[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/22507145/UCEC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UCEC-TP/22534123/transformed.cor.cli.txt"

nPatients in clinical file=548, in cluster file=539, common to both=539
[1]  82 539
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               54               485 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               54               485 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              189               350 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              189               350 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               93               446 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               93               446 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               78               461 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               78               461 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               48               491 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               48               491 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               85               454 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               85               454 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               14               525 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               14               525 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                8               531 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                8               531 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               52               487 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               52               487 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               20               519 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               20               519 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               81               458 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               81               458 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               66               473 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               66               473 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               68               471 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               68               471 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               65               474 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               65               474 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              116               423 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              116               423 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              159               380 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              159               380 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               22               517 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               22               517 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               10               529 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               10               529 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               116                423 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               116                423 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               108                431 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               108                431 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                23                516 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                23                516 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                20                519 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                20                519 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                69                470 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                69                470 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                51                488 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                51                488 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                30                509 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                30                509 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                36                503 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                36                503 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                11                528 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                11                528 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                25                514 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                25                514 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                10                529 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                10                529 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                13                526 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                13                526 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                30                509 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                30                509 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                73                466 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                73                466 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                46                493 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                46                493 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                55                484 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                55                484 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                58                481 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                58                481 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               109                430 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               109                430 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               130                409 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               130                409 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                39                500 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                39                500 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                30                509 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                30                509 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               63               476 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               63               476 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               64               475 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               64               475 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               27               512 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               27               512 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               16               523 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               16               523 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               12               527 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               12               527 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               18               521 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               18               521 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               52               487 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               52               487 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               31               508 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               31               508 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              106               433 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              106               433 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              104               435 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              104               435 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               53               486 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               53               486 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               73               466 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               73               466 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               20               519 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               20               519 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               25               514 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               25               514 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               45               494 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               45               494 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               45               494 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               45               494 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               78               461 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               78               461 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               22               517 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               22               517 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               99               440 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               99               440 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              117               422 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              117               422 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                44                495 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                44                495 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                40                499 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                40                499 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                76                463 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                76                463 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                73                466 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                73                466 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                45                494 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                45                494 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                40                499 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                40                499 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                93                446 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                93                446 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                62                477 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                62                477 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               109                430 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               109                430 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                99                440 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                99                440 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               140                399 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               140                399 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               129                410 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               129                410 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                93                446 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                93                446 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                51                488 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                51                488 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                63                476 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                63                476 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                57                482 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                57                482 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                54                485 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                54                485 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                22                517 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                22                517 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                11                528 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                11                528 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                54                485 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                54                485 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               110                429 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               110                429 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               86               453 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               86               453 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               70               469 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               70               469 
[1] "data2feature, selection=ALL"
 [1] "VITAL_STATUS"                        
 [2] "DAYS_TO_DEATH"                       
 [3] "DAYS_TO_LAST_FOLLOWUP"               
 [4] "TUMOR_TISSUE_SITE"                   
 [5] "PATHOLOGIC_STAGE"                    
 [6] "PATHOLOGY_T_STAGE"                   
 [7] "PATHOLOGY_N_STAGE"                   
 [8] "PATHOLOGY_M_STAGE"                   
 [9] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[10] "DAYS_TO_LAST_KNOWN_ALIVE"            
[11] "RADIATION_THERAPY"                   
[12] "HISTOLOGICAL_TYPE"                   
[13] "RESIDUAL_TUMOR"                      

Input Data has 13 rows and 539 columns.

[1] "Last Follow UP"
Variable 1:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 2:'DAYS_TO_DEATH':	nDistinctValues=88,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 3:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=411,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 4:'TUMOR_TISSUE_SITE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE excluded in the analysis because there is no case of (both >= 3) in the table below"
              ENDOMETRIAL OTHER  SPECIFY
freq.values   "538"       "1"           
freq.contrast "1"         "538"         
both >= 3     "FALSE"     "FALSE"       
Variable 5:'PATHOLOGIC_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGIC_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'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 7:'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 8:'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 9:'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 10:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 11:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 539 columns, 1 survival variables, and 3 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "RADIATION_THERAPY" "HISTOLOGICAL_TYPE" "RESIDUAL_TUMOR"   
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED    41  13
  1P GAIN WILD-TYPE 406  77
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               54               483 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               13                77 
$`1P GAIN MUTATED`
TCGA-A5-A1OK TCGA-AJ-A3IA TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-EY-A212 TCGA-5B-A90C 
       30.15        20.81         1.38        80.38        10.19        39.52 
TCGA-A5-A0G5 TCGA-A5-A0GA TCGA-A5-A0GN TCGA-A5-A1OG TCGA-A5-A3LP TCGA-AJ-A3BD 
       37.02        17.85        60.53        31.99        14.96        34.16 
TCGA-AJ-A3QS TCGA-AJ-A8CW TCGA-AP-A052 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
       16.87         0.13        21.99        51.12        21.90        36.13 
TCGA-AX-A060 TCGA-AX-A0IW TCGA-AX-A1CI TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G4 
       35.34        37.78        85.48        43.82        20.52         0.30 
TCGA-B5-A0JT TCGA-B5-A1MZ TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A0RY TCGA-BG-A18C 
       55.30        52.54        29.65        34.13        15.42        15.45 
TCGA-BG-A222 TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-D1-A16I TCGA-D1-A16S 
        9.57        16.64        61.87        92.88        11.51        18.67 
TCGA-D1-A177 TCGA-DF-A2KS TCGA-DI-A1NO TCGA-E6-A2P9 TCGA-EO-A3AS TCGA-EO-A3KU 
       18.02       109.08         9.37        45.57        34.39        22.26 
TCGA-EY-A1GC TCGA-EY-A2ON TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-JU-AAVI 
       54.15        20.05        14.70        77.33        59.01        17.75 
TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-QS-A744 TCGA-SL-A6J9 
        9.47        26.10        38.70        22.59        14.83         0.07 

$`1P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       41.06        88.18        60.53        16.83        29.39        18.08 
TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B 
       10.19       110.63        57.80        93.99        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-B5-A0KB 
       12.26        36.39        23.05        61.18        27.88        27.09 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 
       22.06        66.41        61.87        51.55        12.56        14.27 
TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 
        1.81        19.79         4.44        47.84        16.93        33.30 
TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 
        6.21        22.78        17.88        14.40        18.87        17.92 
TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 
       19.89         5.88        66.77        13.84        73.32        36.00 
TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 
       23.74         0.43        10.29       106.88       149.56        83.51 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ 
       32.78       112.54       105.37       123.68        74.10        65.75 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        73.87        36.82        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 
       42.35        15.95        31.99        36.33        33.07       118.19 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A7WJ 
       66.15        28.64        24.72        34.95        25.51        11.21 
TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       18.41        20.25        14.43        10.26        21.14        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       35.15        34.36        18.12        18.90        33.90         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-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-A8CV TCGA-AP-A051 
       22.32        12.82        20.78         2.70        35.11       129.80 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07        48.03        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        12.62        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        90.97        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        60.23        45.86        27.85 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       71.51        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        61.08        35.74        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       77.39        13.28        32.91        34.65        25.51        26.37 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CJ TCGA-AX-A1CK 
       32.02        25.91        34.09        76.83        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA 
       37.58         4.77        30.12        71.24        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       34.32        46.49        38.24        17.75        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ 
       31.13        64.93         0.23         0.20         0.56         0.20 
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-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       56.91        86.37        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       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        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       85.78        52.04        32.09        77.23        73.28        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       225.50 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      102.31        50.89        51.45        14.70        48.43        11.87 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       31.36       136.60        96.30        93.50        71.84        39.35 
TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       27.65        41.06        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        35.21        71.24        63.68        74.63        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        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       21.17        20.28        51.06        52.01        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-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
       15.45        20.02        23.70        20.12        11.31        22.39 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       35.90        34.98        35.90        35.08        31.00        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 
       24.33        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       114.90        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        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       83.64        86.99        66.48        16.83        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-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-A16J TCGA-D1-A16N 
       36.36        37.51        36.79        27.42        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-A179 TCGA-D1-A17A TCGA-D1-A17B 
       19.53         6.64        30.15        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        48.79 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ 
        8.48        58.95        15.88         4.27        18.84        17.29 
TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        2.20        71.61       100.83        89.33        10.92        27.16 
TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
       25.91        16.31        39.29        36.62        24.30        35.38 
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        79.10        58.95 
TCGA-E6-A2P8 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
        2.37        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-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       51.52        51.42        19.40        50.73        35.15        38.07 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       27.16        46.42        26.96        16.34        38.47        51.09 
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-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR 
       23.90        33.34        32.71        19.27        18.84        17.62 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       22.03        16.11        32.78        15.81        11.08        37.05 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       19.33        12.59        22.82        45.76        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CY 
       27.35        32.52        11.38        14.14        16.96        68.38 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY 
       39.88         7.99        25.22        96.69         9.34        28.93 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ 
       30.67        59.28        41.56        78.38         1.74        14.04 
TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A915 TCGA-PG-A916 
       13.28        18.21        23.24        21.30         8.19        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A8F1 
        6.97        22.65        39.95        24.95        23.64         4.44 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       20.75        18.28         0.23 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.07              0.20 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           109.08            225.50 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           24.345            30.020 
[1] "0.1 - 109.1 (24.3)" "0.2 - 225.5 (30.0)"
[1] "hr=" "1.8"
D1V2, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    24  26
  1P GAIN WILD-TYPE 266 198
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     24   26
  1P GAIN WILD-TYPE  266  198
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               24               266
  YES              26               198
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  1P GAIN MUTATED                                        27
  1P GAIN WILD-TYPE                                     377
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  1P GAIN MUTATED                               2
  1P GAIN WILD-TYPE                            20
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  1P GAIN MUTATED                                  25
  1P GAIN WILD-TYPE                                88
D1V3, multiclass
                                         clus
vv                                        1P GAIN MUTATED 1P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              27               377
  MIXED SEROUS AND ENDOMETRIOID                         2                20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    25                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"
                   vv
clus                 R0  R1  R2  RX
  1P GAIN MUTATED    31   1   2   8
  1P GAIN WILD-TYPE 340  21  14  32
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              31               340
  R1               1                21
  R2               2                14
  RX               8                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"

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED   152  37
  1Q GAIN WILD-TYPE 295  53
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              189               348 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               37                53 
$`1Q GAIN MUTATED`
TCGA-A5-A0GI TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AX-A3G3 
       88.18        30.15        16.83        20.81        10.19         1.38 
TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A221 TCGA-D1-A102 TCGA-D1-A2G5 
       22.06        61.87        51.55         1.81         4.44        47.84 
TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 
       33.30         6.21        22.78        17.88        10.19        14.40 
TCGA-EY-A549 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 
       19.89        73.32        36.00         0.43        39.52        10.29 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GG TCGA-A5-A0GN TCGA-A5-A0GU 
       83.51        17.85        32.78       123.68        60.53        28.27 
TCGA-A5-A0GV TCGA-A5-A0GX TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K3 
       54.02        68.65        31.99        36.33        33.07        66.15 
TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-AJ-A23O TCGA-AJ-A3BD TCGA-AJ-A3EJ TCGA-AJ-A3EM 
       14.96        11.21        10.26        34.16         1.64        22.26 
TCGA-AJ-A3NC TCGA-AJ-A3NF TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A8CW TCGA-AP-A051 
       36.99        21.21        14.76        16.87         0.13       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LH 
       21.99        23.31        20.91       117.99       110.37        36.36 
TCGA-AP-A0LI TCGA-AP-A0LL TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1E1 
       97.71        83.97        55.89        31.30        35.54        45.86 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05W TCGA-AX-A05Y 
       51.12        21.90        36.13        13.58        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A0IS TCGA-AX-A0IW 
       71.51        35.34        79.46        49.87        61.08        37.78 
TCGA-AX-A0J1 TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       77.39        25.51        32.02        85.48        73.41        80.25 
TCGA-AX-A2HA TCGA-AX-A2HH TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FX TCGA-AX-A3G1 
       81.37        17.75        31.13        64.93        43.82        20.52 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G8 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR 
        0.30         0.26         1.18        14.47         0.39        56.91 
TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0K0 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       55.30        86.01        48.59        57.76        64.21        63.55 
TCGA-B5-A0K9 TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11Z TCGA-B5-A1MU 
       13.45        32.09        77.23        73.28        17.36        50.89 
TCGA-B5-A1MZ TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-BG-A0LX TCGA-BG-A0M0 
       52.54        27.65        29.65        41.06        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       20.94        35.21        71.24        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0W1 TCGA-BG-A186 TCGA-BG-A18C TCGA-BG-A222 
       20.28        15.42        52.83        13.78        15.45         9.57 
TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A26L 
       11.31        35.90        35.08        31.00        31.76        24.13 
TCGA-BS-A0TI TCGA-BS-A0U7 TCGA-BS-A0U9 TCGA-BS-A0UT TCGA-BS-A0V4 TCGA-BS-A0VI 
       61.87        30.74        92.88        72.72        59.51        86.99 
TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A160 TCGA-D1-A165 TCGA-D1-A16I 
       16.83         8.55         0.56         3.68         0.66        11.51 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       18.67         3.95        30.15        18.02         1.58         7.00 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A2G6 TCGA-D1-A3DA 
       26.37        10.22        16.87        18.02         8.48        15.88 
TCGA-D1-A3JQ TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1NO 
       17.29        71.61       109.08        27.16        16.31         9.37 
TCGA-E6-A2P9 TCGA-EC-A1QX TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EY-A1GC TCGA-EY-A1GD 
       45.57         7.36        51.52        34.39        54.15        53.88 
TCGA-EY-A1GF TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       27.16        19.27        18.84        22.03        16.11        32.78 
TCGA-EY-A1GX TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A4KR TCGA-EY-A54A 
       37.05        20.05        45.76        31.04        11.38        14.70 
TCGA-EY-A5W2 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A3PV TCGA-FI-A3PX TCGA-JU-AAVI 
       16.96        77.33        59.01        41.56        78.38        17.75 
TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A917 TCGA-QS-A744 
       13.28        26.10        38.70        22.59         6.97        14.83 
TCGA-QS-A8F1 TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44         0.07         0.23 

$`1Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GM TCGA-AJ-A2QM TCGA-AJ-A3BG TCGA-AP-A053 TCGA-AP-A05D 
       41.06        60.53        29.39        18.08       110.63        57.80 
TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR 
       93.99        95.47        67.66        12.26        36.39        23.05 
TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M8 TCGA-BG-A0YV 
       61.18        27.88        80.38        27.09        66.41        12.56 
TCGA-BG-A220 TCGA-D1-A0ZO TCGA-D1-A3JP TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A72D 
       14.27        19.79        16.93        18.87        17.92         5.88 
TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-KP-A3VZ TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       66.77        13.84        23.74       106.88       149.56        37.02 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GP TCGA-A5-A0GQ 
      112.54       105.37        74.10        65.75        46.55        73.87 
TCGA-A5-A0GR TCGA-A5-A0GW TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       36.82        23.21        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A2K2 TCGA-A5-A2K4 
       29.06        42.35        15.95        31.99       118.19        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N 
       24.72        34.95        25.51        18.41        20.25        14.43 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BI 
       21.14        19.79        35.15        34.36        18.12        18.90 
TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NE TCGA-AJ-A3NG 
       33.90        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-AJ-A8CV TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
        2.70        35.11        86.07        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LG 
       36.89        23.87        12.62        48.79       125.42        66.25 
TCGA-AP-A0LJ TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       46.72        27.12        82.52        33.40        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DQ TCGA-AP-A1DR 
       49.22        25.08        71.67        90.97        46.78        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E3 TCGA-AW-A1PO TCGA-AX-A05T TCGA-AX-A05U 
        6.71        60.23        27.85         0.56        33.21        29.69 
TCGA-AX-A062 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IU 
       45.99        57.47        27.39        30.02        60.66        35.74 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C9 
       43.82        40.11        13.28        32.91        34.65        26.37 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 
       25.91        34.09        76.83        37.58         4.77        30.12 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HJ 
       71.24        40.80        34.32        46.49        38.24        30.74 
TCGA-AX-A2HK TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G7 
        2.96         0.23         0.20         0.56         0.20         0.30 
TCGA-AX-A3G9 TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       18.35        86.37        59.24        58.75        69.27        71.44 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11E TCGA-B5-A11F 
       36.49        72.62        27.29        27.85        59.84       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        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       85.78        52.04        16.73        19.56        19.50        18.41 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       16.57       225.50       102.31        51.45        14.70        48.43 
TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       11.87        31.36       136.60        96.30        93.50        71.84 
TCGA-B5-A3FD TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0M7 TCGA-BG-A0M9 
       39.35        34.13        34.95        18.61        63.68        74.63 
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        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A187 
       52.01        34.29        52.64        56.58        14.83        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3PP 
       14.01        15.45        20.02        23.70        20.12        22.39 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
       34.98        35.90        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        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       77.95        67.99        96.49        97.41       114.90        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       82.39        81.57        73.25        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZP TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
       66.48        29.95         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-A161 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       29.33        32.58        15.72        36.10        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-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       10.65         0.69         3.65        17.49        19.53         6.64 
TCGA-D1-A179 TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
       14.73         0.99        30.44         1.28        28.01        28.08 
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-A1O0 TCGA-D1-A1O5 
        1.41        13.22         0.72        18.25         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G7 TCGA-D1-A3DG TCGA-D1-A3DH 
        1.05         3.95        48.79        58.95         4.27        18.84 
TCGA-DF-A2KN TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2L0 TCGA-DI-A1BU 
        2.20       100.83        89.33        10.92        25.91        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY 
       36.62        24.30        35.38        12.39        31.10       110.10 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-EC-A1NJ TCGA-EC-A24G 
       23.38        79.10        58.95         2.37        16.04        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-A2CG TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV 
       46.26        57.60        51.42        19.40        50.73        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW 
       38.07        27.16        46.42        26.96        22.26        16.34 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GE TCGA-EY-A1GH TCGA-EY-A1GI 
       38.47        51.09        14.99        24.36        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GV TCGA-EY-A1GW 
       23.90        33.34        32.71        17.62        15.81        11.08 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX 
       19.33        12.59        22.82        29.10        27.35        32.52 
TCGA-EY-A548 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU 
       14.14        68.38        39.88         7.99        25.22        96.69 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-K6-A3WQ 
        9.34        28.93        30.67        59.28         1.74        14.04 
TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A915 TCGA-PG-A916 
        9.47        18.21        23.24        21.30         8.19        17.16 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       22.65        39.95        24.95        23.64        20.75        18.28 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.07              0.20 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            129.8             225.5 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            30.15             29.90 
[1] "0.1 - 129.8 (30.1)" "0.2 - 225.5 (29.9)"
[1] "hr=" "1.4"
D2V2, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   102  78
  1Q GAIN WILD-TYPE 188 146
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    102   78
  1Q GAIN WILD-TYPE  188  146
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO              102               188
  YES              78               146
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  1Q GAIN MUTATED                                       141
  1Q GAIN WILD-TYPE                                     263
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  1Q GAIN MUTATED                               5
  1Q GAIN WILD-TYPE                            17
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  1Q GAIN MUTATED                                  43
  1Q GAIN WILD-TYPE                                70
D2V3, multiclass
                                         clus
vv                                        1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             141               263
  MIXED SEROUS AND ENDOMETRIOID                         5                17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    43                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  1Q GAIN MUTATED   128   8   6  15
  1Q GAIN WILD-TYPE 243  14  10  25
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0             128               243
  R1               8                14
  R2               6                10
  RX              15                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"

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    61  31
  2P GAIN WILD-TYPE 386  59
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               92               445 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               31                59 
$`2P GAIN MUTATED`
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AX-A3G3 TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0VT 
       20.81        10.19         1.38        22.06        66.41        51.55 
TCGA-D1-A0ZO TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A214 TCGA-EY-A72D 
       19.79        16.93        33.30         6.21        14.40         5.88 
TCGA-KP-A3VZ TCGA-A5-A0G2 TCGA-A5-A0GN TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0R7 
       23.74       149.56        60.53        28.27        54.02        17.59 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N 
       31.99        36.33        28.64        14.96        20.25        14.43 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A05A TCGA-AP-A0L8 
       33.90         1.64        16.87        16.87        63.91        48.79 
TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05W TCGA-AX-A0IU TCGA-AX-A0IW 
       46.78        21.90        36.13        80.55        35.74        37.78 
TCGA-AX-A1C7 TCGA-AX-A1CK TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A2HH TCGA-AX-A2HK 
       34.65        80.25         4.77        40.80        17.75         2.96 
TCGA-AX-A3G6 TCGA-B5-A0JT TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11I TCGA-B5-A1MU 
        0.26        55.30        63.55        13.45        75.72        50.89 
TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0RY TCGA-BG-A2AE 
       31.36        29.65        19.33        20.94        15.42        23.70 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TE 
       22.39        35.90        31.00        24.13        16.64         4.80 
TCGA-BS-A0TI TCGA-BS-A0UT TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-D1-A0ZP TCGA-D1-A168 
       61.87        72.72        63.58        83.64        29.95        36.10 
TCGA-D1-A17R TCGA-D1-A1NW TCGA-D1-A2G6 TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KR 
       11.15         0.72         8.48        18.84        17.29        71.61 
TCGA-DI-A1NN TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A2CG TCGA-EO-A3B1 TCGA-EO-A3KU 
       35.38       110.10        79.10        51.42        26.96        22.26 
TCGA-EY-A1GH TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A54A TCGA-FI-A2D2 
       23.34        32.71        19.27        22.03        14.70        77.33 
TCGA-FI-A2D4 TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-PG-A7D5 
        7.99        78.38        17.75        14.04         9.47        38.70 
TCGA-QS-A8F1 TCGA-SL-A6J9 
        4.44         0.07 

$`2P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B 
       18.08       110.63        57.80        93.99        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-B5-A0JN 
       12.26        36.39        23.05        61.18        27.88        80.38 
TCGA-B5-A0KB TCGA-BG-A0MS TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A102 
       27.09        61.87        12.56        14.27         1.81         4.44 
TCGA-D1-A2G5 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A547 
       47.84        22.78        17.88        10.19        18.87        17.92 
TCGA-EY-A549 TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E 
       19.89        66.77        13.84        73.32        36.00         0.43 
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
       39.52        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-A0GJ 
       32.78       112.54       105.37       123.68        74.10        65.75 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       46.55        73.87        36.82        23.21        68.65        37.91 
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        31.99 
TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
       33.07       118.19        66.15        24.72        34.95        25.51 
TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       11.21        18.41        10.26        21.14        19.79        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EK TCGA-AJ-A3EL 
       34.36        34.16        18.12        18.90        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-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.35        15.95        14.76        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
        2.70        35.11         0.13       129.80        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       86.07        48.03        45.53        36.89        23.87        12.62 
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        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        46.72        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       61.64        80.78        49.22        25.08        71.67        90.97 
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        60.23 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       45.86        27.85        51.12         0.56        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        88.24        71.51        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       49.87        57.47        27.39        30.02        60.66        61.08 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 
       43.82        40.11        77.39        13.28        32.91        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       26.37        32.02        25.91        34.09        76.83        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CN TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HA TCGA-AX-A2HC 
       73.41        37.58        30.12        71.24        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       46.49        38.24        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-A0JR 
        0.30         1.18        18.35        14.47         0.39        56.91 
TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       86.37        59.24        86.01        58.75        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K8 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J 
       27.85        59.84       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 
       73.64        61.68        85.78        52.04        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       73.28        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       225.50       102.31        51.45        14.70        48.43 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       11.87        52.54       136.60        96.30        93.50        71.84 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW 
       39.35        27.65        41.06        34.13        34.95        18.61 
TCGA-BG-A0LX TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.19        35.21        71.24        63.68        74.63        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        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       21.17        20.28        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW 
       15.45        15.45         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        35.90        35.08        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        24.33        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        92.88 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV TCGA-BS-A0V4 
      114.90        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 
       89.59        86.99        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-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-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-A2G7 
        2.07        15.06         1.05         3.95        48.79        58.95 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KN TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV 
       15.88         4.27         2.20       109.08       100.83        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       10.92        27.16        25.91        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        58.95 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37        45.57        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        50.73        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       38.07        27.16        46.42        16.34        38.47        51.09 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GI 
       14.99        54.15        53.88        24.36        27.16        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU 
       23.90        33.34        18.84        17.62        16.11        32.78 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM 
       15.81        11.08        37.05        19.33        12.59        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX 
       20.05        45.76        31.04        29.10        27.35        32.52 
TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D6 
       11.38        14.14        16.96        68.38        39.88        25.22 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 
       96.69        59.01         9.34        28.93        30.67        59.28 
TCGA-FI-A3PV TCGA-H5-A2HR TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
       41.56         1.74        13.28        26.10        18.21        23.24 
TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       21.30        22.59         8.19        17.16         6.97        22.65 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       39.95        24.95        23.64        14.83        20.75        18.28 
TCGA-SL-A6JA 
        0.23 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.07              0.13 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           149.56            225.50 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           23.935            30.150 
[1] "0.1 - 149.6 (23.9)" "0.1 - 225.5 (30.1)"
[1] "hr=" "2.9"
D3V2, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    44  43
  2P GAIN WILD-TYPE 246 181
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     44   43
  2P GAIN WILD-TYPE  246  181
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               44               246
  YES              43               181
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  2P GAIN MUTATED                                        43
  2P GAIN WILD-TYPE                                     361
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  2P GAIN MUTATED                               5
  2P GAIN WILD-TYPE                            17
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  2P GAIN MUTATED                                  45
  2P GAIN WILD-TYPE                                68
D3V3, multiclass
                                         clus
vv                                        2P GAIN MUTATED 2P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              43               361
  MIXED SEROUS AND ENDOMETRIOID                         5                17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    45                68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  2P GAIN MUTATED    65   3   4   8
  2P GAIN WILD-TYPE 306  19  12  32
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0              65               306
  R1               3                19
  R2               4                12
  RX               8                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"

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    51  26
  2Q GAIN WILD-TYPE 396  64
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               77               460 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               26                64 
$`2Q GAIN MUTATED`
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AX-A3G3 TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0VT 
       20.81        10.19         1.38        22.06        66.41        51.55 
TCGA-D1-A0ZO TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A214 TCGA-EY-A72D 
       19.79        16.93        33.30         6.21        14.40         5.88 
TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0GN TCGA-A5-A0GV TCGA-A5-A0R7 TCGA-A5-A1OG 
       23.74        39.52        60.53        54.02        17.59        31.99 
TCGA-A5-A1OH TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3BK 
       36.33        28.64        14.96        20.25        14.43        33.90 
TCGA-AJ-A3EJ TCGA-AJ-A3TW TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05W 
        1.64        16.87        46.78        21.90        36.13        80.55 
TCGA-AX-A0IW TCGA-AX-A2HH TCGA-AX-A2HK TCGA-B5-A0JT TCGA-B5-A0K7 TCGA-B5-A0K9 
       37.78        17.75         2.96        55.30        63.55        13.45 
TCGA-B5-A11I TCGA-B5-A1MU TCGA-B5-A3S1 TCGA-BG-A0M2 TCGA-BG-A0RY TCGA-BG-A2AE 
       75.72        50.89        29.65        20.94        15.42        23.70 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD 
       22.39        35.90        35.08        31.00        24.13        16.64 
TCGA-BS-A0TE TCGA-BS-A0UT TCGA-BS-A0V7 TCGA-D1-A0ZP TCGA-D1-A168 TCGA-D1-A17R 
        4.80        72.72        63.58        29.95        36.10        11.15 
TCGA-D1-A2G6 TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DI-A1NN TCGA-DI-A2QY TCGA-E6-A1LZ 
        8.48        18.84        17.29        35.38       110.10        79.10 
TCGA-EO-A2CG TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1GH TCGA-EY-A1GM TCGA-EY-A1GO 
       51.42        26.96        22.26        23.34        32.71        19.27 
TCGA-EY-A1GS TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A3PX TCGA-JU-AAVI 
       22.03        14.70        77.33         7.99        78.38        17.75 
TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-PG-A7D5 TCGA-QS-A8F1 TCGA-SL-A6J9 
       14.04         9.47        38.70         4.44         0.07 

$`2Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B 
       18.08       110.63        57.80        93.99        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-B5-A0JN 
       12.26        36.39        23.05        61.18        27.88        80.38 
TCGA-B5-A0KB TCGA-BG-A0MS TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A102 
       27.09        61.87        12.56        14.27         1.81         4.44 
TCGA-D1-A2G5 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A547 
       47.84        22.78        17.88        10.19        18.87        17.92 
TCGA-EY-A549 TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E 
       19.89        66.77        13.84        73.32        36.00         0.43 
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-A0GJ 
       32.78       112.54       105.37       123.68        74.10        65.75 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        73.87        36.82        28.27        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       37.91        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 
       31.99        33.07       118.19        66.15        24.72        34.95 
TCGA-A5-A3LO TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       25.51        11.21        18.41        10.26        21.14        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EK 
       35.15        34.36        34.16        18.12        18.90        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-A3QS 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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 
       12.82        20.78         2.70        35.11         0.13       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
       21.99        23.31        86.07        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       36.89        23.87        12.62        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      117.99       110.37        66.25        36.36        97.71        46.72 
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-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        90.97        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        60.23        45.86        27.85 
TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y 
       51.12         0.56        13.58        33.21        29.69        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ 
       27.39        30.02        60.66        61.08        35.74        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        77.39        13.28        32.91        34.65        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       26.37        32.02        25.91        34.09        76.83        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       73.41        80.25        37.58         4.77        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HJ 
       40.80        81.37        34.32        46.49        38.24        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-A0JR TCGA-B5-A0JS TCGA-B5-A0JU 
       18.35        14.47         0.39        56.91        86.37        59.24 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.01        58.75        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K8 TCGA-B5-A11E 
       72.62        27.29        57.76        64.21        27.85        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      185.79       113.36        88.34        54.44        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       85.78        52.04        32.09        77.23        73.28        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       225.50 
TCGA-B5-A1MS TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
      102.31        51.45        14.70        48.43        11.87        52.54 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       31.36       136.60        96.30        93.50        71.84        39.35 
TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       27.65        41.06        34.13        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       19.33        35.21        71.24        63.68        74.63        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        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       21.17        20.28        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW 
       15.45        15.45         9.57        20.02        20.12        11.31 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 
       34.98        35.90        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        24.33        85.55        78.21        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        92.88 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV TCGA-BS-A0V4 
      114.90        85.84        82.39        81.57        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ 
       89.59        83.64        86.99        66.48        16.83         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-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-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-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-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KN TCGA-DF-A2KR 
       48.79        58.95        15.88         4.27         2.20        71.61 
TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 
      109.08       100.83        89.33        10.92        27.16        25.91 
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        58.95         2.37        45.57        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        50.73        35.15        38.07        27.16        46.42 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       16.34        38.47        51.09        14.99        54.15        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GP 
       24.36        27.16        23.34        23.90        33.34        18.84 
TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       17.62        16.11        32.78        15.81        11.08        37.05 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       19.33        12.59        22.82        20.05        45.76        31.04 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A5W2 
       29.10        27.35        32.52        11.38        14.14        16.96 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
       68.38        39.88        25.22        96.69        59.01         9.34 
TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-KP-A3W0 
       28.93        30.67        59.28        41.56         1.74        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        21.30        22.59         8.19 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       17.16         6.97        22.65        39.95        24.95        23.64 
TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       14.83        20.75        18.28         0.23 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.07              0.13 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            110.1             225.5 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           23.340            30.555 
[1] "0.1 - 110.1 (23.3)" "0.1 - 225.5 (30.6)"
[1] "hr=" "3"  
D4V2, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    35  38
  2Q GAIN WILD-TYPE 255 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     35   38
  2Q GAIN WILD-TYPE  255  186
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               35               255
  YES              38               186
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  2Q GAIN MUTATED                                        37
  2Q GAIN WILD-TYPE                                     367
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  2Q GAIN MUTATED                               4
  2Q GAIN WILD-TYPE                            18
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  2Q GAIN MUTATED                                  37
  2Q GAIN WILD-TYPE                                76
D4V3, multiclass
                                         clus
vv                                        2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              37               367
  MIXED SEROUS AND ENDOMETRIOID                         4                18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    37                76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  2Q GAIN MUTATED    52   2   4   8
  2Q GAIN WILD-TYPE 319  20  12  32
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0              52               319
  R1               2                20
  R2               4                12
  RX               8                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"

