42        27.85        16.24 
TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       21.90         0.56        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       28.54        37.78        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       19.20        16.96        13.55        15.25        20.28        12.43 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       20.05        76.83        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
       36.39        30.12        71.24        40.80        61.18        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       34.32        46.49        19.36        26.33        17.75        30.74 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        64.93         0.23         0.20         0.56        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.20         1.38         0.26         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       14.47        80.38        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        27.29        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       11.01         8.71       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q 
       54.44        45.90        43.96        40.50        36.82        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       33.50        27.35        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW 
       17.36        16.57       191.84        50.89        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       11.70        11.87        15.29        12.79       116.25        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       78.81        62.14        14.27        29.65        41.06        34.13 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       34.98        22.06        38.37        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        52.64        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 
       13.78        14.73        14.01        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 
        9.57        20.02        23.70        20.12        11.31        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       34.98         6.21        10.22        10.16        31.76        24.99 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.13        16.64        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        30.74        97.41        88.34        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       63.58        49.55        63.16        66.48        16.83        19.79 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       27.42        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02        14.73         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
        1.28        28.01        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
        0.72        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 
        1.05         3.95         3.52        41.42         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        0.26         4.27        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU 
       39.29        36.62        24.30         9.37        12.39        31.10 
TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
      110.10        23.38        48.36        17.06         2.37         6.67 
TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       27.32        16.04         7.36        16.80        10.92        49.15 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       37.71        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       51.52        51.42        19.40        34.39        26.43        35.15 
TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KX TCGA-EO-A3L0 
       17.19        17.88        26.96        22.26        14.53        24.89 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
        6.21        14.99         4.54        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       23.34        23.34        23.90        22.78        13.97         6.90 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       19.27        18.84        17.88        15.09        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 
       15.81        11.08         6.48        19.33        12.59        10.19 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       14.40        18.87        22.82        20.05        45.76        31.04 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 
       29.10        27.35        13.84        11.38        17.92        14.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY 
       19.89        14.70        16.96         5.88        40.01        41.06 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EX 
       39.88         7.99        13.84         8.98        59.01         9.07 
TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-KP-A3VZ 
       28.93        28.96        25.02        29.23         1.74        23.74 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 
       13.28         9.47        23.24        15.45        23.97        12.92 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        7.00        11.24         6.97        18.84        39.95        12.92 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       23.64        14.83         4.44        14.07        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.30               0.07 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            125.42             191.84 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             20.52              23.34 
[1] "0.3 - 125.4 (20.5)" "0.1 - 191.8 (23.3)"
[1] "hr=" "1.9"
D61V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  10Q LOSS MUTATED                                        12
  10Q LOSS WILD-TYPE                                     383
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  10Q LOSS MUTATED                               4
  10Q LOSS WILD-TYPE                            17
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  10Q LOSS MUTATED                                  23
  10Q LOSS WILD-TYPE                                89
D61V3, multiclass
                                         clus
vv                                        10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               12                383
  MIXED SEROUS AND ENDOMETRIOID                          4                 17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     23                 89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V4, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     6  33
  10Q LOSS WILD-TYPE 135 354
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      6   33
  10Q LOSS WILD-TYPE  135  354
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                 6                135
  YES               33                354
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10Q LOSS MUTATED    27   1   1   4
  10Q LOSS WILD-TYPE 336  22  16  31
D61V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               27                336
  R1                1                 22
  R2                1                 16
  RX                4                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q LOSS MUTATED                                  0     0
  10Q LOSS WILD-TYPE                                4    20
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  10Q LOSS MUTATED                           9
  10Q LOSS WILD-TYPE                        92
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10Q LOSS MUTATED                                           2    25
  10Q LOSS WILD-TYPE                                         7   341
D61V6, multiclass
                                           clus
vv                                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    0                 20
  BLACK OR AFRICAN AMERICAN                                9                 92
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                2                  7
  WHITE                                                   25                341
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     1  28
  10Q LOSS WILD-TYPE  13 339
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1   28
  10Q LOSS WILD-TYPE   13  339
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 13
  NOT HISPANIC OR LATINO               28                339
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    57  16
  11P LOSS WILD-TYPE 400  53
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                73                453 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                16                 53 
$`11P LOSS MUTATED`
TCGA-5B-A90C TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A1OG TCGA-A5-A1OH 
       36.69        65.75        60.53        36.82        11.44        36.33 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AJ-A3BF 
       91.04        46.32        28.64         1.18        34.16         1.12 
TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AP-A05A 
       18.90         1.64        21.21        10.19        16.87        63.91 
TCGA-AP-A0LF TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A06B TCGA-AX-A1CA 
        3.39        46.78        21.90        36.13        53.92        20.28 
TCGA-AX-A1CR TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3GI 
       11.08        20.52         1.38         0.30         0.26         0.39 
TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A1MS TCGA-B5-A1N2 
       27.29        17.85        36.82        32.09       102.31        12.79 
TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OD TCGA-BG-A0YV TCGA-BK-A139 TCGA-BK-A4ZD 
      116.25        33.11        34.13        12.56        10.16        16.64 
TCGA-D1-A0ZZ TCGA-D1-A16S TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-D1-A3DH 
       22.55        18.67        18.25         2.07         4.27         4.11 
TCGA-D1-A3JP TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A8L9 TCGA-EO-A1Y8 
       16.93         9.37        12.39        31.10        27.32        37.71 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS 
       19.40        34.39        19.27        18.84        17.62        15.09 
TCGA-EY-A214 TCGA-EY-A2OO TCGA-EY-A3L3 TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2EY 
       14.40        45.76        27.35        14.70        39.95        28.93 
TCGA-FI-A2F8 TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W1 
       25.02         7.76        14.04         2.43        23.74         9.47 
TCGA-PG-A5BC 
       23.24 

$`11P LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       57.53        60.53        46.55        38.37        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        19.96        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK 
       29.06        42.35        15.95         7.92         9.60         8.02 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O 
        5.33         5.16         7.33        14.96        14.43        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG 
        0.39        19.79        29.39         2.40        34.36         0.76 
TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA 
        1.68        14.66        22.49        22.26        17.06        20.81 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       36.99        20.65        15.62        15.35        15.95        14.76 
TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW 
       16.87        22.32        12.82        20.78         2.70         0.13 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       83.67        21.99         5.95        23.31        86.07         8.22 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       57.80        45.53        36.89        23.87        12.20        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       60.36        55.89        31.30        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S 
       30.90        10.42        27.85        16.24         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       45.99        66.58        34.98        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        35.01        28.54        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        65.88        13.28        19.20        16.96        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       15.25        12.43        20.05        76.83        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       67.50        25.12        36.39         4.77        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       40.80        61.18        81.37        34.32        46.49        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       26.33        17.75        30.74         2.96        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G7 
        0.23         0.20         0.56        43.82         0.20         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
        1.18        18.35        14.47        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       28.34        30.51        25.91        17.88        13.74        17.10 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       11.01         4.11         8.71       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11R 
       75.72        54.44        45.90        43.96        40.50        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       16.57       191.84        50.89        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH 
       11.87        15.29        96.30        78.81        62.14        14.27 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       29.65        41.06        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98        22.06        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        20.02        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31         6.81        35.90        34.98         6.21 
TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 
       10.22        31.76        24.99        24.13        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        23.47        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       67.20        88.34        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI 
       73.25        59.51        62.79        63.58        49.55        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
        4.87        28.67        23.93         1.74         4.44        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       37.51        36.79        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NY 
        2.33        22.92         1.41        13.22         0.72        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 
       18.02        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        8.48        44.88         0.26        89.33        10.92        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QY 
       16.31        39.29        36.62        24.30        35.38       110.10 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       23.38        48.36        17.06         2.37         6.67        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S 
        7.36        16.80        10.92        49.15        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AU 
       66.90        46.26        57.60        51.52        51.42        26.43 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU 
       35.15        17.19        27.16        17.88        26.96        22.26 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC 
       16.34        14.53        24.89         6.21        14.99         4.54 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU 
       22.78        13.97         6.90        17.88        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 
       15.81        11.08         6.48        19.33        12.59        10.19 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX 
       18.87        22.82        20.05        31.04        29.10        13.84 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D 
       11.38        17.92        14.14        19.89        16.96         5.88 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       40.01        41.06        39.88         7.99        13.84         8.98 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-FI-A3PV 
       96.69        59.01         9.07        28.96        29.23        41.06 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A6IB 
       45.01         1.74        13.28        26.10        18.21        15.45 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       23.97        12.92         7.00        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       39.95        12.92        23.64        14.83         4.44        14.07 
TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       18.28         0.07         0.23 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.26               0.07 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            116.25             191.84 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             19.40              23.87 
[1] "0.3 - 116.2 (19.4)" "0.1 - 191.8 (23.9)"
[1] "hr=" "2.3"
D62V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  11P LOSS MUTATED                                        26
  11P LOSS WILD-TYPE                                     369
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  11P LOSS MUTATED                               6
  11P LOSS WILD-TYPE                            15
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  11P LOSS MUTATED                                  41
  11P LOSS WILD-TYPE                                71
D62V3, multiclass
                                         clus
vv                                        11P LOSS MUTATED 11P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               26                369
  MIXED SEROUS AND ENDOMETRIOID                          6                 15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     41                 71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V4, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    11  62
  11P LOSS WILD-TYPE 130 325
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     11   62
  11P LOSS WILD-TYPE  130  325
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                11                130
  YES               62                325
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11P LOSS MUTATED    42   3   4   6
  11P LOSS WILD-TYPE 321  20  13  29
D62V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0               42                321
  R1                3                 20
  R2                4                 13
  RX                6                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  1     1
  11P LOSS WILD-TYPE                                3    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  11P LOSS MUTATED                          21
  11P LOSS WILD-TYPE                        80
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11P LOSS MUTATED                                           1    45
  11P LOSS WILD-TYPE                                         8   321
D62V6, multiclass
                                           clus
vv                                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  3
  ASIAN                                                    1                 19
  BLACK OR AFRICAN AMERICAN                               21                 80
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   45                321
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     2  51
  11P LOSS WILD-TYPE  12 316
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      2   51
  11P LOSS WILD-TYPE   12  316
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 12
  NOT HISPANIC OR LATINO               51                316
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    57  15
  11Q LOSS WILD-TYPE 400  54
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                72                454 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                15                 54 
$`11Q LOSS MUTATED`
TCGA-5B-A90C TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A1OG TCGA-A5-A1OH 
       36.69        65.75        60.53        36.82        11.44        36.33 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-AJ-A23M TCGA-AJ-A2QM TCGA-AJ-A3BD 
       91.04        46.32        28.64         1.18        29.39        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW 
        1.12        18.90         1.64        10.19        16.87        16.87 
TCGA-AP-A0LF TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A1CR TCGA-AX-A2IO TCGA-AX-A3G1 
        3.39        21.90        36.13        11.08        64.93        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11P 
        1.38         0.26         0.39        27.29        17.85        36.82 
TCGA-B5-A11Q TCGA-B5-A1MS TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OD TCGA-BG-A0YV 
       32.09       102.31       116.25        33.11        34.13        12.56 
TCGA-BG-A3PP TCGA-BK-A4ZD TCGA-D1-A0ZZ TCGA-D1-A169 TCGA-D1-A16S TCGA-D1-A1NX 
        6.81        16.64        22.55        37.32        18.67        18.25 
TCGA-D1-A3DG TCGA-D1-A3JP TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU 
        4.27        16.93        35.38         9.37        12.39        31.10 
TCGA-E6-A8L9 TCGA-EO-A1Y8 TCGA-EO-A2CH TCGA-EO-A3KU TCGA-EY-A1GO TCGA-EY-A1GP 
       27.32        37.71        19.40        22.26        19.27        18.84 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A2OO 
       17.62        15.09        11.08        12.59        14.40        45.76 
TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-JU-AAVI 
       27.35        11.38        14.70        39.95        96.69         7.76 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A915 
       14.04         2.43        23.74         9.47        26.10         7.00 

$`11Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       57.53        60.53        46.55        38.37        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        19.96        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK 
       29.06        42.35        15.95         7.92         9.60         8.02 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O 
        5.33         5.16         7.33        14.96        14.43        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BK 
        0.39        19.79         2.40        34.36         0.76         1.68 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC 
       14.66        22.49        22.26        17.06        20.81        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65        21.21        15.62        15.35        15.95        14.76 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       22.32        12.82        20.78         2.70         0.13        83.67 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
       21.99         5.95        23.31        86.07         8.22        63.91 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       57.80        45.53        36.89        23.87        12.20        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       60.36        55.89        31.30        35.54        46.78        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO 
        6.71        30.90        10.42        27.85        16.24         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D 
       35.34        45.99        66.58        34.98        53.92        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       51.09        27.39        30.02        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       16.96        13.55        15.25        20.28        12.43        20.05 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       76.83        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
        4.77        30.12        71.24        40.80        61.18        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       34.32        46.49        19.36        26.33        17.75        30.74 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
        2.96        31.13         0.23         0.20         0.56        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.20         0.30         0.30         1.18        18.35        14.47 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       80.38        56.91        46.75        43.13        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       44.71        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E 
       17.88        13.74        17.10        11.01         4.11         8.71 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L 
      185.79       113.36        88.34        75.72        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       43.96        40.50        33.50        27.35        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU 
       19.50        18.41        17.36        16.57       191.84        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 
       14.40        14.70        11.70        11.87        15.29        12.79 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       96.30        78.81        62.14        14.27        29.65        41.06 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       34.98        22.06        38.37        36.49        28.27        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 
       13.78        14.73        14.01        15.45        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
        1.81         9.57        20.02        23.70        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       35.90        34.98         6.21        10.22        10.16        31.76 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.99        24.13        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        67.20        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       62.79        63.58        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93         1.74         4.44        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       15.72        36.10        36.36        37.51        36.79        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02        14.73         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
       13.22         0.72        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 
        1.05         3.95         3.52        41.42         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DH TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        0.26         4.11        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ 
       39.29        36.62        24.30       110.10        23.38        48.36 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       17.06         2.37         6.67        16.04         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       10.92        49.15        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       57.60        51.52        51.42        34.39        26.43        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EO-A3KX 
       17.19        27.16        17.88        26.96        16.34        14.53 
TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       24.89         6.21        14.99         4.54        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL 
       27.16        23.34        23.34        23.90        22.78        13.97 
TCGA-EY-A1GM TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX 
        6.90        17.88        16.11        12.43        15.81         6.48 
TCGA-EY-A1H0 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP 
       19.33        10.19        18.87        22.82        20.05        31.04 
TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 
       29.10        13.84        17.92        14.14        19.89        16.96 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 
        5.88        40.01        41.06        39.88         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 
        8.98        59.01         9.07        28.93        28.96        25.02 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-KP-A3W0 TCGA-KP-A3W4 
       29.23        41.06        45.01         1.74        13.28        18.21 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 
       23.24        15.45        23.97        12.92        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 
       18.84        39.95        12.92        23.64        14.83         4.44 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.07        18.28         0.07         0.23 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.26               0.07 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            116.25             191.84 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            19.085             23.785 
[1] "0.3 - 116.2 (19.1)" "0.1 - 191.8 (23.8)"
[1] "hr=" "2.1"
D63V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  11Q LOSS MUTATED                                        23
  11Q LOSS WILD-TYPE                                     372
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  11Q LOSS MUTATED                               7
  11Q LOSS WILD-TYPE                            14
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  11Q LOSS MUTATED                                  42
  11Q LOSS WILD-TYPE                                70
D63V3, multiclass
                                         clus
vv                                        11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               23                372
  MIXED SEROUS AND ENDOMETRIOID                          7                 14
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     42                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V4, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     8  64
  11Q LOSS WILD-TYPE 133 323
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      8   64
  11Q LOSS WILD-TYPE  133  323
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 8                133
  YES               64                323
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11Q LOSS MUTATED    42   4   4   7
  11Q LOSS WILD-TYPE 321  19  13  28
D63V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0               42                321
  R1                4                 19
  R2                4                 13
  RX                7                 28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  1     1
  11Q LOSS WILD-TYPE                                3    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  11Q LOSS MUTATED                          21
  11Q LOSS WILD-TYPE                        80
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11Q LOSS MUTATED                                           0    44
  11Q LOSS WILD-TYPE                                         9   322
D63V6, multiclass
                                           clus
vv                                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  3
  ASIAN                                                    1                 19
  BLACK OR AFRICAN AMERICAN                               21                 80
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  9
  WHITE                                                   44                322
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     3  51
  11Q LOSS WILD-TYPE  11 316
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3   51
  11Q LOSS WILD-TYPE   11  316
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 11
  NOT HISPANIC OR LATINO               51                316
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    30  12
  12P LOSS WILD-TYPE 427  57
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                42                484 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                12                 57 
$`12P LOSS MUTATED`
TCGA-A5-A0R6 TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-AJ-A2QM TCGA-AJ-A3BI TCGA-AJ-A3EM 
       19.96        91.04        28.64        29.39        18.90        22.26 
TCGA-AJ-A3NF TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A3K1 
       21.21        21.99        45.53        97.71        33.40        21.90 
TCGA-AX-A06B TCGA-AX-A2H4 TCGA-AX-A3FX TCGA-B5-A0K3 TCGA-B5-A1MS TCGA-B5-A3S1 
       53.92        30.12        43.82        27.29       102.31        29.65 
TCGA-B5-A5OE TCGA-BG-A0YV TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0V8 TCGA-D1-A0ZZ 
       34.95        12.56        10.16        16.64        49.55        22.55 
TCGA-D1-A15V TCGA-D1-A16S TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-EO-A3B1 TCGA-EO-A3KW 
       39.48        18.67        44.88         4.11        26.96        16.34 
TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A212 TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A54A 
       15.09        11.08        10.19        29.10        11.38        14.70 
TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A3PV TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-PG-A915 
       96.69         9.07        41.06        13.28        26.10         7.00 

$`12P LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       38.37        36.82        28.27        20.81        23.21        68.65 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 
        7.92        11.44        36.33         9.60         8.02        46.32 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N 
        5.33         5.16         7.33        14.96         1.18        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
       10.26         0.39        19.79         2.40        34.36        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        1.12         0.76         1.68         1.64        14.66        22.49 
TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3NH 
       17.06        20.81        36.99        20.65        15.62        10.19 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV 
       15.35        15.95        14.76        16.87        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A053 
       12.82        20.78         2.70         0.13        83.67         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J 
       23.31        86.07         8.22        63.91        57.80        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       23.87        12.20        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37         3.39        63.16        36.36        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       27.12        82.52        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        55.89        31.30        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       46.78        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       16.24        36.13         0.56        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       34.98        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       35.01        28.54        37.78        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       13.28        19.20        16.96        13.55        15.25        20.28 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       12.43        20.05        76.83        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 
       25.12        36.39        11.08         4.77        71.24        40.80 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       61.18        81.37        34.32        46.49        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       17.75        30.74         2.96        31.13        64.93         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 
        0.20         0.56         0.20        20.52         1.38         0.30 
TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
        0.26         0.30         1.18        18.35        14.47         0.39 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       80.38        56.91        46.75        43.13        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       44.71        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB 
       17.88        13.74        17.10        17.85        11.01         4.11 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
        8.71       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R 
       45.90        43.96        40.50        36.82        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       16.57       191.84        50.89        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       11.87        15.29        12.79       116.25        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW 
       62.14        33.11        14.27        41.06        34.13        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 
       20.19        19.33        20.94        35.21        34.98        22.06 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       38.37        36.49        28.27        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       23.47        43.30        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.01        15.45        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 
       20.02        23.70        20.12        11.31         6.81        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
       34.98         6.21        10.22        31.76        24.99        24.13 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        23.47        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       30.74        97.41        67.20        88.34        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        72.72        73.25        59.51        62.79        63.58 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.16        66.48        16.83        19.79        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 
        0.56         4.87        28.67        23.93         1.74         4.44 
TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       21.99        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       37.51        36.79        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
        2.33        22.92         1.41        13.22         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JP 
        3.52        41.42         8.48         0.26         4.27        16.93 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY 
       24.30        35.38         9.37        12.39        31.10       110.10 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 
       23.38        48.36        17.06         2.37         6.67        27.32 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       16.04         7.36        16.80        10.92        49.15        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       51.42        19.40        34.39        26.43        35.15        17.19 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 
       27.16        17.88        22.26        14.53        24.89         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99         4.54        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       23.34        23.90        22.78        13.97         6.90        19.27 
TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       18.84        17.88        17.62        16.11        12.43        15.81 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM 
        6.48        19.33        12.59        14.40        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A547 
       20.05        45.76        31.04        27.35        13.84        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY 
       14.14        19.89        16.96         5.88        40.01        41.06 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EW 
       39.88        39.95         7.99        13.84         8.98        59.01 
TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR 
       28.93        28.96        25.02        29.23        45.01         1.74 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W1 TCGA-KP-A3W4 
        7.76        14.04         2.43        23.74         9.47        18.21 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 
       23.24        15.45        23.97        12.92        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 
       18.84        39.95        12.92        23.64        14.83         4.44 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.07        18.28         0.07         0.23 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              4.11               0.07 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            102.31             191.84 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            24.325             23.340 
[1] "4.1 - 102.3 (24.3)" "0.1 - 191.8 (23.3)"
[1] "hr=" "2.5"
D64V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  12P LOSS MUTATED                                        13
  12P LOSS WILD-TYPE                                     382
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  12P LOSS MUTATED                               1
  12P LOSS WILD-TYPE                            20
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  12P LOSS MUTATED                                  28
  12P LOSS WILD-TYPE                                84
D64V3, multiclass
                                         clus
vv                                        12P LOSS MUTATED 12P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               13                382
  MIXED SEROUS AND ENDOMETRIOID                          1                 20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     28                 84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V4, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     7  35
  12P LOSS WILD-TYPE 134 352
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      7   35
  12P LOSS WILD-TYPE  134  352
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 7                134
  YES               35                352
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12P LOSS MUTATED    27   3   4   3
  12P LOSS WILD-TYPE 336  20  13  32
D64V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               27                336
  R1                3                 20
  R2                4                 13
  RX                3                 32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P LOSS MUTATED                                  0     0
  12P LOSS WILD-TYPE                                4    20
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  12P LOSS MUTATED                          10
  12P LOSS WILD-TYPE                        91
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12P LOSS MUTATED                                           1    26
  12P LOSS WILD-TYPE                                         8   340
D64V6, multiclass
                                           clus
vv                                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    0                 20
  BLACK OR AFRICAN AMERICAN                               10                 91
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   26                340
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     1  29
  12P LOSS WILD-TYPE  13 338
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1   29
  12P LOSS WILD-TYPE   13  338
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 13
  NOT HISPANIC OR LATINO               29                338
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    25  10
  12Q LOSS WILD-TYPE 432  59
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                35                491 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                10                 59 
$`12Q LOSS MUTATED`
TCGA-A5-A0R6 TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-AJ-A3IA TCGA-AJ-A3NF TCGA-AJ-A3NH 
       19.96        91.04        28.64        20.81        21.21        10.19 
TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A3K1 TCGA-B5-A0K3 
       21.99        45.53        97.71        33.40        21.90        27.29 
TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BG-A0YV TCGA-BK-A139 TCGA-BK-A4ZD TCGA-D1-A0ZZ 
       29.65        34.95        12.56        10.16        16.64        22.55 
TCGA-D1-A15V TCGA-D1-A16S TCGA-D1-A3DH TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1GW 
       39.48        18.67         4.11        26.96        16.34        11.08 
TCGA-EY-A212 TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2EU TCGA-FI-A2EX 
       10.19        29.10        11.38        14.70        96.69         9.07 
TCGA-FI-A3PV TCGA-JU-AAVI TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-PG-A915 
       41.06         7.76        13.28        26.10         7.00 

$`12Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       38.37        36.82        28.27        20.81        23.21        68.65 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 
        7.92        11.44        36.33         9.60         8.02        46.32 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N 
        5.33         5.16         7.33        14.96         1.18        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
       10.26         0.39        19.79        29.39         2.40        34.36 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       34.16         1.12         0.76        18.90         1.68         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE 
       14.66        22.49        22.26        17.06        36.99        20.65 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW 
       15.62        15.35        15.95        14.76        16.87        16.87 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       22.32        12.82        20.78         2.70         0.13        83.67 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D 
        5.95        23.31        86.07         8.22        63.91        57.80 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       36.89        23.87        12.20        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
      117.99       110.37         3.39        63.16        36.36        31.73 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       83.97        27.12        82.52        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        46.78        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       27.85        16.24        36.13         0.56        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       66.58        34.98        53.92        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        35.01        28.54        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        65.88        13.28        19.20        16.96        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       15.25        20.28        12.43        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 
       54.12        67.50        25.12        36.39        11.08         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       30.12        71.24        40.80        61.18        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       46.49        19.36        26.33        17.75        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        64.93         0.23         0.20         0.56        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
        0.20        20.52         1.38         0.30         0.26         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR 
        1.18        18.35        14.47         0.39        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       46.75        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.64        28.34        30.51        25.91        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F 
       17.10        17.85        11.01         4.11         8.71       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       40.50        36.82        32.09        33.50        27.35        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       191.84 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      102.31        50.89        14.40        14.70        11.70        11.87 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       15.29        12.79       116.25        96.30        78.81        62.14 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX 
       33.11        14.27        41.06        34.13        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98        22.06        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       36.49        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       43.30        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       15.45        15.45        14.27         1.81         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31         6.81        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F 
        6.21        10.22        31.76        24.99        24.13        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        23.47        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        67.20        88.34        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       72.72        73.25        59.51        62.79        63.58        49.55 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.16        66.48        16.83        19.79        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 
        0.56         4.87        28.67        23.93         1.74         4.44 
TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       21.99        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       37.51        36.79        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
        2.33        22.92         1.41        13.22         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.52        41.42         8.48        44.88         0.26         4.27 
TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
       16.93        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU 
       36.62        24.30        35.38         9.37        12.39        31.10 
TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
      110.10        23.38        48.36        17.06         2.37         6.67 
TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       27.32        16.04         7.36        16.80        10.92        49.15 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       37.71        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       51.52        51.42        19.40        34.39        26.43        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KX TCGA-EO-A3L0 
       17.19        27.16        17.88        22.26        14.53        24.89 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
        6.21        14.99         4.54        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       23.34        23.34        23.90        22.78        13.97         6.90 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT 
       19.27        18.84        17.88        17.62        15.09        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 
       12.43        15.81         6.48        19.33        12.59        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 
       18.87        22.82        20.05        45.76        31.04        27.35 
TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D 
       13.84        17.92        14.14        19.89        16.96         5.88 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
       40.01        41.06        39.88        39.95         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 
        8.98        59.01        28.93        28.96        25.02        29.23 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W1 
       45.01         1.74        14.04         2.43        23.74         9.47 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 
       18.21        23.24        15.45        23.97        12.92        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        18.84        39.95        12.92        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44        14.07        18.28         0.07         0.23 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              4.11               0.07 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             97.71             191.84 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             21.21              23.47 
[1] "4.1 - 97.7 (21.2)"  "0.1 - 191.8 (23.5)"
[1] "hr=" "3"  
D65V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  12Q LOSS MUTATED                                         8
  12Q LOSS WILD-TYPE                                     387
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  12Q LOSS MUTATED                               1
  12Q LOSS WILD-TYPE                            20
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  12Q LOSS MUTATED                                  26
  12Q LOSS WILD-TYPE                                86
D65V3, multiclass
                                         clus
vv                                        12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                8                387
  MIXED SEROUS AND ENDOMETRIOID                          1                 20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     26                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V4, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     6  29
  12Q LOSS WILD-TYPE 135 358
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      6   29
  12Q LOSS WILD-TYPE  135  358
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 6                135
  YES               29                358
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12Q LOSS MUTATED    26   2   2   2
  12Q LOSS WILD-TYPE 337  21  15  33
D65V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               26                337
  R1                2                 21
  R2                2                 15
  RX                2                 33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q LOSS MUTATED                                  0     0
  12Q LOSS WILD-TYPE                                4    20
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  12Q LOSS MUTATED                          10
  12Q LOSS WILD-TYPE                        91
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12Q LOSS MUTATED                                           0    20
  12Q LOSS WILD-TYPE                                         9   346
D65V6, multiclass
                                           clus
vv                                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    0                 20
  BLACK OR AFRICAN AMERICAN                               10                 91
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  9
  WHITE                                                   20                346
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     1  23
  12Q LOSS WILD-TYPE  13 344
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1   23
  12Q LOSS WILD-TYPE   13  344
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 13
  NOT HISPANIC OR LATINO               23                344
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    69  19
  13Q LOSS WILD-TYPE 388  50
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                88                438 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                19                 50 
$`13Q LOSS MUTATED`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G2 TCGA-A5-A0GN TCGA-A5-A0R7 TCGA-A5-A0VP 
       41.06        10.29       149.56        60.53        17.59        42.35 
TCGA-A5-A2K2 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A2QK TCGA-AJ-A2QM TCGA-AJ-A3BI 
       91.04         7.33        14.96         0.39        29.39        18.90 
TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NH TCGA-AJ-A3TW TCGA-AJ-A6NU 
        1.64        22.26        17.06        10.19        16.87        20.78 
TCGA-AP-A05H TCGA-AP-A05P TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A5FX TCGA-AW-A1PO 
       45.53        20.91        97.71        33.40        36.13         0.56 
TCGA-AX-A06B TCGA-AX-A1C9 TCGA-AX-A1CF TCGA-AX-A1CK TCGA-AX-A1CP TCGA-AX-A2H4 
       53.92        15.25        76.83        67.50        36.39        30.12 
TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 
        2.96        64.93        43.82        20.52         1.38         0.30 
TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0K3 TCGA-B5-A0KB TCGA-B5-A11P TCGA-B5-A1MY 
        0.26         0.39        27.29         4.11        36.82        11.87 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A5OE TCGA-BG-A0M6 TCGA-BG-A0YV TCGA-BG-A18C 
       12.79       116.25        34.95        22.06        12.56        15.45 
TCGA-BG-A2AE TCGA-BG-A3PP TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0U9 
       23.70         6.81        10.16        16.64        61.87        67.20 
TCGA-D1-A169 TCGA-D1-A16N TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A179 TCGA-D1-A1NU 
       37.32        31.07         0.69         3.95        14.73        13.22 
TCGA-D1-A3DG TCGA-D1-A3JP TCGA-DI-A1NN TCGA-DI-A1NO TCGA-E6-A8L9 TCGA-EO-A1Y7 
        4.27        16.93        35.38         9.37        27.32        49.15 
TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EY-A1GC TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GV 
       34.39        27.16         4.54        18.84        17.62        15.81 
TCGA-EY-A1GW TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A547 
       11.08        20.05        45.76        29.10        13.84        17.92 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-KJ-A3U4 
        9.07        28.93        25.02        45.01        14.04         2.43 
TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-PG-A7D5 
       23.74        13.28         9.47        23.97 

$`13Q LOSS WILD-TYPE`
TCGA-5B-A90C TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
       36.69       106.88        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
      112.54       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       23.21        68.65        19.96        19.59        24.62        29.06 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK 
       15.95         7.92        11.44        36.33         9.60         8.02 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23M TCGA-AJ-A23N 
       46.32        28.64         5.33         5.16         1.18        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF 
       10.26        19.79         2.40        34.36        34.16         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3IA TCGA-AJ-A3NC 
        0.76         1.68        14.66        22.49        20.81        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65        21.21        15.62        15.35        15.95        14.76 
TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       16.87        22.32        12.82         2.70         0.13        83.67 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
       21.99         5.95        23.31        86.07         8.22        63.91 
TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A0L8 TCGA-AP-A0L9 
       57.80        36.89        23.87        12.20        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
      117.99       110.37         3.39        63.16        36.36        31.73 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       83.97        27.12        82.52        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        46.78        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       27.85        16.24        21.90        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       34.98        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       35.01        28.54        37.78        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CC 
       13.28        19.20        16.96        13.55        20.28        12.43 
TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CN TCGA-AX-A1CR TCGA-AX-A2H2 
       20.05        72.56        54.12        25.12        11.08         4.77 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       71.24        40.80        61.18        81.37        34.32        46.49 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS 
       19.36        26.33        17.75        30.74        31.13         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.20         0.56         0.20         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       14.47        80.38        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       25.91        17.88        13.74        17.10        17.85        11.01 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
        8.71       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       45.90        43.96        40.50        32.09        33.50        27.35 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
      191.84       102.31        50.89        14.40        14.70        11.70 
TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH 
       15.29        96.30        78.81        62.14        33.11        14.27 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       29.65        41.06        34.13        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       20.94        35.21        34.98        38.37        36.49        28.27 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 
       14.83        13.78        14.73        14.01        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 
        1.81         9.57        20.02        20.12        11.31        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
       34.98         6.21        10.22        31.76        24.99        24.13 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        23.47        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
       78.21         4.80        77.95        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       97.41        88.34        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI 
       73.25        59.51        62.79        63.58        49.55        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B 
       29.33        32.58         0.66        15.72        36.10        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16O 
       37.51        36.79        27.42        11.51        29.92        33.63 
TCGA-D1-A16Q TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       10.65        18.67         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
        0.72        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 
        1.05         3.95         3.52        41.42         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DH TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        0.26         4.11        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY 
       39.29        36.62        24.30        12.39        31.10       110.10 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       23.38        48.36        17.06         2.37         6.67        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
        7.36        16.80        10.92        37.71        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH 
       66.90        46.26        57.60        51.52        51.42        19.40 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU 
       26.43        35.15        17.19        17.88        26.96        22.26 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD 
       16.34        14.53        24.89         6.21        14.99        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK 
       24.36        27.16        23.34        23.34        23.90        22.78 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT 
       13.97         6.90        19.27        17.88        15.09        16.11 
TCGA-EY-A1GU TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 
       12.43         6.48        19.33        12.59        10.19        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A548 
       18.87        22.82        31.04        27.35        11.38        14.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY 
       19.89        14.70        16.96         5.88        40.01        41.06 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       39.88        39.95         7.99        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI 
       59.01        28.96        29.23        41.06         1.74         7.76 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A915 
       26.10        18.21        23.24        15.45        12.92         7.00 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       11.24         6.97        18.84        39.95        12.92        23.64 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83         4.44        14.07        18.28         0.07         0.23 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.26               0.07 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            149.56             191.84 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            19.475             23.885 
[1] "0.3 - 149.6 (19.5)" "0.1 - 191.8 (23.9)"
[1] "hr=" "2.2"
D66V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  13Q LOSS MUTATED                                        46
  13Q LOSS WILD-TYPE                                     349
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  13Q LOSS MUTATED                               5
  13Q LOSS WILD-TYPE                            16
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  13Q LOSS MUTATED                                  38
  13Q LOSS WILD-TYPE                                74
D66V3, multiclass
                                         clus
vv                                        13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               46                349
  MIXED SEROUS AND ENDOMETRIOID                          5                 16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     38                 74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V4, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    15  74
  13Q LOSS WILD-TYPE 126 313
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     15   74
  13Q LOSS WILD-TYPE  126  313
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                15                126
  YES               74                313
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  13Q LOSS MUTATED    58   3   5   5
  13Q LOSS WILD-TYPE 305  20  12  30
D66V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0               58                305
  R1                3                 20
  R2                5                 12
  RX                5                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  0     2
  13Q LOSS WILD-TYPE                                4    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  13Q LOSS MUTATED                          20
  13Q LOSS WILD-TYPE                        81
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  13Q LOSS MUTATED                                           2    60
  13Q LOSS WILD-TYPE                                         7   306
D66V6, multiclass
                                           clus
vv                                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    2                 18
  BLACK OR AFRICAN AMERICAN                               20                 81
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                2                  7
  WHITE                                                   60                306
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     4  66
  13Q LOSS WILD-TYPE  10 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4   66
  13Q LOSS WILD-TYPE   10  301
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 10
  NOT HISPANIC OR LATINO               66                301
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    46  13
  14Q LOSS WILD-TYPE 411  56
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                59                467 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                13                 56 
$`14Q LOSS MUTATED`
TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A2K4 TCGA-AJ-A23M 
       60.53        19.96        17.59        11.44        28.64         1.18 
TCGA-AJ-A3BD TCGA-AJ-A3NH TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0L9 
       34.16        10.19        45.53        36.89        48.79       125.42 
TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AX-A0IW TCGA-AX-A1CA TCGA-AX-A3G1 TCGA-AX-A3G4 
       97.71        33.40        37.78        20.28        20.52         0.30 
TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K3 TCGA-B5-A0KB 
        0.26         0.30         0.39        80.38        27.29         4.11 
TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MY TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A0M6 
       75.72        36.82        11.87        29.65        34.13        22.06 
TCGA-BG-A18C TCGA-BK-A0CC TCGA-BK-A139 TCGA-D1-A16I TCGA-D1-A179 TCGA-D1-A1NU 
       15.45        10.22        10.16        11.51        14.73        13.22 
TCGA-D1-A1NW TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-E6-A8L9 TCGA-EO-A2CG 
        0.72        35.38         9.37        12.39        27.32        51.42 
TCGA-EO-A3AS TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GO TCGA-EY-A1GR TCGA-EY-A1GS 
       34.39        22.26        16.34        19.27        17.62        15.09 
TCGA-EY-A214 TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2F9 
       14.40        45.76        29.10        14.70        41.06        29.23 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-PG-A915 TCGA-QS-A8F1 
       45.01         1.74         7.76         7.00         4.44 