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    37  11
  3P GAIN WILD-TYPE 410  79
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               48               489 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               11                79 
$`3P GAIN MUTATED`
TCGA-AJ-A3IA TCGA-AX-A06D TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1GQ 
       20.81        12.26        47.84        16.93        33.30        17.88 
TCGA-EY-A212 TCGA-EY-A72D TCGA-A5-A2K2 TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3QS 
       10.19         5.88       118.19        34.16        18.90        16.87 
TCGA-AJ-A8CW TCGA-AP-A0LO TCGA-AP-A1DO TCGA-AX-A05W TCGA-AX-A1CA TCGA-AX-A2H4 
        0.13        33.40        31.30        80.55        32.02        30.12 
TCGA-AX-A2H7 TCGA-AX-A3G6 TCGA-B5-A0K4 TCGA-B5-A11R TCGA-B5-A1MR TCGA-B5-A1MY 
       40.80         0.26        57.76        77.23       225.50        11.87 
TCGA-BG-A0M4 TCGA-BG-A0RY TCGA-BG-A0W1 TCGA-BS-A0U9 TCGA-BS-A0UV TCGA-BS-A0V8 
       71.24        15.42        52.83        92.88        73.25        83.64 
TCGA-D1-A2G6 TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KS TCGA-DI-A2QY TCGA-EO-A22Y 
        8.48        18.84        17.29       109.08       110.10        51.52 
TCGA-EO-A3B1 TCGA-EY-A1GC TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A4KR 
       26.96        54.15        17.62        22.03        11.08        11.38 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A3PX TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A744 
       59.01         9.34        78.38        22.59         8.19        14.83 

$`3P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS 
       18.08        10.19       110.63        57.80        93.99        95.47 
TCGA-AX-A06B TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 
       67.66        36.39        23.05        61.18        27.88         1.38 
TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       80.38        27.09        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A1G7 
       12.56        14.27         1.81        19.79         4.44         6.21 
TCGA-EY-A1GK TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-FI-A2CX 
       22.78        14.40        18.87        17.92        19.89        66.77 
TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C 
       13.84        73.32        36.00        23.74         0.43        39.52 
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-A0GJ 
       32.78       112.54       105.37       123.68        74.10        65.75 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        73.87        36.82        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        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        31.99        31.99        36.33 
TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
       33.07        66.15        28.64        24.72        34.95        25.51 
TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O 
       14.96        11.21        18.41        20.25        14.43        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BK 
       21.14        19.79        35.15        34.36        18.12        33.90 
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-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65        21.21        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-A8CV 
       16.87        22.32        12.82        20.78         2.70        35.11 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
      129.80        21.99        23.31        86.07        48.03        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        12.62        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      125.42       117.99       110.37        66.25        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ 
       46.72        83.97        27.12        82.52        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP 
       49.22        25.08        71.67        90.97        55.89        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        60.23        45.86        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       51.12        21.90        36.13         0.56        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        88.24        71.51        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       49.87        57.47        27.39        30.02        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       35.74        37.78        43.82        40.11        77.39        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE 
       32.91        34.65        25.51        26.37        25.91        34.09 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 
       76.83        85.48        73.41        80.25        37.58         4.77 
TCGA-AX-A2H5 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       71.24        81.37        34.32        46.49        38.24        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-A3G7 
        0.56        43.82         0.20        20.52         0.30         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS 
        1.18        18.35        14.47         0.39        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       55.30        59.24        86.01        58.75        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 
       48.59        36.49        72.62        27.29        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       27.85        13.45        59.84       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        73.64        61.68        85.78        52.04 
TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       32.09        73.28        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        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       48.43        52.54        31.36       136.60        96.30        93.50 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       71.84        39.35        27.65        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-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       63.68        74.63        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-A0VV 
       43.30        43.04        59.74        21.17        20.28        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       52.01        34.29        52.64        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD 
       14.73        14.01        15.45        15.45         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        22.39        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
       35.90        35.08        31.00        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        24.33 
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       114.90        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        89.59        63.58        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        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-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-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KN TCGA-DF-A2KR 
       48.79        58.95        15.88         4.27         2.20        71.61 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH 
      100.83        89.33        10.92        27.16        25.91        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-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       31.10        23.38        79.10        58.95         2.37        45.57 
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-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        50.73        35.15        38.07        27.16 
TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 
       46.42        22.26        16.34        38.47        51.09        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-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU 
       33.34        32.71        19.27        18.84        16.11        32.78 
TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON 
       15.81        37.05        19.33        12.59        22.82        20.05 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 
       45.76        31.04        29.10        27.35        32.52        14.14 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
       14.70        16.96        68.38        39.88        77.33         7.99 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV 
       25.22        96.69        28.93        30.67        59.28        41.56 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 
        1.74        17.75        14.04        13.28         9.47        26.10 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A916 TCGA-PG-A917 
       18.21        23.24        21.30        38.70        17.16         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       22.65        39.95        24.95        23.64         4.44        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       18.28         0.07         0.23 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.13              0.07 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           225.50            185.79 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            28.54             29.92 
[1] "0.1 - 225.5 (28.5)" "0.1 - 185.8 (29.9)"
[1] "hr=" "1.3"
D5V2, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    24  21
  3P GAIN WILD-TYPE 266 203
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     24   21
  3P GAIN WILD-TYPE  266  203
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               24               266
  YES              21               203
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  3P GAIN MUTATED                                        27
  3P GAIN WILD-TYPE                                     377
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  3P GAIN MUTATED                               0
  3P GAIN WILD-TYPE                            22
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  3P GAIN MUTATED                                  21
  3P GAIN WILD-TYPE                                92
D5V3, multiclass
                                         clus
vv                                        3P GAIN MUTATED 3P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              27               377
  MIXED SEROUS AND ENDOMETRIOID                         0                22
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    21                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"
                   vv
clus                 R0  R1  R2  RX
  3P GAIN MUTATED    33   4   2   4
  3P GAIN WILD-TYPE 338  18  14  36
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              33               338
  R1               4                18
  R2               2                14
  RX               4                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    60  25
  3Q GAIN WILD-TYPE 387  65
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               85               452 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               25                65 
$`3Q GAIN MUTATED`
TCGA-AJ-A3IA TCGA-AX-A06D TCGA-AX-A1CR TCGA-BG-A0M6 TCGA-BG-A0YV TCGA-D1-A2G5 
       20.81        12.26        23.05        22.06        12.56        47.84 
TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A72D TCGA-FI-A2CX 
       16.93        33.30        17.88        10.19         5.88        66.77 
TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A3LP 
       39.52        37.02        31.99        36.33       118.19        14.96 
TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3QS TCGA-AJ-A8CW 
       20.25        34.16        18.90         1.64        16.87         0.13 
TCGA-AP-A0L8 TCGA-AP-A0LO TCGA-AP-A1DO TCGA-AX-A05W TCGA-AX-A1CA TCGA-AX-A1CF 
       48.79        33.40        31.30        80.55        32.02        76.83 
TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A3FW TCGA-AX-A3G6 TCGA-B5-A0K4 TCGA-B5-A11I 
       30.12        40.80         0.56         0.26        57.76        75.72 
TCGA-B5-A11R TCGA-B5-A1MR TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-BG-A0M4 TCGA-BG-A0RY 
       77.23       225.50        11.87        31.36        71.24        15.42 
TCGA-BG-A0W1 TCGA-BK-A0CC TCGA-BS-A0TE TCGA-BS-A0U9 TCGA-BS-A0UV TCGA-BS-A0V8 
       52.83        35.08         4.80        92.88        73.25        83.64 
TCGA-D1-A168 TCGA-D1-A16G TCGA-D1-A1NW TCGA-D1-A2G6 TCGA-D1-A3DH TCGA-D1-A3JQ 
       36.10        27.42         0.72         8.48        18.84        17.29 
TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EC-A1QX TCGA-EO-A1Y5 
       71.61       109.08       110.10        79.10         7.36        10.92 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GM 
       51.52        51.42        26.96        16.34        54.15        32.71 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A2ON TCGA-EY-A3QX TCGA-EY-A4KR 
       17.62        22.03        11.08        20.05        32.52        11.38 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ 
       59.01         9.34        28.93        78.38        17.75        14.04 
TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A744 
        9.47        26.10        38.70        22.59         8.19        14.83 
TCGA-SL-A6J9 
        0.07 

$`3Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS 
       18.08        10.19       110.63        57.80        93.99        95.47 
TCGA-AX-A06B TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN 
       67.66        36.39        61.18        27.88         1.38        80.38 
TCGA-B5-A0KB TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A220 TCGA-BG-A221 
       27.09        66.41        61.87        51.55        14.27         1.81 
TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A214 TCGA-EY-A215 
       19.79         4.44         6.21        22.78        14.40        18.87 
TCGA-EY-A547 TCGA-EY-A549 TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       17.92        19.89        13.84        73.32        36.00        23.74 
TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA 
        0.43        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-A0GJ 
       32.78       112.54       105.37       123.68        74.10        65.75 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        73.87        36.82        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A2K3 
       29.06        42.35        15.95        31.99        33.07        66.15 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A7WJ TCGA-A5-A7WK 
       28.64        24.72        34.95        25.51        11.21        18.41 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       14.43        10.26        21.14        19.79        35.15        34.36 
TCGA-AJ-A3BF TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
       18.12        33.90        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-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-A8CV TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       35.11       129.80        21.99        23.31        86.07        48.03 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       63.91        45.53        36.89        23.87        12.62        20.91 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      125.42       117.99       110.37        66.25        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ 
       46.72        83.97        27.12        82.52        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP 
       49.22        25.08        71.67        90.97        55.89        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        60.23        45.86        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       51.12        21.90        36.13         0.56        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        88.24        71.51        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       49.87        57.47        27.39        30.02        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       35.74        37.78        43.82        40.11        77.39        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE 
       32.91        34.65        25.51        26.37        25.91        34.09 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H5 
       85.48        73.41        80.25        37.58         4.77        71.24 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       81.37        34.32        46.49        38.24        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-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.20        20.52         0.30         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        86.37        55.30        59.24 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.01        58.75        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       72.62        27.29        64.21        63.55        27.85        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
       59.84       185.79       113.36        88.34        54.44        73.64 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U 
       61.68        85.78        52.04        32.09        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MS 
       19.56        19.50        18.41        17.36        16.57       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 
       50.89        51.45        14.70        48.43        52.54       136.60 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 
       96.30        93.50        71.84        39.35        27.65        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-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       20.94        35.21        63.68        74.63        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       48.56        23.47        43.30        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 
       20.28        51.06        52.01        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-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        22.39 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       35.90        34.98        35.90        31.00        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-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       24.33        85.55        78.21        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       114.90        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        89.59        63.58        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        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-A165 TCGA-D1-A167 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
        0.66        15.72        37.32        36.36        37.51        36.79 
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-A2G7 TCGA-D1-A3DA 
       15.06         1.05         3.95        48.79        58.95        15.88 
TCGA-D1-A3DG TCGA-DF-A2KN TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        4.27         2.20       100.83        89.33        10.92        27.16 
TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
       25.91        16.31        39.29        36.62        24.30        35.38 
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        58.95         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
       45.57        16.04        16.80        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-A3KU 
       50.73        35.15        38.07        27.16        46.42        22.26 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       38.47        51.09        14.99        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP 
       23.34        23.34        23.90        33.34        19.27        18.84 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       16.11        32.78        15.81        37.05        19.33        12.59 
TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A548 
       22.82        45.76        31.04        29.10        27.35        14.14 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
       14.70        16.96        68.38        39.88        77.33         7.99 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR 
       25.22        96.69        30.67        59.28        41.56         1.74 
TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 
       13.28        18.21        23.24        21.30        17.16         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       22.65        39.95        24.95        23.64         4.44        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.07              0.20 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           225.50            185.79 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           27.420            29.985 
[1] "0.1 - 225.5 (27.4)" "0.2 - 185.8 (30.0)"
[1] "hr=" "2.2"
D6V2, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    34  46
  3Q GAIN WILD-TYPE 256 178
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     34   46
  3Q GAIN WILD-TYPE  256  178
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               34               256
  YES              46               178
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  3Q GAIN MUTATED                                        37
  3Q GAIN WILD-TYPE                                     367
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  3Q GAIN MUTATED                               4
  3Q GAIN WILD-TYPE                            18
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  3Q GAIN MUTATED                                  44
  3Q GAIN WILD-TYPE                                69
D6V3, multiclass
                                         clus
vv                                        3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              37               367
  MIXED SEROUS AND ENDOMETRIOID                         4                18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    44                69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  3Q GAIN MUTATED    56   5   5   8
  3Q GAIN WILD-TYPE 315  17  11  32
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              56               315
  R1               5                17
  R2               5                11
  RX               8                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"

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED     9   5
  4P GAIN WILD-TYPE 438  85
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               14               523 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5                85 
$`4P GAIN MUTATED`
TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-EY-A72D TCGA-A5-A0G5 TCGA-A5-A1OG TCGA-AJ-A23N 
       80.38        22.06         5.88        37.02        31.99        14.43 
TCGA-AP-A0LI TCGA-BK-A139 TCGA-BK-A4ZD TCGA-D1-A3DH TCGA-EO-A1Y5 TCGA-EO-A2CG 
       97.71        31.00        16.64        18.84        10.92        51.42 
TCGA-EY-A1GW TCGA-PG-A914 
       11.08        22.59 

$`4P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF 
       18.08        20.81        10.19       110.63        57.80        93.99 
TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 
       95.47        67.66        12.26        36.39        23.05        61.18 
TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0KB TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       27.88         1.38        27.09        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 
       12.56        14.27         1.81        19.79         4.44        47.84 
TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 
       16.93        33.30         6.21        22.78        17.88        10.19 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-FI-A2CX TCGA-FI-A2D5 
       14.40        18.87        17.92        19.89        66.77        13.84 
TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 
       73.32        36.00        23.74         0.43        39.52        10.29 
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88       149.56        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP 
      105.37       123.68        74.10        65.75        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       73.87        36.82        28.27        54.02        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       37.91        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 
       15.95        31.99        36.33        33.07       118.19        66.15 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ 
       28.64        24.72        34.95        25.51        14.96        11.21 
TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       18.41        20.25        10.26        21.14        19.79        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       34.36        34.16        18.12        18.90        33.90         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-A8CV 
       16.87        22.32        12.82        20.78         2.70        35.11 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        0.13       129.80        21.99        23.31        86.07        48.03 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       63.91        45.53        36.89        23.87        12.62        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        66.25        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       46.72        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       80.78        49.22        25.08        71.67        90.97        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        60.23 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
       45.86        27.85        51.12        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        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        61.08        35.74        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        77.39        13.28        32.91        34.65        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       26.37        32.02        25.91        34.09        76.83        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       73.41        80.25        37.58         4.77        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       40.80        81.37        34.32        46.49        38.24        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-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 
       86.37        55.30        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       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        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       85.78        52.04        32.09        77.23        73.28        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       225.50 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      102.31        50.89        51.45        14.70        48.43        11.87 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       52.54        31.36       136.60        96.30        93.50        71.84 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       39.35        27.65        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        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       63.68        74.63        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        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        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-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
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        22.39 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        31.76        24.99 
TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       24.13        13.18        10.03         9.86        46.95        24.33 
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        92.88       114.90        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        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       63.58        83.64        86.99        66.48        16.83        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-A2G6 TCGA-D1-A2G7 
       15.06         1.05         3.95        48.79         8.48        58.95 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS 
       15.88         4.27        17.29         2.20        71.61       109.08 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH 
      100.83        89.33        10.92        27.16        25.91        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        79.10        58.95         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       45.57        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        50.73        35.15        38.07        27.16 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       46.42        26.96        22.26        16.34        38.47        51.09 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99        54.15        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.34        23.90        33.34        32.71        19.27        18.84 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX 
       17.62        22.03        16.11        32.78        15.81        37.05 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       19.33        12.59        22.82        20.05        45.76        31.04 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A 
       29.10        27.35        32.52        11.38        14.14        14.70 
TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 
       16.96        68.38        39.88        77.33         7.99        25.22 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 
       96.69        59.01         9.34        28.93        30.67        59.28 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 
       41.56        78.38         1.74        17.75        14.04        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        21.30        38.70 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        8.19        17.16         6.97        22.65        39.95        24.95 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       23.64        14.83         4.44        20.75        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             5.88              0.07 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            97.71            225.50 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           22.325            29.950 
[1] "5.9 - 97.7 (22.3)"  "0.1 - 225.5 (29.9)"
[1] "hr=" "2.7"
D7V2, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     6   8
  4P GAIN WILD-TYPE 284 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      6    8
  4P GAIN WILD-TYPE  284  216
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                6               284
  YES               8               216
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  4P GAIN MUTATED                                         5
  4P GAIN WILD-TYPE                                     399
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  4P GAIN MUTATED                               0
  4P GAIN WILD-TYPE                            22
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  4P GAIN MUTATED                                   9
  4P GAIN WILD-TYPE                               104
D7V3, multiclass
                                         clus
vv                                        4P GAIN MUTATED 4P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               5               399
  MIXED SEROUS AND ENDOMETRIOID                         0                22
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     9               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"
                   vv
clus                 R0  R1  R2  RX
  4P GAIN MUTATED    10   1   2   0
  4P GAIN WILD-TYPE 361  21  14  40
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0              10               361
  R1               1                21
  R2               2                14
  RX               0                40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     6   2
  4Q GAIN WILD-TYPE 441  88
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                8               529 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                88 
$`4Q GAIN MUTATED`
TCGA-AX-A3G3 TCGA-A5-A0G5 TCGA-AP-A0LI TCGA-B5-A0K8 TCGA-BK-A139 TCGA-BK-A4ZD 
        1.38        37.02        97.71        27.85        31.00        16.64 
TCGA-EO-A2CG TCGA-EY-A1GW 
       51.42        11.08 

$`4Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF 
       18.08        20.81        10.19       110.63        57.80        93.99 
TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 
       95.47        67.66        12.26        36.39        23.05        61.18 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       27.88        80.38        27.09        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 
       51.55        12.56        14.27         1.81        19.79         4.44 
TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ 
       47.84        16.93        33.30         6.21        22.78        17.88 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D 
       10.19        14.40        18.87        17.92        19.89         5.88 
TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E 
       66.77        13.84        73.32        36.00        23.74         0.43 
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA 
       39.52        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-A0GJ 
       32.78       112.54       105.37       123.68        74.10        65.75 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        73.87        36.82        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        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        31.99        31.99        36.33 
TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
       33.07       118.19        66.15        28.64        24.72        34.95 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N 
       25.51        14.96        11.21        18.41        20.25        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
       10.26        21.14        19.79        35.15        34.36        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
       18.12        18.90        33.90         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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 
       12.82        20.78         2.70        35.11         0.13       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
       21.99        23.31        86.07        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       36.89        23.87        12.62        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL 
      117.99       110.37        66.25        36.36        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        90.97        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        60.23        45.86        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       51.12        21.90        36.13         0.56        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        80.55        88.24        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       79.46        49.87        57.47        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       61.08        35.74        37.78        43.82        40.11        77.39 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       13.28        32.91        34.65        25.51        26.37        32.02 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       25.91        34.09        76.83        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA 
       37.58         4.77        30.12        71.24        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       34.32        46.49        38.24        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-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       18.35        14.47         0.39        56.91        86.37        55.30 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       59.24        86.01        58.75        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       13.45        59.84       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        73.64        61.68        85.78        52.04        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       77.23        73.28        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       225.50       102.31        50.89        51.45 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       14.70        48.43        11.87        52.54        31.36       136.60 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 
       96.30        93.50        71.84        39.35        27.65        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-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        35.21        71.24        63.68        74.63        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        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       14.01        15.45        15.45         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        22.39        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 
       35.08        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        24.33        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 
       92.88       114.90        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        89.59        63.58        83.64        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        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-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-A3DH 
       48.79         8.48        58.95        15.88         4.27        18.84 
TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV 
       17.29         2.20        71.61       109.08       100.83        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       10.92        27.16        25.91        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-EC-A1NJ 
       23.38        79.10        58.95         2.37        45.57        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        50.73        35.15        38.07        27.16        46.42 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 
       26.96        22.26        16.34        38.47        51.09        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       54.15        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR 
       23.90        33.34        32.71        19.27        18.84        17.62 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 
       22.03        16.11        32.78        15.81        37.05        19.33 
TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       12.59        22.82        20.05        45.76        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 
       27.35        32.52        11.38        14.14        14.70        16.96 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU 
       68.38        39.88        77.33         7.99        25.22        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV 
       59.01         9.34        28.93        30.67        59.28        41.56 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 
       78.38         1.74        17.75        14.04        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        21.30        38.70        22.59 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        8.19        17.16         6.97        22.65        39.95        24.95 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       23.64        14.83         4.44        20.75        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             1.38              0.07 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            97.71            225.50 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           29.425            29.920 
[1] "1.4 - 97.7 (29.4)"  "0.1 - 225.5 (29.9)"
[1] "hr=" "1.7"
D8V2, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     5   2
  4Q GAIN WILD-TYPE 285 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      5    2
  4Q GAIN WILD-TYPE  285  222
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                5               285
  YES               2               222
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  4Q GAIN MUTATED                                         3
  4Q GAIN WILD-TYPE                                     401
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  4Q GAIN MUTATED                               0
  4Q GAIN WILD-TYPE                            22
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  4Q GAIN MUTATED                                   5
  4Q GAIN WILD-TYPE                               108
D8V3, multiclass
                                         clus
vv                                        4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               3               401
  MIXED SEROUS AND ENDOMETRIOID                         0                22
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     5               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"
                   vv
clus                 R0  R1  R2  RX
  4Q GAIN MUTATED     4   1   1   0
  4Q GAIN WILD-TYPE 367  21  15  40
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0               4               367
  R1               1                21
  R2               1                15
  RX               0                40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    32  20
  5P GAIN WILD-TYPE 415  70
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               52               485 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               20                70 
$`5P GAIN MUTATED`
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AX-A3G3 TCGA-BG-A0M6 TCGA-BG-A0VT TCGA-EY-A547 
       20.81        10.19         1.38        22.06        51.55        17.92 
TCGA-KP-A3VZ TCGA-A5-A0G5 TCGA-A5-A1OH TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A2QK 
       23.74        37.02        36.33        14.96        14.43        21.14 
TCGA-AP-A0LH TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AX-A0IS TCGA-AX-A0IW TCGA-AX-A2H2 
       36.36        31.30        46.78        61.08        37.78         4.77 
TCGA-AX-A2H5 TCGA-AX-A2HK TCGA-AX-A3GI TCGA-B5-A1MY TCGA-B5-A5OD TCGA-BG-A0M3 
       71.24         2.96         0.39        11.87        34.13        35.21 
TCGA-BG-A18C TCGA-BK-A139 TCGA-BS-A0TE TCGA-BS-A0TI TCGA-D1-A16N TCGA-D1-A1NW 
       15.45        31.00         4.80        61.87        31.07         0.72 
TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY 
       18.84        17.29        35.38         9.37        12.39       110.10 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A3B1 TCGA-EY-A1GC TCGA-EY-A1GR 
       79.10        10.92        37.71        26.96        54.15        17.62 
TCGA-EY-A1GS TCGA-EY-A2ON TCGA-EY-A3QX TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       22.03        20.05        32.52        77.33        59.01         9.34 
TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-JU-AAVI TCGA-PG-A915 
       28.93        30.67        17.75         8.19 

$`5P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B 
       18.08       110.63        57.80        93.99        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-B5-A0JN 
       12.26        36.39        23.05        61.18        27.88        80.38 
TCGA-B5-A0KB TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 
       27.09        66.41        61.87        12.56        14.27         1.81 
TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 
       19.79         4.44        47.84        16.93        33.30         6.21 
TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A549 
       22.78        17.88        10.19        14.40        18.87        19.89 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E 
        5.88        66.77        13.84        73.32        36.00         0.43 
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA 
       39.52        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-A0GJ 
       32.78       112.54       105.37       123.68        74.10        65.75 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        73.87        36.82        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ 
       29.06        42.35        15.95        31.99        31.99        33.07 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
      118.19        66.15        28.64        24.72        34.95        25.51 
TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN 
       11.21        18.41        20.25        10.26        19.79        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       34.36        34.16        18.12        18.90        33.90         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-A8CV 
       16.87        22.32        12.82        20.78         2.70        35.11 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        0.13       129.80        21.99        23.31        86.07        48.03 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       63.91        45.53        36.89        23.87        12.62        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LI 
       48.79       125.42       117.99       110.37        66.25        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       46.72        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       80.78        49.22        25.08        71.67        90.97        55.89 
TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       35.54        49.15         6.71        60.23        45.86        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       51.12        21.90        36.13         0.56        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        80.55        88.24        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       79.46        49.87        57.47        27.39        30.02        60.66 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       35.74        43.82        40.11        77.39        13.28        32.91 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       34.65        25.51        26.37        32.02        25.91        34.09 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H4 
       76.83        85.48        73.41        80.25        37.58        30.12 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       40.80        81.37        34.32        46.49        38.24        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-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
       43.82         0.20        20.52         0.30         0.26         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        86.37        55.30 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       59.24        86.01        58.75        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       27.85        13.45        59.84       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        73.64        61.68        85.78        52.04 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        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       225.50       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       51.45        14.70        48.43        52.54        31.36       136.60 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 
       96.30        93.50        71.84        39.35        27.65        29.65 
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-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       71.24        63.68        74.63        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        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        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-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        22.39 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        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-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 
       24.33        85.55        78.21        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        92.88       114.90        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        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       83.64        86.99        66.48        16.83        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-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-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-A1NX 
       24.30         2.33        22.92         1.41        13.22        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-DF-A2KN 
       48.79         8.48        58.95        15.88         4.27         2.20 
TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
       71.61       109.08       100.83        89.33        10.92        27.16 
TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QU 
       25.91        16.31        39.29        36.62        24.30        31.10 
TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       23.38        58.95         2.37        45.57        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       16.80        49.15        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        50.73 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KW 
       35.15        38.07        27.16        46.42        22.26        16.34 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       38.47        51.09        14.99        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       23.34        23.34        23.90        33.34        32.71        19.27 
TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       18.84        16.11        32.78        15.81        11.08        37.05 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       19.33        12.59        22.82        45.76        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY 
       27.35        11.38        14.14        14.70        16.96        68.38 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2F9 TCGA-FI-A3PV 
       39.88         7.99        25.22        96.69        59.28        41.56 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 
       78.38         1.74        14.04        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        21.30        38.70        22.59        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        22.65        39.95        24.95        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44        20.75        18.28         0.07         0.23 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.39              0.07 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            110.1             225.5 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            22.90             30.08 
[1] "0.4 - 110.1 (22.9)" "0.1 - 225.5 (30.1)"
[1] "hr=" "3.4"
D9V2, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    29  19
  5P GAIN WILD-TYPE 261 205
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     29   19
  5P GAIN WILD-TYPE  261  205
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               29               261
  YES              19               205
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  5P GAIN MUTATED                                        16
  5P GAIN WILD-TYPE                                     388
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  5P GAIN MUTATED                               3
  5P GAIN WILD-TYPE                            19
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  5P GAIN MUTATED                                  33
  5P GAIN WILD-TYPE                                80
D9V3, multiclass
                                         clus
vv                                        5P GAIN MUTATED 5P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              16               388
  MIXED SEROUS AND ENDOMETRIOID                         3                19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    33                80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  5P GAIN MUTATED    37   2   5   4
  5P GAIN WILD-TYPE 334  20  11  36
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0              37               334
  R1               2                20
  R2               5                11
  RX               4                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    13   7
  5Q GAIN WILD-TYPE 434  83
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               20               517 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                7                83 
$`5Q GAIN MUTATED`
TCGA-AX-A3G3 TCGA-BG-A0VT TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AX-A0IS TCGA-B5-A1MY 
        1.38        51.55        31.30        46.78        61.08        11.87 
TCGA-BG-A18C TCGA-BS-A0TE TCGA-D1-A16N TCGA-D1-A3JQ TCGA-DI-A1NN TCGA-E6-A1LZ 
       15.45         4.80        31.07        17.29        35.38        79.10 
TCGA-EO-A1Y5 TCGA-EO-A3B1 TCGA-EY-A1GC TCGA-EY-A1GR TCGA-EY-A1GS TCGA-FI-A2EW 
       10.92        26.96        54.15        17.62        22.03        59.01 
TCGA-FI-A2EY TCGA-JU-AAVI 
       28.93        17.75 