$`14Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ 
       74.10        57.53        65.75        60.53        46.55        38.37 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 
       36.82        28.27        20.81        23.21        68.65        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH 
       24.62        29.06        42.35        15.95         7.92        36.33 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 
        9.60         8.02        91.04        46.32         5.33         5.16 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
        7.33        14.96        14.43        10.26         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI 
       29.39         2.40        34.36         1.12         0.76        18.90 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
        1.68         1.64        14.66        22.49        22.26        17.06 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       20.81        36.99        20.65        21.21        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.95        14.76        16.87        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       20.78         2.70         0.13        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05N 
       23.31        86.07         8.22        63.91        57.80        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       12.20        20.91       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP 
       36.36        31.73        83.97        27.12        82.52        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       55.89        31.30        35.54        46.78        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
       30.90        10.42        27.85        16.24        21.90        36.13 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       28.54        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       16.96        13.55        15.25        12.43        20.05        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR 
       72.56        54.12        67.50        25.12        36.39        11.08 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
        4.77        30.12        71.24        40.80        61.18        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       34.32        46.49        19.36        26.33        17.75        30.74 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
        2.96        31.13        64.93         0.23         0.20         0.56 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
       43.82         0.20         1.38         1.18        18.35        14.47 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        46.75        43.13        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 
       32.55        28.64        28.34        30.51        25.91        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       13.74        17.10        17.85        11.01         8.71       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
      113.36        88.34        54.44        45.90        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU 
       18.41        17.36        16.57       191.84       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       14.40        14.70        11.70        15.29        12.79       116.25 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC 
       96.30        78.81        62.14        33.11        14.27        41.06 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       34.98        38.37        36.49        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        52.64        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 
       13.78        14.73        14.01        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        9.57        20.02        23.70        20.12        11.31         6.81 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
       35.90        34.98         6.21        31.76        24.99        24.13 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       16.64        13.18        10.03         9.86        46.95        23.47 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF 
       96.49        30.74        97.41        67.20        88.34        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       63.58        49.55        63.16        66.48        16.83        19.79 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       27.42        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       18.67         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
       18.25        16.87        18.02         2.07        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        3.95         3.52        41.42         8.48        44.88         0.26 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        4.27         4.11        16.93        89.33        10.92        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QU TCGA-DI-A2QY 
       16.31        39.29        36.62        24.30        31.10       110.10 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       23.38        48.36        17.06         2.37         6.67        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
        7.36        16.80        10.92        49.15        37.71        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH 
       61.55        66.90        46.26        57.60        51.52        19.40 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 
       26.43        35.15        17.19        27.16        17.88        26.96 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       14.53        24.89         6.21        14.99         4.54        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK 
       24.36        27.16        23.34        23.34        23.90        22.78 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU 
       13.97         6.90        18.84        17.88        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 
       15.81        11.08         6.48        19.33        12.59        10.19 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX 
       18.87        22.82        20.05        31.04        27.35        13.84 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D 
       11.38        17.92        14.14        19.89        16.96         5.88 
TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       40.01        39.88        39.95         7.99        13.84         8.98 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 
       96.69        59.01         9.07        28.93        28.96        25.02 
TCGA-FI-A3PV TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 
       41.06        14.04         2.43        23.74        13.28         9.47 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 
       26.10        18.21        23.24        15.45        23.97        12.92 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       11.24         6.97        18.84        39.95        12.92        23.64 
TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83        14.07        18.28         0.07         0.23 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.26               0.07 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            125.42             191.84 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             19.96              23.64 
[1] "0.3 - 125.4 (20.0)" "0.1 - 191.8 (23.6)"
[1] "hr=" "2.2"
D67V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  14Q LOSS MUTATED                                        19
  14Q LOSS WILD-TYPE                                     376
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  14Q LOSS MUTATED                               3
  14Q LOSS WILD-TYPE                            18
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  14Q LOSS MUTATED                                  37
  14Q LOSS WILD-TYPE                                75
D67V3, multiclass
                                         clus
vv                                        14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               19                376
  MIXED SEROUS AND ENDOMETRIOID                          3                 18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     37                 75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V4, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    19  40
  14Q LOSS WILD-TYPE 122 347
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     19   40
  14Q LOSS WILD-TYPE  122  347
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                19                122
  YES               40                347
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  14Q LOSS MUTATED    35   2   3   3
  14Q LOSS WILD-TYPE 328  21  14  32
D67V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0               35                328
  R1                2                 21
  R2                3                 14
  RX                3                 32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q LOSS MUTATED                                  1     2
  14Q LOSS WILD-TYPE                                3    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  14Q LOSS MUTATED                          21
  14Q LOSS WILD-TYPE                        80
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  14Q LOSS MUTATED                                           1    30
  14Q LOSS WILD-TYPE                                         8   336
D67V6, multiclass
                                           clus
vv                                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  3
  ASIAN                                                    2                 18
  BLACK OR AFRICAN AMERICAN                               21                 80
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   30                336
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     3  36
  14Q LOSS WILD-TYPE  11 331
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      3   36
  14Q LOSS WILD-TYPE   11  331
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 11
  NOT HISPANIC OR LATINO               36                331
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    82  23
  15Q LOSS WILD-TYPE 375  46
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               105                421 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                23                 46 
$`15Q LOSS MUTATED`
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A2K2 
       65.75        60.53        19.96        17.59        11.44        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N 
       46.32        28.64         7.33        14.96         1.18        14.43 
TCGA-AJ-A2QK TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM 
        0.39        29.39        34.16        18.90         1.64        22.26 
TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A052 
       21.21        10.19        16.87        16.87        20.78        21.99 
TCGA-AP-A053 TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A3K1 TCGA-AP-A5FX 
        5.95        45.53        48.79       125.42        21.90        36.13 
TCGA-AX-A06B TCGA-AX-A0IW TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CR 
       53.92        37.78        15.25        20.28        12.43        11.08 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H8 TCGA-AX-A2HK TCGA-AX-A3FS TCGA-AX-A3FZ 
        4.77        30.12        61.18         2.96         0.23         0.20 
TCGA-AX-A3G3 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K3 
        1.38         0.26         0.30         0.39        80.38        27.29 
TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1N2 TCGA-B5-A3F9 
       17.85         4.11        36.82       102.31        12.79       116.25 
TCGA-B5-A3S1 TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-BS-A0V8 
       29.65        15.45         6.81        16.64        67.20        49.55 
TCGA-D1-A0ZQ TCGA-D1-A0ZZ TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A16V 
        8.55        22.55        11.51        31.07        18.67         3.95 
TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A3DH TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y8 
       14.73        13.22         4.11       110.10        48.36        37.71 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU 
       51.42        19.40        34.39        27.16        26.96        22.26 
TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 
        4.54        19.27        18.84        12.59        10.19        14.40 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A547 
       20.05        45.76        29.10        27.35        11.38        17.92 
TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX 
       39.95        96.69        59.01        25.02        29.23        45.01 
TCGA-K6-A3WQ TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-PG-A914 
       14.04        23.74        13.28        26.10        23.97        12.92 
TCGA-PG-A915 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
        7.00         4.44        14.07 

$`15Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       74.10        57.53        60.53        46.55        38.37        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 
       28.27        20.81        23.21        68.65        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ 
       29.06        42.35        15.95         7.92        36.33         9.60 
TCGA-A5-A1OK TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN 
        8.02         5.33         5.16        10.26        19.79         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
       34.36         1.12         0.76         1.68        14.66        22.49 
TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       17.06        20.81        36.99        20.65        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW 
       15.95        14.76        22.32        12.82         2.70         0.13 
TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D 
       83.67        23.31        86.07         8.22        63.91        57.80 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE 
       36.89        23.87        12.20        20.91       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        46.78        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       27.85        16.24         0.56        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       34.98        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       35.01        28.54        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       19.20        16.96        13.55        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2H7 
       54.12        67.50        25.12        36.39        71.24        40.80 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       81.37        34.32        46.49        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       30.74        31.13        64.93         0.20         0.56        43.82 
TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR 
       20.52         0.30         1.18        18.35        14.47        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       46.75        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.64        28.34        30.51        25.91        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.10        11.01         8.71       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       75.72        54.44        45.90        43.96        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       33.50        27.35        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW 
       17.36        16.57       191.84        50.89        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       11.70        11.87        15.29        96.30        78.81        62.14 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW 
       33.11        14.27        41.06        34.13        34.95        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 
       20.19        19.33        20.94        35.21        34.98        22.06 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       38.37        36.49        28.27        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       23.47        43.30        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       52.64        52.83        56.58        14.83        12.56        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.73        14.01        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA 
       20.02        23.70        20.12        11.31        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
        6.21        10.22        10.16        31.76        24.99        24.13 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        23.47        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41        88.34        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI 
       72.72        73.25        59.51        62.79        63.58        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        19.79        29.95         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93         1.74         4.44        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       36.79        27.42        29.92        33.63        10.65         0.69 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NW TCGA-D1-A1NX 
       24.30         2.33        22.92         1.41         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.52        41.42         8.48        44.88         0.26         4.27 
TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
       16.93        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU 
       36.62        24.30        35.38         9.37        12.39        31.10 
TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ 
       23.38        17.06         2.37         6.67        27.32        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S 
        7.36        16.80        10.92        49.15        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AU TCGA-EO-A3AV 
       66.90        46.26        57.60        51.52        26.43        35.15 
TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 
       17.19        17.88        16.34        14.53        24.89         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       14.99        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GQ TCGA-EY-A1GR 
       23.90        22.78        13.97         6.90        17.88        17.62 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       15.09        16.11        12.43        15.81        11.08         6.48 
TCGA-EY-A1H0 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A548 
       19.33        18.87        22.82        31.04        13.84        14.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY 
       19.89        14.70        16.96         5.88        40.01        41.06 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EX TCGA-FI-A2EY 
       39.88         7.99        13.84         8.98         9.07        28.93 
TCGA-FI-A2F4 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KJ-A3U4 TCGA-KP-A3W1 
       28.96        41.06         1.74         7.76         2.43         9.47 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       18.21        23.24        15.45        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       39.95        12.92        23.64        14.83        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.20               0.07 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            125.42             191.84 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             19.96              24.13 
[1] "0.2 - 125.4 (20.0)" "0.1 - 191.8 (24.1)"
[1] "hr=" "2.2"
D68V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  15Q LOSS MUTATED                                        36
  15Q LOSS WILD-TYPE                                     359
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  15Q LOSS MUTATED                               8
  15Q LOSS WILD-TYPE                            13
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  15Q LOSS MUTATED                                  61
  15Q LOSS WILD-TYPE                                51
D68V3, multiclass
                                         clus
vv                                        15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               36                359
  MIXED SEROUS AND ENDOMETRIOID                          8                 13
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     61                 51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V4, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    20  85
  15Q LOSS WILD-TYPE 121 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     20   85
  15Q LOSS WILD-TYPE  121  302
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                20                121
  YES               85                302
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  15Q LOSS MUTATED    68   4   6   8
  15Q LOSS WILD-TYPE 295  19  11  27
D68V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0               68                295
  R1                4                 19
  R2                6                 11
  RX                8                 27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q LOSS MUTATED                                  0     2
  15Q LOSS WILD-TYPE                                4    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  15Q LOSS MUTATED                          27
  15Q LOSS WILD-TYPE                        74
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  15Q LOSS MUTATED                                           2    65
  15Q LOSS WILD-TYPE                                         7   301
D68V6, multiclass
                                           clus
vv                                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    2                 18
  BLACK OR AFRICAN AMERICAN                               27                 74
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                2                  7
  WHITE                                                   65                301
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     2  74
  15Q LOSS WILD-TYPE  12 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2   74
  15Q LOSS WILD-TYPE   12  293
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 12
  NOT HISPANIC OR LATINO               74                293
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    75  20
  16P LOSS WILD-TYPE 382  49
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                95                431 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                20                 49 
$`16P LOSS MUTATED`
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K4 TCGA-A5-A3LO 
       65.75        60.53        11.44        36.33        28.64         7.33 
TCGA-AJ-A23M TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3EM TCGA-AJ-A3NF TCGA-AJ-A3NH 
        1.18        29.39        34.16        22.26        21.21        10.19 
TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 
       16.87        20.78        21.99        45.53        36.89        48.79 
TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AX-A06B TCGA-AX-A0IU 
        3.39        97.71        46.78        21.90        53.92        28.54 
TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H5 
       15.25        12.43        76.83        11.08        30.12        71.24 
TCGA-AX-A2IO TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 
       64.93        43.82         0.20         1.38         0.30         0.26 
TCGA-AX-A3GI TCGA-B5-A0JT TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A11P 
        0.39        43.13        17.85         4.11        75.72        36.82 
TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BG-A0MU 
      102.31        11.87        33.11        29.65        34.95        20.28 
TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0V8 
       15.45         6.81        10.22        10.16        16.64        49.55 
TCGA-D1-A0ZZ TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A179 TCGA-D1-A17K 
       22.55        27.42        29.92        31.07        14.73        28.08 
TCGA-D1-A17R TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-D1-A3DH 
       11.15        13.22         0.72         2.07         4.27         4.11 
TCGA-D1-A3JP TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QY TCGA-E6-A8L9 TCGA-EO-A1Y5 
       16.93        35.38         9.37       110.10        27.32        10.92 
TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1GM 
       37.71        51.42        19.40        27.16        26.96         6.90 
TCGA-EY-A1GR TCGA-EY-A210 TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       17.62        12.59        29.10        27.35        13.84        11.38 
TCGA-FI-A2EU TCGA-FI-A3PV TCGA-FI-A3PX TCGA-JU-AAVI TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       96.69        41.06        45.01         7.76         2.43        23.74 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-QS-A8F1 
       26.10        18.21        23.24        23.97         4.44 