$`5Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF 
       18.08        20.81        10.19       110.63        57.80        93.99 
TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 
       95.47        67.66        12.26        36.39        23.05        61.18 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       27.88        80.38        27.09        22.06        66.41        61.87 
TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 
       12.56        14.27         1.81        19.79         4.44        47.84 
TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 
       16.93        33.30         6.21        22.78        17.88        10.19 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX 
       14.40        18.87        17.92        19.89         5.88        66.77 
TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C 
       13.84        73.32        36.00        23.74         0.43        39.52 
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-A0GJ 
       32.78       112.54       105.37       123.68        74.10        65.75 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        73.87        36.82        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        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        31.99        31.99        36.33 
TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
       33.07       118.19        66.15        28.64        24.72        34.95 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N 
       25.51        14.96        11.21        18.41        20.25        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
       10.26        21.14        19.79        35.15        34.36        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
       18.12        18.90        33.90         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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 
       12.82        20.78         2.70        35.11         0.13       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
       21.99        23.31        86.07        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       36.89        23.87        12.62        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      117.99       110.37        66.25        36.36        97.71        46.72 
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-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP 
       49.22        25.08        71.67        90.97        55.89        35.54 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        60.23        45.86        27.85        51.12 
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        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       80.55        88.24        71.51        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IU 
       49.87        57.47        27.39        30.02        60.66        35.74 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        77.39        13.28        32.91 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       34.65        25.51        26.37        32.02        25.91        34.09 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 
       76.83        85.48        73.41        80.25        37.58         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-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       38.24        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-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
        0.39        56.91        86.37        55.30        59.24        86.01 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       58.75        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       59.84       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 
       73.64        61.68        85.78        52.04        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       73.28        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       225.50       102.31        50.89        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       48.43        52.54        31.36       136.60        96.30        93.50 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       71.84        39.35        27.65        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-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       71.24        63.68        74.63        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        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        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-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        22.39 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       35.90        34.98        35.90        35.08        31.00        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        24.33        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        92.88       114.90 
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 
       89.59        63.58        83.64        86.99        66.48        16.83 
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-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74        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-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       11.51        29.92        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-A2G6 TCGA-D1-A2G7 
       15.06         1.05         3.95        48.79         8.48        58.95 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS 
       15.88         4.27        18.84         2.20        71.61       109.08 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH 
      100.83        89.33        10.92        27.16        25.91        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-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
      110.10        23.38        58.95         2.37        45.57        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        50.73        35.15        38.07        27.16        46.42 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD 
       22.26        16.34        38.47        51.09        14.99        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        23.90        33.34 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       32.71        19.27        18.84        16.11        32.78        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON 
       11.08        37.05        19.33        12.59        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        32.52        11.38 
TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
       14.14        14.70        16.96        68.38        39.88        77.33 
TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2F8 TCGA-FI-A2F9 
        7.99        25.22        96.69         9.34        30.67        59.28 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 
       41.56        78.38         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-A914 
       26.10        18.21        23.24        21.30        38.70        22.59 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        8.19        17.16         6.97        22.65        39.95        24.95 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       23.64        14.83         4.44        20.75        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             1.38              0.07 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             79.1             225.5 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           27.945            29.950 
[1] "1.4 - 79.1 (27.9)"  "0.1 - 225.5 (29.9)"
[1] "hr=" "2.6"
D10V2, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    12   7
  5Q GAIN WILD-TYPE 278 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     12    7
  5Q GAIN WILD-TYPE  278  217
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               12               278
  YES               7               217
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  5Q GAIN MUTATED                                         8
  5Q GAIN WILD-TYPE                                     396
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  5Q GAIN MUTATED                               0
  5Q GAIN WILD-TYPE                            22
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  5Q GAIN MUTATED                                  12
  5Q GAIN WILD-TYPE                               101
D10V3, multiclass
                                         clus
vv                                        5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               8               396
  MIXED SEROUS AND ENDOMETRIOID                         0                22
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    12               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"
                   vv
clus                 R0  R1  R2  RX
  5Q GAIN MUTATED    14   1   2   1
  5Q GAIN WILD-TYPE 357  21  14  39
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              14               357
  R1               1                21
  R2               2                14
  RX               1                39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    62  19
  6P GAIN WILD-TYPE 385  71
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               81               456 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               19                71 
$`6P GAIN MUTATED`
TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M8 TCGA-D1-A2G5 TCGA-EY-A1GQ 
        1.38        80.38        27.09        66.41        47.84        17.88 
TCGA-EY-A214 TCGA-FI-A2CX TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A1OG 
       14.40        66.77        23.74        39.52        37.02        31.99 
TCGA-A5-A1OH TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A8CW 
       36.33        20.25        34.16        18.12        18.90         0.13 
TCGA-AP-A0L8 TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A1DQ TCGA-AP-A5FX TCGA-AX-A06J 
       48.79        97.71        33.40        46.78        36.13        30.02 
TCGA-AX-A0IW TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A2H7 TCGA-AX-A2HA 
       37.78        32.02        25.91        76.83        40.80        81.37 
TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3GI TCGA-B5-A0JS TCGA-B5-A11E TCGA-B5-A11I 
       43.82        20.52         0.39        86.37        59.84        75.72 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A1MU TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OD 
       77.23        73.28        50.89        31.36        29.65        34.13 
TCGA-BG-A18C TCGA-BK-A0C9 TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0U9 
       15.45        35.90        35.08        24.13        16.64        92.88 
TCGA-BS-A0V8 TCGA-D1-A168 TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A3DH TCGA-DF-A2KS 
       83.64        36.10        31.07        18.67        18.84       109.08 
TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QY TCGA-EO-A22Y TCGA-EO-A2CG 
       25.91        35.38         9.37       110.10        51.52        51.42 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GR 
       26.96        22.26        16.34        54.15        19.27        17.62 
TCGA-EY-A2ON TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A54A TCGA-FI-A2D0 TCGA-FI-A2EW 
       20.05        27.35        32.52        14.70        39.88        59.01 
TCGA-FI-A2EY TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-KP-A3W3 TCGA-PG-A7D5 
       28.93        59.28        78.38        14.04        26.10        38.70 
TCGA-PG-A915 TCGA-QS-A8F1 TCGA-SL-A6J9 
        8.19         4.44         0.07 

$`6P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF 
       18.08        20.81        10.19       110.63        57.80        93.99 
TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 
       95.47        67.66        12.26        36.39        23.05        61.18 
TCGA-AX-A2HF TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 
       27.88        22.06        61.87        51.55        12.56        14.27 
TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 
        1.81        19.79         4.44        16.93        33.30         6.21 
TCGA-EY-A1GK TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D 
       22.78        10.19        18.87        17.92        19.89         5.88 
TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 
       13.84        73.32        36.00         0.43        10.29       106.88 
TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
      149.56        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
      123.68        74.10        65.75        60.53        46.55        73.87 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       36.82        28.27        54.02        23.21        68.65        37.91 
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-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
       31.99        33.07       118.19        66.15        28.64        24.72 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23N 
       34.95        25.51        14.96        11.21        18.41        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BK 
       10.26        21.14        19.79        35.15        34.36        33.90 
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-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-A8CV TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       35.11       129.80        21.99        23.31        86.07        48.03 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       63.91        45.53        36.89        23.87        12.62        20.91 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
      125.42       117.99       110.37        66.25        36.36        46.72 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       83.97        27.12        82.52        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        90.97        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        60.23        45.86        27.85        51.12 
TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       21.90         0.56        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ 
       57.47        27.39        60.66        61.08        35.74        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        77.39        13.28        32.91        34.65        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       26.37        34.09        85.48        73.41        80.25        37.58 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG 
        4.77        30.12        71.24        34.32        46.49        38.24 
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-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
        0.20         0.56         0.20         0.30         0.26         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JT TCGA-B5-A0JU 
        1.18        18.35        14.47        56.91        55.30        59.24 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.01        58.75        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
       13.45       185.79       113.36        88.34        54.44        73.64 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11U TCGA-B5-A11V 
       61.68        85.78        52.04        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       225.50       102.31 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 
       51.45        14.70        48.43        11.87        52.54       136.60 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC 
       96.30        93.50        71.84        39.35        27.65        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-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       71.24        63.68        74.63        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        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        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-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        22.39 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F 
       34.98        35.90        31.00        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        24.33        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       114.90        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        89.59        63.58        86.99        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        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-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-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V 
       11.51        29.92        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-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-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        1.05         3.95        48.79         8.48        58.95        15.88 
TCGA-D1-A3DG TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KU TCGA-DF-A2KV 
        4.27        17.29         2.20        71.61       100.83        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-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       12.39        31.10        23.38        79.10        58.95         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       45.57        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        50.73        35.15        38.07        27.16 
TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       46.42        38.47        51.09        14.99        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM 
       27.16        23.34        23.34        23.90        33.34        32.71 
TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       18.84        22.03        16.11        32.78        15.81        11.08 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP 
       37.05        19.33        12.59        22.82        45.76        31.04 
TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D2 
       29.10        11.38        14.14        16.96        68.38        77.33 
TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2F8 TCGA-FI-A3PV 
        7.99        25.22        96.69         9.34        30.67        41.56 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A5BC 
        1.74        17.75        13.28         9.47        18.21        23.24 
TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       21.30        22.59        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       24.95        23.64        14.83        20.75        18.28         0.23 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.07              0.20 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            110.1             225.5 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           33.400            28.865 
[1] "0.1 - 110.1 (33.4)" "0.2 - 225.5 (28.9)"
[1] "hr=" "1.4"
D11V2, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    35  41
  6P GAIN WILD-TYPE 255 183
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     35   41
  6P GAIN WILD-TYPE  255  183
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               35               255
  YES              41               183
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  6P GAIN MUTATED                                        40
  6P GAIN WILD-TYPE                                     364
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  6P GAIN MUTATED                               1
  6P GAIN WILD-TYPE                            21
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  6P GAIN MUTATED                                  40
  6P GAIN WILD-TYPE                                73
D11V3, multiclass
                                         clus
vv                                        6P GAIN MUTATED 6P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              40               364
  MIXED SEROUS AND ENDOMETRIOID                         1                21
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    40                73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  6P GAIN MUTATED    46   2   3  11
  6P GAIN WILD-TYPE 325  20  13  29
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0              46               325
  R1               2                20
  R2               3                13
  RX              11                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"

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    50  16
  6Q GAIN WILD-TYPE 397  74
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               66               471 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               16                74 
$`6Q GAIN MUTATED`
TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M8 TCGA-D1-A2G5 TCGA-EY-A1GQ TCGA-EY-A214 
       80.38        27.09        66.41        47.84        17.88        14.40 
TCGA-FI-A2CX TCGA-KP-A3VZ TCGA-A5-A0G5 TCGA-AJ-A23M TCGA-AJ-A3BI TCGA-AJ-A8CW 
       66.77        23.74        37.02        20.25        18.90         0.13 
TCGA-AP-A0L8 TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A1DQ TCGA-AP-A5FX TCGA-AX-A06J 
       48.79        97.71        33.40        46.78        36.13        30.02 
TCGA-AX-A0IW TCGA-AX-A1CC TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A3FW TCGA-AX-A3FX 
       37.78        25.91        40.80        81.37         0.56        43.82 
TCGA-AX-A3G1 TCGA-AX-A3GI TCGA-B5-A11E TCGA-B5-A11I TCGA-B5-A11R TCGA-B5-A1MU 
       20.52         0.39        59.84        75.72        77.23        50.89 
TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A18C TCGA-BK-A0C9 TCGA-BK-A0CC 
       31.36        29.65        34.13        15.45        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A168 
       31.00        24.13        16.64        92.88        83.64        36.10 
TCGA-D1-A16N TCGA-D1-A16S TCGA-DF-A2KR TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-DI-A2QY 
       31.07        18.67        71.61        25.91        35.38       110.10 
TCGA-E6-A1LZ TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3KU TCGA-EY-A1GC TCGA-EY-A1GO 
       79.10        51.52        51.42        22.26        54.15        19.27 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A2ON TCGA-EY-A3L3 TCGA-EY-A54A TCGA-FI-A2D0 
       17.62        22.03        20.05        27.35        14.70        39.88 
TCGA-FI-A2EW TCGA-FI-A2F8 TCGA-FI-A3PX TCGA-PG-A915 TCGA-QS-A8F1 TCGA-SL-A6J9 
       59.01        30.67        78.38         8.19         4.44         0.07 

$`6Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF 
       18.08        20.81        10.19       110.63        57.80        93.99 
TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 
       95.47        67.66        12.26        36.39        23.05        61.18 
TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV 
       27.88         1.38        22.06        61.87        51.55        12.56 
TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A3JP TCGA-E6-A8L9 
       14.27         1.81        19.79         4.44        16.93        33.30 
TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 
        6.21        22.78        10.19        18.87        17.92        19.89 
TCGA-EY-A72D TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5B-A90C 
        5.88        13.84        73.32        36.00         0.43        39.52 
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-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN 
      112.54       105.37       123.68        74.10        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        73.87        36.82        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ 
       42.35        15.95        31.99        31.99        36.33        33.07 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
      118.19        66.15        28.64        24.72        34.95        25.51 
TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
       14.96        11.21        18.41        14.43        10.26        21.14 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BK 
       19.79        35.15        34.36        34.16        18.12        33.90 
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-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-A8CV TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       35.11       129.80        21.99        23.31        86.07        48.03 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       63.91        45.53        36.89        23.87        12.62        20.91 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
      125.42       117.99       110.37        66.25        36.36        46.72 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       83.97        27.12        82.52        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        90.97        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        60.23        45.86        27.85        51.12 
TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       21.90         0.56        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ 
       57.47        27.39        60.66        61.08        35.74        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        77.39        13.28        32.91        34.65        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       26.37        32.02        34.09        76.83        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HC 
       80.25        37.58         4.77        30.12        71.24        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       46.49        38.24        17.75        30.74         2.96        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G4 TCGA-AX-A3G6 
       64.93         0.23         0.20         0.20         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        86.37 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       55.30        59.24        86.01        58.75        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        27.85        13.45       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        73.64        61.68        85.78        52.04        32.09 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       73.28        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       225.50       102.31        51.45        14.70        48.43 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       11.87        52.54       136.60        96.30        93.50        71.84 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       39.35        27.65        41.06        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        71.24        63.68        74.63 
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-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
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-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       14.73        14.01        15.45         9.57        20.02        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B 
       20.12        11.31        22.39        34.98        35.90        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        24.33 
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       114.90        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        89.59        63.58 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       86.99        66.48        16.83        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-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        48.79         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN 
       58.95        15.88         4.27        18.84        17.29         2.20 
TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
      109.08       100.83        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-EC-A1NJ TCGA-EC-A1QX 
       23.38        58.95         2.37        45.57        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-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       66.90        46.26        57.60        19.40        34.39        50.73 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KW 
       35.15        38.07        27.16        46.42        26.96        16.34 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       38.47        51.09        14.99        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP 
       23.34        23.34        23.90        33.34        32.71        18.84 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        32.78        15.81        11.08        37.05        19.33 
TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX 
       12.59        22.82        45.76        31.04        29.10        32.52 
TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2D4 
       11.38        14.14        16.96        68.38        77.33         7.99 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F9 TCGA-FI-A3PV 
       25.22        96.69         9.34        28.93        59.28        41.56 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 
        1.74        17.75        14.04        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        21.30        38.70        22.59        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        22.65        39.95        24.95        23.64        14.83 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       20.75        18.28         0.23 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.07              0.20 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            110.1             225.5 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           33.765            29.060 
[1] "0.1 - 110.1 (33.8)" "0.2 - 225.5 (29.1)"
[1] "hr=" "1.5"
D12V2, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    31  30
  6Q GAIN WILD-TYPE 259 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     31   30
  6Q GAIN WILD-TYPE  259  194
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               31               259
  YES              30               194
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  6Q GAIN MUTATED                                        35
  6Q GAIN WILD-TYPE                                     369
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  6Q GAIN MUTATED                               1
  6Q GAIN WILD-TYPE                            21
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  6Q GAIN MUTATED                                  30
  6Q GAIN WILD-TYPE                                83
D12V3, multiclass
                                         clus
vv                                        6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              35               369
  MIXED SEROUS AND ENDOMETRIOID                         1                21
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    30                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"
                   vv
clus                 R0  R1  R2  RX
  6Q GAIN MUTATED    37   1   3  10
  6Q GAIN WILD-TYPE 334  21  13  30
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              37               334
  R1               1                21
  R2               3                13
  RX              10                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"

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    50  17
  7P GAIN WILD-TYPE 397  73
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               67               470 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               17                73 
$`7P GAIN MUTATED`
TCGA-2E-A9G8 TCGA-A5-AB3J TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AX-A3G3 
       41.06        16.83        20.81        10.19        57.80         1.38 
TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A3JP TCGA-EY-A1G7 TCGA-EY-A549 
       61.87        51.55        12.56        16.93         6.21        19.89 
TCGA-EY-A72D TCGA-A5-A0GV TCGA-A5-A3LO TCGA-AJ-A2QN TCGA-AJ-A3BF TCGA-AJ-A3BI 
        5.88        54.02        25.51        35.15        18.12        18.90 
TCGA-AJ-A3EJ TCGA-AJ-A3NG TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A3K1 
        1.64        15.62       125.42        97.71        33.40        21.90 
TCGA-AX-A05W TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G6 TCGA-B5-A0JR TCGA-B5-A0JT 
       80.55         0.20        20.52         0.26        56.91        55.30 
TCGA-B5-A0K0 TCGA-B5-A0K4 TCGA-B5-A1MV TCGA-B5-A1MY TCGA-BG-A0M3 TCGA-BG-A0RY 
       48.59        57.76        51.45        11.87        35.21        15.42 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TE 
       23.70        35.90        31.00        24.13        16.64         4.80 
TCGA-BS-A0TI TCGA-BS-A0UT TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A17C TCGA-D1-A17R 
       61.87        72.72        83.64        22.55         0.99        11.15 
TCGA-D1-A1NY TCGA-D1-A2G6 TCGA-D1-A3JQ TCGA-EO-A1Y5 TCGA-EO-A22Y TCGA-EY-A1GH 
       16.87         8.48        17.29        10.92        51.52        23.34 
TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A2ON TCGA-EY-A54A 
       33.34        19.27        11.08        37.05        20.05        14.70 
TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W1 
       77.33        96.69        78.38        17.75        14.04         9.47 
TCGA-PG-A914 
       22.59 

$`7P GAIN WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-AJ-A2QM TCGA-AJ-A3BG TCGA-AP-A053 
       88.18        60.53        30.15        29.39        18.08       110.63 
TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR 
       93.99        95.47        67.66        12.26        36.39        23.05 
TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 
       61.18        27.88        80.38        27.09        22.06        66.41 
TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 
       14.27         1.81        19.79         4.44        47.84        33.30 
TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 
       22.78        17.88        10.19        14.40        18.87        17.92 
TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E 
       66.77        13.84        73.32        36.00        23.74         0.43 
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       39.52        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       123.68        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       65.75        60.53        46.55        73.87        36.82        28.27 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        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        31.99        31.99        36.33 
TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
       33.07       118.19        66.15        28.64        24.72        34.95 
TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O 
       14.96        11.21        18.41        20.25        14.43        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BK TCGA-AJ-A3EK 
       21.14        19.79        34.36        34.16        33.90        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-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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 
       12.82        20.78         2.70        35.11         0.13       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
       21.99        23.31        86.07        48.03        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        12.62        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        66.25        36.36        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       82.52        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       90.97        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        60.23        45.86        27.85        51.12        36.13 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z 
        0.56        13.58        33.21        29.69        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        61.08        35.74        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        77.39        13.28        32.91        34.65        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       26.37        32.02        25.91        34.09        76.83        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       73.41        80.25        37.58         4.77        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       40.80        81.37        34.32        46.49        38.24        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-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.56        43.82         0.30         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       14.47         0.39        86.37        59.24        86.01        58.75 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 
       69.27        71.44        36.49        72.62        27.29        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       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        73.64        61.68        85.78 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       52.04        32.09        77.23        73.28        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       225.50       102.31 
TCGA-B5-A1MU TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       50.89        14.70        48.43        52.54        31.36       136.60 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 
       96.30        93.50        71.84        39.35        27.65        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-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       20.94        71.24        63.68        74.63        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       48.56        23.47        43.30        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       20.28        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
       15.45         9.57        20.02        20.12        11.31        22.39 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F 
       34.98        35.90        35.08        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        24.33        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        92.88 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV TCGA-BS-A0V4 
      114.90        85.84        82.39        81.57        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        86.99        66.48        16.83        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-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-A17D TCGA-D1-A17F TCGA-D1-A17H 
       14.73         1.58         7.00        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-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        48.79 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KN TCGA-DF-A2KR 
       58.95        15.88         4.27        18.84         2.20        71.61 
TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 
      109.08       100.83        89.33        10.92        27.16        25.91 
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        79.10        58.95 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 
        2.37        45.57        16.04         7.36        16.80        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-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       51.42        19.40        34.39        50.73        35.15        38.07 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX 
       27.16        46.42        26.96        22.26        16.34        38.47 
TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       51.09        14.99        54.15        53.88        24.36        27.16 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS 
       23.34        23.90        32.71        18.84        17.62        22.03 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM 
       16.11        32.78        15.81        19.33        12.59        22.82 
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        32.52        11.38 
TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 
       14.14        16.96        68.38        39.88         7.99        25.22 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV 
       59.01         9.34        28.93        30.67        59.28        41.56 
TCGA-H5-A2HR TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
        1.74        13.28        26.10        18.21        23.24        21.30 
TCGA-PG-A7D5 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       38.70         8.19        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       24.95        23.64        14.83         4.44        20.75        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.20              0.07 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           125.42            225.50 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           21.900            30.295 
[1] "0.2 - 125.4 (21.9)" "0.1 - 225.5 (30.3)"
[1] "hr=" "2"  
D13V2, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    35  28
  7P GAIN WILD-TYPE 255 196
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     35   28
  7P GAIN WILD-TYPE  255  196
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               35               255
  YES              28               196
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  7P GAIN MUTATED                                        42
  7P GAIN WILD-TYPE                                     362
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  7P GAIN MUTATED                               4
  7P GAIN WILD-TYPE                            18
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  7P GAIN MUTATED                                  22
  7P GAIN WILD-TYPE                                91
D13V3, multiclass
                                         clus
vv                                        7P GAIN MUTATED 7P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              42               362
  MIXED SEROUS AND ENDOMETRIOID                         4                18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    22                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"
                   vv
clus                 R0  R1  R2  RX
  7P GAIN MUTATED    48   2   3   2
  7P GAIN WILD-TYPE 323  20  13  38
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0              48               323
  R1               2                20
  R2               3                13
  RX               2                38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    46  18
  7Q GAIN WILD-TYPE 401  72
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               64               473 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               18                72 
$`7Q GAIN MUTATED`
TCGA-2E-A9G8 TCGA-A5-AB3J TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AX-A3G3 TCGA-BG-A0MS 
       41.06        16.83        20.81        10.19         1.38        61.87 
TCGA-BG-A0VT TCGA-D1-A3JP TCGA-EY-A1G7 TCGA-EY-A549 TCGA-EY-A72D TCGA-KP-A3VZ 
       51.55        16.93         6.21        19.89         5.88        23.74 
TCGA-A5-A0GV TCGA-A5-A3LP TCGA-AJ-A2QN TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3NG 
       54.02        14.96        35.15        18.90         1.64        15.62 
TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A3K1 TCGA-AX-A05W TCGA-AX-A2HJ 
      125.42        97.71        33.40        21.90        80.55        30.74 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JT 
        0.20        20.52         0.26         0.39        56.91        55.30 
TCGA-B5-A0K0 TCGA-B5-A0K4 TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MY TCGA-BG-A0M3 
       48.59        57.76        50.89        51.45        11.87        35.21 
TCGA-BG-A0RY TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A4ZD TCGA-BS-A0TE TCGA-BS-A0TI 
       15.42        23.70        35.90        16.64         4.80        61.87 
TCGA-BS-A0UT TCGA-D1-A0ZN TCGA-D1-A0ZZ TCGA-D1-A17C TCGA-D1-A17R TCGA-D1-A1NY 
       72.72        16.83        22.55         0.99        11.15        16.87 
TCGA-D1-A2G6 TCGA-D1-A3JQ TCGA-EC-A1NJ TCGA-EO-A22Y TCGA-EY-A1GH TCGA-EY-A1GL 
        8.48        17.29        16.04        51.52        23.34        33.34 
TCGA-EY-A1GO TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2EY 
       19.27        11.08        37.05        14.70        77.33        28.93 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-QS-A8F1 
       17.75        14.04         9.47         4.44 

$`7Q GAIN WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-AJ-A2QM TCGA-AJ-A3BG TCGA-AP-A053 
       88.18        60.53        30.15        29.39        18.08       110.63 
TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP 
       57.80        93.99        95.47        67.66        12.26        36.39 
TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 
       23.05        61.18        27.88        80.38        27.09        22.06 
TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 
       66.41        12.56        14.27         1.81        19.79         4.44 
TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 
       47.84        33.30        22.78        17.88        10.19        14.40 
TCGA-EY-A215 TCGA-EY-A547 TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 
       18.87        17.92        66.77        13.84        73.32        36.00 
TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
        0.43        39.52        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       123.68 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       74.10        65.75        60.53        46.55        73.87        36.82 
TCGA-A5-A0GU TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       28.27        23.21        68.65        37.91        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        31.99        31.99 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
       36.33        33.07       118.19        66.15        28.64        24.72 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N 
       34.95        25.51        11.21        18.41        20.25        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF 
       10.26        21.14        19.79        34.36        34.16        18.12 
TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC 
       33.90        14.66        22.49        22.26        17.06        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       20.65        21.21        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-A8CV 
       16.87        22.32        12.82        20.78         2.70        35.11 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        0.13       129.80        21.99        23.31        86.07        48.03 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       63.91        45.53        36.89        23.87        12.62        20.91 
TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
       48.79       117.99       110.37        66.25        36.36        46.72 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       83.97        27.12        82.52        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        90.97        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        60.23        45.86        27.85 
TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       51.12        36.13         0.56        13.58        33.21        29.69 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       57.47        27.39        30.02        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        77.39        13.28        32.91 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       34.65        25.51        26.37        32.02        25.91        34.09 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 
       76.83        85.48        73.41        80.25        37.58         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-A2HG TCGA-AX-A2HH TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       38.24        17.75         2.96        31.13        64.93         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.20         0.56        43.82         0.30         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       18.35        14.47        86.37        59.24        86.01        58.75 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 
       69.27        71.44        36.49        72.62        27.29        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       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        73.64        61.68        85.78 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       52.04        32.09        77.23        73.28        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       225.50       102.31 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       14.70        48.43        52.54        31.36       136.60        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       93.50        71.84        39.35        27.65        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-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       71.24        63.68        74.63        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        59.74        21.17        20.28 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        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-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
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        22.39        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
       35.90        35.08        31.00        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        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       78.21        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-A0UV 
       92.88       114.90        85.84        82.39        81.57        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ 
       59.51        89.59        63.58        83.64        86.99        66.48 
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-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-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-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KN 
       48.79        58.95        15.88         4.27        18.84         2.20 
TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
       71.61       109.08       100.83        89.33        10.92        27.16 
TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
       25.91        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        79.10 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
       58.95         2.37        45.57         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-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       57.60        51.42        19.40        34.39        50.73        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW 
       38.07        27.16        46.42        26.96        22.26        16.34 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       38.47        51.09        14.99        54.15        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GR 
       27.16        23.34        23.90        32.71        18.84        17.62 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1H0 TCGA-EY-A210 
       22.03        16.11        32.78        15.81        19.33        12.59 
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-A548 TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 
       32.52        11.38        14.14        16.96        68.38        39.88 
TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
        7.99        25.22        96.69        59.01         9.34        30.67 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-KP-A3W0 TCGA-KP-A3W3 
       59.28        41.56        78.38         1.74        13.28        26.10 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       18.21        23.24        21.30        38.70        22.59         8.19 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       17.16         6.97        22.65        39.95        24.95        23.64 
TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83        20.75        18.28         0.07         0.23 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.20              0.07 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           125.42            225.50 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           20.205            30.670 
[1] "0.2 - 125.4 (20.2)" "0.1 - 225.5 (30.7)"
[1] "hr=" "2.4"
D14V2, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    34  24
  7Q GAIN WILD-TYPE 256 200
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     34   24
  7Q GAIN WILD-TYPE  256  200
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               34               256
  YES              24               200
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  7Q GAIN MUTATED                                        42
  7Q GAIN WILD-TYPE                                     362
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  7Q GAIN MUTATED                               4
  7Q GAIN WILD-TYPE                            18
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  7Q GAIN MUTATED                                  19
  7Q GAIN WILD-TYPE                                94
D14V3, multiclass
                                         clus
vv                                        7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              42               362
  MIXED SEROUS AND ENDOMETRIOID                         4                18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    19                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"
                   vv
clus                 R0  R1  R2  RX
  7Q GAIN MUTATED    44   1   2   2
  7Q GAIN WILD-TYPE 327  21  14  38
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0              44               327
  R1               1                21
  R2               2                14
  RX               2                38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    90  25
  8P GAIN WILD-TYPE 357  65
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              115               422 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               25                65 
$`8P GAIN MUTATED`
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-BG-A221 TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 
       20.81        10.19         1.81         4.44        47.84        33.30 
TCGA-EY-A1GQ TCGA-EY-A549 TCGA-EY-A72D TCGA-A5-A0G5 TCGA-A5-A0GE TCGA-A5-A0GW 
       17.88        19.89         5.88        37.02       105.37        23.21 
TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A2QK 
       17.59        31.99        33.07        25.51        14.96        21.14 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A3BD TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EM 
       19.79        35.15        34.16        33.90         1.64        22.26 
TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A8CW TCGA-AP-A0L9 
       20.65        15.62        14.76        16.87         0.13       125.42 
TCGA-AP-A0LD TCGA-AP-A0LO TCGA-AP-A1DO TCGA-AP-A1E0 TCGA-AP-A3K1 TCGA-AP-A5FX 
      117.99        33.40        31.30        60.23        21.90        36.13 
TCGA-AX-A1CA TCGA-AX-A1CI TCGA-AX-A1CK TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A2HA 
       32.02        85.48        80.25         4.77        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G6 TCGA-B5-A0JT 
       34.32         0.20         0.20        20.52         0.26        55.30 
TCGA-B5-A0K4 TCGA-B5-A11E TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11V 
       57.76        59.84        32.09        77.23        73.28        19.56 
TCGA-B5-A1MR TCGA-B5-A1MW TCGA-B5-A3FD TCGA-B5-A5OE TCGA-BG-A0M0 TCGA-BG-A0M2 
      225.50        14.70        39.35        34.95        19.33        20.94 
TCGA-BG-A0M4 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MQ TCGA-BG-A18C TCGA-BK-A0C9 
       71.24        74.63        10.72        59.74        15.45        35.90 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0T9 TCGA-BS-A0TE 
       35.90        35.08        31.00        16.64        46.95         4.80 
TCGA-BS-A0TG TCGA-BS-A0U9 TCGA-BS-A0UV TCGA-BS-A0VI TCGA-D1-A0ZU TCGA-D1-A15V 
       77.95        92.88        73.25        86.99        28.67        39.48 
TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16N TCGA-D1-A16R TCGA-D1-A16S 
        0.66        36.10        37.32        31.07         0.69        18.67 
TCGA-D1-A17R TCGA-D1-A1O0 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-DF-A2KR TCGA-DI-A1C3 
       11.15         2.07        48.79         8.48        71.61        24.30 
TCGA-DI-A2QU TCGA-E6-A1M0 TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22T TCGA-EO-A22Y 
       31.10        58.95        10.92        37.71        66.90        51.52 
TCGA-EO-A2CH TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC 
       19.40        27.16        46.42        51.09        14.99        54.15 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GR TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM 
       32.71        19.27        17.62        37.05        19.33        22.82 
TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-FI-A2D4 TCGA-FI-A2F9 TCGA-K6-A3WQ TCGA-KP-A3W0 
       20.05        29.10         7.99        59.28        14.04        13.28 
TCGA-QS-A744 
       14.83 

$`8P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B 
       18.08       110.63        57.80        93.99        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 
       12.26        36.39        23.05        61.18        27.88         1.38 
TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       80.38        27.09        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-BG-A220 TCGA-D1-A0ZO TCGA-D1-A3JP TCGA-EY-A1G7 TCGA-EY-A1GK 
       12.56        14.27        19.79        16.93         6.21        22.78 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-FI-A2CX TCGA-FI-A2D5 
       10.19        14.40        18.87        17.92        66.77        13.84 
TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 
       73.32        36.00        23.74         0.43        39.52        10.29 
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88       149.56        83.51        17.85        32.78       112.54 
TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
      123.68        74.10        65.75        60.53        46.55        73.87 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 
       36.82        28.27        54.02        68.65        37.91        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        31.99        36.33 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A7WJ 
      118.19        66.15        28.64        24.72        34.95        11.21 
TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QO TCGA-AJ-A3BF 
       18.41        20.25        14.43        10.26        34.36        18.12 
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-AJ-A8CV TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 
        2.70        35.11       129.80        21.99        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       48.03        63.91        45.53        36.89        23.87        12.62 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
       20.91        48.79       110.37        66.25        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ 
       46.72        83.97        27.12        82.52        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP 
       49.22        25.08        71.67        90.97        55.89        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       46.78        49.15         6.71        45.86        27.85        51.12 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        61.08        35.74        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        77.39        13.28        32.91        34.65 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CJ 
       25.51        26.37        25.91        34.09        76.83        73.41 
TCGA-AX-A1CN TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       37.58        30.12        71.24        46.49        38.24        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FW 
       30.74         2.96        31.13        64.93         0.23         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-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
        0.39        56.91        86.37        59.24        86.01        58.75 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       69.27        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       64.21        63.55        27.85        13.45       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        73.64        61.68        85.78 
TCGA-B5-A11P TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       52.04        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        51.45        48.43        11.87        52.54 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH 
       31.36       136.60        96.30        93.50        71.84        27.65 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M3 
       29.65        41.06        34.13        18.61        20.19        35.21 
TCGA-BG-A0M7 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       63.68        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.01        15.45         9.57        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
       11.31        22.39        34.98        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        24.33        85.55        78.21 
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       114.90 
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        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        83.64        66.48        16.83        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-A16I 
       15.72        36.36        37.51        36.79        27.42        11.51 
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-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-A2G7 TCGA-D1-A3DA 
       18.02        15.06         1.05         3.95        58.95        15.88 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KS TCGA-DF-A2KU 
        4.27        18.84        17.29         2.20       109.08       100.83 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU 
       89.33        10.92        27.16        25.91        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LX 
       36.62        35.38         9.37        12.39       110.10        23.38 
TCGA-E6-A1LZ TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       79.10         2.37        45.57        16.04         7.36        16.80 
TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG 
       49.15        61.74        61.55        46.26        57.60        51.42 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B1 TCGA-EO-A3KU 
       34.39        50.73        35.15        38.07        26.96        22.26 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       16.34        38.47        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GT 
       23.34        23.90        33.34        18.84        22.03        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A2OO TCGA-EY-A2OP 
       32.78        15.81        11.08        12.59        45.76        31.04 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 
       27.35        32.52        11.38        14.14        14.70        16.96 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       68.38        39.88        77.33        25.22        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR 
        9.34        28.93        30.67        41.56        78.38         1.74 
TCGA-JU-AAVI TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       17.75         9.47        26.10        18.21        23.24        21.30 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       38.70        22.59         8.19        17.16         6.97        22.65 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       39.95        24.95        23.64         4.44        20.75        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 
           225.50            185.79 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           31.070            29.785 
[1] "0.1 - 225.5 (31.1)" "0.1 - 185.8 (29.8)"
[1] "hr=" "1.5"
D15V2, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    70  38
  8P GAIN WILD-TYPE 220 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     70   38
  8P GAIN WILD-TYPE  220  186
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               70               220
  YES              38               186
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  8P GAIN MUTATED                                        87
  8P GAIN WILD-TYPE                                     317
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  8P GAIN MUTATED                               6
  8P GAIN WILD-TYPE                            16
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  8P GAIN MUTATED                                  23
  8P GAIN WILD-TYPE                                90
D15V3, multiclass
                                         clus
vv                                        8P GAIN MUTATED 8P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              87               317
  MIXED SEROUS AND ENDOMETRIOID                         6                16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    23                90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  8P GAIN MUTATED    82   1   5   9
  8P GAIN WILD-TYPE 289  21  11  31
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0              82               289
  R1               1                21
  R2               5                11
  RX               9                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"

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   120  37
  8Q GAIN WILD-TYPE 327  53
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              157               380 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               37                53 
$`8Q GAIN MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A0LF TCGA-BG-A0M6 TCGA-BG-A0M8 
       41.06        20.81        10.19        93.99        22.06        66.41 
TCGA-BG-A221 TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1GQ TCGA-EY-A547 
        1.81         4.44        47.84        33.30        17.88        17.92 
TCGA-EY-A549 TCGA-EY-A72D TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A0GE TCGA-A5-A0GJ 
       19.89         5.88        39.52        37.02       105.37        65.75 
TCGA-A5-A0GW TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K4 
       23.21        17.59        31.99        36.33        33.07        28.64 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A3BD 
       25.51        14.96        21.14        19.79        35.15        34.16 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NE 
       18.90        33.90         1.64        22.26        17.06        20.65 
TCGA-AJ-A3NG TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A8CW TCGA-AP-A05A 
       15.62        14.76        16.87        16.87         0.13        63.91 
TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LO TCGA-AP-A1DO 
       45.53        48.79       125.42       117.99        33.40        31.30 
TCGA-AP-A1E0 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1C8 
       60.23        21.90        36.13         0.56        37.78        25.51 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CI TCGA-AX-A1CK TCGA-AX-A2H2 TCGA-AX-A2H4 
       32.02        25.91        85.48        80.25         4.77        30.12 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G1 
       40.80        81.37        34.32         0.20         0.20        20.52 
TCGA-B5-A0JT TCGA-B5-A0K4 TCGA-B5-A11E TCGA-B5-A11H TCGA-B5-A11Q TCGA-B5-A11R 
       55.30        57.76        59.84        88.34        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11V TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MW TCGA-B5-A3F9 
       73.28        19.56       225.50       102.31        14.70       136.60 
TCGA-B5-A3FD TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M4 
       39.35        34.13        34.95        19.33        20.94        71.24 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MT TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       74.63        10.72        21.17        15.45        23.70        35.90 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0T9 TCGA-BS-A0TE 
       35.90        35.08        31.00        16.64        46.95         4.80 
TCGA-BS-A0TG TCGA-BS-A0U9 TCGA-BS-A0UV TCGA-BS-A0VI TCGA-D1-A0ZP TCGA-D1-A0ZU 
       77.95        92.88        73.25        86.99        29.95        28.67 
TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16N 
       22.55        39.48         0.66        36.10        37.32        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        48.79 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DI-A1C3 
        8.48        58.95        18.84        71.61       109.08        24.30 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       31.10       110.10        79.10        58.95        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        46.42 
TCGA-EO-A3B1 TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GM TCGA-EY-A1GO 
       26.96        51.09        14.99        54.15        32.71        19.27 
TCGA-EY-A1GR TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2ON 
       17.62        15.81        37.05        19.33        22.82        20.05 
TCGA-EY-A2OQ TCGA-FI-A2D4 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-JU-AAVI TCGA-K6-A3WQ 
       29.10         7.99        59.28        41.56        17.75        14.04 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A744 
       13.28         9.47        18.21        22.59         8.19        14.83 
TCGA-SL-A6J9 
        0.07 

$`8Q GAIN WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP 
      110.63        57.80        95.47        67.66        12.26        36.39 
TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB 
       23.05        61.18        27.88         1.38        80.38        27.09 
TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-D1-A0ZO TCGA-D1-A3JP 
       61.87        51.55        12.56        14.27        19.79        16.93 
TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-FI-A2CX 
        6.21        22.78        10.19        14.40        18.87        66.77 
TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5S-A9Q8 
       13.84        73.32        36.00        23.74         0.43        10.29 
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88       149.56        83.51        17.85        32.78       112.54 
TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
      123.68        74.10        60.53        46.55        73.87        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 
       28.27        54.02        68.65        37.91        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A2K2 TCGA-A5-A2K3 
       29.06        42.35        15.95        31.99       118.19        66.15 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N 
       24.72        34.95        11.21        18.41        20.25        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3NC 
       10.26        34.36        18.12        14.66        22.49        36.99 
TCGA-AJ-A3NF TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       21.21        15.35        15.95        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 
        2.70        35.11       129.80        21.99        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LE 
       48.03        36.89        23.87        12.62        20.91       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       82.52        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       90.97        55.89        35.54        46.78        49.15         6.71 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       45.86        27.85        51.12        13.58        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       80.55        88.24        71.51        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       49.87        57.47        27.39        30.02        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       35.74        43.82        40.11        77.39        13.28        32.91 
TCGA-AX-A1C7 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CJ TCGA-AX-A1CN 
       34.65        26.37        34.09        76.83        73.41        37.58 
TCGA-AX-A2H5 TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       71.24        46.49        38.24        17.75        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G4 
       31.13        64.93         0.23         0.56        43.82         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-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       56.91        86.37        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 
       71.44        48.59        36.49        72.62        27.29        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11I 
       63.55        27.85        13.45       185.79       113.36        75.72 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11U 
       54.44        73.64        61.68        85.78        52.04        16.73 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MV 
       19.50        18.41        17.36        16.57        50.89        51.45 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB 
       48.43        11.87        52.54        31.36        96.30        93.50 
TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX 
       71.84        27.65        29.65        41.06        18.61        20.19 
TCGA-BG-A0M3 TCGA-BG-A0M7 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       35.21        63.68        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       43.04        59.74        20.28        15.42        51.06        52.01 
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-A222 TCGA-BG-A2AD TCGA-BG-A2L7 
       14.73        14.01        15.45         9.57        20.02        20.12 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
       11.31        22.39        34.98        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        24.33        85.55        78.21 
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       114.90 
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        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       63.58        83.64        66.48        16.83         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X 
        4.87        23.93         1.74        21.99        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A16B 
        1.91         3.68        29.33        32.58        15.72        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-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       10.65         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-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-A3DA TCGA-D1-A3DG TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KU 
        3.95        15.88         4.27        17.29         2.20       100.83 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU 
       89.33        10.92        27.16        25.91        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A2P8 
       36.62        35.38         9.37        12.39        23.38         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S 
       45.57        16.04         7.36        16.80        61.74        61.55 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       46.26        57.60        51.42        34.39        50.73        35.15 
TCGA-EO-A3AY TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EY-A1GD TCGA-EY-A1GE 
       38.07        22.26        16.34        38.47        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GP 
       27.16        23.34        23.34        23.90        33.34        18.84 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A2OO 
       22.03        16.11        32.78        11.08        12.59        45.76 
TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A 
       31.04        27.35        32.52        11.38        14.14        14.70 
TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D6 TCGA-FI-A2EU 
       16.96        68.38        39.88        77.33        25.22        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PX TCGA-H5-A2HR 
       59.01         9.34        28.93        30.67        78.38         1.74 
TCGA-KP-A3W3 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A916 TCGA-PG-A917 
       26.10        23.24        21.30        38.70        17.16         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       22.65        39.95        24.95        23.64         4.44        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.07              0.23 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           225.50            185.79 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           30.120            29.785 
[1] "0.1 - 225.5 (30.1)" "0.2 - 185.8 (29.8)"
[1] "hr=" "1.7"
D16V2, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    88  61
  8Q GAIN WILD-TYPE 202 163
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     88   61
  8Q GAIN WILD-TYPE  202  163
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               88               202
  YES              61               163
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  8Q GAIN MUTATED                                       104
  8Q GAIN WILD-TYPE                                     300
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  8Q GAIN MUTATED                               8
  8Q GAIN WILD-TYPE                            14
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  8Q GAIN MUTATED                                  47
  8Q GAIN WILD-TYPE                                66
D16V3, multiclass
                                         clus
vv                                        8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             104               300
  MIXED SEROUS AND ENDOMETRIOID                         8                14
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    47                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  8Q GAIN MUTATED   112   3   7  14
  8Q GAIN WILD-TYPE 259  19   9  26
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0             112               259
  R1               3                19
  R2               7                 9
  RX              14                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"

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    16   6
  9P GAIN WILD-TYPE 431  84
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               22               515 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                6                84 
$`9P GAIN MUTATED`
TCGA-AX-A06B TCGA-AX-A3G3 TCGA-A5-A1OG TCGA-AJ-A2QK TCGA-AX-A05Z TCGA-AX-A2HK 
       67.66         1.38        31.99        21.14        71.51         2.96 
TCGA-B5-A11H TCGA-B5-A11I TCGA-BS-A0U9 TCGA-D1-A1NW TCGA-DF-A2KS TCGA-E6-A1M0 
       88.34        75.72        92.88         0.72       109.08        58.95 
TCGA-EO-A1Y8 TCGA-EO-A22X TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A2ON TCGA-EY-A2OQ 
       37.71        57.60        22.03        11.08        20.05        29.10 
TCGA-EY-A3QX TCGA-FI-A3PX TCGA-PG-A7D5 TCGA-SL-A6J9 
       32.52        78.38        38.70         0.07 

$`9P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF 
       18.08        20.81        10.19       110.63        57.80        93.99 
TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF 
       95.47        12.26        36.39        23.05        61.18        27.88 
TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       80.38        27.09        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 
       12.56        14.27         1.81        19.79         4.44        47.84 
TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 
       16.93        33.30         6.21        22.78        17.88        10.19 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX 
       14.40        18.87        17.92        19.89         5.88        66.77 
TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C 
       13.84        73.32        36.00        23.74         0.43        39.52 
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-A0GJ 
       32.78       112.54       105.37       123.68        74.10        65.75 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        73.87        36.82        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        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        31.99        36.33        33.07 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
      118.19        66.15        28.64        24.72        34.95        25.51 
TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O 
       14.96        11.21        18.41        20.25        14.43        10.26 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI 
       19.79        35.15        34.36        34.16        18.12        18.90 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
       33.90         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-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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
        2.70        35.11         0.13       129.80        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07        48.03        63.91        45.53        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       12.62        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        90.97        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        60.23        45.86        27.85        51.12 
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        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       80.55        88.24        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       57.47        27.39        30.02        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        77.39        13.28        32.91 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       34.65        25.51        26.37        32.02        25.91        34.09 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 
       76.83        85.48        73.41        80.25        37.58         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-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       38.24        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-A3G4 
        0.20         0.56        43.82         0.20        20.52         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-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        86.37        55.30        59.24        86.01        58.75 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       69.27        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       57.76        64.21        63.55        27.85        13.45        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
      185.79       113.36        54.44        73.64        61.68        85.78 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       52.04        32.09        77.23        73.28        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       225.50       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        51.45        14.70        48.43        11.87        52.54 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       31.36       136.60        96.30        93.50        71.84        39.35 
TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW 
       27.65        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        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       74.63        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        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-A222 
       13.78        14.73        14.01        15.45        15.45         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        22.39        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       34.98        35.90        35.08        31.00        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 
       24.33        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       114.90        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        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       63.58        83.64        86.99        66.48        16.83        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-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
       13.22        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        1.05         3.95        48.79         8.48        58.95        15.88 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KU 
        4.27        18.84        17.29         2.20        71.61       100.83 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU 
       89.33        10.92        27.16        25.91        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-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
      110.10        23.38        79.10         2.37        45.57        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-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       66.90        46.26        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 
       50.73        35.15        38.07        27.16        46.42        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC 
       22.26        16.34        38.47        51.09        14.99        54.15 
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-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GT 
       33.34        32.71        19.27        18.84        17.62        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM 
       32.78        15.81        37.05        19.33        12.59        22.82 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A 
       45.76        31.04        27.35        11.38        14.14        14.70 
TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 
       16.96        68.38        39.88        77.33         7.99        25.22 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 
       96.69        59.01         9.34        28.93        30.67        59.28 
TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 
       41.56         1.74        17.75        14.04        13.28         9.47 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A915 
       26.10        18.21        23.24        21.30        22.59         8.19 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       17.16         6.97        22.65        39.95        24.95        23.64 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       14.83         4.44        20.75        18.28         0.23 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.07              0.13 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           109.08            225.50 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           35.115            29.690 
[1] "0.1 - 109.1 (35.1)" "0.1 - 225.5 (29.7)"
[1] "hr=" "1.5"
D17V2, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    15   5
  9P GAIN WILD-TYPE 275 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     15    5
  9P GAIN WILD-TYPE  275  219
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               15               275
  YES               5               219
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  9P GAIN MUTATED                                        13
  9P GAIN WILD-TYPE                                     391
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  9P GAIN MUTATED                               1
  9P GAIN WILD-TYPE                            21
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  9P GAIN MUTATED                                   8
  9P GAIN WILD-TYPE                               105
D17V3, multiclass
                                         clus
vv                                        9P GAIN MUTATED 9P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              13               391
  MIXED SEROUS AND ENDOMETRIOID                         1                21
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     8               105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  9P GAIN MUTATED    12   2   2   3
  9P GAIN WILD-TYPE 359  20  14  37
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              12               359
  R1               2                20
  R2               2                14
  RX               3                37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED     7   3
  9Q GAIN WILD-TYPE 440  87
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               10               527 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3                87 
$`9Q GAIN MUTATED`
TCGA-AX-A3G3 TCGA-A5-A1OG TCGA-B5-A11H TCGA-BS-A0U9 TCGA-D1-A1NW TCGA-DF-A2KS 
        1.38        31.99        88.34        92.88         0.72       109.08 
TCGA-E6-A1M0 TCGA-EY-A1GS TCGA-EY-A1GW TCGA-SL-A6J9 
       58.95        22.03        11.08         0.07 

$`9Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF 
       18.08        20.81        10.19       110.63        57.80        93.99 
TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 
       95.47        67.66        12.26        36.39        23.05        61.18 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       27.88        80.38        27.09        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 
       51.55        12.56        14.27         1.81        19.79         4.44 
TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ 
       47.84        16.93        33.30         6.21        22.78        17.88 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D 
       10.19        14.40        18.87        17.92        19.89         5.88 
TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E 
       66.77        13.84        73.32        36.00        23.74         0.43 
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       39.52        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       123.68        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       65.75        60.53        46.55        73.87        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        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        31.99        36.33 
TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
       33.07       118.19        66.15        28.64        24.72        34.95 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N 
       25.51        14.96        11.21        18.41        20.25        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
       10.26        21.14        19.79        35.15        34.36        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
       18.12        18.90        33.90         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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 
       12.82        20.78         2.70        35.11         0.13       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
       21.99        23.31        86.07        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       36.89        23.87        12.62        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      117.99       110.37        66.25        36.36        97.71        46.72 
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-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        90.97        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        60.23        45.86 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       27.85        51.12        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 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       45.99        79.46        49.87        57.47        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       60.66        61.08        35.74        37.78        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       77.39        13.28        32.91        34.65        25.51        26.37 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       32.02        25.91        34.09        76.83        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       80.25        37.58         4.77        30.12        71.24        40.80 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       81.37        34.32        46.49        38.24        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-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
       43.82         0.20        20.52         0.30         0.26         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS 
        1.18        18.35        14.47         0.39        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       55.30        59.24        86.01        58.75        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       185.79       113.36 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
       75.72        54.44        73.64        61.68        85.78        52.04 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        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       225.50       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 
       51.45        14.70        48.43        11.87        52.54        31.36 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH 
      136.60        96.30        93.50        71.84        39.35        27.65 
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        71.24        63.68        74.63 
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-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
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-A222 TCGA-BG-A2AD 
       14.73        14.01        15.45        15.45         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        22.39        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
       35.90        35.08        31.00        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        24.33 
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       114.90        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        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       83.64        86.99        66.48        16.83        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-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-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        48.79         8.48        58.95        15.88         4.27 
TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KU TCGA-DF-A2KV 
       18.84        17.29         2.20        71.61       100.83        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       10.92        27.16        25.91        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-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       23.38        79.10         2.37        45.57        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        50.73        35.15        38.07        27.16        46.42 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 
       26.96        22.26        16.34        38.47        51.09        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       54.15        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR 
       23.90        33.34        32.71        19.27        18.84        17.62 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       16.11        32.78        15.81        37.05        19.33        12.59 
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-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY 
       32.52        11.38        14.14        14.70        16.96        68.38 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       39.88        77.33         7.99        25.22        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
        9.34        28.93        30.67        59.28        41.56        78.38 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 
        1.74        17.75        14.04        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        21.30        38.70        22.59         8.19 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       17.16         6.97        22.65        39.95        24.95        23.64 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       14.83         4.44        20.75        18.28         0.23 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.07              0.13 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           109.08            225.50 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            27.01             29.92 
[1] "0.1 - 109.1 (27.0)" "0.1 - 225.5 (29.9)"
[1] "hr=" "1.9"
D18V2, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     6   2
  9Q GAIN WILD-TYPE 284 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      6    2
  9Q GAIN WILD-TYPE  284  222
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                6               284
  YES               2               222
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  9Q GAIN MUTATED                                         6
  9Q GAIN WILD-TYPE                                     398
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  9Q GAIN MUTATED                               1
  9Q GAIN WILD-TYPE                            21
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  9Q GAIN MUTATED                                   3
  9Q GAIN WILD-TYPE                               110
D18V3, multiclass
                                         clus
vv                                        9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               6               398
  MIXED SEROUS AND ENDOMETRIOID                         1                21
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     3               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"
                   vv
clus                 R0  R1  R2  RX
  9Q GAIN MUTATED     3   1   1   3
  9Q GAIN WILD-TYPE 368  21  15  37
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0               3               368
  R1               1                21
  R2               1                15
  RX               3                37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    96  20
  10P GAIN WILD-TYPE 351  70
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               116                421 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                20                 70 
$`10P GAIN MUTATED`
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A0LF TCGA-AX-A06D TCGA-BG-A0M6 TCGA-BG-A0MS 
       20.81        10.19        93.99        12.26        22.06        61.87 
TCGA-BG-A0VT TCGA-BG-A221 TCGA-D1-A102 TCGA-D1-A2G5 TCGA-EY-A1G7 TCGA-EY-A1GK 
       51.55         1.81         4.44        47.84         6.21        22.78 
TCGA-EY-A1GQ TCGA-EY-A214 TCGA-EY-A72D TCGA-A5-A0G5 TCGA-A5-A0GE TCGA-A5-A0GU 
       17.88        14.40         5.88        37.02       105.37        28.27 
TCGA-A5-A0GV TCGA-A5-A0R9 TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A3LP 
       54.02        24.62        31.99        33.07       118.19        14.96 
TCGA-AJ-A23O TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3NC TCGA-AJ-A3QS 
       10.26        18.90         1.64        22.26        36.99        16.87 
TCGA-AJ-A3TW TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LJ TCGA-AP-A0LN TCGA-AP-A0LQ 
       16.87        20.91       117.99        46.72        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        51.12        13.58        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A06J TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C4 TCGA-AX-A1CA 
       80.55        30.02        35.74        37.78        13.28        32.02 
TCGA-AX-A1CC TCGA-AX-A1CJ TCGA-AX-A2HH TCGA-AX-A3FX TCGA-B5-A0JT TCGA-B5-A0JX 
       25.91        73.41        17.75        43.82        55.30        58.75 
TCGA-B5-A11F TCGA-B5-A11L TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A1MV TCGA-BG-A0LX 
      185.79        73.64        77.23        73.28        51.45        20.19 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0MG TCGA-BG-A0RY TCGA-BG-A0W2 
       20.94        35.21        71.24        48.56        15.42        56.58 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BK-A0C9 TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0T9 
       14.73        14.01        35.90        31.00        16.64        46.95 
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-A3DH TCGA-DF-A2KR TCGA-DF-A2KS 
        2.33        18.25         2.07        18.84        71.61       109.08 
TCGA-DI-A2QY TCGA-E6-A1M0 TCGA-E6-A2P9 TCGA-EO-A1Y7 TCGA-EO-A22Y TCGA-EO-A2CG 
      110.10        58.95        45.57        49.15        51.52        51.42 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3L0 TCGA-EY-A1GC TCGA-EY-A1GH TCGA-EY-A1GO 
       26.96        22.26        51.09        54.15        23.34        19.27 
TCGA-EY-A1GT TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OO 
       16.11        11.08        37.05        19.33        12.59        45.76 
TCGA-EY-A2OP TCGA-FI-A2D4 TCGA-FI-A2EX TCGA-KP-A3W1 TCGA-PG-A7D5 TCGA-QS-A744 
       31.04         7.99         9.34         9.47        38.70        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZJ 
        4.44        18.28 

$`10P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A1CP 
       18.08       110.63        57.80        95.47        67.66        36.39 
TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB 
       23.05        61.18        27.88         1.38        80.38        27.09 
TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-BG-A220 TCGA-D1-A0ZO TCGA-D1-A3JP TCGA-E6-A8L9 
       66.41        12.56        14.27        19.79        16.93        33.30 
TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-FI-A2CX TCGA-FI-A2D5 
       10.19        18.87        17.92        19.89        66.77        13.84 
TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 
       73.32        36.00        23.74         0.43        39.52        10.29 
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88       149.56        83.51        17.85        32.78       112.54 
TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
      123.68        74.10        65.75        60.53        46.55        73.87 
TCGA-A5-A0GR TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       36.82        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A2K3 
       29.06        42.35        15.95        31.99        36.33        66.15 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A7WJ TCGA-A5-A7WK 
       28.64        24.72        34.95        25.51        11.21        18.41 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       20.25        14.43        21.14        19.79        35.15        34.36 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 
       34.16        18.12        33.90        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-A8CV TCGA-AJ-A8CW 
       22.32        12.82        20.78         2.70        35.11         0.13 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
      129.80        21.99        23.31        86.07        48.03        63.91 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A0L8 TCGA-AP-A0L9 
       45.53        36.89        23.87        12.62        48.79       125.42 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LL TCGA-AP-A0LM 
      110.37        66.25        36.36        97.71        83.97        27.12 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       33.40        61.64        49.22        25.08        71.67        90.97 
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        60.23 
TCGA-AP-A1E1 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05Y TCGA-AX-A05Z 
       45.86        21.90        36.13         0.56        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C5 
       60.66        61.08        43.82        40.11        77.39        32.91 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       34.65        25.51        26.37        34.09        76.83        85.48 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       80.25        37.58         4.77        30.12        71.24        40.80 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK 
       81.37        34.32        46.49        38.24        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ 
       31.13        64.93         0.23         0.20         0.56         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
       20.52         0.30         0.26         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV 
       14.47         0.39        56.91        86.37        59.24        86.01 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       69.27        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       57.76        64.21        63.55        27.85        13.45        59.84 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11N TCGA-B5-A11O 
      113.36        88.34        75.72        54.44        61.68        85.78 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       52.04        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-A1MW 
       17.36        16.57       225.50       102.31        50.89        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       48.43        11.87        52.54        31.36       136.60        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       93.50        71.84        39.35        27.65        29.65        41.06 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0M0 TCGA-BG-A0M7 TCGA-BG-A0M9 
       34.13        34.95        18.61        19.33        63.68        74.63 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       10.72        41.52        23.47        43.30        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       21.17        20.28        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A222 
       52.83        14.83        13.78        15.45        15.45         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0CA 
       20.02        23.70        20.12        11.31        22.39        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F 
       35.90        35.08        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-A0TE 
       10.03         9.86        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U8 TCGA-BS-A0U9 
       77.95        61.87        67.99        96.49        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0V4 
      114.90        85.84        82.39        81.57        72.72        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZR 
       89.59        83.64        86.99        16.83        29.95         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W 
        4.87        23.93        22.55         1.74        21.99        30.08 
TCGA-D1-A15X TCGA-D1-A160 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B 
       29.88         3.68        32.58        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-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-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A1NZ 
       22.92         1.41        13.22         0.72        16.87        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 
       15.06         1.05         3.95        48.79         8.48        58.95 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KU TCGA-DF-A2KV 
       15.88         4.27        17.29         2.20       100.83        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       10.92        27.16        25.91        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-A2P8 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
       79.10         2.37        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        50.73        35.15        38.07        27.16 
TCGA-EO-A3B0 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       46.42        16.34        38.47        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        33.34        32.71        18.84 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A2OM TCGA-EY-A2ON 
       17.62        22.03        32.78        15.81        22.82        20.05 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A 
       29.10        27.35        32.52        11.38        14.14        14.70 
TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D6 TCGA-FI-A2EU 
       16.96        68.38        39.88        77.33        25.22        96.69 
TCGA-FI-A2EW TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
       59.01        28.93        30.67        59.28        41.56        78.38 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 
        1.74        17.75        14.04        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        21.30        22.59         8.19        17.16         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-SJ-A6ZI TCGA-SL-A6J9 
       22.65        39.95        24.95        23.64        20.75         0.07 
TCGA-SL-A6JA 
        0.23 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.66               0.07 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            185.79             225.50 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             30.38              29.88 
[1] "0.7 - 185.8 (30.4)" "0.1 - 225.5 (29.9)"
[1] "hr=" "1"  
D19V2, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    69  47
  10P GAIN WILD-TYPE 221 177
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     69   47
  10P GAIN WILD-TYPE  221  177
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                69                221
  YES               47                177
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  10P GAIN MUTATED                                        88
  10P GAIN WILD-TYPE                                     316
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  10P GAIN MUTATED                               3
  10P GAIN WILD-TYPE                            19
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  10P GAIN MUTATED                                  25
  10P GAIN WILD-TYPE                                88
D19V3, multiclass
                                         clus
vv                                        10P GAIN MUTATED 10P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               88                316
  MIXED SEROUS AND ENDOMETRIOID                          3                 19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     25                 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"
                    vv
clus                  R0  R1  R2  RX
  10P GAIN MUTATED    90   5   4   7
  10P GAIN WILD-TYPE 281  17  12  33
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               90                281
  R1                5                 17
  R2                4                 12
  RX                7                 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"