$`16P LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       74.10        57.53        60.53        46.55        38.37        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        20.81        23.21        68.65        19.96        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       19.59        24.62        29.06        42.35        15.95         7.92 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 
        9.60         8.02        91.04        46.32         5.33         5.16 
TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       14.96        14.43        10.26         0.39        19.79         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       34.36         1.12         0.76        18.90         1.68         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE 
       14.66        22.49        17.06        20.81        36.99        20.65 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DV 
       15.62        15.35        15.95        14.76        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 
       12.82         2.70         0.13        83.67         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05N TCGA-AP-A05O 
       86.07         8.22        63.91        57.80        23.87        12.20 
TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       20.91       125.42       117.99       110.37        63.16        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       31.73        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       55.89        31.30        35.54        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       10.42        27.85        16.24        36.13         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       45.99        66.58        34.98        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        35.01        37.78        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA 
       65.88        13.28        19.20        16.96        13.55        20.28 
TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       20.05        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
        4.77        40.80        61.18        81.37        34.32        46.49 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       19.36        26.33        17.75        30.74         2.96        31.13 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3G1 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.23         0.20         0.56        20.52         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU 
       18.35        14.47        80.38        56.91        46.75        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       25.91        27.29        17.88        13.74        17.10        11.01 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
        8.71       185.79       113.36        88.34        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       43.96        40.50        32.09        33.50        27.35        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       191.84 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 
       50.89        14.40        14.70        11.70        15.29        12.79 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC 
      116.25        96.30        78.81        62.14        14.27        41.06 
TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.13        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       34.98        22.06        38.37        36.49        28.27        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       30.81        21.17        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        52.64        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 
       13.78        14.73        14.01        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 
        9.57        20.02        23.70        20.12        11.31        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F 
       34.98         6.21        31.76        24.99        24.13        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        23.47        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        67.20        88.34        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI 
       72.72        73.25        59.51        62.79        63.58        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
        4.87        28.67        23.93         1.74         4.44        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16I TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       37.51        36.79        11.51        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       18.67         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
        1.28        28.01        26.37        10.22         1.51         1.78 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NX TCGA-D1-A1NY 
       24.30         2.33        22.92         1.41        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 
       18.02        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        8.48        44.88         0.26        89.33        10.92        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QU 
       16.31        39.29        36.62        24.30        12.39        31.10 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       23.38        48.36        17.06         2.37         6.67        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
        7.36        16.80        49.15        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       46.26        57.60        51.52        34.39        26.43        35.15 
TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       17.19        17.88        22.26        16.34        14.53        24.89 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
        6.21        14.99         4.54        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GO 
       23.34        23.34        23.90        22.78        13.97        19.27 
TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       18.84        17.88        15.09        16.11        12.43        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 
       11.08         6.48        19.33        10.19        14.40        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A547 TCGA-EY-A548 
       22.82        20.05        45.76        31.04        17.92        14.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY 
       19.89        14.70        16.96         5.88        40.01        41.06 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EW 
       39.88        39.95         7.99        13.84         8.98        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-H5-A2HR 
        9.07        28.93        28.96        25.02        29.23         1.74 
TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A915 
       14.04        13.28         9.47        15.45        12.92         7.00 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       11.24         6.97        18.84        39.95        12.92        23.64 
TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83        14.07        18.28         0.07         0.23 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.20               0.07 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            110.10             191.84 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             22.26              23.47 
[1] "0.2 - 110.1 (22.3)" "0.1 - 191.8 (23.5)"
[1] "hr=" "2.2"
D69V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  16P LOSS MUTATED                                        32
  16P LOSS WILD-TYPE                                     363
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  16P LOSS MUTATED                               6
  16P LOSS WILD-TYPE                            15
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  16P LOSS MUTATED                                  58
  16P LOSS WILD-TYPE                                54
D69V3, multiclass
                                         clus
vv                                        16P LOSS MUTATED 16P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               32                363
  MIXED SEROUS AND ENDOMETRIOID                          6                 15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     58                 54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V4, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    19  77
  16P LOSS WILD-TYPE 122 310
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     19   77
  16P LOSS WILD-TYPE  122  310
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                19                122
  YES               77                310
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16P LOSS MUTATED    55   5   7   9
  16P LOSS WILD-TYPE 308  18  10  26
D69V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0               55                308
  R1                5                 18
  R2                7                 10
  RX                9                 26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P LOSS MUTATED                                  0     2
  16P LOSS WILD-TYPE                                4    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  16P LOSS MUTATED                          26
  16P LOSS WILD-TYPE                        75
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16P LOSS MUTATED                                           2    60
  16P LOSS WILD-TYPE                                         7   306
D69V6, multiclass
                                           clus
vv                                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    2                 18
  BLACK OR AFRICAN AMERICAN                               26                 75
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                2                  7
  WHITE                                                   60                306
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     3  66
  16P LOSS WILD-TYPE  11 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3   66
  16P LOSS WILD-TYPE   11  301
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 11
  NOT HISPANIC OR LATINO               66                301
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED   110  25
  16Q LOSS WILD-TYPE 347  44
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               135                391 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                25                 44 
$`16Q LOSS MUTATED`
TCGA-5B-A90C TCGA-A5-A0GG TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R7 TCGA-A5-A1OG 
       36.69        87.32        65.75        60.53        17.59        11.44 
TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N 
       36.33        91.04        28.64         7.33         1.18        14.43 
TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3EM TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3TW 
       29.39        34.16        22.26        21.21        10.19        16.87 
TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 
       20.78        21.99        57.80        45.53        36.89        48.79 
TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AX-A05U TCGA-AX-A06B 
        3.39        97.71        46.78        21.90        29.69        53.92 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       28.54        37.78        16.96        15.25        20.28        12.43 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 
       76.83        72.56        25.12        36.39        11.08        30.12 
TCGA-AX-A2H5 TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FW 
       71.24        46.49        19.36         2.96        64.93         0.56 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 
       43.82         0.20        20.52         1.38         0.30         0.26 
TCGA-AX-A3GI TCGA-B5-A0JT TCGA-B5-A0K6 TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11G 
        0.39        43.13        13.74        17.85         4.11       113.36 
TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3FD 
       75.72        36.82       102.31        11.87        12.79        33.11 
TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BG-A0M8 TCGA-BG-A0MU TCGA-BG-A0VT TCGA-BG-A0VW 
       29.65        34.95        36.49        20.28        24.39        16.34 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A18C TCGA-BG-A2AE TCGA-BG-A3PP TCGA-BK-A0CC 
       12.56        13.78        15.45        23.70         6.81        10.22 
TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A16G TCGA-D1-A16J 
       16.64        61.87        49.55        22.55        27.42        29.92 
TCGA-D1-A16N TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A17R TCGA-D1-A1NU TCGA-D1-A1NW 
       31.07        14.73        28.08        11.15        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DI-A1NN 
       18.25         2.07         4.27         4.11        16.93        35.38 
TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
        9.37        31.10       110.10        48.36        10.92        37.71 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU 
       51.42        19.40        34.39        27.16        26.96        22.26 
TCGA-EO-A3KW TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A2OQ 
       16.34         6.90        17.62        12.59        14.40        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-FI-A2CY TCGA-FI-A2EU 
       27.35        13.84        11.38        17.92        41.06        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A3PV TCGA-FI-A3PX TCGA-KJ-A3U4 
       59.01         9.07        28.93        41.06        45.01         2.43 
TCGA-KP-A3VZ TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A915 
       23.74        26.10        18.21        23.24        23.97         7.00 
TCGA-QS-A8F1 TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44         0.07         0.23 

$`16Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI 
       17.85        32.78       112.54       105.37        74.10        57.53 
TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       23.21        68.65        19.96        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 
       42.35        15.95         7.92         9.60         8.02        46.32 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
        5.33         5.16        14.96        10.26         0.39        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
        2.40        34.36         1.12         0.76        18.90         1.68 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC 
        1.64        14.66        22.49        17.06        20.81        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       20.65        15.62        15.35        15.95        14.76        16.87 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A053 
       22.32        12.82         2.70         0.13        83.67         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05N TCGA-AP-A05O 
       23.31        86.07         8.22        63.91        23.87        12.20 
TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       20.91       125.42       117.99       110.37        63.16        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       31.73        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       55.89        31.30        35.54        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       10.42        27.85        16.24        36.13         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       19.82        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       66.58        34.98        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       60.66        35.01        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1CE TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A2H2 
       19.20        13.55        20.05        54.12        67.50         4.77 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HG TCGA-AX-A2HH 
       40.80        61.18        81.37        34.32        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3G7 TCGA-AX-A3G8 
       30.74        31.13         0.23         0.20         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU 
       18.35        14.47        80.38        56.91        46.75        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E 
       25.91        27.29        17.88        17.10        11.01         8.71 
TCGA-B5-A11F TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
      185.79        88.34        54.44        45.90        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV 
       18.41        17.36        16.57       191.84        50.89        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       14.70        11.70        15.29       116.25        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX 
       62.14        14.27        41.06        34.13        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98        22.06        38.37 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        39.32        30.81        21.17        15.42        26.66 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A187 
       34.29        52.64        52.83        56.58        14.83        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       14.01        15.45        14.27         1.81         9.57        20.02 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 
       20.12        11.31        35.90        34.98         6.21        10.16 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       31.76        24.99        24.13        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        85.55        78.21         4.80        77.95 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        67.20        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       62.79        63.58        63.16        66.48        16.83        19.79 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16I 
       36.10        37.32        36.36        37.51        36.79        11.51 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X 
       33.63        10.65         0.69        18.67         3.95         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
       17.49        19.53         6.64        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L 
        7.00         0.99        30.44         1.28        28.01        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
       10.22         1.51         1.78        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
        1.41        16.87        18.02        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-DF-A2KV 
        3.52        41.42         8.48        44.88         0.26        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 
       12.39        23.38        17.06         2.37         6.67        27.32 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S 
       16.04         7.36        16.80        49.15        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AU TCGA-EO-A3AV 
       66.90        46.26        57.60        51.52        26.43        35.15 
TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       17.19        17.88        14.53        24.89         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ 
       23.90        22.78        13.97        19.27        18.84        17.88 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       15.09        16.11        12.43        15.81        11.08         6.48 
TCGA-EY-A1H0 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       19.33        10.19        18.87        22.82        20.05        45.76 
TCGA-EY-A2OP TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D 
       31.04        14.14        19.89        14.70        16.96         5.88 
TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       40.01        39.88        39.95         7.99        13.84         8.98 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ 
       28.96        25.02        29.23         1.74         7.76        14.04 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 
       13.28         9.47        15.45        12.92        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI 
       18.84        39.95        12.92        23.64        14.83        14.07 
TCGA-SJ-A6ZJ 
       18.28 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.07               0.13 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            113.36             191.84 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             22.26              23.47 
[1] "0.1 - 113.4 (22.3)" "0.1 - 191.8 (23.5)"
[1] "hr=" "1.8"
D70V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  16Q LOSS MUTATED                                        55
  16Q LOSS WILD-TYPE                                     340
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  16Q LOSS MUTATED                               7
  16Q LOSS WILD-TYPE                            14
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  16Q LOSS MUTATED                                  74
  16Q LOSS WILD-TYPE                                38
D70V3, multiclass
                                         clus
vv                                        16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               55                340
  MIXED SEROUS AND ENDOMETRIOID                          7                 14
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     74                 38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V4, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    27 109
  16Q LOSS WILD-TYPE 114 278
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     27  109
  16Q LOSS WILD-TYPE  114  278
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                27                114
  YES              109                278
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16Q LOSS MUTATED    79   8   8  12
  16Q LOSS WILD-TYPE 284  15   9  23
D70V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0               79                284
  R1                8                 15
  R2                8                  9
  RX               12                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q LOSS MUTATED                                  1     2
  16Q LOSS WILD-TYPE                                3    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  16Q LOSS MUTATED                          37
  16Q LOSS WILD-TYPE                        64
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16Q LOSS MUTATED                                           2    85
  16Q LOSS WILD-TYPE                                         7   281
D70V6, multiclass
                                           clus
vv                                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  3
  ASIAN                                                    2                 18
  BLACK OR AFRICAN AMERICAN                               37                 64
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                2                  7
  WHITE                                                   85                281
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     3  95
  16Q LOSS WILD-TYPE  11 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3   95
  16Q LOSS WILD-TYPE   11  272
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 11
  NOT HISPANIC OR LATINO               95                272
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    97  27
  17P LOSS WILD-TYPE 360  42
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               124                402 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                27                 42 
$`17P LOSS MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 
       41.06        36.69        65.75        60.53        36.82        19.96 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M 
       11.44        36.33        91.04        28.64         7.33         1.18 
TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EM 
       14.43         0.39        34.16         1.12        18.90        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A053 
       17.06        21.21        10.19        16.87        16.87         5.95 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LH 
       63.91        57.80        45.53        48.79       125.42        36.36 
TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A06B TCGA-AX-A0IU 
       97.71        46.78        36.13         0.56        53.92        28.54 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CF TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 
       16.96        13.55        76.83        11.08         4.77        71.24 
TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A2HH TCGA-AX-A2IO TCGA-AX-A3FW TCGA-AX-A3FX 
       61.18        19.36        17.75        64.93         0.56        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
        0.20        20.52         1.38         0.30         0.26         0.30 
TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A11N TCGA-B5-A1MS TCGA-B5-A1MY 
       17.85         4.11        75.72        43.96       102.31        11.87 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-BG-A0M6 TCGA-BG-A0M8 
       12.79       116.25        33.11        29.65        22.06        36.49 
TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A139 TCGA-BK-A26L TCGA-BS-A0U9 TCGA-BS-A0V8 
       15.45         6.81        10.16        24.13        67.20        49.55 
TCGA-D1-A0ZP TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16N 
       29.95        22.55        39.48        37.32        11.51        31.07 
TCGA-D1-A16S TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A3DH TCGA-D1-A3JP 
       18.67        13.22         0.72        18.25         4.11        16.93 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LZ TCGA-E6-A8L9 
       35.38         9.37        12.39        31.10        48.36        27.32 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CH TCGA-EO-A3KU TCGA-EO-A3KW 
       10.92        49.15        37.71        19.40        22.26        16.34 
TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GW 
        4.54        23.90         6.90        17.62        15.09        11.08 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A54A 
       12.59        10.19        29.10        11.38        17.92        14.70 
TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX 
       41.06        39.95        28.93        25.02        41.06        45.01 
TCGA-JU-AAVI TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A5BC 
        7.76         2.43        23.74        13.28        18.21        23.24 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A8F1 
       23.97        12.92         7.00         4.44 

$`17P LOSS WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
       10.29       106.88       149.56        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       32.78       112.54       105.37        87.32        74.10        57.53 
TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       60.53        46.55        38.37        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       68.65        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K5 
       15.95         7.92         9.60         8.02        46.32         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
        5.16        14.96        10.26        19.79        29.39         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
       34.36         0.76         1.68         1.64        14.66        22.49 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       20.81        36.99        20.65        15.62        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW 
       14.76        22.32        12.82        20.78         2.70         0.13 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05J 
       83.67        21.99        23.31        86.07         8.22        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       23.87        12.20        20.91       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       63.16        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       60.36        55.89        31.30        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AX-A05S 
       30.90        10.42        27.85        16.24        21.90        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       45.99        66.58        34.98        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        35.01        37.78        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       65.88        13.28        19.20        15.25        20.28        12.43 
TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       20.05        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG 
       30.12        40.80        81.37        34.32        46.49        26.33 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3G8 
       30.74         2.96        31.13         0.23         0.20         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       18.35        14.47         0.39        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        27.29        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.10        11.01         8.71       185.79       113.36        88.34 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        45.90        40.50        36.82        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       16.57       191.84        50.89        14.40        14.70        11.70 
TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC 
       15.29        96.30        78.81        62.14        14.27        41.06 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       34.13        34.95        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       35.21        34.98        38.37        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        52.64        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 
       13.78        14.73        14.01        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 
        9.57        20.02        23.70        20.12        11.31        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD 
       34.98         6.21        10.22        31.76        24.99        16.64 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        23.47        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41        88.34        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI 
       72.72        73.25        59.51        62.79        63.58        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        19.79         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W 
       28.67        23.93         1.74         4.44        21.99        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       15.72        36.10        36.36        37.51        36.79        27.42 
TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X 
       29.92        33.63        10.65         0.69         3.95         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
       17.49        19.53         6.64        30.15        18.02        14.73 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NY TCGA-D1-A1NZ 
       24.30         2.33        22.92         1.41        16.87        18.02 
TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 
        2.07        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KV TCGA-DF-A2KY 
        8.48        44.88         0.26         4.27        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QY 
       27.16        16.31        39.29        36.62        24.30       110.10 
TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       23.38        17.06         2.37         6.67        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       16.80        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       51.52        51.42        34.39        26.43        35.15        17.19 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 
       27.16        17.88        26.96        14.53        24.89         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       14.99        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GT 
       22.78        13.97        19.27        18.84        17.88        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A214 TCGA-EY-A215 
       12.43        15.81         6.48        19.33        14.40        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX 
       22.82        20.05        45.76        31.04        27.35        13.84 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 
       14.14        19.89        16.96         5.88        40.01        39.88 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
        7.99        13.84         8.98        96.69        59.01         9.07 
TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-KP-A3W3 
       28.96        29.23         1.74        14.04         9.47        26.10 
TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       15.45        11.24         6.97        18.84        39.95        12.92 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       23.64        14.83        14.07        18.28         0.07         0.23 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.20               0.07 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            125.42             191.84 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             20.24              23.90 
[1] "0.2 - 125.4 (20.2)" "0.1 - 191.8 (23.9)"
[1] "hr=" "2.3"
D71V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  17P LOSS MUTATED                                        44
  17P LOSS WILD-TYPE                                     351
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  17P LOSS MUTATED                               9
  17P LOSS WILD-TYPE                            12
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  17P LOSS MUTATED                                  72
  17P LOSS WILD-TYPE                                40
D71V3, multiclass
                                         clus
vv                                        17P LOSS MUTATED 17P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               44                351
  MIXED SEROUS AND ENDOMETRIOID                          9                 12
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     72                 40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V4, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    28  97
  17P LOSS WILD-TYPE 113 290
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     28   97
  17P LOSS WILD-TYPE  113  290
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                28                113
  YES               97                290
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17P LOSS MUTATED    79   8   6  10
  17P LOSS WILD-TYPE 284  15  11  25
D71V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0               79                284
  R1                8                 15
  R2                6                 11
  RX               10                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P LOSS MUTATED                                  1     1
  17P LOSS WILD-TYPE                                3    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  17P LOSS MUTATED                          35
  17P LOSS WILD-TYPE                        66
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17P LOSS MUTATED                                           3    77
  17P LOSS WILD-TYPE                                         6   289
D71V6, multiclass
                                           clus
vv                                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  3
  ASIAN                                                    1                 19
  BLACK OR AFRICAN AMERICAN                               35                 66
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                3                  6
  WHITE                                                   77                289
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     4  88
  17P LOSS WILD-TYPE  10 279
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4   88
  17P LOSS WILD-TYPE   10  279
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 10
  NOT HISPANIC OR LATINO               88                279
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    68  20
  17Q LOSS WILD-TYPE 389  49
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                88                438 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                20                 49 
$`17Q LOSS MUTATED`
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 
       65.75        60.53        19.96        11.44        36.33        91.04 
TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QM TCGA-AJ-A3BD 
        7.33         1.18        14.43         0.39        29.39        34.16 
TCGA-AJ-A3BI TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3TW 
       18.90        22.26        17.06        21.21        10.19        16.87 
TCGA-AP-A053 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 
        5.95        63.91        57.80        45.53        48.79       125.42 
TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A1CR TCGA-AX-A2H5 
       97.71        46.78        36.13         0.56        11.08        71.24 
TCGA-AX-A2H8 TCGA-AX-A2HH TCGA-AX-A2IO TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
       61.18        17.75        64.93        43.82         0.20        20.52 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-B5-A11N TCGA-B5-A1MS TCGA-B5-A3F9 
        0.30         0.26         0.30        43.96       102.31       116.25 
TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-BG-A0M8 TCGA-BG-A18C TCGA-BK-A139 TCGA-BK-A26L 
       33.11        29.65        36.49        15.45        10.16        24.13 
TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16N 
       67.20        49.55        22.55        37.32        11.51        31.07 
TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A3DH TCGA-DI-A1NO 
       14.73        13.22         0.72        18.25         4.11         9.37 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       12.39        31.10        48.36        27.32        10.92        49.15 
TCGA-EO-A1Y8 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GR 
       37.71        22.26        16.34         4.54        23.90        17.62 
TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A2OQ TCGA-EY-A547 TCGA-FI-A2CY 
       11.08        12.59        10.19        29.10        17.92        41.06 
TCGA-FI-A2D2 TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-JU-AAVI TCGA-KJ-A3U4 TCGA-KP-A3W0 
       39.95        28.93        25.02         7.76         2.43        13.28 
TCGA-KP-A3W4 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-QS-A8F1 
       18.21        23.97        12.92         4.44 