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    88  20
  10Q GAIN WILD-TYPE 359  70
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               108                429 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                20                 70 
$`10Q GAIN MUTATED`
TCGA-AJ-A3NH TCGA-AP-A0LF TCGA-AX-A06D TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0VT 
       10.19        93.99        12.26        22.06        61.87        51.55 
TCGA-D1-A2G5 TCGA-EY-A1G7 TCGA-EY-A1GQ TCGA-EY-A214 TCGA-EY-A72D TCGA-A5-A0GE 
       47.84         6.21        17.88        14.40         5.88       105.37 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0R9 TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A2K2 
       28.27        54.02        24.62        31.99        33.07       118.19 
TCGA-AJ-A23O TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3NC TCGA-AJ-A3QS 
       10.26        18.90         1.64        22.26        36.99        16.87 
TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LJ TCGA-AP-A0LN TCGA-AP-A0LQ TCGA-AP-A1DQ 
       20.91       117.99        46.72        82.52        80.78        46.78 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       27.85        51.12        13.58        33.21        29.69        80.55 
TCGA-AX-A06J TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C4 TCGA-AX-A1CA TCGA-AX-A1CC 
       30.02        35.74        37.78        13.28        32.02        25.91 
TCGA-AX-A1CJ TCGA-AX-A2HH TCGA-AX-A3FX TCGA-B5-A0JT TCGA-B5-A0JX TCGA-B5-A11F 
       73.41        17.75        43.82        55.30        58.75       185.79 
TCGA-B5-A11L TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A1MV TCGA-BG-A0LX TCGA-BG-A0M2 
       73.64        77.23        73.28        51.45        20.19        20.94 
TCGA-BG-A0M3 TCGA-BG-A0MG TCGA-BG-A0RY TCGA-BG-A0W2 TCGA-BG-A187 TCGA-BG-A18A 
       35.21        48.56        15.42        56.58        14.73        14.01 
TCGA-BK-A0C9 TCGA-BK-A0CC TCGA-BK-A4ZD TCGA-BS-A0T9 TCGA-BS-A0TI TCGA-BS-A0U7 
       35.90        35.08        16.64        46.95        61.87        30.74 
TCGA-BS-A0UV TCGA-BS-A0V7 TCGA-BS-A0WQ TCGA-D1-A0ZQ TCGA-D1-A0ZU TCGA-D1-A15V 
       73.25        63.58        66.48         8.55        28.67        39.48 
TCGA-D1-A15Z TCGA-D1-A161 TCGA-D1-A165 TCGA-D1-A169 TCGA-D1-A16S TCGA-D1-A17T 
        1.91        29.33         0.66        37.32        18.67         2.33 
TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-DF-A2KR TCGA-DI-A2QT TCGA-E6-A1M0 TCGA-E6-A2P9 
       18.25         2.07        71.61        12.39        58.95        45.57 
TCGA-EO-A1Y7 TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3B1 TCGA-EO-A3L0 TCGA-EY-A1GC 
       49.15        51.52        51.42        26.96        51.09        54.15 
TCGA-EY-A1GH TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GW TCGA-EY-A1GX 
       23.34        19.27        22.03        16.11        11.08        37.05 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OO TCGA-EY-A2OP TCGA-FI-A2D4 TCGA-FI-A2EX 
       19.33        12.59        45.76        31.04         7.99         9.34 
TCGA-FI-A2EY TCGA-KP-A3W1 TCGA-PG-A7D5 TCGA-PG-A915 TCGA-QS-A744 TCGA-SJ-A6ZJ 
       28.93         9.47        38.70         8.19        14.83        18.28 

$`10Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06B 
       18.08        20.81       110.63        57.80        95.47        67.66 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN 
       36.39        23.05        61.18        27.88         1.38        80.38 
TCGA-B5-A0KB TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       27.09        66.41        12.56        14.27         1.81        19.79 
TCGA-D1-A102 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1GK TCGA-EY-A212 TCGA-EY-A215 
        4.44        16.93        33.30        22.78        10.19        18.87 
TCGA-EY-A547 TCGA-EY-A549 TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 
       17.92        19.89        66.77        13.84        73.32        36.00 
TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 
       23.74         0.43        39.52        10.29       106.88       149.56 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GG 
       37.02        83.51        17.85        32.78       112.54       123.68 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       74.10        65.75        60.53        46.55        73.87        36.82 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0RA 
       23.21        68.65        37.91        17.59        19.59        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A2K3 TCGA-A5-A2K4 
       42.35        15.95        31.99        36.33        66.15        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK 
       24.72        34.95        25.51        14.96        11.21        18.41 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       20.25        14.43        21.14        19.79        35.15        34.36 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 
       34.16        18.12        33.90        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-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV 
       16.87        22.32        12.82        20.78         2.70        35.11 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        0.13       129.80        21.99        23.31        86.07        48.03 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A0L8 
       63.91        45.53        36.89        23.87        12.62        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LL 
      125.42       110.37        66.25        36.36        97.71        83.97 
TCGA-AP-A0LM TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       27.12        33.40        61.64        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       90.97        55.89        31.30        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05Y 
       60.23        45.86        21.90        36.13         0.56        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       27.39        60.66        61.08        43.82        40.11        77.39 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CF 
       32.91        34.65        25.51        26.37        34.09        76.83 
TCGA-AX-A1CI TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       85.48        80.25        37.58         4.77        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HJ 
       40.80        81.37        34.32        46.49        38.24        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-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-A0JR TCGA-B5-A0JS TCGA-B5-A0JU 
       18.35        14.47         0.39        56.91        86.37        59.24 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       86.01        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11E TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11N 
       59.84       113.36        88.34        75.72        54.44        61.68 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       85.78        52.04        32.09        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       225.50       102.31        50.89 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       14.70        48.43        11.87        52.54        31.36       136.60 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 
       96.30        93.50        71.84        39.35        27.65        29.65 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0M0 TCGA-BG-A0M4 
       41.06        34.13        34.95        18.61        19.33        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MI TCGA-BG-A0MK 
       63.68        74.63        10.72        41.52        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VV TCGA-BG-A0VW 
       43.04        59.74        21.17        20.28        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A18B 
       34.29        52.64        52.83        14.83        13.78        15.45 
TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       15.45         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 
       22.39        34.98        35.90        31.00        31.76        24.99 
TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0TA TCGA-BS-A0TC 
       24.13        13.18        10.03         9.86        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U8 
       78.21         4.80        77.95        67.99        96.49        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       92.88       114.90        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-A0ZP 
       59.51        89.59        83.64        86.99        16.83        29.95 
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-A160 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A168 
       30.08        29.88         3.68        32.58        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-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-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NY 
       24.30        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-A2G6 
       18.02        15.06         1.05         3.95        48.79         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN 
       58.95        15.88         4.27        18.84        17.29         2.20 
TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 
      109.08       100.83        89.33        10.92        27.16        25.91 
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-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A2P8 TCGA-EC-A1NJ 
       31.10       110.10        23.38        79.10         2.37        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-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       66.90        46.26        57.60        19.40        34.39        50.73 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KW 
       35.15        38.07        27.16        46.42        22.26        16.34 
TCGA-EO-A3KX TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GI 
       38.47        14.99        53.88        24.36        27.16        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GU 
       23.90        33.34        32.71        18.84        17.62        32.78 
TCGA-EY-A1GV TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX 
       15.81        22.82        20.05        29.10        27.35        32.52 
TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 
       11.38        14.14        14.70        16.96        68.38        39.88 
TCGA-FI-A2D2 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F8 TCGA-FI-A2F9 
       77.33        25.22        96.69        59.01        30.67        59.28 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 
       41.56        78.38         1.74        17.75        14.04        13.28 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 
       26.10        18.21        23.24        21.30        22.59        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A8F1 
        6.97        22.65        39.95        24.95        23.64         4.44 
TCGA-SJ-A6ZI TCGA-SL-A6J9 TCGA-SL-A6JA 
       20.75         0.07         0.23 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.66               0.07 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            185.79             225.50 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             30.89              29.65 
[1] "0.7 - 185.8 (30.9)" "0.1 - 225.5 (29.6)"
[1] "hr=" "1.1"
D20V2, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    66  41
  10Q GAIN WILD-TYPE 224 183
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     66   41
  10Q GAIN WILD-TYPE  224  183
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                66                224
  YES               41                183
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  10Q GAIN MUTATED                                        82
  10Q GAIN WILD-TYPE                                     322
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  10Q GAIN MUTATED                               3
  10Q GAIN WILD-TYPE                            19
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  10Q GAIN MUTATED                                  23
  10Q GAIN WILD-TYPE                                90
D20V3, multiclass
                                         clus
vv                                        10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               82                322
  MIXED SEROUS AND ENDOMETRIOID                          3                 19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     23                 90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED    84   5   6   5
  10Q GAIN WILD-TYPE 287  17  10  35
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0               84                287
  R1                5                 17
  R2                6                 10
  RX                5                 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"

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    17   6
  11P GAIN WILD-TYPE 430  84
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                23                514 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 6                 84 
$`11P GAIN MUTATED`
TCGA-BG-A0VT TCGA-A5-A3LO TCGA-AJ-A23N TCGA-AJ-A3TW TCGA-AP-A0L8 TCGA-AX-A0IU 
       51.55        25.51        14.43        16.87        48.79        35.74 
TCGA-AX-A0IW TCGA-AX-A2H2 TCGA-B5-A0JT TCGA-B5-A0K4 TCGA-B5-A1MU TCGA-B5-A5OE 
       37.78         4.77        55.30        57.76        50.89        34.95 
TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BS-A0U9 TCGA-D1-A169 TCGA-D1-A16I 
       15.45        22.39        35.08        92.88        37.32        11.51 
TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-FI-A3PX TCGA-KP-A3W3 TCGA-PG-A915 
       25.91        35.38        78.38        26.10         8.19 

$`11P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF 
       18.08        20.81        10.19       110.63        57.80        93.99 
TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 
       95.47        67.66        12.26        36.39        23.05        61.18 
TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 
       27.88         1.38        80.38        27.09        22.06        66.41 
TCGA-BG-A0MS TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 
       61.87        12.56        14.27         1.81        19.79         4.44 
TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ 
       47.84        16.93        33.30         6.21        22.78        17.88 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D 
       10.19        14.40        18.87        17.92        19.89         5.88 
TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E 
       66.77        13.84        73.32        36.00        23.74         0.43 
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       39.52        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       123.68        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       65.75        60.53        46.55        73.87        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        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        31.99        31.99 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
       36.33        33.07       118.19        66.15        28.64        24.72 
TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23O 
       34.95        14.96        11.21        18.41        20.25        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF 
       21.14        19.79        35.15        34.36        34.16        18.12 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       18.90        33.90         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-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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
        2.70        35.11         0.13       129.80        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07        48.03        63.91        45.53        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       12.62        20.91       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       33.40        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       90.97        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        60.23        45.86        27.85        51.12        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        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ 
       57.47        27.39        30.02        60.66        61.08        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        77.39        13.28        32.91        34.65        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       26.37        32.02        25.91        34.09        76.83        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       73.41        80.25        37.58        30.12        71.24        40.80 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       81.37        34.32        46.49        38.24        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-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
       43.82         0.20        20.52         0.30         0.26         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS 
        1.18        18.35        14.47         0.39        56.91        86.37 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       59.24        86.01        58.75        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       36.49        72.62        27.29        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       13.45        59.84       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        73.64        61.68        85.78        52.04        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       77.23        73.28        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       225.50       102.31        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       48.43        11.87        52.54        31.36       136.60        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       93.50        71.84        39.35        27.65        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-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       71.24        63.68        74.63        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        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        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-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        35.90        31.00        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        24.33 
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       114.90        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        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       83.64        86.99        66.48        16.83        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-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-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-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-A3DH 
       48.79         8.48        58.95        15.88         4.27        18.84 
TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV 
       17.29         2.20        71.61       109.08       100.83        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        79.10 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       58.95         2.37        45.57        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 
       50.73        35.15        38.07        27.16        46.42        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC 
       22.26        16.34        38.47        51.09        14.99        54.15 
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-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS 
       33.34        32.71        19.27        18.84        17.62        22.03 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        32.78        15.81        11.08        37.05        19.33 
TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       12.59        22.82        20.05        45.76        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 
       27.35        32.52        11.38        14.14        14.70        16.96 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU 
       68.38        39.88        77.33         7.99        25.22        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV 
       59.01         9.34        28.93        30.67        59.28        41.56 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W4 
        1.74        17.75        14.04        13.28         9.47        18.21 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 
       23.24        21.30        38.70        22.59        17.16         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 
       22.65        39.95        24.95        23.64        14.83         4.44 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       20.75        18.28         0.07         0.23 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              4.77               0.07 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             92.88             225.50 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            35.080             29.785 
[1] "4.8 - 92.9 (35.1)"  "0.1 - 225.5 (29.8)"
[1] "hr=" "1.6"
D21V2, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    14   9
  11P GAIN WILD-TYPE 276 215
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     14    9
  11P GAIN WILD-TYPE  276  215
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                14                276
  YES                9                215
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  11P GAIN MUTATED                                         8
  11P GAIN WILD-TYPE                                     396
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  11P GAIN MUTATED                               0
  11P GAIN WILD-TYPE                            22
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  11P GAIN MUTATED                                  15
  11P GAIN WILD-TYPE                                98
D21V3, multiclass
                                         clus
vv                                        11P GAIN MUTATED 11P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                8                396
  MIXED SEROUS AND ENDOMETRIOID                          0                 22
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     15                 98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  11P GAIN MUTATED    14   0   1   4
  11P GAIN WILD-TYPE 357  22  15  36
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0               14                357
  R1                0                 22
  R2                1                 15
  RX                4                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    12   8
  11Q GAIN WILD-TYPE 435  82
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                20                517 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 8                 82 
$`11Q GAIN MUTATED`
TCGA-BG-A0VT TCGA-A5-A3LO TCGA-AJ-A23N TCGA-AP-A0L8 TCGA-AX-A0IW TCGA-AX-A1CA 
       51.55        25.51        14.43        48.79        37.78        32.02 
TCGA-AX-A2H2 TCGA-AX-A2HK TCGA-B5-A0JT TCGA-B5-A0K4 TCGA-B5-A1MU TCGA-B5-A5OE 
        4.77         2.96        55.30        57.76        50.89        34.95 
TCGA-BG-A0M2 TCGA-BG-A18C TCGA-BS-A0U9 TCGA-D1-A16I TCGA-D1-A1O0 TCGA-DF-A2L0 
       20.94        15.45        92.88        11.51         2.07        25.91 
TCGA-FI-A2EY TCGA-FI-A3PX 
       28.93        78.38 

$`11Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF 
       18.08        20.81        10.19       110.63        57.80        93.99 
TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 
       95.47        67.66        12.26        36.39        23.05        61.18 
TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 
       27.88         1.38        80.38        27.09        22.06        66.41 
TCGA-BG-A0MS TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 
       61.87        12.56        14.27         1.81        19.79         4.44 
TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ 
       47.84        16.93        33.30         6.21        22.78        17.88 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D 
       10.19        14.40        18.87        17.92        19.89         5.88 
TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E 
       66.77        13.84        73.32        36.00        23.74         0.43 
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       39.52        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       123.68        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       65.75        60.53        46.55        73.87        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        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        31.99        31.99 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
       36.33        33.07       118.19        66.15        28.64        24.72 
TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23O 
       34.95        14.96        11.21        18.41        20.25        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF 
       21.14        19.79        35.15        34.36        34.16        18.12 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       18.90        33.90         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-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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       20.78         2.70        35.11         0.13       129.80        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07        48.03        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        12.62        20.91       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        90.97        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        60.23        45.86        27.85        51.12 
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        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       80.55        88.24        71.51        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       49.87        57.47        27.39        30.02        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       35.74        43.82        40.11        77.39        13.28        32.91 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       34.65        25.51        26.37        25.91        34.09        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H4 TCGA-AX-A2H5 
       85.48        73.41        80.25        37.58        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       40.80        81.37        34.32        46.49        38.24        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-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
       43.82         0.20        20.52         0.30         0.26         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS 
        1.18        18.35        14.47         0.39        56.91        86.37 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       59.24        86.01        58.75        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       36.49        72.62        27.29        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       13.45        59.84       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        73.64        61.68        85.78        52.04        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       77.23        73.28        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       225.50       102.31        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       48.43        11.87        52.54        31.36       136.60        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       93.50        71.84        39.35        27.65        29.65        41.06 
TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M3 TCGA-BG-A0M4 
       34.13        18.61        20.19        19.33        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       63.68        74.63        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        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        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-A222 
       14.83        13.78        14.73        14.01        15.45         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        22.39        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       34.98        35.90        35.08        31.00        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 
       24.33        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       114.90        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        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       63.58        83.64        86.99        66.48        16.83        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-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-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-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.95        48.79         8.48        58.95        15.88         4.27 
TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU 
       18.84        17.29         2.20        71.61       109.08       100.83 
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-EC-A1NJ 
       23.38        79.10        58.95         2.37        45.57        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        50.73        35.15        38.07        27.16 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       46.42        26.96        22.26        16.34        38.47        51.09 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99        54.15        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.34        23.90        33.34        32.71        19.27        18.84 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       17.62        22.03        16.11        32.78        15.81        11.08 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       37.05        19.33        12.59        22.82        20.05        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        32.52        11.38        14.14 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
       14.70        16.96        68.38        39.88        77.33         7.99 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 TCGA-FI-A2F9 
       25.22        96.69        59.01         9.34        30.67        59.28 
TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 
       41.56         1.74        17.75        14.04        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        21.30        38.70        22.59 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        8.19        17.16         6.97        22.65        39.95        24.95 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       23.64        14.83         4.44        20.75        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              2.07               0.07 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             92.88             225.50 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            30.475             29.920 
[1] "2.1 - 92.9 (30.5)"  "0.1 - 225.5 (29.9)"
[1] "hr=" "2.7"
D22V2, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    14   6
  11Q GAIN WILD-TYPE 276 218
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     14    6
  11Q GAIN WILD-TYPE  276  218
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                14                276
  YES                6                218
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  11Q GAIN MUTATED                                        10
  11Q GAIN WILD-TYPE                                     394
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  11Q GAIN MUTATED                               0
  11Q GAIN WILD-TYPE                            22
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  11Q GAIN MUTATED                                  10
  11Q GAIN WILD-TYPE                               103
D22V3, multiclass
                                         clus
vv                                        11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               10                394
  MIXED SEROUS AND ENDOMETRIOID                          0                 22
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     10                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"
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN MUTATED    11   1   1   3
  11Q GAIN WILD-TYPE 360  21  15  37
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0               11                360
  R1                1                 21
  R2                1                 15
  RX                3                 37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    56  12
  12P GAIN WILD-TYPE 391  78
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                68                469 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                12                 78 
$`12P GAIN MUTATED`
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-BG-A0M6 
       20.81        10.19        27.88         1.38        80.38        22.06 
TCGA-BG-A0M8 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A72D TCGA-KP-A3VZ 
       66.41        47.84        16.93        33.30         5.88        23.74 
TCGA-5B-A90C TCGA-A5-A0G2 TCGA-A5-A0GE TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A2K3 
       39.52       149.56       105.37        17.59        31.99        66.15 
TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AP-A05P TCGA-AP-A1DO TCGA-AP-A1DQ 
       14.96        20.25        34.16        20.91        31.30        46.78 
TCGA-AP-A1E4 TCGA-AX-A05W TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1CA TCGA-AX-A2HA 
       51.12        80.55        37.78        77.39        32.02        81.37 
TCGA-AX-A3GI TCGA-B5-A11R TCGA-B5-A11V TCGA-B5-A1N2 TCGA-B5-A5OC TCGA-B5-A5OD 
        0.39        77.23        19.56        31.36        41.06        34.13 
TCGA-BG-A0M2 TCGA-BG-A0MG TCGA-BG-A0W1 TCGA-BG-A18C TCGA-BG-A2AE TCGA-BG-A3PP 
       20.94        48.56        52.83        15.45        23.70        22.39 
TCGA-BS-A0TE TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-BS-A0V7 TCGA-D1-A16O TCGA-D1-A17K 
        4.80        61.87        92.88        63.58        33.63        28.08 
TCGA-D1-A1O0 TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A2CG 
        2.07        24.30        35.38       110.10        79.10        51.42 
TCGA-EO-A3AV TCGA-EO-A3AZ TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GR TCGA-EY-A1H0 
       35.15        27.16        54.15        19.27        17.62        19.33 
TCGA-EY-A210 TCGA-FI-A2D2 TCGA-FI-A2D6 TCGA-FI-A2EY TCGA-FI-A3PX TCGA-JU-AAVI 
       12.59        77.33        25.22        28.93        78.38        17.75 
TCGA-PG-A7D5 TCGA-PG-A914 
       38.70        22.59 

$`12P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B 
       18.08       110.63        57.80        93.99        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-B5-A0KB TCGA-BG-A0MS 
       12.26        36.39        23.05        61.18        27.09        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 
       51.55        12.56        14.27         1.81        19.79         4.44 
TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 
        6.21        22.78        17.88        10.19        14.40        18.87 
TCGA-EY-A547 TCGA-EY-A549 TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 
       17.92        19.89        66.77        13.84        73.32        36.00 
TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        0.43        10.29       106.88        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN 
       32.78       112.54       123.68        74.10        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        73.87        36.82        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       68.65        37.91        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K4 
       15.95        31.99        36.33        33.07       118.19        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23N 
       24.72        34.95        25.51        11.21        18.41        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF 
       10.26        21.14        19.79        35.15        34.36        18.12 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       18.90        33.90         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-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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       20.78         2.70        35.11         0.13       129.80        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07        48.03        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        12.62        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       71.67        90.97        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 
       60.23        45.86        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        33.21        29.69        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       45.99        79.46        49.87        57.47        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A1C4 
       60.66        61.08        35.74        43.82        40.11        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE 
       32.91        34.65        25.51        26.37        25.91        34.09 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 
       76.83        85.48        73.41        80.25        37.58         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG 
       30.12        71.24        40.80        34.32        46.49        38.24 
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-A3G4 
        0.20         0.56        43.82         0.20        20.52         0.30 
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 
       86.37        55.30        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       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        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11W 
       85.78        52.04        32.09        73.28        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       225.50       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 
       51.45        14.70        48.43        11.87        52.54       136.60 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 
       96.30        93.50        71.84        39.35        27.65        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        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MI TCGA-BG-A0MK 
       63.68        74.63        10.72        41.52        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       52.01        34.29        52.64        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 
       14.73        14.01        15.45         9.57        20.02        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        35.90        35.08        31.00 
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        24.33        85.55        78.21        77.95 
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       114.90        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        89.59 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       83.64        86.99        66.48        16.83        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-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-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X 
       31.07        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-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        48.79 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ 
        8.48        58.95        15.88         4.27        18.84        17.29 
TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY 
        2.20        71.61       109.08       100.83        89.33        10.92 
TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1NO 
       27.16        25.91        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        58.95         2.37        45.57 
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        50.73        38.07        46.42        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD 
       22.26        16.34        38.47        51.09        14.99        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        23.90        33.34 
TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       32.71        18.84        22.03        16.11        32.78        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       11.08        37.05        22.82        20.05        45.76        31.04 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A 
       29.10        27.35        32.52        11.38        14.14        14.70 
TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2EU TCGA-FI-A2EW 
       16.96        68.38        39.88         7.99        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ 
        9.34        30.67        59.28        41.56         1.74        14.04 
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        21.30 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        8.19        17.16         6.97        22.65        39.95        24.95 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       23.64        14.83         4.44        20.75        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             225.50 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            32.005             29.650 
[1] "0.4 - 149.6 (32.0)" "0.1 - 225.5 (29.6)"
[1] "hr=" "1"  
D23V2, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    37  28
  12P GAIN WILD-TYPE 253 196
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     37   28
  12P GAIN WILD-TYPE  253  196
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                37                253
  YES               28                196
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  12P GAIN MUTATED                                        35
  12P GAIN WILD-TYPE                                     369
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  12P GAIN MUTATED                               3
  12P GAIN WILD-TYPE                            19
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  12P GAIN MUTATED                                  31
  12P GAIN WILD-TYPE                                82
D23V3, multiclass
                                         clus
vv                                        12P GAIN MUTATED 12P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               35                369
  MIXED SEROUS AND ENDOMETRIOID                          3                 19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     31                 82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  12P GAIN MUTATED    51   1   2   4
  12P GAIN WILD-TYPE 320  21  14  36
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               51                320
  R1                1                 21
  R2                2                 14
  RX                4                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    44   7
  12Q GAIN WILD-TYPE 403  83
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                51                486 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 7                 83 
$`12Q GAIN MUTATED`
TCGA-BG-A0M8 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A214 TCGA-EY-A72D 
       66.41        47.84        16.93        33.30        14.40         5.88 
TCGA-KP-A3VZ TCGA-A5-A0G2 TCGA-A5-A0GE TCGA-A5-A0R7 TCGA-A5-A2K3 TCGA-AJ-A23M 
       23.74       149.56       105.37        17.59        66.15        20.25 
TCGA-AJ-A3BD TCGA-AJ-A3EM TCGA-AP-A05P TCGA-AP-A1DO TCGA-AP-A1E4 TCGA-AX-A05W 
       34.16        22.26        20.91        31.30        51.12        80.55 
TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1CA TCGA-AX-A2H4 TCGA-AX-A2HA TCGA-B5-A11R 
       37.78        77.39        32.02        30.12        81.37        77.23 
TCGA-B5-A11V TCGA-B5-A1N2 TCGA-B5-A5OC TCGA-BG-A0M2 TCGA-BG-A0MG TCGA-BG-A0W1 
       19.56        31.36        41.06        20.94        48.56        52.83 
TCGA-BG-A18C TCGA-BG-A2AE TCGA-BG-A3PP TCGA-BS-A0TE TCGA-BS-A0U9 TCGA-BS-A0V7 
       15.45        23.70        22.39         4.80        92.88        63.58 
TCGA-D1-A16O TCGA-D1-A1O0 TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-EO-A2CG TCGA-EO-A3AV 
       33.63         2.07        24.30        35.38        51.42        35.15 
TCGA-EY-A1GO TCGA-EY-A1GR TCGA-EY-A1H0 TCGA-EY-A210 TCGA-FI-A2D2 TCGA-FI-A2D6 
       19.27        17.62        19.33        12.59        77.33        25.22 
TCGA-FI-A2EY TCGA-FI-A3PX TCGA-PG-A7D5 
       28.93        78.38        38.70 

$`12Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF 
       18.08        20.81        10.19       110.63        57.80        93.99 
TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 
       95.47        67.66        12.26        36.39        23.05        61.18 
TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0MS 
       27.88         1.38        80.38        27.09        22.06        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 
       51.55        12.56        14.27         1.81        19.79         4.44 
TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A547 
        6.21        22.78        17.88        10.19        18.87        17.92 
TCGA-EY-A549 TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E 
       19.89        66.77        13.84        73.32        36.00         0.43 
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
       39.52        10.29       106.88        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN 
       32.78       112.54       123.68        74.10        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        73.87        36.82        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       68.65        37.91        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-A2K2 
       15.95        31.99        31.99        36.33        33.07       118.19 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ 
       28.64        24.72        34.95        25.51        14.96        11.21 
TCGA-A5-A7WK TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       18.41        14.43        10.26        21.14        19.79        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
       34.36        18.12        18.90        33.90         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       22.49        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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 
       12.82        20.78         2.70        35.11         0.13       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
       21.99        23.31        86.07        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        12.62        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DQ 
       25.08        71.67        90.97        55.89        35.54        46.78 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A3K1 
       49.15         6.71        60.23        45.86        27.85        21.90 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y 
       36.13         0.56        13.58        33.21        29.69        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ 
       27.39        30.02        60.66        61.08        35.74        43.82 
TCGA-AX-A0J0 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       40.11        13.28        32.91        34.65        25.51        26.37 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       25.91        34.09        76.83        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HC TCGA-AX-A2HD 
       37.58         4.77        71.24        40.80        34.32        46.49 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       38.24        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-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
        0.39        56.91        86.37        55.30        59.24        86.01 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       58.75        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       59.84       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-A11S 
       73.64        61.68        85.78        52.04        32.09        73.28 
TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       16.73        19.50        18.41        17.36        16.57       225.50 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      102.31        50.89        51.45        14.70        48.43        11.87 
TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       52.54       136.60        96.30        93.50        71.84        39.35 
TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       27.65        29.65        34.13        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       19.33        35.21        71.24        63.68        74.63        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        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
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-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA 
        9.57        20.02        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 
       35.90        35.08        31.00        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        24.33 
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-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41       114.90        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V8 TCGA-BS-A0VI 
       72.72        73.25        59.51        89.59        83.64        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        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-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-A16Q 
       36.79        27.42        11.51        29.92        31.07        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        48.79         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN 
       58.95        15.88         4.27        18.84        17.29         2.20 
TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
       71.61       109.08       100.83        89.33        10.92        27.16 
TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1NO TCGA-DI-A2QT 
       25.91        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        79.10        58.95         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       45.57        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-A3AZ 
       51.52        19.40        34.39        50.73        38.07        27.16 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       46.42        26.96        22.26        16.34        38.47        51.09 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99        54.15        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GS 
       23.34        23.90        33.34        32.71        18.84        22.03 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A2OM 
       16.11        32.78        15.81        11.08        37.05        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX 
       20.05        45.76        31.04        29.10        27.35        32.52 
TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 
       11.38        14.14        14.70        16.96        68.38        39.88 
TCGA-FI-A2D4 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 TCGA-FI-A2F9 
        7.99        96.69        59.01         9.34        30.67        59.28 
TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 
       41.56         1.74        17.75        14.04        13.28         9.47 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A915 
       26.10        18.21        23.24        21.30        22.59         8.19 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       17.16         6.97        22.65        39.95        24.95        23.64 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83         4.44        20.75        18.28         0.07         0.23 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              2.07               0.07 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            149.56             225.50 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             32.02              29.52 
[1] "2.1 - 149.6 (32.0)" "0.1 - 225.5 (29.5)"
[1] "hr=" "1.4"
D24V2, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    30  20
  12Q GAIN WILD-TYPE 260 204
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     30   20
  12Q GAIN WILD-TYPE  260  204
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                30                260
  YES               20                204
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  12Q GAIN MUTATED                                        32
  12Q GAIN WILD-TYPE                                     372
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  12Q GAIN MUTATED                               2
  12Q GAIN WILD-TYPE                            20
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  12Q GAIN MUTATED                                  17
  12Q GAIN WILD-TYPE                                96
D24V3, multiclass
                                         clus
vv                                        12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               32                372
  MIXED SEROUS AND ENDOMETRIOID                          2                 20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     17                 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"
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN MUTATED    39   1   3   3
  12Q GAIN WILD-TYPE 332  21  13  37
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               39                332
  R1                1                 21
  R2                3                 13
  RX                3                 37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    23   7
  13Q GAIN WILD-TYPE 424  83
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                30                507 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 7                 83 
$`13Q GAIN MUTATED`
TCGA-AP-A0LF TCGA-B5-A0JN TCGA-EY-A214 TCGA-A5-A1OG TCGA-AJ-A23M TCGA-AJ-A23N 
       93.99        80.38        14.40        31.99        20.25        14.43 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AX-A0IW TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A1MS 
       48.79       125.42        37.78        27.85        75.72       102.31 
TCGA-B5-A5OD TCGA-BK-A26L TCGA-D1-A15V TCGA-D1-A165 TCGA-D1-A16I TCGA-D1-A16S 
       34.13        24.13        39.48         0.66        11.51        18.67 
TCGA-D1-A3JQ TCGA-DI-A2QY TCGA-EO-A1Y5 TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3B1 
       17.29       110.10        10.92        51.52        51.42        26.96 
TCGA-EY-A1GO TCGA-EY-A210 TCGA-EY-A54A TCGA-FI-A2F9 TCGA-PG-A914 TCGA-PG-A915 
       19.27        12.59        14.70        59.28        22.59         8.19 

$`13Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LS 
       18.08        20.81        10.19       110.63        57.80        95.47 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF 
       67.66        12.26        36.39        23.05        61.18        27.88 
TCGA-AX-A3G3 TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
        1.38        27.09        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 
       12.56        14.27         1.81        19.79         4.44        47.84 
TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 
       16.93        33.30         6.21        22.78        17.88        10.19 
TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 
       18.87        17.92        19.89         5.88        66.77        13.84 
TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 
       73.32        36.00        23.74         0.43        39.52        10.29 
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN 
      112.54       105.37       123.68        74.10        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        73.87        36.82        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 
       42.35        15.95        31.99        36.33        33.07       118.19 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       66.15        28.64        24.72        34.95        25.51        14.96 
TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       11.21        18.41        10.26        21.14        19.79        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       34.36        34.16        18.12        18.90        33.90         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-A8CV 
       16.87        22.32        12.82        20.78         2.70        35.11 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        0.13       129.80        21.99        23.31        86.07        48.03 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       63.91        45.53        36.89        23.87        12.62        20.91 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      117.99       110.37        66.25        36.36        97.71        46.72 
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-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        90.97        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        60.23        45.86 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       27.85        51.12        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 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       45.99        79.46        49.87        57.47        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        61.08        35.74        43.82        40.11        77.39 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       13.28        32.91        34.65        25.51        26.37        32.02 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       25.91        34.09        76.83        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA 
       37.58         4.77        30.12        71.24        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       34.32        46.49        38.24        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-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       18.35        14.47         0.39        56.91        86.37        55.30 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       59.24        86.01        58.75        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J 
       13.45        59.84       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 
       73.64        61.68        85.78        52.04        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       73.28        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       225.50        50.89        51.45        14.70        48.43 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       11.87        52.54        31.36       136.60        96.30        93.50 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE 
       71.84        39.35        27.65        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        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       63.68        74.63        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        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        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-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
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        22.39 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       35.90        34.98        35.90        35.08        31.00        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 
       24.33        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        92.88       114.90 
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 
       89.59        63.58        83.64        86.99        66.48        16.83 
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-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
       22.55         1.74        21.99        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
        3.68        29.33        32.58        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N 
       36.36        37.51        36.79        27.42        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-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
       48.79         8.48        58.95        15.88         4.27        18.84 
TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY 
        2.20        71.61       109.08       100.83        89.33        10.92 
TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       27.16        25.91        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        79.10 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       58.95         2.37        45.57        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-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       57.60        19.40        34.39        50.73        35.15        38.07 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       27.16        46.42        22.26        16.34        38.47        51.09 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99        54.15        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GR 
       23.34        23.90        33.34        32.71        18.84        17.62 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       22.03        16.11        32.78        15.81        11.08        37.05 
TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       19.33        22.82        20.05        45.76        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CY 
       27.35        32.52        11.38        14.14        16.96        68.38 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       39.88        77.33         7.99        25.22        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR 
        9.34        28.93        30.67        41.56        78.38         1.74 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 
       17.75        14.04        13.28         9.47        26.10        18.21 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       23.24        21.30        38.70        17.16         6.97        22.65 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       39.95        24.95        23.64        14.83         4.44        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       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             225.50 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            27.405             29.950 
[1] "0.7 - 125.4 (27.4)" "0.1 - 225.5 (29.9)"
[1] "hr=" "1.3"
D25V2, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    11  19
  13Q GAIN WILD-TYPE 279 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     11   19
  13Q GAIN WILD-TYPE  279  205
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                11                279
  YES               19                205
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  13Q GAIN MUTATED                                         8
  13Q GAIN WILD-TYPE                                     396
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  13Q GAIN MUTATED                               1
  13Q GAIN WILD-TYPE                            21
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  13Q GAIN MUTATED                                  21
  13Q GAIN WILD-TYPE                                92
D25V3, multiclass
                                         clus
vv                                        13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                8                396
  MIXED SEROUS AND ENDOMETRIOID                          1                 21
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     21                 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"
                    vv
clus                  R0  R1  R2  RX
  13Q GAIN MUTATED    20   0   2   3
  13Q GAIN WILD-TYPE 351  22  14  37
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0               20                351
  R1                0                 22
  R2                2                 14
  RX                3                 37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    27   9
  14Q GAIN WILD-TYPE 420  81
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                36                501 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 9                 81 
$`14Q GAIN MUTATED`
TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3IA TCGA-AX-A1CR TCGA-D1-A2G5 TCGA-A5-A1OH 
       30.15        16.83        20.81        23.05        47.84        36.33 
TCGA-A5-A2K2 TCGA-A5-A3LP TCGA-AJ-A3EM TCGA-AJ-A3NF TCGA-AJ-A3TW TCGA-AP-A3K1 
      118.19        14.96        22.26        21.21        16.87        21.90 
TCGA-AX-A1CC TCGA-AX-A2H4 TCGA-B5-A0JR TCGA-B5-A0K4 TCGA-B5-A1MU TCGA-BG-A3PP 
       25.91        30.12        56.91        57.76        50.89        22.39 
TCGA-BK-A0C9 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-D1-A169 TCGA-D1-A1O0 
       35.90        24.13        16.64        92.88        37.32         2.07 
TCGA-DI-A2QY TCGA-E6-A1M0 TCGA-EO-A22Y TCGA-EO-A3B1 TCGA-EY-A1GC TCGA-EY-A1GW 
      110.10        58.95        51.52        26.96        54.15        11.08 
TCGA-EY-A4KR TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-K6-A3WQ 
       11.38        77.33        59.01         9.34        28.93        14.04 

$`14Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AJ-A2QM TCGA-AJ-A3BG TCGA-AJ-A3NH 
       41.06        88.18        60.53        29.39        18.08        10.19 
TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D 
      110.63        57.80        93.99        95.47        67.66        12.26 
TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB 
       36.39        61.18        27.88         1.38        80.38        27.09 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 
       22.06        66.41        61.87        51.55        12.56        14.27 
TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 
        1.81        19.79         4.44        16.93        33.30         6.21 
TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 
       22.78        17.88        10.19        14.40        18.87        17.92 
TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 
       19.89         5.88        66.77        13.84        73.32        36.00 
TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 
       23.74         0.43        39.52        10.29       106.88       149.56 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
      123.68        74.10        65.75        60.53        46.55        73.87 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       36.82        28.27        54.02        23.21        68.65        37.91 
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-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
       31.99        31.99        33.07        66.15        28.64        24.72 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N 
       34.95        25.51        11.21        18.41        20.25        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
       10.26        21.14        19.79        35.15        34.36        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
       18.12        18.90        33.90         1.64        14.66        22.49 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       17.06        36.99        20.65        15.62        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS 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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 
       35.11         0.13       129.80        21.99        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       48.03        63.91        45.53        36.89        23.87        12.62 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       33.40        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       90.97        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        60.23        45.86        27.85        51.12        36.13 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        61.08        35.74        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        77.39        13.28        32.91        34.65 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       25.51        26.37        32.02        34.09        76.83        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 
       73.41        80.25        37.58         4.77        71.24        40.80 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       81.37        34.32        46.49        38.24        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-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
       43.82         0.20        20.52         0.30         0.26         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JS TCGA-B5-A0JT 
        1.18        18.35        14.47         0.39        86.37        55.30 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       59.24        86.01        58.75        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       36.49        72.62        27.29        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       13.45        59.84       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        73.64        61.68        85.78        52.04        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       77.23        73.28        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       225.50       102.31        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       48.43        11.87        52.54        31.36       136.60        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       93.50        71.84        39.35        27.65        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-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       35.21        71.24        63.68        74.63        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       48.56        23.47        43.30        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       15.45        15.45         9.57        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       11.31        34.98        35.90        35.08        31.00        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        24.33 
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       114.90        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        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       83.64        86.99        66.48        16.83        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-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-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-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       18.25        16.87        18.02        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
       48.79         8.48        58.95        15.88         4.27        18.84 
TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV 
       17.29         2.20        71.61       109.08       100.83        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       10.92        27.16        25.91        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-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       79.10         2.37        45.57        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-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       46.26        57.60        51.42        19.40        34.39        50.73 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KW 
       35.15        38.07        27.16        46.42        22.26        16.34 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       38.47        51.09        14.99        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       23.34        23.34        23.90        33.34        32.71        19.27 
TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       18.84        17.62        22.03        16.11        32.78        15.81 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       37.05        19.33        12.59        22.82        20.05        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A54A 
       31.04        29.10        27.35        32.52        14.14        14.70 
TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU 
       16.96        68.38        39.88         7.99        25.22        96.69 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
       30.67        59.28        41.56        78.38         1.74        17.75 
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        21.30 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       38.70        22.59         8.19        17.16         6.97        22.65 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       39.95        24.95        23.64        14.83         4.44        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       18.28         0.07         0.23 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              2.07               0.07 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            118.19             225.50 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            27.945             29.950 
[1] "2.1 - 118.2 (27.9)" "0.1 - 225.5 (29.9)"
[1] "hr=" "1.5"
D26V2, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    22  14
  14Q GAIN WILD-TYPE 268 210
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     22   14
  14Q GAIN WILD-TYPE  268  210
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                22                268
  YES               14                210
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  14Q GAIN MUTATED                                        15
  14Q GAIN WILD-TYPE                                     389
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  14Q GAIN MUTATED                               2
  14Q GAIN WILD-TYPE                            20
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  14Q GAIN MUTATED                                  19
  14Q GAIN WILD-TYPE                                94
D26V3, multiclass
                                         clus
vv                                        14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               15                389
  MIXED SEROUS AND ENDOMETRIOID                          2                 20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     19                 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"
                    vv
clus                  R0  R1  R2  RX
  14Q GAIN MUTATED    24   2   1   5
  14Q GAIN WILD-TYPE 347  20  15  35
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0               24                347
  R1                2                 20
  R2                1                 15
  RX                5                 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"

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED     7   4
  15Q GAIN WILD-TYPE 440  86
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                11                526 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 4                 86 
$`15Q GAIN MUTATED`
TCGA-AJ-A3IA TCGA-D1-A102 TCGA-EY-A72D TCGA-AX-A3G1 TCGA-B5-A11I TCGA-BS-A0TE 
       20.81         4.44         5.88        20.52        75.72         4.80 
TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-E6-A1M0 TCGA-EY-A1GW TCGA-PG-A5BC 
       25.91        35.38        58.95        11.08        23.24 

$`15Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS 
       18.08        10.19       110.63        57.80        93.99        95.47 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF 
       67.66        12.26        36.39        23.05        61.18        27.88 
TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
        1.38        80.38        27.09        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A2G5 
       51.55        12.56        14.27         1.81        19.79        47.84 
TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 
       16.93        33.30         6.21        22.78        17.88        10.19 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-FI-A2CX TCGA-FI-A2D5 
       14.40        18.87        17.92        19.89        66.77        13.84 
TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 
       73.32        36.00        23.74         0.43        39.52        10.29 
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN 
      112.54       105.37       123.68        74.10        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        73.87        36.82        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ 
       42.35        15.95        31.99        31.99        36.33        33.07 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
      118.19        66.15        28.64        24.72        34.95        25.51 
TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O 
       14.96        11.21        18.41        20.25        14.43        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF 
       21.14        19.79        35.15        34.36        34.16        18.12 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       18.90        33.90         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-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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       20.78         2.70        35.11         0.13       129.80        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07        48.03        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        12.62        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        90.97        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        60.23        45.86        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       51.12        21.90        36.13         0.56        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        80.55        88.24        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       79.46        49.87        57.47        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       61.08        35.74        37.78        43.82        40.11        77.39 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       13.28        32.91        34.65        25.51        26.37        32.02 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       25.91        34.09        76.83        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA 
       37.58         4.77        30.12        71.24        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       34.32        46.49        38.24        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-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.20         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        86.37        55.30        59.24 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.01        58.75        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J 
       13.45        59.84       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 
       73.64        61.68        85.78        52.04        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       73.28        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       225.50       102.31        50.89        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       48.43        11.87        52.54        31.36       136.60        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       93.50        71.84        39.35        27.65        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-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       35.21        71.24        63.68        74.63        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       48.56        23.47        43.30        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       15.45        15.45         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        22.39        35.90        34.98        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F 
       31.00        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        24.33        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-A0UT 
       92.88       114.90        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        89.59        63.58        83.64        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        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-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-A3DH 
       48.79         8.48        58.95        15.88         4.27        18.84 
TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV 
       17.29         2.20        71.61       109.08       100.83        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        79.10 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37        45.57        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        50.73 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU 
       35.15        38.07        27.16        46.42        26.96        22.26 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       16.34        38.47        51.09        14.99        54.15        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        23.90        33.34 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT 
       32.71        19.27        18.84        17.62        22.03        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM 
       32.78        15.81        37.05        19.33        12.59        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX 
       20.05        45.76        31.04        29.10        27.35        32.52 
TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 
       11.38        14.14        14.70        16.96        68.38        39.88 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
       77.33         7.99        25.22        96.69        59.01         9.34 
TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR 
       28.93        30.67        59.28        41.56        78.38         1.74 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 
       17.75        14.04        13.28         9.47        26.10        18.21 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 
       21.30        38.70        22.59         8.19        17.16         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 
       22.65        39.95        24.95        23.64        14.83         4.44 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       20.75        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             225.50 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             20.81              30.05 
[1] "4.4 - 75.7 (20.8)"  "0.1 - 225.5 (30.0)"
[1] "hr=" "3.3"
D27V2, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     9   2
  15Q GAIN WILD-TYPE 281 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      9    2
  15Q GAIN WILD-TYPE  281  222
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 9                281
  YES                2                222
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  15Q GAIN MUTATED                                         8
  15Q GAIN WILD-TYPE                                     396
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  15Q GAIN MUTATED                               0
  15Q GAIN WILD-TYPE                            22
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  15Q GAIN MUTATED                                   3
  15Q GAIN WILD-TYPE                               110
D27V3, multiclass
                                         clus
vv                                        15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                8                396
  MIXED SEROUS AND ENDOMETRIOID                          0                 22
  SEROUS ENDOMETRIAL ADENOCARCINOMA                      3                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"
                    vv
clus                  R0  R1  R2  RX
  15Q GAIN MUTATED     4   1   1   2
  15Q GAIN WILD-TYPE 367  21  15  38
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0                4                367
  R1                1                 21
  R2                1                 15
  RX                2                 38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    21   4
  16P GAIN WILD-TYPE 426  86
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                25                512 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 4                 86 
$`16P GAIN MUTATED`
TCGA-BG-A0M8 TCGA-D1-A102 TCGA-EY-A547 TCGA-EY-A72D TCGA-A5-A2K2 TCGA-A5-A3LP 
       66.41         4.44        17.92         5.88       118.19        14.96 
TCGA-AX-A0IW TCGA-AX-A1C8 TCGA-AX-A3G1 TCGA-B5-A11G TCGA-B5-A11V TCGA-B5-A1N2 
       37.78        25.51        20.52       113.36        19.56        31.36 
TCGA-BK-A26L TCGA-BS-A0U9 TCGA-D1-A168 TCGA-EO-A1Y7 TCGA-EO-A3KU TCGA-EO-A3KW 
       24.13        92.88        36.10        49.15        22.26        16.34 
TCGA-EY-A1GW TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-PG-A914 TCGA-PG-A915 
       11.08        14.70        77.33        59.01        22.59         8.19 
TCGA-SL-A6J9 
        0.07 

$`16P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF 
       18.08        20.81        10.19       110.63        57.80        93.99 
TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 
       95.47        67.66        12.26        36.39        23.05        61.18 
TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0MS 
       27.88         1.38        80.38        27.09        22.06        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A2G5 
       51.55        12.56        14.27         1.81        19.79        47.84 
TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 
       16.93        33.30         6.21        22.78        17.88        10.19 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A549 TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 
       14.40        18.87        19.89        66.77        13.84        73.32 
TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 
       36.00        23.74         0.43        39.52        10.29       106.88 
TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      149.56        37.02        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP 
      105.37       123.68        74.10        65.75        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       73.87        36.82        28.27        54.02        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       37.91        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-A2K3 
       15.95        31.99        31.99        36.33        33.07        66.15 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A7WJ TCGA-A5-A7WK 
       28.64        24.72        34.95        25.51        11.21        18.41 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       20.25        14.43        10.26        21.14        19.79        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       34.36        34.16        18.12        18.90        33.90         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-A8CV 
       16.87        22.32        12.82        20.78         2.70        35.11 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        0.13       129.80        21.99        23.31        86.07        48.03 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       63.91        45.53        36.89        23.87        12.62        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        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        46.72        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       61.64        80.78        49.22        25.08        71.67        90.97 
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 
       60.23        45.86        27.85        51.12        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        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ 
       27.39        30.02        60.66        61.08        35.74        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C9 
       40.11        77.39        13.28        32.91        34.65        26.37 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       32.02        25.91        34.09        76.83        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       80.25        37.58         4.77        30.12        71.24        40.80 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       81.37        34.32        46.49        38.24        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-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
       43.82         0.20         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        86.37        55.30 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       59.24        86.01        58.75        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11H TCGA-B5-A11I 
       27.85        13.45        59.84       185.79        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q 
       54.44        73.64        61.68        85.78        52.04        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       77.23        73.28        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       225.50       102.31        50.89        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       48.43        11.87        52.54       136.60        96.30        93.50 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       71.84        39.35        27.65        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-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       71.24        63.68        74.63        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        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       15.45         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 
       22.39        35.90        34.98        35.90        35.08        31.00 
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        24.33        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       114.90 
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 
       89.59        63.58        83.64        86.99        66.48        16.83 
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-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74        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-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-A2G6 TCGA-D1-A2G7 
       15.06         1.05         3.95        48.79         8.48        58.95 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR 
       15.88         4.27        18.84        17.29         2.20        71.61 
TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 
      109.08       100.83        89.33        10.92        27.16        25.91 
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        79.10        58.95 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37        45.57        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        50.73        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KX TCGA-EO-A3L0 
       38.07        27.16        46.42        26.96        38.47        51.09 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99        54.15        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.34        23.90        33.34        32.71        19.27        18.84 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX 
       17.62        22.03        16.11        32.78        15.81        37.05 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       19.33        12.59        22.82        20.05        45.76        31.04 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A5W2 
       29.10        27.35        32.52        11.38        14.14        16.96 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EX 
       68.38        39.88         7.99        25.22        96.69         9.34 
TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR 
       28.93        30.67        59.28        41.56        78.38         1.74 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 
       17.75        14.04        13.28         9.47        26.10        18.21 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       23.24        21.30        38.70        17.16         6.97        22.65 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       39.95        24.95        23.64        14.83         4.44        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.07               0.13 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            118.19             225.50 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             22.59              30.05 
[1] "0.1 - 118.2 (22.6)" "0.1 - 225.5 (30.0)"
[1] "hr=" "1.1"
D28V2, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    15   9
  16P GAIN WILD-TYPE 275 215
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     15    9
  16P GAIN WILD-TYPE  275  215
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                15                275
  YES                9                215
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  16P GAIN MUTATED                                        13
  16P GAIN WILD-TYPE                                     391
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  16P GAIN MUTATED                               1
  16P GAIN WILD-TYPE                            21
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  16P GAIN MUTATED                                  11
  16P GAIN WILD-TYPE                               102
D28V3, multiclass
                                         clus
vv                                        16P GAIN MUTATED 16P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               13                391
  MIXED SEROUS AND ENDOMETRIOID                          1                 21
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     11                102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  16P GAIN MUTATED    15   2   0   4
  16P GAIN WILD-TYPE 356  20  16  36
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               15                356
  R1                2                 20
  R2                0                 16
  RX                4                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED     7   3
  16Q GAIN WILD-TYPE 440  87
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                10                527 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 3                 87 
$`16Q GAIN MUTATED`
TCGA-B5-A0JN TCGA-AX-A1C8 TCGA-AX-A2HH TCGA-B5-A11V TCGA-BS-A0U9 TCGA-EO-A1Y7 
       80.38        25.51        17.75        19.56        92.88        49.15 
TCGA-EY-A1GW TCGA-EY-A54A TCGA-FI-A2D2 TCGA-JU-AAVI 
       11.08        14.70        77.33        17.75 

$`16Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF 
       18.08        20.81        10.19       110.63        57.80        93.99 
TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 
       95.47        67.66        12.26        36.39        23.05        61.18 
TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       27.88         1.38        27.09        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 
       51.55        12.56        14.27         1.81        19.79         4.44 
TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ 
       47.84        16.93        33.30         6.21        22.78        17.88 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D 
       10.19        14.40        18.87        17.92        19.89         5.88 
TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E 
       66.77        13.84        73.32        36.00        23.74         0.43 
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       39.52        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       123.68        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       65.75        60.53        46.55        73.87        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        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        31.99        31.99 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
       36.33        33.07       118.19        66.15        28.64        24.72 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M 
       34.95        25.51        14.96        11.21        18.41        20.25 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       14.43        10.26        21.14        19.79        35.15        34.36 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
       34.16        18.12        18.90        33.90         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-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-A8CV TCGA-AJ-A8CW 
       22.32        12.82        20.78         2.70        35.11         0.13 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
      129.80        21.99        23.31        86.07        48.03        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        12.62        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      125.42       117.99       110.37        66.25        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       46.72        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       80.78        49.22        25.08        71.67        90.97        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        60.23 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
       45.86        27.85        51.12        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        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        61.08        35.74        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C9 
       40.11        77.39        13.28        32.91        34.65        26.37 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       32.02        25.91        34.09        76.83        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       80.25        37.58         4.77        30.12        71.24        40.80 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK 
       81.37        34.32        46.49        38.24        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-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       18.35        14.47         0.39        56.91        86.37        55.30 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       59.24        86.01        58.75        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       27.85        13.45        59.84       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        73.64        61.68        85.78        52.04 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y 
       32.09        77.23        73.28        16.73        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       225.50       102.31        50.89        51.45 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       14.70        48.43        11.87        52.54        31.36       136.60 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 
       96.30        93.50        71.84        39.35        27.65        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-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        35.21        71.24        63.68        74.63        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        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       14.01        15.45        15.45         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        22.39        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD 
       35.08        31.00        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        24.33        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       114.90        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        89.59        63.58        83.64 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       86.99        66.48        16.83        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-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-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.95        48.79         8.48        58.95        15.88         4.27 
TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU 
       18.84        17.29         2.20        71.61       109.08       100.83 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU 
       89.33        10.92        27.16        25.91        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        79.10        58.95         2.37        45.57 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22R 
       16.04         7.36        16.80        10.92        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        50.73        35.15        38.07        27.16 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       46.42        26.96        22.26        16.34        38.47        51.09 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99        54.15        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.34        23.90        33.34        32.71        19.27        18.84 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX 
       17.62        22.03        16.11        32.78        15.81        37.05 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       19.33        12.59        22.82        20.05        45.76        31.04 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A5W2 
       29.10        27.35        32.52        11.38        14.14        16.96 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       68.38        39.88         7.99        25.22        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
        9.34        28.93        30.67        59.28        41.56        78.38 
TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 
        1.74        14.04        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        21.30        38.70        22.59         8.19        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        22.65        39.95        24.95        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44        20.75        18.28         0.07         0.23 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             11.08               0.07 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             92.88             225.50 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            22.535             29.950 
[1] "11.1 - 92.9 (22.5)" "0.1 - 225.5 (29.9)"
[1] "hr=" "1.8"
D29V2, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     7   3
  16Q GAIN WILD-TYPE 283 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      7    3
  16Q GAIN WILD-TYPE  283  221
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 7                283
  YES                3                221
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  16Q GAIN MUTATED                                         6
  16Q GAIN WILD-TYPE                                     398
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  16Q GAIN MUTATED                               1
  16Q GAIN WILD-TYPE                            21
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  16Q GAIN MUTATED                                   3
  16Q GAIN WILD-TYPE                               110
D29V3, multiclass
                                         clus
vv                                        16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                6                398
  MIXED SEROUS AND ENDOMETRIOID                          1                 21
  SEROUS ENDOMETRIAL ADENOCARCINOMA                      3                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"
                    vv
clus                  R0  R1  R2  RX
  16Q GAIN MUTATED     4   3   0   1
  16Q GAIN WILD-TYPE 367  19  16  39
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0                4                367
  R1                3                 19
  R2                0                 16
  RX                1                 39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    10   3
  17P GAIN WILD-TYPE 437  87
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                13                524 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                 87 
$`17P GAIN MUTATED`
TCGA-AJ-A3IA TCGA-A5-A0R7 TCGA-AX-A0IW TCGA-AX-A1C4 TCGA-AX-A2HK TCGA-BG-A0M4 
       20.81        17.59        37.78        13.28         2.96        71.24 
TCGA-BK-A0CC TCGA-D1-A1O0 TCGA-DI-A2QY TCGA-EO-A3B1 TCGA-EY-A1GO TCGA-K6-A3WQ 
       35.08         2.07       110.10        26.96        19.27        14.04 
TCGA-SL-A6J9 
        0.07 

$`17P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS 
       18.08        10.19       110.63        57.80        93.99        95.47 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF 
       67.66        12.26        36.39        23.05        61.18        27.88 
TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
        1.38        80.38        27.09        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 
       51.55        12.56        14.27         1.81        19.79         4.44 
TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ 
       47.84        16.93        33.30         6.21        22.78        17.88 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D 
       10.19        14.40        18.87        17.92        19.89         5.88 
TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E 
       66.77        13.84        73.32        36.00        23.74         0.43 
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       39.52        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       123.68        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       65.75        60.53        46.55        73.87        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 
       54.02        23.21        68.65        37.91        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        31.99        31.99        36.33 
TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
       33.07       118.19        66.15        28.64        24.72        34.95 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N 
       25.51        14.96        11.21        18.41        20.25        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
       10.26        21.14        19.79        35.15        34.36        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
       18.12        18.90        33.90         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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 
       12.82        20.78         2.70        35.11         0.13       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
       21.99        23.31        86.07        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       36.89        23.87        12.62        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      117.99       110.37        66.25        36.36        97.71        46.72 
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-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        90.97        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        60.23        45.86 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       27.85        51.12        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 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       45.99        79.46        49.87        57.47        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        61.08        35.74        43.82        40.11        77.39 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       32.91        34.65        25.51        26.37        32.02        25.91 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       34.09        76.83        85.48        73.41        80.25        37.58 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
        4.77        30.12        71.24        40.80        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO 
       46.49        38.24        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-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        86.37        55.30        59.24        86.01 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       58.75        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       59.84       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 
       73.64        61.68        85.78        52.04        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       73.28        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       225.50       102.31        50.89        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       48.43        11.87        52.54        31.36       136.60        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       93.50        71.84        39.35        27.65        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-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       35.21        63.68        74.63        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        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       15.45         9.57        20.02        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B 
       22.39        35.90        34.98        35.90        31.00        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        24.33        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        92.88 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
      114.90        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        89.59        63.58        83.64        86.99        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        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-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-A2G6 
       18.02        15.06         1.05         3.95        48.79         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN 
       58.95        15.88         4.27        18.84        17.29         2.20 
TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
       71.61       109.08       100.83        89.33        10.92        27.16 
TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
       25.91        16.31        39.29        36.62        24.30        35.38 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
        9.37        12.39        31.10        23.38        79.10        58.95 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37        45.57        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        50.73 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KW 
       35.15        38.07        27.16        46.42        22.26        16.34 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       38.47        51.09        14.99        54.15        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM 
       27.16        23.34        23.34        23.90        33.34        32.71 
TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       18.84        17.62        22.03        16.11        32.78        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON 
       11.08        37.05        19.33        12.59        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        32.52        11.38 
TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
       14.14        14.70        16.96        68.38        39.88        77.33 
TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
        7.99        25.22        96.69        59.01         9.34        28.93 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
       30.67        59.28        41.56        78.38         1.74        17.75 
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        21.30 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       38.70        22.59         8.19        17.16         6.97        22.65 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       39.95        24.95        23.64        14.83         4.44        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.07               0.13 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             110.1              225.5 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             19.27              30.05 
[1] "0.1 - 110.1 (19.3)" "0.1 - 225.5 (30.0)"
[1] "hr=" "1.8"
D30V2, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     6   6
  17P GAIN WILD-TYPE 284 218
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      6    6
  17P GAIN WILD-TYPE  284  218
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 6                284
  YES                6                218
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  17P GAIN MUTATED                                         7
  17P GAIN WILD-TYPE                                     397
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  17P GAIN MUTATED                               0
  17P GAIN WILD-TYPE                            22
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  17P GAIN MUTATED                                   6
  17P GAIN WILD-TYPE                               107
D30V3, multiclass
                                         clus
vv                                        17P GAIN MUTATED 17P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                7                397
  MIXED SEROUS AND ENDOMETRIOID                          0                 22
  SEROUS ENDOMETRIAL ADENOCARCINOMA                      6                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"
                    vv
clus                  R0  R1  R2  RX
  17P GAIN MUTATED     8   1   0   3
  17P GAIN WILD-TYPE 363  21  16  37
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0                8                363
  R1                1                 21
  R2                0                 16
  RX                3                 37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    22   8
  17Q GAIN WILD-TYPE 425  82
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                30                507 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 8                 82 
$`17Q GAIN MUTATED`
TCGA-AJ-A3IA TCGA-B5-A0KB TCGA-D1-A3JP TCGA-A5-A0GR TCGA-A5-A0R7 TCGA-AJ-A3QS 
       20.81        27.09        16.93        36.82        17.59        16.87 
TCGA-AX-A0IW TCGA-AX-A1C4 TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2HK TCGA-B5-A11I 
       37.78        13.28        76.83         4.77         2.96        75.72 
TCGA-B5-A1MY TCGA-BG-A0M2 TCGA-BG-A0M4 TCGA-BG-A3PP TCGA-BK-A0CC TCGA-D1-A1O0 
       11.87        20.94        71.24        22.39        35.08         2.07 
TCGA-DI-A1NN TCGA-EO-A2CH TCGA-EO-A3B1 TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A2ON 
       35.38        19.40        26.96        19.27        22.03        20.05 
TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-PG-A915 TCGA-SL-A6J9 
       27.35        11.38        78.38        14.04         8.19         0.07 