$`17Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       74.10        57.53        60.53        46.55        38.37        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 
       28.27        20.81        23.21        68.65        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ 
       24.62        29.06        42.35        15.95         7.92         9.60 
TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP 
        8.02        46.32        28.64         5.33         5.16        14.96 
TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG 
       10.26        19.79         2.40        34.36         1.12         0.76 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3IA TCGA-AJ-A3NC 
        1.68         1.64        14.66        22.49        20.81        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       20.65        15.62        15.35        15.95        14.76        16.87 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       22.32        12.82        20.78         2.70         0.13        83.67 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05J TCGA-AP-A05N 
       21.99        23.31        86.07         8.22        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       12.20        20.91       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       60.36        55.89        31.30        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AX-A05S 
       30.90        10.42        27.85        16.24        21.90        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       45.99        66.58        34.98        53.92        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        35.01        28.54        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        65.88        13.28        19.20        16.96 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       13.55        15.25        20.28        12.43        20.05        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H2 
       72.56        54.12        67.50        25.12        36.39         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       30.12        40.80        81.37        34.32        46.49        19.36 
TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT 
       26.33        30.74         2.96        31.13         0.23         0.20 
TCGA-AX-A3FW TCGA-AX-A3G3 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
        0.56         1.38         1.18        18.35        14.47         0.39 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       80.38        56.91        46.75        43.13        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       44.71        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        17.88        13.74        17.10        17.85        11.01 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
        4.11         8.71       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        45.90        40.50        36.82        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       16.57       191.84        50.89        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       11.87        15.29        12.79        96.30        78.81        62.14 
TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       14.27        41.06        34.13        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98        22.06        38.37 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        20.02        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31         6.81        35.90        34.98         6.21 
TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
       10.22        31.76        24.99        16.64        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        23.47        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       59.51        62.79        63.58        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93         1.74         4.44        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       15.72        36.10        36.36        37.51        36.79        27.42 
TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
       29.92        33.63        10.65         0.69        18.67         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NY TCGA-D1-A1NZ 
       24.30         2.33        22.92         1.41        16.87        18.02 
TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 
        2.07        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JP TCGA-DF-A2KV 
        8.48        44.88         0.26         4.27        16.93        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       35.38       110.10        23.38        17.06         2.37         6.67 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       16.04         7.36        16.80        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       46.26        57.60        51.52        51.42        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 
       26.43        35.15        17.19        27.16        17.88        26.96 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       14.53        24.89         6.21        14.99        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       27.16        23.34        23.34        22.78        13.97         6.90 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       19.27        18.84        17.88        15.09        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM 
       15.81         6.48        19.33        14.40        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       20.05        45.76        31.04        27.35        13.84        11.38 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX 
       14.14        19.89        14.70        16.96         5.88        40.01 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       39.88         7.99        13.84         8.98        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR 
        9.07        28.96        29.23        41.06        45.01         1.74 
TCGA-K6-A3WQ TCGA-KP-A3VZ TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A5BC TCGA-PG-A6IB 
       14.04        23.74         9.47        26.10        23.24        15.45 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        7.00        11.24         6.97        18.84        39.95        12.92 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       23.64        14.83        14.07        18.28         0.07         0.23 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.20               0.07 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            125.42             191.84 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            21.735             23.470 
[1] "0.2 - 125.4 (21.7)" "0.1 - 191.8 (23.5)"
[1] "hr=" "2.1"
D72V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  17Q LOSS MUTATED                                        35
  17Q LOSS WILD-TYPE                                     360
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  17Q LOSS MUTATED                               7
  17Q LOSS WILD-TYPE                            14
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  17Q LOSS MUTATED                                  47
  17Q LOSS WILD-TYPE                                65
D72V3, multiclass
                                         clus
vv                                        17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               35                360
  MIXED SEROUS AND ENDOMETRIOID                          7                 14
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     47                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V4, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    19  70
  17Q LOSS WILD-TYPE 122 317
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     19   70
  17Q LOSS WILD-TYPE  122  317
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                19                122
  YES               70                317
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS MUTATED    59   6   3   7
  17Q LOSS WILD-TYPE 304  17  14  28
D72V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0               59                304
  R1                6                 17
  R2                3                 14
  RX                7                 28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q LOSS MUTATED                                  1     1
  17Q LOSS WILD-TYPE                                3    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  17Q LOSS MUTATED                          18
  17Q LOSS WILD-TYPE                        83
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17Q LOSS MUTATED                                           3    59
  17Q LOSS WILD-TYPE                                         6   307
D72V6, multiclass
                                           clus
vv                                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  3
  ASIAN                                                    1                 19
  BLACK OR AFRICAN AMERICAN                               18                 83
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                3                  6
  WHITE                                                   59                307
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     5  60
  17Q LOSS WILD-TYPE   9 307
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      5   60
  17Q LOSS WILD-TYPE    9  307
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  9
  NOT HISPANIC OR LATINO               60                307
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    42   7
  18P LOSS WILD-TYPE 415  62
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                49                477 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 7                 62 
$`18P LOSS MUTATED`
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R7 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LO 
       65.75        60.53        17.59        46.32        28.64         7.33 
TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A2QM TCGA-AJ-A3BF TCGA-AP-A05H TCGA-AP-A0LH 
       14.96         1.18        29.39         1.12        45.53        36.36 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
       11.08         4.77        71.24         0.20        20.52         1.38 
TCGA-B5-A11P TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A139 
       36.82       116.25        33.11        15.45         6.81        10.16 
TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A16I TCGA-D1-A16S 
       16.64        61.87        49.55        22.55        11.51        18.67 
TCGA-D1-A17K TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-DI-A2QU TCGA-EO-A2CG TCGA-EO-A3KW 
       28.08         0.72         2.07        31.10        51.42        16.34 
TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A214 
        4.54        19.27        18.84        15.09        11.08        14.40 
TCGA-EY-A2OO TCGA-EY-A3QX TCGA-FI-A2EW TCGA-FI-A2EX TCGA-KP-A3VZ TCGA-KP-A3W0 
       45.76        13.84        59.01         9.07        23.74        13.28 
TCGA-SL-A6J9 
        0.07 

$`18P LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       74.10        57.53        60.53        46.55        38.37        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 
       28.27        20.81        23.21        68.65        19.96        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95         7.92        11.44 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K5 TCGA-A5-A2K7 
       36.33         9.60         8.02        91.04         5.33         5.16 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       14.43        10.26         0.39        19.79         2.40        34.36 
TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
       34.16         0.76        18.90         1.68         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE 
       22.49        22.26        17.06        20.81        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       21.21        15.62        10.19        15.35        15.95        14.76 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
       16.87        16.87        22.32        12.82        20.78         2.70 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        0.13        83.67        21.99         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
        8.22        63.91        57.80        36.89        23.87        12.20 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       63.16        97.71        31.73        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       33.40        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        60.36        55.89        31.30        35.54        46.78 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        30.90        10.42        27.85        16.24 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       21.90        36.13         0.56        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       34.98        53.92        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       60.66        35.01        28.54        37.78        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       65.88        13.28        19.20        16.96        13.55        15.25 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       20.28        12.43        20.05        76.83        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2H8 
       67.50        25.12        36.39        30.12        40.80        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       81.37        34.32        46.49        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       30.74         2.96        31.13        64.93         0.23         0.20 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.56        43.82         0.30         0.26         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       18.35        14.47         0.39        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        27.29        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F 
       17.10        17.85        11.01         4.11         8.71       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       40.50        32.09        33.50        27.35        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS 
       19.50        18.41        17.36        16.57       191.84       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        14.40        14.70        11.70        11.87        15.29 
TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 
       12.79        96.30        78.81        62.14        14.27        29.65 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       41.06        34.13        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98        22.06        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        20.02        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       20.12        11.31        35.90        34.98         6.21        10.22 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       31.76        24.99        24.13        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        85.55        78.21         4.80        77.95 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        67.20        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       62.79        63.58        63.16        66.48        16.83        19.79 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       36.10        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V 
       29.92        31.07        33.63        10.65         0.69         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.01        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX 
       24.30         2.33        22.92         1.41        13.22        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       16.87        18.02        15.06         1.05         3.95         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
       41.42         8.48        44.88         0.26         4.27         4.11 
TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
       16.93        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY 
       36.62        24.30        35.38         9.37        12.39       110.10 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 
       23.38        48.36        17.06         2.37         6.67        27.32 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       16.04         7.36        16.80        10.92        49.15        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       19.40        34.39        26.43        35.15        17.19        27.16 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 
       17.88        26.96        22.26        14.53        24.89         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       14.99        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GQ TCGA-EY-A1GR 
       23.90        22.78        13.97         6.90        17.88        17.62 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       16.11        12.43        15.81         6.48        19.33        12.59 
TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A2OQ 
       10.19        18.87        22.82        20.05        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       27.35        11.38        17.92        14.14        19.89        14.70 
TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
       16.96         5.88        40.01        41.06        39.88        39.95 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A2F4 
        7.99        13.84         8.98        96.69        28.93        28.96 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
       25.02        29.23        41.06        45.01         1.74         7.76 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
       14.04         2.43         9.47        26.10        18.21        23.24 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 
       15.45        23.97        12.92         7.00        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 
       18.84        39.95        12.92        23.64        14.83         4.44 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       14.07        18.28         0.23 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.07               0.13 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            116.25             191.84 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             17.59              23.70 
[1] "0.1 - 116.2 (17.6)" "0.1 - 191.8 (23.7)"
[1] "hr=" "1.3"
D73V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  18P LOSS MUTATED                                        24
  18P LOSS WILD-TYPE                                     371
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  18P LOSS MUTATED                               5
  18P LOSS WILD-TYPE                            16
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  18P LOSS MUTATED                                  21
  18P LOSS WILD-TYPE                                91
D73V3, multiclass
                                         clus
vv                                        18P LOSS MUTATED 18P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               24                371
  MIXED SEROUS AND ENDOMETRIOID                          5                 16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     21                 91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V4, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     9  41
  18P LOSS WILD-TYPE 132 346
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      9   41
  18P LOSS WILD-TYPE  132  346
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 9                132
  YES               41                346
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18P LOSS MUTATED    31   5   1   4
  18P LOSS WILD-TYPE 332  18  16  31
D73V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0               31                332
  R1                5                 18
  R2                1                 16
  RX                4                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P LOSS MUTATED                                  0     1
  18P LOSS WILD-TYPE                                4    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  18P LOSS MUTATED                           9
  18P LOSS WILD-TYPE                        92
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18P LOSS MUTATED                                           1    37
  18P LOSS WILD-TYPE                                         8   329
D73V6, multiclass
                                           clus
vv                                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    1                 19
  BLACK OR AFRICAN AMERICAN                                9                 92
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   37                329
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     1  38
  18P LOSS WILD-TYPE  13 329
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      1   38
  18P LOSS WILD-TYPE   13  329
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 13
  NOT HISPANIC OR LATINO               38                329
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    53   9
  18Q LOSS WILD-TYPE 404  60
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                62                464 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 9                 60 
$`18Q LOSS MUTATED`
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A2K3 
       65.75        60.53        36.82        17.59        11.44        46.32 
TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AJ-A3BF 
       28.64         7.33        14.96         1.18        34.16         1.12 
TCGA-AP-A05H TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AX-A1CA TCGA-AX-A1CR TCGA-AX-A2H2 
       45.53        36.36        97.71        20.28        11.08         4.77 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A11P 
        0.20        20.52         1.38         0.30         0.39        36.82 
TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OE TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A0CC 
      116.25        33.11        34.95        15.45         6.81        10.22 
TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A169 TCGA-D1-A16S 
       10.16        16.64        49.55        22.55        37.32        18.67 
TCGA-D1-A16V TCGA-D1-A17K TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-D1-A3DH TCGA-D1-A3JP 
        3.95        28.08         0.72         2.07         4.11        16.93 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A2CG TCGA-EY-A1GC TCGA-EY-A1GO 
       31.10       110.10        48.36        51.42         4.54        19.27 
TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OO 
       18.84        15.09        11.08        14.40        20.05        45.76 
TCGA-EY-A3QX TCGA-FI-A2CY TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A3PX TCGA-KP-A3VZ 
       13.84        41.06        59.01         9.07        45.01        23.74 
TCGA-KP-A3W0 TCGA-SL-A6J9 
       13.28         0.07 

$`18Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        57.53        60.53        46.55        38.37        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 
       20.81        23.21        68.65        19.96        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ 
       29.06        42.35        15.95         7.92        36.33         9.60 
TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23N TCGA-AJ-A23O 
        8.02        91.04         5.33         5.16        14.43        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG 
        0.39        19.79        29.39         2.40        34.36         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       18.90         1.68         1.64        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       17.06        20.81        36.99        20.65        21.21        15.62 
TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW 
       10.19        15.35        15.95        14.76        16.87        16.87 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       22.32        12.82        20.78         2.70         0.13        83.67 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
       21.99         5.95        23.31        86.07         8.22        63.91 
TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 
       57.80        36.89        23.87        12.20        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LJ 
      125.42       117.99       110.37         3.39        63.16        31.73 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       83.97        27.12        82.52        33.40        61.64        80.78 
TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        46.78        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
       10.42        27.85        16.24        21.90        36.13         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D 
       35.34        45.99        66.58        34.98        53.92        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       51.09        27.39        30.02        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       16.96        13.55        15.25        12.43        20.05        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H4 
       72.56        54.12        67.50        25.12        36.39        30.12 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       71.24        40.80        61.18        81.37        34.32        46.49 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       19.36        26.33        17.75        30.74         2.96        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G6 
       64.93         0.23         0.20         0.56        43.82         0.26 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR 
        0.30         1.18        18.35        14.47        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       46.75        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        27.29        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E 
       13.74        17.10        17.85        11.01         4.11         8.71 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L 
      185.79       113.36        88.34        75.72        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       43.96        40.50        32.09        33.50        27.35        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       191.84 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      102.31        50.89        14.40        14.70        11.70        11.87 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH 
       15.29        12.79        96.30        78.81        62.14        14.27 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       29.65        41.06        34.13        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98        22.06        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        20.02        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B 
       20.12        11.31        35.90        34.98         6.21        31.76 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.99        24.13        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        67.20        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       62.79        63.58        63.16        66.48        16.83        19.79 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I 
       36.10        36.36        37.51        36.79        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X 
       29.92        31.07        33.63        10.65         0.69         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
       17.49        19.53         6.64        30.15        18.02        14.73 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1NY 
        2.33        22.92         1.41        13.22        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 
       18.02        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KV TCGA-DF-A2KY 
        8.48        44.88         0.26         4.27        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
       27.16        16.31        39.29        36.62        24.30        35.38 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
        9.37        12.39        23.38        17.06         2.37         6.67 
TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       27.32        16.04         7.36        16.80        10.92        49.15 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       37.71        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       51.52        19.40        34.39        26.43        35.15        17.19 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX 
       27.16        17.88        26.96        22.26        16.34        14.53 
TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       24.89         6.21        14.99        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       23.34        23.34        23.90        22.78        13.97         6.90 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX 
       17.88        17.62        16.11        12.43        15.81         6.48 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OP 
       19.33        12.59        10.19        18.87        22.82        31.04 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       29.10        27.35        11.38        17.92        14.14        19.89 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D2 
       14.70        16.96         5.88        40.01        39.88        39.95 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A2F4 
        7.99        13.84         8.98        96.69        28.93        28.96 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ 
       25.02        29.23        41.06         1.74         7.76        14.04 
TCGA-KJ-A3U4 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
        2.43         9.47        26.10        18.21        23.24        15.45 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       23.97        12.92         7.00        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       39.95        12.92        23.64        14.83         4.44        14.07 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.07               0.13 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            116.25             191.84 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            18.755             23.785 
[1] "0.1 - 116.2 (18.8)" "0.1 - 191.8 (23.8)"
[1] "hr=" "1.3"
D74V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  18Q LOSS MUTATED                                        27
  18Q LOSS WILD-TYPE                                     368
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  18Q LOSS MUTATED                               6
  18Q LOSS WILD-TYPE                            15
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  18Q LOSS MUTATED                                  30
  18Q LOSS WILD-TYPE                                82
D74V3, multiclass
                                         clus
vv                                        18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               27                368
  MIXED SEROUS AND ENDOMETRIOID                          6                 15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     30                 82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V4, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    12  51
  18Q LOSS WILD-TYPE 129 336
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     12   51
  18Q LOSS WILD-TYPE  129  336
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                12                129
  YES               51                336
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18Q LOSS MUTATED    38   5   3   6
  18Q LOSS WILD-TYPE 325  18  14  29
D74V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0               38                325
  R1                5                 18
  R2                3                 14
  RX                6                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q LOSS MUTATED                                  0     2
  18Q LOSS WILD-TYPE                                4    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  18Q LOSS MUTATED                          17
  18Q LOSS WILD-TYPE                        84
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18Q LOSS MUTATED                                           2    41
  18Q LOSS WILD-TYPE                                         7   325
D74V6, multiclass
                                           clus
vv                                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    2                 18
  BLACK OR AFRICAN AMERICAN                               17                 84
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                2                  7
  WHITE                                                   41                325
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     2  49
  18Q LOSS WILD-TYPE  12 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      2   49
  18Q LOSS WILD-TYPE   12  318
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 12
  NOT HISPANIC OR LATINO               49                318
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    44  15
  19P LOSS WILD-TYPE 413  54
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                59                467 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                15                 54 
$`19P LOSS MUTATED`
TCGA-2E-A9G8 TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A1OG TCGA-A5-A2K3 TCGA-A5-A2K4 
       41.06        65.75        60.53        11.44        46.32        28.64 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3BF 
        7.33        14.96         1.18        14.43        34.16         1.12 
TCGA-AJ-A3EJ TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A3K1 TCGA-AX-A1CA TCGA-AX-A1CF 
        1.64        63.91        45.53        21.90        20.28        76.83 
TCGA-AX-A2H5 TCGA-AX-A2HK TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G6 TCGA-AX-A3G7 
       71.24         2.96         0.20         1.38         0.26         0.30 
TCGA-AX-A3GI TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MU TCGA-B5-A3F9 
        0.39         4.11        75.72        36.82        50.89       116.25 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A18C TCGA-BS-A0U9 TCGA-D1-A15V TCGA-D1-A16G 
       22.06        36.49        15.45        67.20        39.48        27.42 
TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A3JP TCGA-DI-A2QT TCGA-E6-A8L9 TCGA-EO-A1Y8 
       11.51        31.07        16.93        12.39        27.32        37.71 
TCGA-EO-A2CH TCGA-EY-A1GP TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A214 TCGA-EY-A3L3 
       19.40        18.84        15.81        11.08        14.40        27.35 
TCGA-EY-A3QX TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY 
       13.84        41.06        39.95        96.69         9.07        28.93 
TCGA-JU-AAVI TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-PG-A914 TCGA-QS-A8F1 
        7.76         2.43        23.74        12.92         4.44 

$`19P LOSS WILD-TYPE`
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       36.69        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       57.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH 
       24.62        29.06        42.35        15.95         7.92        36.33 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23O 
        9.60         8.02        91.04         5.33         5.16        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG 
        0.39        19.79        29.39         2.40        34.36         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
       18.90         1.68        14.66        22.49        22.26        17.06 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH 
       20.81        36.99        20.65        21.21        15.62        10.19 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV 
       15.35        15.95        14.76        16.87        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       12.82        20.78         2.70         0.13        83.67        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05D TCGA-AP-A05J 
        5.95        23.31        86.07         8.22        57.80        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       23.87        12.20        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      110.37         3.39        63.16        36.36        97.71        31.73 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       83.97        27.12        82.52        33.40        61.64        80.78 
TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        46.78        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       10.42        27.85        16.24        36.13         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       45.99        66.58        34.98        53.92        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        35.01        28.54        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        65.88        13.28        19.20        16.96 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       13.55        15.25        12.43        20.05        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 
       67.50        25.12        36.39        11.08         4.77        30.12 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       40.80        61.18        81.37        34.32        46.49        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       26.33        17.75        30.74        31.13        64.93         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G8 
        0.20         0.56        43.82        20.52         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       18.35        14.47        80.38        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        27.29        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.85        11.01         8.71       185.79       113.36        88.34 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        45.90        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       16.57       191.84       102.31        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       11.87        15.29        12.79        96.30        78.81        62.14 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       33.11        14.27        29.65        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        34.98 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       43.30        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       14.01        15.45        14.27         1.81         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31         6.81        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
        6.21        10.22        10.16        31.76        24.99        24.13 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       16.64        13.18        10.03         9.86        46.95        23.47 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       96.49        30.74        97.41        88.34        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        72.72        73.25        59.51        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       49.55        63.16        66.48        16.83        19.79        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74         4.44        21.99        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16J TCGA-D1-A16O 
       37.32        36.36        37.51        36.79        29.92        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       10.65         0.69        18.67         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
        2.33        22.92         1.41        13.22         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.52        41.42         8.48        44.88         0.26         4.27 
TCGA-D1-A3DH TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
        4.11        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY 
       36.62        24.30        35.38         9.37        31.10       110.10 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       23.38        48.36        17.06         2.37         6.67        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S 
        7.36        16.80        10.92        49.15        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AS 
       66.90        46.26        57.60        51.52        51.42        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 
       26.43        35.15        17.19        27.16        17.88        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       22.26        16.34        14.53        24.89         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GQ 
       23.90        22.78        13.97         6.90        19.27        17.88 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GX TCGA-EY-A1H0 
       17.62        15.09        16.11        12.43         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       12.59        10.19        18.87        22.82        20.05        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       31.04        29.10        11.38        17.92        14.14        19.89 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D4 
       14.70        16.96         5.88        40.01        39.88         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 
       13.84         8.98        59.01        28.96        25.02        29.23 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 
       41.06        45.01         1.74        14.04        13.28         9.47 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A915 
       26.10        18.21        23.24        15.45        23.97         7.00 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       11.24         6.97        18.84        39.95        12.92        23.64 
TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83        14.07        18.28         0.07         0.23 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.20               0.07 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            116.25             191.84 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             20.28              23.47 
[1] "0.2 - 116.2 (20.3)" "0.1 - 191.8 (23.5)"
[1] "hr=" "2.4"
D75V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  19P LOSS MUTATED                                        18
  19P LOSS WILD-TYPE                                     377
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  19P LOSS MUTATED                               4
  19P LOSS WILD-TYPE                            17
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  19P LOSS MUTATED                                  37
  19P LOSS WILD-TYPE                                75
D75V3, multiclass
                                         clus
vv                                        19P LOSS MUTATED 19P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               18                377
  MIXED SEROUS AND ENDOMETRIOID                          4                 17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     37                 75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V4, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    14  45
  19P LOSS WILD-TYPE 127 342
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     14   45
  19P LOSS WILD-TYPE  127  342
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                14                127
  YES               45                342
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19P LOSS MUTATED    34   4   4   5
  19P LOSS WILD-TYPE 329  19  13  30
D75V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0               34                329
  R1                4                 19
  R2                4                 13
  RX                5                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P LOSS MUTATED                                  1     1
  19P LOSS WILD-TYPE                                3    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  19P LOSS MUTATED                          14
  19P LOSS WILD-TYPE                        87
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19P LOSS MUTATED                                           1    39
  19P LOSS WILD-TYPE                                         8   327
D75V6, multiclass
                                           clus
vv                                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  3
  ASIAN                                                    1                 19
  BLACK OR AFRICAN AMERICAN                               14                 87
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   39                327
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     3  41
  19P LOSS WILD-TYPE  11 326
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3   41
  19P LOSS WILD-TYPE   11  326
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 11
  NOT HISPANIC OR LATINO               41                326
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    41  15
  19Q LOSS WILD-TYPE 416  54
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                56                470 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                15                 54 
$`19Q LOSS MUTATED`
TCGA-2E-A9G8 TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M 
       41.06        65.75        60.53        28.64         7.33         1.18 
TCGA-AJ-A23N TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ 
       14.43        29.39        34.16         1.12        18.90         1.64 
TCGA-AJ-A3NF TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A0L9 TCGA-AP-A0LH TCGA-AP-A3K1 
       21.21        63.91        45.53       125.42        36.36        21.90 
TCGA-AX-A2H5 TCGA-AX-A2HK TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G6 TCGA-AX-A3G7 
       71.24         2.96         0.20         1.38         0.26         0.30 
TCGA-AX-A3GI TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A3F9 
        0.39        75.72        36.82       102.31        50.89       116.25 
TCGA-BG-A0M8 TCGA-BG-A18C TCGA-BG-A3PP TCGA-BS-A0U9 TCGA-D1-A16G TCGA-D1-A16I 
       36.49        15.45         6.81        67.20        27.42        11.51 
TCGA-D1-A16N TCGA-D1-A3JP TCGA-DI-A2QT TCGA-E6-A8L9 TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       31.07        16.93        12.39        27.32        49.15        37.71 
TCGA-EO-A2CH TCGA-EY-A1GJ TCGA-EY-A1GW TCGA-EY-A214 TCGA-EY-A3L3 TCGA-EY-A3QX 
       19.40        23.90        11.08        14.40        27.35        13.84 
TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       41.06        39.95        96.69         9.07         2.43        23.74 
TCGA-PG-A914 TCGA-QS-A8F1 
       12.92         4.44 

$`19Q LOSS WILD-TYPE`
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       36.69        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       57.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95         7.92        11.44 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K5 
       36.33         9.60         8.02        91.04        46.32         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
        5.16        14.96        10.26         0.39        19.79         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       34.36         0.76         1.68        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3NH 
       17.06        20.81        36.99        20.65        15.62        10.19 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV 
       15.35        15.95        14.76        16.87        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       12.82        20.78         2.70         0.13        83.67        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05D TCGA-AP-A05J 
        5.95        23.31        86.07         8.22        57.80        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        12.20        20.91        48.79       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
        3.39        63.16        97.71        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        55.89        31.30        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       46.78        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       16.24        36.13         0.56        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       34.98        53.92        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       60.66        35.01        28.54        37.78        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       65.88        13.28        19.20        16.96        13.55        15.25 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       20.28        12.43        20.05        76.83        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 
       67.50        25.12        36.39        11.08         4.77        30.12 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       40.80        61.18        81.37        34.32        46.49        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       26.33        17.75        30.74        31.13        64.93         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G8 
        0.20         0.56        43.82        20.52         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       18.35        14.47        80.38        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        27.29        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.85        11.01         4.11         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       88.34        54.44        45.90        43.96        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       33.50        27.35        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       17.36        16.57       191.84        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       11.87        15.29        12.79        96.30        78.81        62.14 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       33.11        14.27        29.65        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       22.06        38.37        28.27        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       23.47        43.30        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       52.64        52.83        56.58        14.83        12.56        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.73        14.01        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA 
       20.02        23.70        20.12        11.31        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
        6.21        10.22        10.16        31.76        24.99        24.13 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       16.64        13.18        10.03         9.86        46.95        23.47 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       96.49        30.74        97.41        88.34        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        72.72        73.25        59.51        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       49.55        63.16        66.48        16.83        19.79        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16J 
       36.10        37.32        36.36        37.51        36.79        29.92 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X 
       33.63        10.65         0.69        18.67         3.95         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
       17.49        19.53         6.64        30.15        18.02        14.73 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW 
       24.30         2.33        22.92         1.41        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
       18.25        16.87        18.02         2.07        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        3.95         3.52        41.42         8.48        44.88         0.26 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        4.27         4.11        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU 
       39.29        36.62        24.30        35.38         9.37        31.10 
TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
      110.10        23.38        48.36        17.06         2.37         6.67 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A22R TCGA-EO-A22S 
       16.04         7.36        16.80        10.92        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AS 
       66.90        46.26        57.60        51.52        51.42        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 
       26.43        35.15        17.19        27.16        17.88        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       22.26        16.34        14.53        24.89         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ 
       22.78        13.97         6.90        19.27        18.84        17.88 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX 
       17.62        15.09        16.11        12.43        15.81         6.48 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
       19.33        12.59        10.19        18.87        22.82        20.05 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 
       45.76        31.04        29.10        11.38        17.92        14.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 
       19.89        14.70        16.96         5.88        40.01        39.88 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EY TCGA-FI-A2F4 
        7.99        13.84         8.98        59.01        28.93        28.96 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
       25.02        29.23        41.06        45.01         1.74         7.76 
TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
       14.04        13.28         9.47        26.10        18.21        23.24 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       15.45        23.97         7.00        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       39.95        12.92        23.64        14.83        14.07        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.20               0.07 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            125.42             191.84 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            23.820             23.325 
[1] "0.2 - 125.4 (23.8)" "0.1 - 191.8 (23.3)"
[1] "hr=" "2.2"
D76V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  19Q LOSS MUTATED                                        18
  19Q LOSS WILD-TYPE                                     377
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  19Q LOSS MUTATED                               4
  19Q LOSS WILD-TYPE                            17
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  19Q LOSS MUTATED                                  34
  19Q LOSS WILD-TYPE                                78
D76V3, multiclass
                                         clus
vv                                        19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               18                377
  MIXED SEROUS AND ENDOMETRIOID                          4                 17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     34                 78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V4, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    11  45
  19Q LOSS WILD-TYPE 130 342
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     11   45
  19Q LOSS WILD-TYPE  130  342
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                11                130
  YES               45                342
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19Q LOSS MUTATED    32   3   3   6
  19Q LOSS WILD-TYPE 331  20  14  29
D76V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0               32                331
  R1                3                 20
  R2                3                 14
  RX                6                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q LOSS MUTATED                                  1     0
  19Q LOSS WILD-TYPE                                3    20
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  19Q LOSS MUTATED                          11
  19Q LOSS WILD-TYPE                        90
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19Q LOSS MUTATED                                           1    39
  19Q LOSS WILD-TYPE                                         8   327
D76V6, multiclass
                                           clus
vv                                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  3
  ASIAN                                                    0                 20
  BLACK OR AFRICAN AMERICAN                               11                 90
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   39                327
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     3  37
  19Q LOSS WILD-TYPE  11 330
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      3   37
  19Q LOSS WILD-TYPE   11  330
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 11
  NOT HISPANIC OR LATINO               37                330
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    15   3
  20P LOSS WILD-TYPE 442  66
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                18                508 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 3                 66 
$`20P LOSS MUTATED`
TCGA-2E-A9G8 TCGA-A5-A0G2 TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-AJ-A3BD TCGA-AP-A05H 
       41.06       149.56        60.53        19.96        34.16        45.53 
TCGA-AP-A0LI TCGA-AW-A1PO TCGA-AX-A1CF TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-B5-A0K8 
       97.71         0.56        76.83        20.52         0.30        17.85 
TCGA-BG-A0M6 TCGA-BG-A0MO TCGA-D1-A3JP TCGA-EY-A1GJ TCGA-EY-A1GW TCGA-FI-A2D2 
       22.06        43.04        16.93        23.90        11.08        39.95 