$`17Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS 
       18.08        10.19       110.63        57.80        93.99        95.47 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF 
       67.66        12.26        36.39        23.05        61.18        27.88 
TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
        1.38        80.38        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 
       12.56        14.27         1.81        19.79         4.44        47.84 
TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 
       33.30         6.21        22.78        17.88        10.19        14.40 
TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 
       18.87        17.92        19.89         5.88        66.77        13.84 
TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 
       73.32        36.00        23.74         0.43        39.52        10.29 
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN 
      112.54       105.37       123.68        74.10        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        73.87        28.27        54.02        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       37.91        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 
       31.99        31.99        36.33        33.07       118.19        66.15 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ 
       28.64        24.72        34.95        25.51        14.96        11.21 
TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       18.41        20.25        14.43        10.26        21.14        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK 
       35.15        34.36        34.16        18.12        18.90        33.90 
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-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65        21.21        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-A8CV 
       16.87        22.32        12.82        20.78         2.70        35.11 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        0.13       129.80        21.99        23.31        86.07        48.03 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       63.91        45.53        36.89        23.87        12.62        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        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        46.72        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       61.64        80.78        49.22        25.08        71.67        90.97 
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 
       60.23        45.86        27.85        51.12        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        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ 
       27.39        30.02        60.66        61.08        35.74        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       40.11        77.39        32.91        34.65        25.51        26.37 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       32.02        25.91        34.09        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
       37.58        30.12        71.24        40.80        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO 
       46.49        38.24        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-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        86.37        55.30        59.24        86.01 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       58.75        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
       59.84       185.79       113.36        88.34        54.44        73.64 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       61.68        85.78        52.04        32.09        77.23        73.28 
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 
      225.50       102.31        50.89        51.45        14.70        48.43 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       52.54        31.36       136.60        96.30        93.50        71.84 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       39.35        27.65        29.65        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M3 TCGA-BG-A0M7 TCGA-BG-A0M9 
       18.61        20.19        19.33        35.21        63.68        74.63 
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-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
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-A222 TCGA-BG-A2AD 
       14.73        14.01        15.45        15.45         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        35.90 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F 
       31.00        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        24.33        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        92.88       114.90        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        89.59        63.58        83.64 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       86.99        66.48        16.83        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-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-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       18.25        16.87        18.02        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
       48.79         8.48        58.95        15.88         4.27        18.84 
TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV 
       17.29         2.20        71.61       109.08       100.83        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       10.92        27.16        25.91        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX 
       24.30         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 
       79.10        58.95         2.37        45.57        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 
       50.73        35.15        38.07        27.16        46.42        22.26 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       16.34        38.47        51.09        14.99        54.15        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        23.90        33.34 
TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       32.71        18.84        17.62        16.11        32.78        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2OO 
       11.08        37.05        19.33        12.59        22.82        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 
       31.04        29.10        32.52        14.14        14.70        16.96 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU 
       68.38        39.88        77.33         7.99        25.22        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV 
       59.01         9.34        28.93        30.67        59.28        41.56 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 
        1.74        17.75        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        21.30        38.70        22.59        17.16         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 
       22.65        39.95        24.95        23.64        14.83         4.44 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       20.75        18.28         0.23 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.07               0.13 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             78.38             225.50 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             20.43              30.44 
[1] "0.1 - 78.4 (20.4)"  "0.1 - 225.5 (30.4)"
[1] "hr=" "2.5"
D31V2, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    14  15
  17Q GAIN WILD-TYPE 276 209
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     14   15
  17Q GAIN WILD-TYPE  276  209
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                14                276
  YES               15                209
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  17Q GAIN MUTATED                                        12
  17Q GAIN WILD-TYPE                                     392
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  17Q GAIN MUTATED                               0
  17Q GAIN WILD-TYPE                            22
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  17Q GAIN MUTATED                                  18
  17Q GAIN WILD-TYPE                                95
D31V3, multiclass
                                         clus
vv                                        17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               12                392
  MIXED SEROUS AND ENDOMETRIOID                          0                 22
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     18                 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"
                    vv
clus                  R0  R1  R2  RX
  17Q GAIN MUTATED    18   1   4   3
  17Q GAIN WILD-TYPE 353  21  12  37
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0               18                353
  R1                1                 21
  R2                4                 12
  RX                3                 37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    53  20
  18P GAIN WILD-TYPE 394  70
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                73                464 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                20                 70 
$`18P GAIN MUTATED`
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A0LF TCGA-BG-A0M6 TCGA-BG-A0M8 
       20.81        10.19       110.63        93.99        22.06        66.41 
TCGA-BG-A0VT TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A212 TCGA-EY-A72D TCGA-KJ-A3U4 
       51.55        16.93        33.30        10.19         5.88        36.00 
TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A0GE TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A1OG 
       39.52        37.02       105.37        36.82        37.91        31.99 
TCGA-A5-A1OH TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3EM TCGA-AJ-A3NF TCGA-AJ-A3QS 
       36.33        14.43        34.16        22.26        21.21        16.87 
TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A0LO 
       16.87        20.78        48.79       125.42        97.71        33.40 
TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A2H4 
       46.78        21.90        36.13        32.02        25.91        30.12 
TCGA-AX-A2HC TCGA-AX-A2HK TCGA-AX-A3GI TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A3S1 
       34.32         2.96         0.39        27.85        75.72        29.65 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A2AE TCGA-BK-A0CC TCGA-BK-A26L TCGA-BS-A0U9 
       34.13        34.95        23.70        35.08        24.13        92.88 
TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A2G0 TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DF-A2KR 
       39.48        37.32        48.79        58.95        18.84        71.61 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A2CH TCGA-EO-A3AZ 
       35.38         9.37       110.10        79.10        19.40        27.16 
TCGA-EO-A3KU TCGA-EY-A1GR TCGA-EY-A210 TCGA-EY-A2ON TCGA-EY-A3L3 TCGA-FI-A2CY 
       22.26        17.62        12.59        20.05        27.35        68.38 
TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A915 
       59.28        78.38        14.04        23.24        38.70         8.19 
TCGA-QS-A8F1 
        4.44 

$`18P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP 
       18.08        57.80        95.47        67.66        12.26        36.39 
TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB 
       23.05        61.18        27.88         1.38        80.38        27.09 
TCGA-BG-A0MS TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 
       61.87        12.56        14.27         1.81        19.79         4.44 
TCGA-D1-A2G5 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A214 TCGA-EY-A215 
       47.84         6.21        22.78        17.88        14.40        18.87 
TCGA-EY-A547 TCGA-EY-A549 TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KP-A3VZ 
       17.92        19.89        66.77        13.84        73.32        23.74 
TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA 
        0.43        10.29       106.88       149.56        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN 
       32.78       112.54       123.68        74.10        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        73.87        28.27        54.02        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-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
       31.99        33.07       118.19        66.15        28.64        24.72 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M 
       34.95        25.51        14.96        11.21        18.41        20.25 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF 
       10.26        21.14        19.79        35.15        34.36        18.12 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 
       18.90        33.90         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-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 
       22.32        12.82         2.70        35.11         0.13       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
       21.99        23.31        86.07        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE 
       36.89        23.87        12.62        20.91       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       66.25        36.36        46.72        83.97        27.12        82.52 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       61.64        80.78        49.22        25.08        71.67        90.97 
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        60.23 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       45.86        27.85        51.12         0.56        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        80.55        88.24        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       79.46        49.87        57.47        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       61.08        35.74        37.78        43.82        40.11        77.39 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CE 
       13.28        32.91        34.65        25.51        26.37        34.09 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 
       76.83        85.48        73.41        80.25        37.58         4.77 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       71.24        40.80        81.37        46.49        38.24        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-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
       43.82         0.20        20.52         0.30         0.26         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        86.37        55.30 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       59.24        86.01        58.75        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J 
       13.45        59.84       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 
       73.64        61.68        85.78        52.04        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       73.28        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       225.50       102.31        50.89        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       48.43        11.87        52.54        31.36       136.60        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-BG-A0LW 
       93.50        71.84        39.35        27.65        41.06        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        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       74.63        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        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-A222 
       13.78        14.73        14.01        15.45        15.45         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        22.39        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F 
       35.90        31.00        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        24.33        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       114.90        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        89.59        63.58        83.64        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        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-A15W 
       28.67        23.93        22.55         1.74        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-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-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-A2G6 TCGA-D1-A3DA 
        2.07        15.06         1.05         3.95         8.48        15.88 
TCGA-D1-A3DG TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV 
        4.27        17.29         2.20       109.08       100.83        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       10.92        27.16        25.91        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 
       24.30        12.39        31.10        23.38        58.95         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       45.57        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-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       51.52        51.42        34.39        50.73        35.15        38.07 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 
       46.42        26.96        16.34        38.47        51.09        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       54.15        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GS 
       23.90        33.34        32.71        19.27        18.84        22.03 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        32.78        15.81        11.08        37.05        19.33 
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        32.52        11.38 
TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
       14.14        14.70        16.96        39.88        77.33         7.99 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 
       25.22        96.69        59.01         9.34        28.93        30.67 
TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 
       41.56         1.74        17.75        13.28         9.47        26.10 
TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       18.21        21.30        22.59        17.16         6.97        22.65 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       39.95        24.95        23.64        14.83        20.75        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.39               0.07 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            125.42             225.50 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             33.30              29.36 
[1] "0.4 - 125.4 (33.3)" "0.1 - 225.5 (29.4)"
[1] "hr=" "1.7"
D32V2, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    39  32
  18P GAIN WILD-TYPE 251 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     39   32
  18P GAIN WILD-TYPE  251  192
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                39                251
  YES               32                192
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  18P GAIN MUTATED                                        22
  18P GAIN WILD-TYPE                                     382
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  18P GAIN MUTATED                               5
  18P GAIN WILD-TYPE                            17
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  18P GAIN MUTATED                                  46
  18P GAIN WILD-TYPE                                67
D32V3, multiclass
                                         clus
vv                                        18P GAIN MUTATED 18P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               22                382
  MIXED SEROUS AND ENDOMETRIOID                          5                 17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     46                 67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  18P GAIN MUTATED    47   1   6   8
  18P GAIN WILD-TYPE 324  21  10  32
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0               47                324
  R1                1                 21
  R2                6                 10
  RX                8                 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"

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    31  15
  18Q GAIN WILD-TYPE 416  75
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                46                491 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                15                 75 
$`18Q GAIN MUTATED`
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A0LF TCGA-BG-A0VT TCGA-EY-A72D 
       20.81        10.19       110.63        93.99        51.55         5.88 
TCGA-KJ-A3U4 TCGA-5B-A90C TCGA-A5-A0GE TCGA-A5-A0R6 TCGA-AJ-A23N TCGA-AJ-A3EM 
       36.00        39.52       105.37        37.91        14.43        22.26 
TCGA-AJ-A3NF TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LO TCGA-AP-A3K1 TCGA-AP-A5FX 
       21.21        48.79       125.42        33.40        21.90        36.13 
TCGA-AX-A1CC TCGA-AX-A2HC TCGA-AX-A2HK TCGA-B5-A11I TCGA-B5-A3S1 TCGA-B5-A5OD 
       25.91        34.32         2.96        75.72        29.65        34.13 
TCGA-BG-A2AE TCGA-BK-A0CC TCGA-BK-A26L TCGA-BS-A0U9 TCGA-D1-A15V TCGA-D1-A16I 
       23.70        35.08        24.13        92.88        39.48        11.51 
TCGA-D1-A2G0 TCGA-D1-A2G7 TCGA-DF-A2KR TCGA-DI-A1NN TCGA-DI-A1NO TCGA-EO-A2CH 
       48.79        58.95        71.61        35.38         9.37        19.40 
TCGA-EO-A3AZ TCGA-EY-A1GR TCGA-EY-A210 TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-FI-A2F9 
       27.16        17.62        12.59        27.35        11.38        59.28 
TCGA-K6-A3WQ TCGA-KP-A3W3 TCGA-PG-A915 TCGA-QS-A8F1 
       14.04        26.10         8.19         4.44 

$`18Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP 
       18.08        57.80        95.47        67.66        12.26        36.39 
TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB 
       23.05        61.18        27.88         1.38        80.38        27.09 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 
       22.06        66.41        61.87        12.56        14.27         1.81 
TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 
       19.79         4.44        47.84        16.93        33.30         6.21 
TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 
       22.78        17.88        10.19        14.40        18.87        17.92 
TCGA-EY-A549 TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KP-A3VZ TCGA-4E-A92E 
       19.89        66.77        13.84        73.32        23.74         0.43 
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-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN 
       32.78       112.54       123.68        74.10        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        73.87        36.82        28.27        54.02        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-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 
       15.95        31.99        31.99        36.33        33.07       118.19 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       66.15        28.64        24.72        34.95        25.51        14.96 
TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       11.21        18.41        20.25        10.26        21.14        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK 
       35.15        34.36        34.16        18.12        18.90        33.90 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE 
        1.64        14.66        22.49        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-A8CV TCGA-AJ-A8CW 
       22.32        12.82        20.78         2.70        35.11         0.13 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
      129.80        21.99        23.31        86.07        48.03        63.91 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD 
       45.53        36.89        23.87        12.62        20.91       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       27.12        82.52        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        90.97        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        60.23        45.86        27.85        51.12 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        61.08        35.74        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        77.39        13.28        32.91        34.65 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       25.51        26.37        32.02        34.09        76.83        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       73.41        80.25        37.58         4.77        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       40.80        81.37        46.49        38.24        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-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       18.35        14.47         0.39        56.91        86.37        55.30 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       59.24        86.01        58.75        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       27.85        13.45        59.84       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        73.64        61.68        85.78        52.04        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       77.23        73.28        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       225.50       102.31        50.89        51.45 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       14.70        48.43        11.87        52.54        31.36       136.60 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC 
       96.30        93.50        71.84        39.35        27.65        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-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       71.24        63.68        74.63        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        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
       15.45         9.57        20.02        20.12        11.31        22.39 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       35.90        34.98        35.90        31.00        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        24.33 
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       114.90        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        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       83.64        86.99        66.48        16.83        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-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-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-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-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN 
        8.48        15.88         4.27        18.84        17.29         2.20 
TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 
      109.08       100.83        89.33        10.92        27.16        25.91 
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-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
      110.10        23.38        79.10        58.95         2.37        45.57 
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-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 
       51.42        34.39        50.73        35.15        38.07        46.42 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 
       26.96        22.26        16.34        38.47        51.09        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       54.15        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GS 
       23.90        33.34        32.71        19.27        18.84        22.03 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        32.78        15.81        11.08        37.05        19.33 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX 
       22.82        20.05        45.76        31.04        29.10        32.52 
TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
       14.14        14.70        16.96        68.38        39.88        77.33 
TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
        7.99        25.22        96.69        59.01         9.34        28.93 
TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KP-A3W0 
       30.67        41.56        78.38         1.74        17.75        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        21.30        38.70        22.59 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       17.16         6.97        22.65        39.95        24.95        23.64 
TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83        20.75        18.28         0.07         0.23 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              2.96               0.07 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            125.42             225.50 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             28.50              29.95 
[1] "3.0 - 125.4 (28.5)" "0.1 - 225.5 (29.9)"
[1] "hr=" "2.1"
D33V2, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    24  21
  18Q GAIN WILD-TYPE 266 203
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     24   21
  18Q GAIN WILD-TYPE  266  203
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                24                266
  YES               21                203
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  18Q GAIN MUTATED                                        17
  18Q GAIN WILD-TYPE                                     387
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  18Q GAIN MUTATED                               4
  18Q GAIN WILD-TYPE                            18
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  18Q GAIN MUTATED                                  25
  18Q GAIN WILD-TYPE                                88
D33V3, multiclass
                                         clus
vv                                        18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               17                387
  MIXED SEROUS AND ENDOMETRIOID                          4                 18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     25                 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"
                    vv
clus                  R0  R1  R2  RX
  18Q GAIN MUTATED    28   0   3   8
  18Q GAIN WILD-TYPE 343  22  13  32
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0               28                343
  R1                0                 22
  R2                3                 13
  RX                8                 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"

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    42  12
  19P GAIN WILD-TYPE 405  78
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                54                483 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                12                 78 
$`19P GAIN MUTATED`
TCGA-AJ-A3IA TCGA-AP-A0LF TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-B5-A0JN TCGA-BG-A0VT 
       20.81        93.99        23.05        61.18        80.38        51.55 
TCGA-EY-A212 TCGA-EY-A547 TCGA-AJ-A3BI TCGA-AJ-A8CW TCGA-AP-A0L8 TCGA-AP-A0L9 
       10.19        17.92        18.90         0.13        48.79       125.42 
TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H2 
       97.71        46.78        37.78        34.65        25.51         4.77 
TCGA-AX-A2H7 TCGA-AX-A3G1 TCGA-B5-A0K8 TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-BG-A3PP 
       40.80        20.52        27.85        31.36        29.65        22.39 
TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A16I 
       35.08        24.13        16.64        83.64        22.55        11.51 
TCGA-D1-A16S TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-D1-A3JQ 
       18.67        18.25         2.07        58.95        18.84        17.29 
TCGA-DF-A2KS TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-EO-A1Y5 TCGA-EO-A22Y 
      109.08         9.37        31.10       110.10        10.92        51.52 
TCGA-EO-A2CG TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GR TCGA-EY-A210 
       51.42        22.26        16.34        23.90        17.62        12.59 
TCGA-EY-A2OQ TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-KP-A3W1 TCGA-PG-A7D5 TCGA-PG-A915 
       29.10        59.28        78.38         9.47        38.70         8.19 

$`19P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06B 
       18.08        10.19       110.63        57.80        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0KB TCGA-BG-A0M6 
       12.26        36.39        27.88         1.38        27.09        22.06 
TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       66.41        61.87        12.56        14.27         1.81        19.79 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK 
        4.44        47.84        16.93        33.30         6.21        22.78 
TCGA-EY-A1GQ TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX 
       17.88        14.40        18.87        19.89         5.88        66.77 
TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C 
       13.84        73.32        36.00        23.74         0.43        39.52 
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-A0GJ 
       32.78       112.54       105.37       123.68        74.10        65.75 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        73.87        36.82        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        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        31.99        31.99        36.33 
TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
       33.07       118.19        66.15        28.64        24.72        34.95 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N 
       25.51        14.96        11.21        18.41        20.25        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
       10.26        21.14        19.79        35.15        34.36        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       18.12        33.90         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-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-A8CV TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
       20.78         2.70        35.11       129.80        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07        48.03        63.91        45.53        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       12.62        20.91       117.99       110.37        66.25        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       46.72        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       80.78        49.22        25.08        71.67        90.97        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        60.23        45.86 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       27.85        51.12        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 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       45.99        79.46        49.87        57.47        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        61.08        35.74        43.82        40.11        77.39 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       13.28        32.91        26.37        32.02        25.91        34.09 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H4 
       76.83        85.48        73.41        80.25        37.58        30.12 
TCGA-AX-A2H5 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       71.24        81.37        34.32        46.49        38.24        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-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
        0.56        43.82         0.20         0.30         0.26         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS 
        1.18        18.35        14.47         0.39        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       55.30        59.24        86.01        58.75        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        13.45        59.84       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        73.64        61.68        85.78        52.04 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        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       225.50       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 
       51.45        14.70        48.43        11.87        52.54       136.60 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC 
       96.30        93.50        71.84        39.35        27.65        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-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       35.21        71.24        63.68        74.63        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       48.56        23.47        43.30        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       15.45        15.45         9.57        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B 
       11.31        35.90        34.98        35.90        31.00        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        24.33 
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        92.88       114.90        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        89.59 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        86.99        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 
        0.56         4.87        28.67        23.93         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-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-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-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-A1NY TCGA-D1-A1NZ 
       22.92         1.41        13.22         0.72        16.87        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A3DA 
       15.06         1.05         3.95        48.79         8.48        15.88 
TCGA-D1-A3DG TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY 
        4.27         2.20        71.61       100.83        89.33        10.92 
TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       27.16        25.91        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       35.38        12.39        23.38        79.10        58.95         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       45.57        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-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        50.73        35.15        38.07        27.16        46.42 
TCGA-EO-A3B1 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       26.96        38.47        51.09        14.99        54.15        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM 
       24.36        27.16        23.34        23.34        33.34        32.71 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       19.27        18.84        22.03        16.11        32.78        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       11.08        37.05        19.33        22.82        20.05        45.76 
TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A 
       31.04        27.35        32.52        11.38        14.14        14.70 
TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 
       16.96        68.38        39.88        77.33         7.99        25.22 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV 
       96.69        59.01         9.34        28.93        30.67        41.56 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 
        1.74        17.75        14.04        13.28        26.10        18.21 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       23.24        21.30        22.59        17.16         6.97        22.65 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       39.95        24.95        23.64        14.83         4.44        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       18.28         0.07         0.23 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.13               0.07 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            125.42             225.50 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             24.82              30.12 
[1] "0.1 - 125.4 (24.8)" "0.1 - 225.5 (30.1)"
[1] "hr=" "1.4"
D34V2, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    27  25
  19P GAIN WILD-TYPE 263 199
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     27   25
  19P GAIN WILD-TYPE  263  199
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                27                263
  YES               25                199
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  19P GAIN MUTATED                                        21
  19P GAIN WILD-TYPE                                     383
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  19P GAIN MUTATED                               3
  19P GAIN WILD-TYPE                            19
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  19P GAIN MUTATED                                  31
  19P GAIN WILD-TYPE                                82
D34V3, multiclass
                                         clus
vv                                        19P GAIN MUTATED 19P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               21                383
  MIXED SEROUS AND ENDOMETRIOID                          3                 19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     31                 82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  19P GAIN MUTATED    38   3   2   6
  19P GAIN WILD-TYPE 333  19  14  34
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0               38                333
  R1                3                 19
  R2                2                 14
  RX                6                 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"

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    39  18
  19Q GAIN WILD-TYPE 408  72
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                57                480 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                18                 72 
$`19Q GAIN MUTATED`
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AX-A1CR TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0VT 
       20.81        10.19        23.05        80.38        22.06        51.55 
TCGA-EY-A212 TCGA-EY-A547 TCGA-A5-A1OG TCGA-A5-A2K3 TCGA-A5-A3LP TCGA-AJ-A23M 
       10.19        17.92        31.99        66.15        14.96        20.25 
TCGA-AJ-A8CW TCGA-AP-A0L8 TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AX-A0IU TCGA-AX-A0IW 
        0.13        48.79        97.71        46.78        35.74        37.78 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A3G1 
       34.65        25.51        32.02         4.77        40.80        20.52 
TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A4ZD TCGA-D1-A0ZZ 
       31.36        29.65        35.08        24.13        16.64        22.55 
TCGA-D1-A15V TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A2G7 
       39.48        11.51        18.67        18.25         2.07        58.95 
TCGA-D1-A3JQ TCGA-DF-A2KS TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ 
       17.29       109.08         9.37        31.10       110.10        79.10 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3KU TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A210 
       51.52        51.42        22.26        17.62        22.03        12.59 
TCGA-EY-A2OQ TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-JU-AAVI TCGA-KP-A3W1 TCGA-KP-A3W3 
       29.10        59.28        78.38        17.75         9.47        26.10 
TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-SL-A6J9 
       23.24        38.70         0.07 

$`19Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B 
       18.08       110.63        57.80        93.99        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0KB 
       12.26        36.39        61.18        27.88         1.38        27.09 
TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       66.41        61.87        12.56        14.27         1.81        19.79 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK 
        4.44        47.84        16.93        33.30         6.21        22.78 
TCGA-EY-A1GQ TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX 
       17.88        14.40        18.87        19.89         5.88        66.77 
TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C 
       13.84        73.32        36.00        23.74         0.43        39.52 
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-A0GJ 
       32.78       112.54       105.37       123.68        74.10        65.75 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        73.87        36.82        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        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        31.99        36.33        33.07 
TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A7WJ 
      118.19        28.64        24.72        34.95        25.51        11.21 
TCGA-A5-A7WK TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       18.41        14.43        10.26        21.14        19.79        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       34.36        34.16        18.12        18.90        33.90         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-A8CV 
       16.87        22.32        12.82        20.78         2.70        35.11 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
      129.80        21.99        23.31        86.07        48.03        63.91 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 
       45.53        36.89        23.87        12.62        20.91       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL 
      117.99       110.37        66.25        36.36        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        90.97        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        60.23        45.86        27.85        51.12 
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        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       80.55        88.24        71.51        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       49.87        57.47        27.39        30.02        60.66        61.08 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 
       43.82        40.11        77.39        13.28        32.91        26.37 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       25.91        34.09        76.83        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       37.58        30.12        71.24        81.37        34.32        46.49 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       38.24        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-A3G4 
        0.23         0.20         0.56        43.82         0.20         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-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        86.37        55.30        59.24        86.01        58.75 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       69.27        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       57.76        64.21        63.55        27.85        13.45        59.84 
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        73.64 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       61.68        85.78        52.04        32.09        77.23        73.28 
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 
      225.50       102.31        50.89        51.45        14.70        48.43 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       11.87        52.54       136.60        96.30        93.50        71.84 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW 
       39.35        27.65        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        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       74.63        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        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-A222 
       13.78        14.73        14.01        15.45        15.45         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        22.39        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F 
       34.98        35.90        31.00        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        24.33        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        92.88       114.90        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        89.59        63.58        83.64 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       86.99        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W 
        4.87        28.67        23.93         1.74        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-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-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-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
        3.95        48.79         8.48        15.88         4.27        18.84 
TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        2.20        71.61       100.83        89.33        10.92        27.16 
TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
       25.91        16.31        39.29        36.62        24.30        35.38 
TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       12.39        23.38        58.95         2.37        45.57        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 
       50.73        35.15        38.07        27.16        46.42        26.96 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       16.34        38.47        51.09        14.99        54.15        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        23.90        33.34 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       32.71        19.27        18.84        16.11        32.78        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       11.08        37.05        19.33        22.82        20.05        45.76 
TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A 
       31.04        27.35        32.52        11.38        14.14        14.70 
TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 
       16.96        68.38        39.88        77.33         7.99        25.22 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV 
       96.69        59.01         9.34        28.93        30.67        41.56 
TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A914 
        1.74        14.04        13.28        18.21        21.30        22.59 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        8.19        17.16         6.97        22.65        39.95        24.95 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       23.64        14.83         4.44        20.75        18.28         0.23 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.07               0.20 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             110.1              225.5 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             25.51              30.10 
[1] "0.1 - 110.1 (25.5)" "0.2 - 225.5 (30.1)"
[1] "hr=" "2.4"
D35V2, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    29  25
  19Q GAIN WILD-TYPE 261 199
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     29   25
  19Q GAIN WILD-TYPE  261  199
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                29                261
  YES               25                199
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  19Q GAIN MUTATED                                        16
  19Q GAIN WILD-TYPE                                     388
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  19Q GAIN MUTATED                               3
  19Q GAIN WILD-TYPE                            19
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  19Q GAIN MUTATED                                  39
  19Q GAIN WILD-TYPE                                74
D35V3, multiclass
                                         clus
vv                                        19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               16                388
  MIXED SEROUS AND ENDOMETRIOID                          3                 19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     39                 74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  19Q GAIN MUTATED    39   3   2   7
  19Q GAIN WILD-TYPE 332  19  14  33
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               39                332
  R1                3                 19
  R2                2                 14
  RX                7                 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"

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    79  30
  20P GAIN WILD-TYPE 368  60
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               109                428 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                30                 60 
$`20P GAIN MUTATED`
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A1CR TCGA-AX-A3G3 
       20.81        10.19        93.99        67.66        23.05         1.38 
TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A221 TCGA-D1-A102 
       80.38        27.09        61.87        51.55         1.81         4.44 
TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A214 TCGA-FI-A2CX TCGA-KP-A3VZ 
       47.84        33.30         6.21        14.40        66.77        23.74 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP 
       31.99        36.33        66.15        28.64        25.51        14.96 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QN TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM 
       20.25        14.43        35.15        18.90         1.64        22.26 
TCGA-AP-A0L9 TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AX-A0IU TCGA-AX-A0IW 
      125.42        31.30        46.78        21.90        35.74        37.78 
TCGA-AX-A1C7 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2HK 
       34.65        32.02        25.91         4.77        30.12         2.96 
TCGA-AX-A3FS TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3GI 
        0.23        43.82         0.20         0.26         0.30         0.39 
TCGA-B5-A0JT TCGA-B5-A11I TCGA-B5-A11L TCGA-B5-A11V TCGA-B5-A1MS TCGA-B5-A1MY 
       55.30        75.72        73.64        19.56       102.31        11.87 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A0W1 
       31.36       136.60        39.35        29.65        34.13        52.83 
TCGA-BG-A18C TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A56F TCGA-BS-A0TE TCGA-BS-A0U9 
       15.45        35.08        24.13        13.18         4.80        92.88 
TCGA-BS-A0UT TCGA-BS-A0V8 TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       72.72        83.64        37.32        11.51        29.92        31.07 
TCGA-D1-A16S TCGA-D1-A1O0 TCGA-D1-A3DH TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A1NN 
       18.67         2.07        18.84       109.08        25.91        35.38 
TCGA-DI-A2QT TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A2CG 
       12.39        10.92        49.15        37.71        51.52        51.42 
TCGA-EO-A2CH TCGA-EO-A3AV TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GM 
       19.40        35.15        26.96        22.26        16.34        32.71 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A54A 
       17.62        22.03        29.10        27.35        11.38        14.70 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ 
       59.01         9.34        28.93        78.38        17.75        14.04 
TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A8F1 
        9.47        26.10        38.70        22.59         8.19         4.44 
TCGA-SL-A6J9 
        0.07 

$`20P GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CP 
       18.08       110.63        57.80        95.47        12.26        36.39 
TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-BG-A220 
       61.18        27.88        22.06        66.41        12.56        14.27 
TCGA-D1-A0ZO TCGA-D1-A3JP TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A215 
       19.79        16.93        22.78        17.88        10.19        18.87 
TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 
       17.92        19.89         5.88        13.84        73.32        36.00 
TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
        0.43        39.52        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       123.68 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       74.10        65.75        60.53        46.55        73.87        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        54.02        23.21        68.65        37.91        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        31.99 
TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A7WJ TCGA-A5-A7WK 
       33.07       118.19        24.72        34.95        11.21        18.41 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF 
       10.26        21.14        19.79        34.36        34.16        18.12 
TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE 
       33.90        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-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-A8CV 
       16.87        22.32        12.82        20.78         2.70        35.11 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        0.13       129.80        21.99        23.31        86.07        48.03 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       63.91        45.53        36.89        23.87        12.62        20.91 
TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
       48.79       117.99       110.37        66.25        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       46.72        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       80.78        49.22        25.08        71.67        90.97        55.89 
TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       35.54        49.15         6.71        60.23        45.86        27.85 
TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       51.12        36.13         0.56        13.58        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       80.55        88.24        71.51        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       49.87        57.47        27.39        30.02        60.66        61.08 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 
       43.82        40.11        77.39        13.28        32.91        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       26.37        34.09        76.83        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       37.58        71.24        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-A3FT 
       38.24        17.75        30.74        31.13        64.93         0.20 
TCGA-AX-A3FW TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.56        20.52         0.30         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        86.37        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
      113.36        88.34        54.44        61.68        85.78        52.04 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y 
       32.09        77.23        73.28        16.73        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       225.50        50.89        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH 
       48.43        52.54        96.30        93.50        71.84        27.65 
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        71.24        63.68        74.63        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       48.56        23.47        43.30        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
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-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        22.39 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       35.90        34.98        35.90        31.00        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        24.33        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       114.90        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        89.59        63.58        86.99        66.48        16.83 
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-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74        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-A16O 
       36.10        36.36        37.51        36.79        27.42        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-A2G6 
       18.02        15.06         1.05         3.95        48.79         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR 
       58.95        15.88         4.27        17.29         2.20        71.61 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
      100.83        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX 
       36.62        24.30         9.37        31.10       110.10        23.38 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       79.10        58.95         2.37        45.57        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-A3AS TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KX 
       34.39        50.73        38.07        27.16        46.42        38.47 
TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       51.09        14.99        54.15        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP 
       23.34        23.34        23.90        33.34        19.27        18.84 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        32.78        15.81        11.08        37.05        19.33 
TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3QX 
       12.59        22.82        20.05        45.76        31.04        32.52 
TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
       14.14        16.96        68.38        39.88        77.33         7.99 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR 
       25.22        96.69        30.67        59.28        41.56         1.74 
TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 
       13.28        18.21        23.24        21.30        17.16         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI 
       22.65        39.95        24.95        23.64        14.83        20.75 
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 
             136.6              225.5 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            26.960             30.705 
[1] "0.1 - 136.6 (27.0)" "0.1 - 225.5 (30.7)"
[1] "hr=" "2.3"
D36V2, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    58  42
  20P GAIN WILD-TYPE 232 182
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     58   42
  20P GAIN WILD-TYPE  232  182
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                58                232
  YES               42                182
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  20P GAIN MUTATED                                        47
  20P GAIN WILD-TYPE                                     357
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  20P GAIN MUTATED                               3
  20P GAIN WILD-TYPE                            19
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  20P GAIN MUTATED                                  59
  20P GAIN WILD-TYPE                                54
D36V3, multiclass
                                         clus
vv                                        20P GAIN MUTATED 20P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               47                357
  MIXED SEROUS AND ENDOMETRIOID                          3                 19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     59                 54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  20P GAIN MUTATED    63   4   7  12
  20P GAIN WILD-TYPE 308  18   9  28
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0               63                308
  R1                4                 18
  R2                7                  9
  RX               12                 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"