$`20P LOSS WILD-TYPE`
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
       36.69        10.29       106.88        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       32.78       112.54       105.37        87.32        74.10        57.53 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       65.75        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       20.81        23.21        68.65        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH 
       29.06        42.35        15.95         7.92        11.44        36.33 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
        9.60         8.02        91.04        46.32        28.64         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O 
        5.16         7.33        14.96         1.18        14.43        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF 
        0.39        19.79        29.39         2.40        34.36         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76        18.90         1.68         1.64        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.26        17.06        20.81        36.99        20.65        21.21 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       15.62        10.19        15.35        15.95        14.76        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW 
       16.87        22.32        12.82        20.78         2.70         0.13 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       83.67        21.99         5.95        23.31        86.07         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       63.91        57.80        36.89        23.87        12.20        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       60.36        55.89        31.30        35.54        46.78        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        30.90        10.42        27.85        16.24        21.90 
TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       36.13        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       28.54        37.78        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       19.20        16.96        13.55        15.25        20.28        12.43 
TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       20.05        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       11.08         4.77        30.12        71.24        40.80        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       81.37        34.32        46.49        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       30.74         2.96        31.13        64.93         0.23         0.20 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G6 TCGA-AX-A3G7 
        0.56        43.82         0.20         1.38         0.26         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR 
        1.18        18.35        14.47         0.39        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       46.75        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        27.29        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F 
       13.74        17.10        11.01         4.11         8.71       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       40.50        36.82        32.09        33.50        27.35        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       191.84 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      102.31        50.89        14.40        14.70        11.70        11.87 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       15.29        12.79       116.25        96.30        78.81        62.14 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       33.11        14.27        29.65        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        34.98 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       38.37        36.49        28.27        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.30        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.01        15.45        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 
       20.02        23.70        20.12        11.31         6.81        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       34.98         6.21        10.22        10.16        31.76        24.99 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.13        16.64        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        67.20        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       62.79        63.58        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       36.79        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       10.65         0.69        18.67         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
        2.33        22.92         1.41        13.22         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.52        41.42         8.48        44.88         0.26         4.27 
TCGA-D1-A3DH TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
        4.11        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU 
       36.62        24.30        35.38         9.37        12.39        31.10 
TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
      110.10        23.38        48.36        17.06         2.37         6.67 
TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       27.32        16.04         7.36        16.80        10.92        49.15 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       37.71        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       51.52        51.42        19.40        34.39        26.43        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW 
       17.19        27.16        17.88        26.96        22.26        16.34 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       14.53        24.89         6.21        14.99         4.54        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        22.78        13.97 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS 
        6.90        19.27        18.84        17.88        17.62        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       16.11        12.43        15.81         6.48        19.33        12.59 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       10.19        14.40        18.87        22.82        20.05        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 
       31.04        29.10        27.35        13.84        11.38        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX 
       14.14        19.89        14.70        16.96         5.88        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       41.06        39.88         7.99        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 
       59.01         9.07        28.93        28.96        25.02        29.23 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 
       41.06        45.01         1.74         7.76        14.04         2.43 
TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
       23.74        13.28         9.47        26.10        18.21        23.24 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 
       15.45        23.97        12.92         7.00        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 
       18.84        39.95        12.92        23.64        14.83         4.44 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.07        18.28         0.07         0.23 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.30               0.07 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            149.56             191.84 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            29.030             23.325 
[1] "0.3 - 149.6 (29.0)" "0.1 - 191.8 (23.3)"
[1] "hr=" "1"  
D77V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  20P LOSS MUTATED                                         8
  20P LOSS WILD-TYPE                                     387
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  20P LOSS MUTATED                               1
  20P LOSS WILD-TYPE                            20
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  20P LOSS MUTATED                                   9
  20P LOSS WILD-TYPE                               103
D77V3, multiclass
                                         clus
vv                                        20P LOSS MUTATED 20P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                8                387
  MIXED SEROUS AND ENDOMETRIOID                          1                 20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                      9                103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V4, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     8  10
  20P LOSS WILD-TYPE 133 377
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      8   10
  20P LOSS WILD-TYPE  133  377
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 8                133
  YES               10                377
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20P LOSS MUTATED    12   1   2   0
  20P LOSS WILD-TYPE 351  22  15  35
D77V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0               12                351
  R1                1                 22
  R2                2                 15
  RX                0                 35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P LOSS MUTATED                                  0     1
  20P LOSS WILD-TYPE                                4    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  20P LOSS MUTATED                           3
  20P LOSS WILD-TYPE                        98
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20P LOSS MUTATED                                           1    12
  20P LOSS WILD-TYPE                                         8   354
D77V6, multiclass
                                           clus
vv                                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    1                 19
  BLACK OR AFRICAN AMERICAN                                3                 98
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   12                354
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     1  13
  20P LOSS WILD-TYPE  13 354
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1   13
  20P LOSS WILD-TYPE   13  354
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 13
  NOT HISPANIC OR LATINO               13                354
[1] 2 2
[1] FALSE

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     9   0
  20Q LOSS WILD-TYPE 448  69
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 9                517 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 0                 69 
$`20Q LOSS MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-AJ-A3BD TCGA-AW-A1PO TCGA-D1-A0ZZ 
      149.56        60.53        19.96        34.16         0.56        22.55 
TCGA-D1-A3JP TCGA-EY-A1GJ TCGA-FI-A2D2 
       16.93        23.90        39.95 

$`20Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       57.53        65.75        60.53        46.55        38.37        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 
       28.27        20.81        23.21        68.65        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95         7.92        11.44 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 
       36.33         9.60         8.02        91.04        46.32        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N 
        5.33         5.16         7.33        14.96         1.18        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
       10.26         0.39        19.79        29.39         2.40        34.36 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
        1.12         0.76        18.90         1.68         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE 
       22.49        22.26        17.06        20.81        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       21.21        15.62        10.19        15.35        15.95        14.76 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
       16.87        16.87        22.32        12.82        20.78         2.70 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        0.13        83.67        21.99         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        63.91        57.80        45.53        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       12.20        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        46.78        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T 
       27.85        16.24        21.90        36.13        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       66.58        34.98        53.92        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        35.01        28.54        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        65.88        13.28        19.20        16.96        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       15.25        20.28        12.43        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 
       54.12        67.50        25.12        36.39        11.08         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       30.12        71.24        40.80        61.18        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       46.49        19.36        26.33        17.75        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        64.93         0.23         0.20         0.56        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
        0.20        20.52         1.38         0.30         0.26         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR 
        1.18        18.35        14.47         0.39        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       46.75        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        27.29        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E 
       13.74        17.10        17.85        11.01         4.11         8.71 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L 
      185.79       113.36        88.34        75.72        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       43.96        40.50        36.82        32.09        33.50        27.35 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
      191.84       102.31        50.89        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       11.87        15.29        12.79       116.25        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       62.14        33.11        14.27        29.65        41.06        34.13 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       34.98        22.06        38.37        36.49        28.27        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       11.31         6.81        35.90        34.98         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F 
       10.16        31.76        24.99        24.13        16.64        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        23.47        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        67.20        88.34        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       72.72        73.25        59.51        62.79        63.58        49.55 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.16        66.48        16.83        19.79        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 
        0.56         4.87        28.67        23.93         1.74         4.44 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       36.36        37.51        36.79        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
       31.07        33.63        10.65         0.69        18.67         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
        0.72        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 
        1.05         3.95         3.52        41.42         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        0.26         4.27         4.11        89.33        10.92        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO 
       16.31        39.29        36.62        24.30        35.38         9.37 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
       12.39        31.10       110.10        23.38        48.36        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
        2.37         6.67        27.32        16.04         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       10.92        49.15        37.71        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       46.26        57.60        51.52        51.42        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 
       26.43        35.15        17.19        27.16        17.88        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       22.26        16.34        14.53        24.89         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ 
       22.78        13.97         6.90        19.27        18.84        17.88 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       17.62        15.09        16.11        12.43        15.81        11.08 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 
        6.48        19.33        12.59        10.19        14.40        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 
       22.82        20.05        45.76        31.04        29.10        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       13.84        11.38        17.92        14.14        19.89        14.70 
TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
       16.96         5.88        40.01        41.06        39.88         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       13.84         8.98        96.69        59.01         9.07        28.93 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR 
       28.96        25.02        29.23        41.06        45.01         1.74 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 
        7.76        14.04         2.43        23.74        13.28         9.47 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 
       26.10        18.21        23.24        15.45        23.97        12.92 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        7.00        11.24         6.97        18.84        39.95        12.92 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       23.64        14.83         4.44        14.07        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              0.56               0.07 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            149.56             191.84 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             23.90              23.34 
[1] "0.6 - 149.6 (23.9)" "0.1 - 191.8 (23.3)"
[1] "hr="     "9500000"
D78V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  20Q LOSS MUTATED                                         3
  20Q LOSS WILD-TYPE                                     392
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  20Q LOSS MUTATED                               2
  20Q LOSS WILD-TYPE                            19
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  20Q LOSS MUTATED                                   4
  20Q LOSS WILD-TYPE                               108
D78V3, multiclass
                                         clus
vv                                        20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                3                392
  MIXED SEROUS AND ENDOMETRIOID                          2                 19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                      4                108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V4, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     5   4
  20Q LOSS WILD-TYPE 136 383
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      5    4
  20Q LOSS WILD-TYPE  136  383
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 5                136
  YES                4                383
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20Q LOSS MUTATED     9   0   0   0
  20Q LOSS WILD-TYPE 354  23  17  35
D78V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0                9                354
  R1                0                 23
  R2                0                 17
  RX                0                 35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q LOSS MUTATED                                  0     1
  20Q LOSS WILD-TYPE                                4    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  20Q LOSS MUTATED                           1
  20Q LOSS WILD-TYPE                       100
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20Q LOSS MUTATED                                           0     6
  20Q LOSS WILD-TYPE                                         9   360
D78V6, multiclass
                                           clus
vv                                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    1                 19
  BLACK OR AFRICAN AMERICAN                                1                100
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  9
  WHITE                                                    6                360
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0   8
  20Q LOSS WILD-TYPE  14 359
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    8
  20Q LOSS WILD-TYPE   14  359
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 14
  NOT HISPANIC OR LATINO                8                359
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    43  10
  21Q LOSS WILD-TYPE 414  59
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                53                473 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                10                 59 
$`21Q LOSS MUTATED`
TCGA-A5-A0GN TCGA-A5-A1OH TCGA-A5-A2K3 TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A3BG 
       60.53        36.33        46.32         1.18        10.26         0.76 
TCGA-AP-A052 TCGA-AP-A05D TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A3K1 
       21.99        57.80       125.42         3.39        97.71        21.90 
TCGA-AX-A06B TCGA-AX-A1CA TCGA-AX-A2HF TCGA-AX-A2IO TCGA-AX-A3G4 TCGA-AX-A3G6 
       53.92        20.28        19.36        64.93         0.30         0.26 
TCGA-B5-A1N2 TCGA-B5-A3FD TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A18C TCGA-BG-A3PP 
       12.79        33.11        22.06        36.49        15.45         6.81 
TCGA-BK-A139 TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A179 TCGA-D1-A3DG TCGA-DI-A1NN 
       10.16        22.55        39.48        14.73         4.27        35.38 
TCGA-DI-A1NO TCGA-E6-A1LX TCGA-EO-A2CH TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GL 
        9.37        23.38        19.40        16.34         4.54        13.97 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2OO TCGA-EY-A4KR 
       19.27        18.84        10.19        14.40        45.76        11.38 
TCGA-EY-A54A TCGA-EY-A72D TCGA-FI-A2D2 TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PX 
       14.70         5.88        39.95        28.93        25.02        45.01 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KP-A3W1 TCGA-PG-A5BC TCGA-PG-A915 
        1.74         7.76         9.47        23.24         7.00 

$`21Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ 
       74.10        57.53        65.75        60.53        46.55        38.37 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       36.82        28.27        20.81        23.21        68.65        19.96 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K4 
        7.92        11.44         9.60         8.02        91.04        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A2QK 
        5.33         5.16         7.33        14.96        14.43         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF 
       19.79        29.39         2.40        34.36        34.16         1.12 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       18.90         1.68         1.64        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       17.06        20.81        36.99        20.65        21.21        15.62 
TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW 
       10.19        15.35        15.95        14.76        16.87        16.87 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       22.32        12.82        20.78         2.70         0.13        83.67 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
        5.95        23.31        86.07         8.22        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD 
       36.89        23.87        12.20        20.91        48.79       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
      110.37        63.16        36.36        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        55.89        31.30        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       46.78        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       16.24        36.13         0.56        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       34.98        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       35.01        28.54        37.78        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC 
       13.28        19.20        16.96        13.55        15.25        12.43 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       20.05        76.83        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       36.39        11.08         4.77        30.12        71.24        40.80 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       61.18        81.37        34.32        46.49        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
       30.74         2.96        31.13         0.23         0.20         0.56 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G7 TCGA-AX-A3G8 
       43.82         0.20        20.52         1.38         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       18.35        14.47         0.39        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        27.29        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F 
       17.10        17.85        11.01         4.11         8.71       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       40.50        36.82        32.09        33.50        27.35        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       191.84 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      102.31        50.89        14.40        14.70        11.70        11.87 
TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH 
       15.29       116.25        96.30        78.81        62.14        14.27 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       29.65        41.06        34.13        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        34.98        38.37        28.27 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B 
       11.31        35.90        34.98         6.21        10.22        31.76 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       24.99        24.13        16.64        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ 
       59.51        62.79        63.58        49.55        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W 
       28.67        23.93         1.74         4.44        21.99        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
        0.69        18.67         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
        6.64        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
        1.41        13.22         0.72        18.25        16.87        18.02 
TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 
        2.07        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV 
        8.48        44.88         0.26         4.11        16.93        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       12.39        31.10       110.10        48.36        17.06         2.37 
TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        6.67        27.32        16.04         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       49.15        37.71        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       57.60        51.52        51.42        34.39        26.43        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KX 
       17.19        27.16        17.88        26.96        22.26        14.53 
TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       24.89         6.21        14.99        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GM TCGA-EY-A1GQ 
       23.34        23.34        23.90        22.78         6.90        17.88 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       17.62        15.09        16.11        12.43        15.81        11.08 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
        6.48        19.33        12.59        18.87        22.82        20.05 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 
       31.04        29.10        27.35        13.84        17.92        14.14 
TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
       19.89        16.96        40.01        41.06        39.88         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 
       13.84         8.98        96.69        59.01         9.07        28.96 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 
       29.23        41.06        14.04         2.43        23.74        13.28 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 
       26.10        18.21        15.45        23.97        12.92        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        18.84        39.95        12.92        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44        14.07        18.28         0.07         0.23 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.26               0.07 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            125.42             191.84 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             19.27              23.93 
[1] "0.3 - 125.4 (19.3)" "0.1 - 191.8 (23.9)"
[1] "hr=" "1.9"
D79V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  21Q LOSS MUTATED                                        19
  21Q LOSS WILD-TYPE                                     376
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  21Q LOSS MUTATED                               4
  21Q LOSS WILD-TYPE                            17
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  21Q LOSS MUTATED                                  30
  21Q LOSS WILD-TYPE                                82
D79V3, multiclass
                                         clus
vv                                        21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               19                376
  MIXED SEROUS AND ENDOMETRIOID                          4                 17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     30                 82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V4, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    14  39
  21Q LOSS WILD-TYPE 127 348
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     14   39
  21Q LOSS WILD-TYPE  127  348
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                14                127
  YES               39                348
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  21Q LOSS MUTATED    37   2   4   4
  21Q LOSS WILD-TYPE 326  21  13  31
D79V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0               37                326
  R1                2                 21
  R2                4                 13
  RX                4                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q LOSS MUTATED                                  0     0
  21Q LOSS WILD-TYPE                                4    20
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  21Q LOSS MUTATED                          14
  21Q LOSS WILD-TYPE                        87
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  21Q LOSS MUTATED                                           1    35
  21Q LOSS WILD-TYPE                                         8   331
D79V6, multiclass
                                           clus
vv                                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    0                 20
  BLACK OR AFRICAN AMERICAN                               14                 87
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   35                331
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     1  38
  21Q LOSS WILD-TYPE  13 329
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1   38
  21Q LOSS WILD-TYPE   13  329
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 13
  NOT HISPANIC OR LATINO               38                329
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    84  21
  22Q LOSS WILD-TYPE 373  48
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               105                421 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                21                 48 
$`22Q LOSS MUTATED`
TCGA-2E-A9G8 TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R7 TCGA-A5-A1OH 
       41.06        65.75        60.53        36.82        17.59        36.33 
TCGA-A5-A2K2 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QL 
       91.04         7.33        14.96        14.43         0.39        19.79 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3I9 TCGA-AJ-A3IA 
       34.16         1.12        18.90         1.64        17.06        20.81 
TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A0L8 
       10.19        16.87        16.87        57.80        45.53        48.79 
TCGA-AP-A1DQ TCGA-AP-A5FX TCGA-AX-A06B TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 
       46.78        36.13        53.92        37.78        16.96        13.55 
TCGA-AX-A1CA TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H8 
       20.28        36.39        11.08        30.12        71.24        61.18 
TCGA-AX-A2HF TCGA-AX-A2HK TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G3 
       19.36         2.96         0.56        43.82        20.52         1.38 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A11P 
        0.30         0.26         0.30         4.11        75.72        36.82 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD 
      102.31        50.89        11.87        12.79       116.25        33.11 
TCGA-B5-A5OD TCGA-BG-A0M8 TCGA-BG-A0VZ TCGA-BG-A0YV TCGA-BG-A18C TCGA-BG-A2AD 
       34.13        36.49        52.64        12.56        15.45        20.02 
TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BS-A0U9 TCGA-D1-A0ZP TCGA-D1-A0ZZ TCGA-D1-A16I 
        6.81        10.22        67.20        29.95        22.55        11.51 
TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1NW 
       31.07        18.67         3.95        28.08        13.22         0.72 
TCGA-D1-A3DG TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A8L9 TCGA-EO-A1Y7 
        4.27        35.38        12.39        31.10        27.32        49.15 
TCGA-EO-A2CG TCGA-EO-A3AZ TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GM 
       51.42        27.16        16.34         4.54        23.90         6.90 
TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A2ON 
       18.84        17.62        11.08        12.59        14.40        20.05 
TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A547 TCGA-FI-A2D2 TCGA-FI-A2F9 TCGA-FI-A3PX 
       45.76        29.10        17.92        39.95        29.23        45.01 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W3 
        1.74         7.76        14.04         2.43        23.74        26.10 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-SL-A6J9 
       23.97        12.92         0.07 

$`22Q LOSS WILD-TYPE`
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       36.69        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       57.53        60.53        46.55        38.37        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       23.21        68.65        19.96        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A1OK 
       42.35        15.95         7.92        11.44         9.60         8.02 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23M TCGA-AJ-A23O 
       46.32        28.64         5.33         5.16         1.18        10.26 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK 
       29.39         2.40        34.36         0.76         1.68        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       22.49        22.26        36.99        20.65        21.21        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.35        15.95        14.76        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        2.70         0.13        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       86.07         8.22        63.91        36.89        23.87        12.20 
TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       20.91       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       33.40        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR 
       71.67        60.36        55.89        31.30        35.54        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        30.90        10.42        27.85        16.24        21.90 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D 
       46.45        35.34        45.99        66.58        34.98        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       51.09        27.39        30.02        60.66        35.01        28.54 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 
       43.82        40.11        65.88        13.28        19.20        15.25 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       12.43        20.05        76.83        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       25.12         4.77        40.80        81.37        34.32        46.49 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       26.33        17.75        30.74        31.13        64.93         0.23 
TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
        0.20         0.20         1.18        18.35        14.47         0.39 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       80.38        56.91        46.75        43.13        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       44.71        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        17.88        13.74        17.10        17.85        11.01 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
        8.71       185.79       113.36        88.34        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       43.96        40.50        32.09        33.50        27.35        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       191.84 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB 
       14.40        14.70        11.70        15.29        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW 
       62.14        14.27        29.65        41.06        34.95        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 
       20.19        19.33        20.94        35.21        34.98        22.06 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       43.30        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0W1 
       15.42        24.39        26.66        16.34        34.29        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       14.27         1.81         9.57        23.70        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       35.90        34.98         6.21        10.16        31.76        24.99 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.13        16.64        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        30.74        97.41        88.34        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       63.58        49.55        63.16        66.48        16.83        19.79 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 
        8.55         0.56         4.87        28.67        23.93         1.74 
TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        4.44        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J 
       37.32        36.36        37.51        36.79        27.42        29.92 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       33.63        10.65         0.69         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M 
        0.99        30.44         1.28        28.01        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
        1.41        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 
        1.05         3.95         3.52        41.42         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        0.26         4.11        16.93        89.33        10.92        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QY 
       16.31        39.29        36.62        24.30         9.37       110.10 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       23.38        48.36        17.06         2.37         6.67        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
        7.36        16.80        10.92        37.71        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS 
       66.90        46.26        57.60        51.52        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU 
       26.43        35.15        17.19        17.88        26.96        22.26 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       14.53        24.89         6.21        14.99        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GO 
       27.16        23.34        23.34        22.78        13.97        19.27 
TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX 
       17.88        15.09        16.11        12.43        15.81         6.48 
TCGA-EY-A1H0 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A3L3 
       19.33        10.19        18.87        22.82        31.04        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
       13.84        11.38        14.14        19.89        14.70        16.96 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 
        5.88        40.01        41.06        39.88         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 
        8.98        96.69        59.01         9.07        28.93        28.96 
TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A5BC 
       25.02        41.06        13.28         9.47        18.21        23.24 
TCGA-PG-A6IB TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       15.45         7.00        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       12.92        23.64        14.83         4.44        14.07        18.28 
TCGA-SL-A6JA 
        0.23 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.07               0.13 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            116.25             191.84 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             20.02              23.70 
[1] "0.1 - 116.2 (20.0)" "0.1 - 191.8 (23.7)"
[1] "hr=" "2"  
D80V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  22Q LOSS MUTATED                                        44
  22Q LOSS WILD-TYPE                                     351
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  22Q LOSS MUTATED                              10
  22Q LOSS WILD-TYPE                            11
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  22Q LOSS MUTATED                                  52
  22Q LOSS WILD-TYPE                                60
D80V3, multiclass
                                         clus
vv                                        22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               44                351
  MIXED SEROUS AND ENDOMETRIOID                         10                 11
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     52                 60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V4, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    20  86
  22Q LOSS WILD-TYPE 121 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     20   86
  22Q LOSS WILD-TYPE  121  301
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                20                121
  YES               86                301
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  22Q LOSS MUTATED    67   6   4   9
  22Q LOSS WILD-TYPE 296  17  13  26
D80V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               67                296
  R1                6                 17
  R2                4                 13
  RX                9                 26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q LOSS MUTATED                                  1     1
  22Q LOSS WILD-TYPE                                3    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  22Q LOSS MUTATED                          28
  22Q LOSS WILD-TYPE                        73
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  22Q LOSS MUTATED                                           2    71
  22Q LOSS WILD-TYPE                                         7   295
D80V6, multiclass
                                           clus
vv                                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  3
  ASIAN                                                    1                 19
  BLACK OR AFRICAN AMERICAN                               28                 73
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                2                  7
  WHITE                                                   71                295
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     5  78
  22Q LOSS WILD-TYPE   9 289
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      5   78
  22Q LOSS WILD-TYPE    9  289
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  9
  NOT HISPANIC OR LATINO               78                289
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    58  21
  XP LOSS WILD-TYPE 399  48
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               79               447 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               21                48 
$`XP LOSS MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-A5-A0R7 
       41.06        36.69        65.75        60.53        19.96        17.59 
TCGA-A5-A2K2 TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3BF 
       91.04        14.96        14.43        29.39        34.16         1.12 
TCGA-AJ-A3I9 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A0L8 
       17.06        21.99         5.95        57.80        36.89        48.79 
TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AW-A1PO TCGA-AX-A06B TCGA-AX-A1C7 TCGA-AX-A1CF 
       97.71        46.78         0.56        53.92        16.96        76.83 
TCGA-AX-A1CK TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-AX-A3G4 
       67.50        11.08         4.77        19.36         1.38         0.30 
TCGA-B5-A0JN TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1N2 
       80.38        27.29        17.85        36.82       102.31        12.79 
TCGA-B5-A3FD TCGA-B5-A5OE TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-BG-A18C 
       33.11        34.95        22.06        36.49        12.56        15.45 
TCGA-BK-A4ZD TCGA-D1-A0ZZ TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A179 
       16.64        22.55        31.07        18.67         3.95        14.73 
TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A1NO 
       28.08        13.22         2.07         4.27         4.11         9.37 
TCGA-DI-A2QT TCGA-DI-A2QY TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AZ TCGA-EO-A3KU 
       12.39       110.10        51.42        19.40        27.16        22.26 
TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GW TCGA-EY-A2OQ 
       16.34        23.90        18.84        17.62        11.08        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-FI-A2D2 TCGA-FI-A2EU 
       27.35        13.84        11.38        17.92        39.95        96.69 
TCGA-FI-A2EY TCGA-FI-A3PV TCGA-KJ-A3U4 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
       28.93        41.06         2.43        26.10        18.21        23.24 
TCGA-QS-A8F1 
        4.44 

$`XP LOSS WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
       10.29       106.88       149.56        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       32.78       112.54       105.37        87.32        74.10        57.53 
TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       23.21        68.65        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK 
       15.95         7.92        11.44        36.33         9.60         8.02 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23M 
       46.32        28.64         5.33         5.16         7.33         1.18 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG 
       10.26         0.39        19.79         2.40        34.36         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       18.90         1.68         1.64        14.66        22.49        22.26 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH 
       20.81        36.99        20.65        21.21        15.62        10.19 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV 
       15.35        15.95        14.76        16.87        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 
       12.82        20.78         2.70         0.13        83.67        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05O 
       86.07         8.22        63.91        45.53        23.87        12.20 
TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       20.91       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       60.36        55.89        31.30        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
       30.90        10.42        27.85        16.24        21.90        36.13 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F 
       35.34        45.99        66.58        34.98        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        35.01        28.54        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 
       43.82        40.11        65.88        13.28        19.20        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       15.25        20.28        12.43        20.05        72.56        54.12 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       25.12        36.39        30.12        71.24        40.80        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       81.37        34.32        46.49        26.33        17.75        30.74 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
        2.96        31.13        64.93         0.23         0.20         0.56 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
       43.82         0.20        20.52         0.26         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       18.35        14.47         0.39        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       30.51        25.91        17.88        13.74        17.10        11.01 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
        4.11         8.71       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        45.90        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       16.57       191.84        50.89        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       11.87        15.29       116.25        96.30        78.81        62.14 
TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX 
       14.27        29.65        41.06        34.13        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        34.98        38.37        28.27 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 
       14.83        13.78        14.73        14.01        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
        1.81         9.57        20.02        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
        6.81        35.90        34.98         6.21        10.22        10.16 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       31.76        24.99        24.13        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ 
       59.51        62.79        63.58        49.55        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93         1.74         4.44        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q 
       36.79        27.42        11.51        29.92        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        0.69         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.01        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NW TCGA-D1-A1NX 
       24.30         2.33        22.92         1.41         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       16.87        18.02        15.06         1.05         3.95         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3JP TCGA-DF-A2KV 
       41.42         8.48        44.88         0.26        16.93        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       35.38        31.10        23.38        48.36        17.06         2.37 
TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        6.67        27.32        16.04         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       49.15        37.71        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       57.60        51.52        34.39        26.43        35.15        17.19 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       17.88        26.96        14.53        24.89         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GS 
       22.78        13.97         6.90        19.27        17.88        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       16.11        12.43        15.81         6.48        19.33        12.59 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       10.19        14.40        18.87        22.82        20.05        45.76 
TCGA-EY-A2OP TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D 
       31.04        14.14        19.89        14.70        16.96         5.88 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       40.01        41.06        39.88         7.99        13.84         8.98 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX 
       59.01         9.07        28.96        25.02        29.23        45.01 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 
        1.74         7.76        14.04        23.74        13.28         9.47 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 
       15.45        23.97        12.92         7.00        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI 
       18.84        39.95        12.92        23.64        14.83        14.07 
TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       18.28         0.07         0.23 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.30              0.07 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           110.10            191.84 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            21.99             23.64 
[1] "0.3 - 110.1 (22.0)" "0.1 - 191.8 (23.6)"
[1] "hr=" "2.7"
D81V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  XP LOSS MUTATED                                        31
  XP LOSS WILD-TYPE                                     364
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  XP LOSS MUTATED                               4
  XP LOSS WILD-TYPE                            17
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  XP LOSS MUTATED                                  45
  XP LOSS WILD-TYPE                                67
D81V3, multiclass
                                         clus
vv                                        XP LOSS MUTATED XP LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              31               364
  MIXED SEROUS AND ENDOMETRIOID                         4                17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    45                67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V4, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    15  65
  XP LOSS WILD-TYPE 126 322
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     15   65
  XP LOSS WILD-TYPE  126  322
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               15               126
  YES              65               322
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XP LOSS MUTATED    53   2   6   5
  XP LOSS WILD-TYPE 310  21  11  30
D81V5, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  R0              53               310
  R1               2                21
  R2               6                11
  RX               5                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP LOSS MUTATED                                  1     1
  XP LOSS WILD-TYPE                                3    19
                   vv
clus                BLACK OR AFRICAN AMERICAN
  XP LOSS MUTATED                          22
  XP LOSS WILD-TYPE                        79
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XP LOSS MUTATED                                           1    49
  XP LOSS WILD-TYPE                                         8   317
D81V6, multiclass
                                           clus
vv                                          XP LOSS MUTATED XP LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 3
  ASIAN                                                   1                19
  BLACK OR AFRICAN AMERICAN                              22                79
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 8
  WHITE                                                  49               317
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     4  56
  XP LOSS WILD-TYPE  10 311
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      4   56
  XP LOSS WILD-TYPE   10  311
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                10
  NOT HISPANIC OR LATINO              56               311
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    53  15
  XQ LOSS WILD-TYPE 404  54
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               68               458 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               15                54 
$`XQ LOSS MUTATED`
TCGA-2E-A9G8 TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-A5-A2K2 TCGA-AJ-A2QM 
       41.06        65.75        60.53        19.96        91.04        29.39 
TCGA-AJ-A3BF TCGA-AJ-A3I9 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A05J 
        1.12        17.06        21.99         5.95        57.80        36.89 
TCGA-AP-A0LF TCGA-AP-A1DQ TCGA-AW-A1PO TCGA-AX-A06B TCGA-AX-A1C7 TCGA-AX-A1CF 
        3.39        46.78         0.56        53.92        16.96        76.83 
TCGA-AX-A1CK TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-AX-A3G4 
       67.50        11.08         4.77        19.36         1.38         0.30 
TCGA-B5-A0JN TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1N2 
       80.38        27.29        17.85        36.82       102.31        12.79 
TCGA-B5-A3FD TCGA-B5-A5OE TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-BG-A18C TCGA-BK-A139 
       33.11        34.95        36.49        12.56        15.45        10.16 
TCGA-D1-A0ZZ TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A179 TCGA-D1-A17K 
       22.55        31.07        18.67         3.95        14.73        28.08 
TCGA-D1-A1NU TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A1NO TCGA-DI-A2QT 
       13.22         2.07         4.27         4.11         9.37        12.39 
TCGA-DI-A2QY TCGA-EO-A3AS TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GP TCGA-EY-A1GR 
      110.10        34.39        16.34        23.90        18.84        17.62 
TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A4KR TCGA-FI-A2D2 
       15.09        11.08        29.10        13.84        11.38        39.95 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A3PV TCGA-KJ-A3U4 TCGA-KP-A3W3 
       59.01         9.07        28.93        41.06         2.43        26.10 
TCGA-PG-A5BC TCGA-PG-A7D5 
       23.24        23.97 

$`XQ LOSS WILD-TYPE`
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       36.69        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       57.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       20.81        23.21        68.65        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH 
       29.06        42.35        15.95         7.92        11.44        36.33 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
        9.60         8.02        46.32        28.64         5.33         5.16 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
        7.33        14.96         1.18        14.43        10.26         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BI 
       19.79         2.40        34.36        34.16         0.76        18.90 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3IA 
        1.68         1.64        14.66        22.49        22.26        20.81 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ 
       36.99        20.65        21.21        15.62        10.19        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.95        14.76        16.87        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 
       20.78         2.70         0.13        83.67        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
        8.22        63.91        45.53        23.87        12.20        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       60.36        55.89        31.30        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
       30.90        10.42        27.85        16.24        21.90        36.13 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F 
       35.34        45.99        66.58        34.98        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        35.01        28.54        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 
       43.82        40.11        65.88        13.28        19.20        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       15.25        20.28        12.43        20.05        72.56        54.12 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       25.12        36.39        30.12        71.24        40.80        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       81.37        34.32        46.49        26.33        17.75        30.74 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
        2.96        31.13        64.93         0.23         0.20         0.56 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
       43.82         0.20        20.52         0.26         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       18.35        14.47         0.39        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       30.51        25.91        17.88        13.74        17.10        11.01 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
        4.11         8.71       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        45.90        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       16.57       191.84        50.89        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       11.87        15.29       116.25        96.30        78.81        62.14 
TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX 
       14.27        29.65        41.06        34.13        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98        22.06        38.37 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       11.31         6.81        35.90        34.98         6.21        10.22 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
       31.76        24.99        24.13        16.64        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        23.47        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       67.20        88.34        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI 
       73.25        59.51        62.79        63.58        49.55        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
        4.87        28.67        23.93         1.74         4.44        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16O 
       37.51        36.79        27.42        11.51        29.92        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       10.65         0.69         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
        1.28        28.01        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NW 
       11.15        24.30         2.33        22.92         1.41         0.72 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       18.25        16.87        18.02        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3JP 
        3.52        41.42         8.48        44.88         0.26        16.93 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
       24.30        35.38        31.10        23.38        48.36        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
        2.37         6.67        27.32        16.04         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       10.92        49.15        37.71        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU 
       46.26        57.60        51.52        51.42        19.40        26.43 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU 
       35.15        17.19        27.16        17.88        26.96        22.26 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       14.53        24.89         6.21        14.99         4.54        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        22.78        13.97 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
        6.90        19.27        17.88        16.11        12.43        15.81 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 
        6.48        19.33        12.59        10.19        14.40        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A547 
       22.82        20.05        45.76        31.04        27.35        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX 
       14.14        19.89        14.70        16.96         5.88        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       41.06        39.88         7.99        13.84         8.98        96.69 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
       28.96        25.02        29.23        45.01         1.74         7.76 
TCGA-K6-A3WQ TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A6IB 
       14.04        23.74        13.28         9.47        18.21        15.45 
TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       12.92         7.00        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       12.92        23.64        14.83         4.44        14.07        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.30              0.07 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           110.10            191.84 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           19.660            23.555 
[1] "0.3 - 110.1 (19.7)" "0.1 - 191.8 (23.6)"
[1] "hr=" "2.1"
D82V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  XQ LOSS MUTATED                                        30
  XQ LOSS WILD-TYPE                                     365
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  XQ LOSS MUTATED                               3
  XQ LOSS WILD-TYPE                            18
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  XQ LOSS MUTATED                                  36
  XQ LOSS WILD-TYPE                                76
D82V3, multiclass
                                         clus
vv                                        XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              30               365
  MIXED SEROUS AND ENDOMETRIOID                         3                18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    36                76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V4, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    12  57
  XQ LOSS WILD-TYPE 129 330
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     12   57
  XQ LOSS WILD-TYPE  129  330
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               12               129
  YES              57               330
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XQ LOSS MUTATED    44   2   5   5
  XQ LOSS WILD-TYPE 319  21  12  30
D82V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              44               319
  R1               2                21
  R2               5                12
  RX               5                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ LOSS MUTATED                                  1     0
  XQ LOSS WILD-TYPE                                3    20
                   vv
clus                BLACK OR AFRICAN AMERICAN
  XQ LOSS MUTATED                          18
  XQ LOSS WILD-TYPE                        83
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XQ LOSS MUTATED                                           1    46
  XQ LOSS WILD-TYPE                                         8   320
D82V6, multiclass
                                           clus
vv                                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 3
  ASIAN                                                   0                20
  BLACK OR AFRICAN AMERICAN                              18                83
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 8
  WHITE                                                  46               320
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     4  49
  XQ LOSS WILD-TYPE  10 318
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      4   49
  XQ LOSS WILD-TYPE   10  318
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                10
  NOT HISPANIC OR LATINO              49               318
[1] 2 2
[1] FALSE