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED    92  37
  20Q GAIN WILD-TYPE 355  53
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               129                408 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                37                 53 
$`20Q GAIN MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A1CR 
       41.06        20.81        10.19        93.99        67.66        23.05 
TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
        1.38        80.38        27.09        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-BG-A221 TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1G7 
       12.56         1.81         4.44        47.84        33.30         6.21 
TCGA-EY-A214 TCGA-EY-A547 TCGA-EY-A72D TCGA-FI-A2CX TCGA-KP-A3VZ TCGA-5B-A90C 
       14.40        17.92         5.88        66.77        23.74        39.52 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP 
       31.99        36.33        66.15        28.64        25.51        14.96 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QN TCGA-AJ-A3BI TCGA-AJ-A3EJ 
       20.25        14.43        21.14        35.15        18.90         1.64 
TCGA-AJ-A3EM TCGA-AJ-A3QS TCGA-AP-A05A TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DO 
       22.26        16.87        63.91       125.42        97.71        31.30 
TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CA 
       46.78        21.90        35.74        37.78        34.65        32.02 
TCGA-AX-A1CC TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2HK TCGA-AX-A3FS TCGA-AX-A3FX 
       25.91         4.77        30.12         2.96         0.23        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3GI 
        0.20        20.52         0.30         0.26         0.30         0.39 
TCGA-B5-A0JT TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A11L TCGA-B5-A11V TCGA-B5-A1MR 
       55.30        27.85        75.72        73.64        19.56       225.50 
TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A3S1 
      102.31        11.87        31.36       136.60        39.35        29.65 
TCGA-B5-A5OD TCGA-BG-A0W1 TCGA-BG-A18C TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A56F 
       34.13        52.83        15.45        35.08        24.13        13.18 
TCGA-BS-A0TE TCGA-BS-A0U9 TCGA-BS-A0UT TCGA-BS-A0V8 TCGA-D1-A169 TCGA-D1-A16I 
        4.80        92.88        72.72        83.64        37.32        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A1O0 TCGA-D1-A3DH TCGA-DF-A2KS 
       29.92        31.07        18.67         2.07        18.84       109.08 
TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y5 
       25.91        35.38        12.39       110.10        79.10        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-A1GM TCGA-EY-A1GR TCGA-EY-A1GS 
       26.96        22.26        16.34        32.71        17.62        22.03 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR 
       11.08        37.05        20.05        29.10        27.35        11.38 
TCGA-EY-A54A TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A3PV TCGA-FI-A3PX 
       14.70        59.01         9.34        28.93        41.56        78.38 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-PG-A914 
       17.75        14.04         9.47        26.10        38.70        22.59 
TCGA-PG-A915 TCGA-QS-A8F1 TCGA-SL-A6J9 
        8.19         4.44         0.07 

$`20Q GAIN WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2H8 
      110.63        57.80        95.47        12.26        36.39        61.18 
TCGA-AX-A2HF TCGA-BG-A0M6 TCGA-BG-A220 TCGA-D1-A0ZO TCGA-D1-A3JP TCGA-EY-A1GK 
       27.88        22.06        14.27        19.79        16.93        22.78 
TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A549 TCGA-FI-A2D5 TCGA-FI-A2F4 
       17.88        10.19        18.87        19.89        13.84        73.32 
TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       36.00         0.43        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       123.68 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       74.10        65.75        60.53        46.55        73.87        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        54.02        23.21        68.65        37.91        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        31.99 
TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A7WJ TCGA-A5-A7WK 
       33.07       118.19        24.72        34.95        11.21        18.41 
TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BK 
       10.26        19.79        34.36        34.16        18.12        33.90 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       14.66        22.49        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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 
       12.82        20.78         2.70        35.11         0.13       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05H TCGA-AP-A05J 
       21.99        23.31        86.07        48.03        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        12.62        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 
       66.25        36.36        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       33.40        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       90.97        55.89        35.54        49.15         6.71        60.23 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       45.86        27.85        51.12        36.13         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       45.99        79.46        49.87        57.47        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       60.66        61.08        43.82        40.11        77.39        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       32.91        25.51        26.37        34.09        76.83        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA 
       73.41        80.25        37.58        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        38.24        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        86.37        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       64.21        63.55        13.45        59.84       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        61.68        85.78        52.04        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       77.23        73.28        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        51.45        14.70        48.43        52.54 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OE 
       96.30        93.50        71.84        27.65        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        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       63.68        74.63        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        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU 
       51.06        52.01        34.29        52.64        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD 
       13.78        14.73        14.01        15.45         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        22.39        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A6W3 
       35.90        31.00        31.76        24.99        16.64        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG 
        9.86        46.95        24.33        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       114.90 
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        89.59 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        86.99        66.48        16.83        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-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-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       37.51        36.79        27.42        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-A1O5 
       13.22         0.72        18.25        16.87        18.02        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        1.05         3.95        48.79         8.48        58.95        15.88 
TCGA-D1-A3DG TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KU TCGA-DF-A2KV 
        4.27        17.29         2.20        71.61       100.83        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-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
        9.37        31.10        23.38        58.95         2.37        45.57 
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-A3AS TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3AZ 
       46.26        57.60        34.39        50.73        38.07        27.16 
TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       46.42        38.47        51.09        14.99        54.15        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        23.90        33.34 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1H0 
       19.27        18.84        16.11        32.78        15.81        19.33 
TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A548 
       12.59        22.82        45.76        31.04        32.52        14.14 
TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 
       16.96        68.38        39.88        77.33         7.99        25.22 
TCGA-FI-A2EU TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-KP-A3W0 TCGA-KP-A3W4 
       96.69        30.67        59.28         1.74        13.28        18.21 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       23.24        21.30        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       24.95        23.64        14.83        20.75        18.28         0.23 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.07               0.13 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            225.50             185.79 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            27.090             30.705 
[1] "0.1 - 225.5 (27.1)" "0.1 - 185.8 (30.7)"
[1] "hr=" "2.5"
D37V2, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    67  51
  20Q GAIN WILD-TYPE 223 173
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     67   51
  20Q GAIN WILD-TYPE  223  173
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                67                223
  YES               51                173
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  20Q GAIN MUTATED                                        58
  20Q GAIN WILD-TYPE                                     346
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  20Q GAIN MUTATED                               3
  20Q GAIN WILD-TYPE                            19
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  20Q GAIN MUTATED                                  69
  20Q GAIN WILD-TYPE                                44
D37V3, multiclass
                                         clus
vv                                        20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               58                346
  MIXED SEROUS AND ENDOMETRIOID                          3                 19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     69                 44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  20Q GAIN MUTATED    74   5   9  13
  20Q GAIN WILD-TYPE 297  17   7  27
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0               74                297
  R1                5                 17
  R2                9                  7
  RX               13                 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"

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    29  10
  21Q GAIN WILD-TYPE 418  80
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                39                498 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                10                 80 
$`21Q GAIN MUTATED`
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-D1-A2G5 TCGA-A5-A0G5 TCGA-A5-A0R6 TCGA-A5-A3LO 
       20.81        10.19        47.84        37.02        37.91        25.51 
TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3EM TCGA-AJ-A3NF TCGA-AJ-A3TW 
       14.96        14.43        34.16        22.26        21.21        16.87 
TCGA-AP-A1DQ TCGA-AX-A0IW TCGA-AX-A1C4 TCGA-AX-A2HK TCGA-AX-A3FW TCGA-AX-A3G1 
       46.78        37.78        13.28         2.96         0.56        20.52 
TCGA-B5-A1MY TCGA-B5-A5OD TCGA-BS-A0U9 TCGA-D1-A3DH TCGA-DF-A2KS TCGA-DI-A2QY 
       11.87        34.13        92.88        18.84       109.08       110.10 
TCGA-E6-A1LZ TCGA-EO-A22Y TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1GS TCGA-EY-A2ON 
       79.10        51.52        27.16        26.96        22.03        20.05 
TCGA-EY-A3L3 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F9 TCGA-KP-A3W3 TCGA-PG-A7D5 
       27.35        59.01         9.34        59.28        26.10        38.70 
TCGA-PG-A914 TCGA-QS-A8F1 TCGA-SL-A6J9 
       22.59         4.44         0.07 

$`21Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B 
       18.08       110.63        57.80        93.99        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 
       12.26        36.39        23.05        61.18        27.88         1.38 
TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       80.38        27.09        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A3JP 
       12.56        14.27         1.81        19.79         4.44        16.93 
TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 
       33.30         6.21        22.78        17.88        10.19        14.40 
TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 
       18.87        17.92        19.89         5.88        66.77        13.84 
TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 
       73.32        36.00        23.74         0.43        39.52        10.29 
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88       149.56        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP 
      105.37       123.68        74.10        65.75        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       73.87        36.82        28.27        54.02        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-A2K2 TCGA-A5-A2K3 
       31.99        31.99        36.33        33.07       118.19        66.15 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M 
       28.64        24.72        34.95        11.21        18.41        20.25 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF 
       10.26        21.14        19.79        35.15        34.36        18.12 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 
       18.90        33.90         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-A8CV 
       16.87        22.32        12.82        20.78         2.70        35.11 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        0.13       129.80        21.99        23.31        86.07        48.03 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       63.91        45.53        36.89        23.87        12.62        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        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        46.72        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       61.64        80.78        49.22        25.08        71.67        90.97 
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        60.23 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
       45.86        27.85        51.12        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        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        61.08        35.74        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       77.39        32.91        34.65        25.51        26.37        32.02 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       25.91        34.09        76.83        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA 
       37.58         4.77        30.12        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        38.24        17.75        30.74        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G4 
       64.93         0.23         0.20        43.82         0.20         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-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        86.37        55.30        59.24        86.01        58.75 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       69.27        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       57.76        64.21        63.55        27.85        13.45        59.84 
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        73.64 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       61.68        85.78        52.04        32.09        77.23        73.28 
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 
      225.50       102.31        50.89        51.45        14.70        48.43 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       52.54        31.36       136.60        96.30        93.50        71.84 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW 
       39.35        27.65        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-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       74.63        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        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-A222 
       13.78        14.73        14.01        15.45        15.45         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        22.39        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       34.98        35.90        35.08        31.00        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 
       24.33        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       114.90        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        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       63.58        83.64        86.99        66.48        16.83        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-A2G6 TCGA-D1-A2G7 
       15.06         1.05         3.95        48.79         8.48        58.95 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KU 
       15.88         4.27        17.29         2.20        71.61       100.83 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU 
       89.33        10.92        27.16        25.91        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-EC-A1NJ TCGA-EC-A1QX 
       23.38        58.95         2.37        45.57        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 
       50.73        35.15        38.07        46.42        22.26        16.34 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       38.47        51.09        14.99        54.15        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM 
       27.16        23.34        23.34        23.90        33.34        32.71 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       19.27        18.84        17.62        16.11        32.78        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2OO 
       11.08        37.05        19.33        12.59        22.82        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A 
       31.04        29.10        32.52        11.38        14.14        14.70 
TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 
       16.96        68.38        39.88        77.33         7.99        25.22 
TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR 
       96.69        28.93        30.67        41.56        78.38         1.74 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A5BC 
       17.75        14.04        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 
       21.30         8.19        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       24.95        23.64        14.83        20.75        18.28         0.23 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.07               0.13 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             110.1              225.5 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            25.510             30.135 
[1] "0.1 - 110.1 (25.5)" "0.1 - 225.5 (30.1)"
[1] "hr=" "1.8"
D38V2, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    17  20
  21Q GAIN WILD-TYPE 273 204
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     17   20
  21Q GAIN WILD-TYPE  273  204
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                17                273
  YES               20                204
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  21Q GAIN MUTATED                                        13
  21Q GAIN WILD-TYPE                                     391
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  21Q GAIN MUTATED                               1
  21Q GAIN WILD-TYPE                            21
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  21Q GAIN MUTATED                                  25
  21Q GAIN WILD-TYPE                                88
D38V3, multiclass
                                         clus
vv                                        21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               13                391
  MIXED SEROUS AND ENDOMETRIOID                          1                 21
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     25                 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"
                    vv
clus                  R0  R1  R2  RX
  21Q GAIN MUTATED    26   1   3   4
  21Q GAIN WILD-TYPE 345  21  13  36
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0               26                345
  R1                1                 21
  R2                3                 13
  RX                4                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    21   8
  22Q GAIN WILD-TYPE 426  82
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                29                508 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 8                 82 
$`22Q GAIN MUTATED`
TCGA-D1-A3JP TCGA-FI-A2CX TCGA-A5-A0G5 TCGA-A5-A2K4 TCGA-AP-A05A TCGA-AP-A0LI 
       16.93        66.77        37.02        28.64        63.91        97.71 
TCGA-AP-A3K1 TCGA-AX-A1CF TCGA-AX-A3GI TCGA-B5-A0K8 TCGA-B5-A1MR TCGA-B5-A3S1 
       21.90        76.83         0.39        27.85       225.50        29.65 
TCGA-BK-A26L TCGA-D1-A1O0 TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A2CH TCGA-EY-A1GO 
       24.13         2.07        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-A2CY 
       22.03        27.35        32.52        11.38        14.70        68.38 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-KP-A3W1 
       96.69        59.01         9.34        28.93         9.47 

$`22Q GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF 
       18.08        20.81        10.19       110.63        57.80        93.99 
TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 
       95.47        67.66        12.26        36.39        23.05        61.18 
TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 
       27.88         1.38        80.38        27.09        22.06        66.41 
TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       61.87        51.55        12.56        14.27         1.81        19.79 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ 
        4.44        47.84        33.30         6.21        22.78        17.88 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D 
       10.19        14.40        18.87        17.92        19.89         5.88 
TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C 
       13.84        73.32        36.00        23.74         0.43        39.52 
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-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN 
      112.54       105.37       123.68        74.10        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        73.87        36.82        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ 
       42.35        15.95        31.99        31.99        36.33        33.07 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
      118.19        66.15        24.72        34.95        25.51        14.96 
TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
       11.21        18.41        20.25        14.43        10.26        21.14 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI 
       19.79        35.15        34.36        34.16        18.12        18.90 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
       33.90         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-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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
        2.70        35.11         0.13       129.80        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       86.07        48.03        45.53        36.89        23.87        12.62 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        46.72        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       61.64        80.78        49.22        25.08        71.67        90.97 
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 
       60.23        45.86        27.85        51.12        36.13         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        61.08        35.74        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        77.39        13.28        32.91        34.65        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       26.37        32.02        25.91        34.09        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       80.25        37.58         4.77        30.12        71.24        40.80 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       81.37        34.32        46.49        38.24        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-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
       43.82         0.20        20.52         0.30         0.26         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        86.37        55.30 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       59.24        86.01        58.75        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       13.45        59.84       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        73.64        61.68        85.78        52.04        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       77.23        73.28        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        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       48.43        11.87        52.54        31.36       136.60        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD 
       93.50        71.84        39.35        27.65        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-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       71.24        63.68        74.63        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        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       15.45         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 
       22.39        35.90        34.98        35.90        35.08        31.00 
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        24.33        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        92.88 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
      114.90        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        89.59        63.58        83.64        86.99        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        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-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-A2G6 
       18.02        15.06         1.05         3.95        48.79         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN 
       58.95        15.88         4.27        18.84        17.29         2.20 
TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
       71.61       109.08       100.83        89.33        10.92        27.16 
TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
       25.91        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        79.10 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       58.95         2.37        45.57        16.04         7.36        16.80 
TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       49.15        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        50.73        35.15        38.07 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX 
       27.16        46.42        26.96        22.26        16.34        38.47 
TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       51.09        14.99        54.15        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP 
       23.34        23.34        23.90        33.34        32.71        18.84 
TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       17.62        16.11        32.78        15.81        11.08        37.05 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       19.33        12.59        22.82        20.05        45.76        31.04 
TCGA-EY-A2OQ TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
       29.10        14.14        16.96        39.88        77.33         7.99 
TCGA-FI-A2D6 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR 
       25.22        30.67        59.28        41.56        78.38         1.74 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
       17.75        14.04        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 
       21.30        38.70        22.59         8.19        17.16         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 
       22.65        39.95        24.95        23.64        14.83         4.44 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       20.75        18.28         0.07         0.23 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.39               0.07 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            225.50             185.79 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             27.85              30.10 
[1] "0.4 - 225.5 (27.9)" "0.1 - 185.8 (30.1)"
[1] "hr=" "1.8"
D39V2, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    16  12
  22Q GAIN WILD-TYPE 274 212
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     16   12
  22Q GAIN WILD-TYPE  274  212
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                16                274
  YES               12                212
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  22Q GAIN MUTATED                                         7
  22Q GAIN WILD-TYPE                                     397
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  22Q GAIN MUTATED                               1
  22Q GAIN WILD-TYPE                            21
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  22Q GAIN MUTATED                                  22
  22Q GAIN WILD-TYPE                                91
D39V3, multiclass
                                         clus
vv                                        22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                7                397
  MIXED SEROUS AND ENDOMETRIOID                          1                 21
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     22                 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"
                    vv
clus                  R0  R1  R2  RX
  22Q GAIN MUTATED    18   1   4   3
  22Q GAIN WILD-TYPE 353  21  12  37
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0               18                353
  R1                1                 21
  R2                4                 12
  RX                3                 37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    50  13
  XP GAIN WILD-TYPE 397  77
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               63               474 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               13                77 
$`XP GAIN MUTATED`
TCGA-AJ-A3IA TCGA-AP-A0LF TCGA-BG-A0MS TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 
       20.81        93.99        61.87         4.44        47.84        33.30 
TCGA-EY-A1G7 TCGA-EY-A1GQ TCGA-EY-A212 TCGA-KP-A3VZ TCGA-A5-A0GV TCGA-AJ-A3EM 
        6.21        17.88        10.19        23.74        54.02        22.26 
TCGA-AJ-A3NG TCGA-AJ-A3TW TCGA-AJ-A8CW TCGA-AP-A0LO TCGA-AP-A1DO TCGA-AP-A1E4 
       15.62        16.87         0.13        33.40        31.30        51.12 
TCGA-AX-A05W TCGA-AX-A0IW TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HH 
       80.55        37.78        30.12        40.80        81.37        17.75 
TCGA-B5-A0JR TCGA-B5-A0JT TCGA-B5-A0K4 TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A5OD 
       56.91        55.30        57.76        77.23        73.28        34.13 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0RY TCGA-BG-A0W1 
       19.33        20.94        35.21        71.24        15.42        52.83 
TCGA-BK-A0C9 TCGA-BK-A139 TCGA-BK-A26L TCGA-BS-A0TE TCGA-BS-A0TI TCGA-BS-A0UT 
       35.90        31.00        24.13         4.80        61.87        72.72 
TCGA-BS-A0V8 TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A17R TCGA-D1-A2G6 TCGA-E6-A1M0 
       83.64         0.66        36.10        11.15         8.48        58.95 
TCGA-EO-A1Y5 TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3B1 TCGA-EY-A1GH TCGA-EY-A1GS 
       10.92        51.52        34.39        26.96        23.34        22.03 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-FI-A2D4 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-K6-A3WQ 
       37.05        19.33         7.99        59.01         9.34        14.04 
TCGA-KP-A3W1 TCGA-QS-A744 TCGA-SL-A6J9 
        9.47        14.83         0.07 

$`XP GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06B 
       18.08        10.19       110.63        57.80        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 
       12.26        36.39        23.05        61.18        27.88         1.38 
TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0VT TCGA-BG-A0YV 
       80.38        27.09        22.06        66.41        51.55        12.56 
TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A3JP TCGA-EY-A1GK TCGA-EY-A214 
       14.27         1.81        19.79        16.93        22.78        14.40 
TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 
       18.87        17.92        19.89         5.88        66.77        13.84 
TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 
       73.32        36.00         0.43        39.52        10.29       106.88 
TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      149.56        37.02        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP 
      105.37       123.68        74.10        65.75        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       73.87        36.82        28.27        23.21        68.65        37.91 
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-A2K2 TCGA-A5-A2K3 
       31.99        31.99        36.33        33.07       118.19        66.15 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ 
       28.64        24.72        34.95        25.51        14.96        11.21 
TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       18.41        20.25        14.43        10.26        21.14        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK 
       35.15        34.36        34.16        18.12        18.90        33.90 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE 
        1.64        14.66        22.49        17.06        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DV 
       21.21        15.35        15.95        14.76        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AP-A051 TCGA-AP-A052 
       12.82        20.78         2.70        35.11       129.80        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07        48.03        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        12.62        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       27.12        82.52        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       71.67        90.97        55.89        35.54        46.78        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A3K1 TCGA-AP-A5FX 
        6.71        60.23        45.86        27.85        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        33.21        29.69        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        61.08        35.74        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       77.39        13.28        32.91        34.65        25.51        26.37 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       32.02        25.91        34.09        76.83        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2HC TCGA-AX-A2HD 
       80.25        37.58         4.77        71.24        34.32        46.49 
TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       38.24        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-A3G4 
        0.20         0.56        43.82         0.20        20.52         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-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       86.37        59.24        86.01        58.75        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 
       48.59        36.49        72.62        27.29        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       27.85        13.45        59.84       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        73.64        61.68        85.78        52.04 
TCGA-B5-A11Q TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       32.09        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       225.50       102.31        50.89        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       48.43        11.87        52.54        31.36       136.60        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       93.50        71.84        39.35        27.65        29.65        41.06 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       34.95        18.61        20.19        63.68        74.63        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        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       21.17        20.28        51.06        52.01        34.29        52.64 
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-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       15.45         9.57        20.02        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C 
       22.39        34.98        35.90        35.08        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        24.33 
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        92.88       114.90        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        89.59        63.58        86.99        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        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-A167 
       29.88         1.91         3.68        29.33        32.58        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-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-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-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        48.79        58.95        15.88         4.27 
TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU 
       18.84        17.29         2.20        71.61       109.08       100.83 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU 
       89.33        10.92        27.16        25.91        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-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
      110.10        23.38        79.10         2.37        45.57        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-A2CG TCGA-EO-A2CH TCGA-EO-A3AU 
       66.90        46.26        57.60        51.42        19.40        50.73 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KW 
       35.15        38.07        27.16        46.42        22.26        16.34 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       38.47        51.09        14.99        54.15        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       27.16        23.34        23.90        33.34        32.71        19.27 
TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       18.84        17.62        16.11        32.78        15.81        11.08 
TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       12.59        22.82        20.05        45.76        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 
       27.35        32.52        11.38        14.14        14.70        16.96 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EY 
       68.38        39.88        77.33        25.22        96.69        28.93 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
       30.67        59.28        41.56        78.38         1.74        17.75 
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        21.30        38.70 
TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       22.59         8.19        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       24.95        23.64         4.44        20.75        18.28         0.23 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.07              0.20 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            93.99            225.50 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           31.000            29.785 
[1] "0.1 - 94.0 (31.0)"  "0.2 - 225.5 (29.8)"
[1] "hr=" "1.4"
D40V2, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    35  24
  XP GAIN WILD-TYPE 255 200
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     35   24
  XP GAIN WILD-TYPE  255  200
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               35               255
  YES              24               200
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  XP GAIN MUTATED                                        46
  XP GAIN WILD-TYPE                                     358
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  XP GAIN MUTATED                               1
  XP GAIN WILD-TYPE                            21
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  XP GAIN MUTATED                                  16
  XP GAIN WILD-TYPE                                97
D40V3, multiclass
                                         clus
vv                                        XP GAIN MUTATED XP GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              46               358
  MIXED SEROUS AND ENDOMETRIOID                         1                21
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    16                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"
                   vv
clus                 R0  R1  R2  RX
  XP GAIN MUTATED    44   2   5   4
  XP GAIN WILD-TYPE 327  20  11  36
D40V4, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  R0              44               327
  R1               2                20
  R2               5                11
  RX               4                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    48  16
  XQ GAIN WILD-TYPE 399  74
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               64               473 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               16                74 
$`XQ GAIN MUTATED`
TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1G7 
       22.06        61.87         4.44        47.84        33.30         6.21 
TCGA-EY-A1GQ TCGA-EY-A547 TCGA-KP-A3VZ TCGA-A5-A0GV TCGA-A5-A3LP TCGA-AJ-A23N 
       17.88        17.92        23.74        54.02        14.96        14.43 
TCGA-AJ-A3EM TCGA-AJ-A3NG TCGA-AJ-A3TW TCGA-AJ-A8CW TCGA-AP-A0L8 TCGA-AP-A0LO 
       22.26        15.62        16.87         0.13        48.79        33.40 
TCGA-AP-A1DO TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AX-A05W TCGA-AX-A2H4 TCGA-AX-A2H7 
       31.30        51.12        36.13        80.55        30.12        40.80 
TCGA-AX-A2HA TCGA-AX-A2HH TCGA-B5-A0JR TCGA-B5-A0JT TCGA-B5-A11R TCGA-B5-A11S 
       81.37        17.75        56.91        55.30        77.23        73.28 
TCGA-B5-A5OD TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0RY 
       34.13        19.33        20.94        35.21        71.24        15.42 
TCGA-BG-A0W1 TCGA-BK-A0C9 TCGA-BK-A26L TCGA-BS-A0TE TCGA-BS-A0TI TCGA-BS-A0UT 
       52.83        35.90        24.13         4.80        61.87        72.72 
TCGA-BS-A0V8 TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A17R TCGA-D1-A2G6 TCGA-DF-A2L0 
       83.64         0.66        36.10        11.15         8.48        25.91 
TCGA-E6-A1M0 TCGA-EO-A1Y5 TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3B1 TCGA-EO-A3KU 
       58.95        10.92        51.52        19.40        26.96        22.26 
TCGA-EY-A1GH TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A3L3 TCGA-FI-A2D4 TCGA-FI-A2EW 
       23.34        37.05        19.33        27.35         7.99        59.01 
TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-QS-A744 TCGA-SL-A6J9 
       14.04         9.47        14.83         0.07 

$`XQ GAIN WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF 
       18.08        20.81        10.19       110.63        57.80        93.99 
TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 
       95.47        67.66        12.26        36.39        23.05        61.18 
TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M8 TCGA-BG-A0VT 
       27.88         1.38        80.38        27.09        66.41        51.55 
TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A3JP TCGA-EY-A1GK 
       12.56        14.27         1.81        19.79        16.93        22.78 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX 
       10.19        14.40        18.87        19.89         5.88        66.77 
TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 
       13.84        73.32        36.00         0.43        39.52        10.29 
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN 
      112.54       105.37       123.68        74.10        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        73.87        36.82        28.27        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       37.91        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-A2K2 
       15.95        31.99        31.99        36.33        33.07       118.19 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A7WJ 
       66.15        28.64        24.72        34.95        25.51        11.21 
TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       18.41        20.25        10.26        21.14        19.79        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       34.36        34.16        18.12        18.90        33.90         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       14.66        22.49        17.06        36.99        20.65        21.21 
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-A8CV TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
       20.78         2.70        35.11       129.80        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07        48.03        63.91        45.53        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       12.62        20.91       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       61.64        80.78        49.22        25.08        71.67        90.97 
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        60.23 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       45.86        27.85        21.90         0.56        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        88.24        71.51        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       49.87        57.47        27.39        30.02        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       35.74        37.78        43.82        40.11        77.39        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       32.91        34.65        25.51        26.37        32.02        25.91 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       34.09        76.83        85.48        73.41        80.25        37.58 
TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HJ 
        4.77        71.24        34.32        46.49        38.24        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-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
       43.82         0.20        20.52         0.30         0.26         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JS TCGA-B5-A0JU 
        1.18        18.35        14.47         0.39        86.37        59.24 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.01        58.75        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       13.45        59.84       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        73.64        61.68        85.78        52.04        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-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
      225.50       102.31        50.89        51.45        14.70        48.43 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       11.87        52.54        31.36       136.60        96.30        93.50 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE 
       71.84        39.35        27.65        29.65        41.06        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       18.61        20.19        63.68        74.63        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       48.56        23.47        43.30        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 
       20.28        51.06        52.01        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-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        22.39 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       34.98        35.90        35.08        31.00        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        24.33 
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        92.88       114.90        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        89.59        63.58        86.99        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        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-A167 
       29.88         1.91         3.68        29.33        32.58        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-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-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-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        48.79        58.95        15.88         4.27 
TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU 
       18.84        17.29         2.20        71.61       109.08       100.83 
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-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       23.38        79.10         2.37        45.57        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-A2CG TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       46.26        57.60        51.42        34.39        50.73        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       38.07        27.16        46.42        16.34        38.47        51.09 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GI 
       14.99        54.15        53.88        24.36        27.16        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR 
       23.90        33.34        32.71        19.27        18.84        17.62 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A210 
       22.03        16.11        32.78        15.81        11.08        12.59 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX 
       22.82        20.05        45.76        31.04        29.10        32.52 
TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 
       11.38        14.14        14.70        16.96        68.38        39.88 
TCGA-FI-A2D2 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 
       77.33        25.22        96.69         9.34        28.93        30.67 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KP-A3W0 
       59.28        41.56        78.38         1.74        17.75        13.28 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 
       26.10        18.21        23.24        21.30        38.70        22.59 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        8.19        17.16         6.97        22.65        39.95        24.95 
TCGA-QS-A5YR TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       23.64         4.44        20.75        18.28         0.23 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.07              0.20 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            83.64            225.50 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           26.435            30.020 
[1] "0.1 - 83.6 (26.4)"  "0.2 - 225.5 (30.0)"
[1] "hr=" "1.8"
D41V2, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    29  31
  XQ GAIN WILD-TYPE 261 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     29   31
  XQ GAIN WILD-TYPE  261  193
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               29               261
  YES              31               193
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  XQ GAIN MUTATED                                        44
  XQ GAIN WILD-TYPE                                     360
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  XQ GAIN MUTATED                               2
  XQ GAIN WILD-TYPE                            20
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  XQ GAIN MUTATED                                  18
  XQ GAIN WILD-TYPE                                95
D41V3, multiclass
                                         clus
vv                                        XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              44               360
  MIXED SEROUS AND ENDOMETRIOID                         2                20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    18                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"
                   vv
clus                 R0  R1  R2  RX
  XQ GAIN MUTATED    45   2   5   6
  XQ GAIN WILD-TYPE 326  20  11  34
D41V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              45               326
  R1               2                20
  R2               5                11
  RX               6                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"

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    20   7
  1P LOSS WILD-TYPE 427  83
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               27               510 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                7                83 
$`1P LOSS MUTATED`
TCGA-AJ-A3NH TCGA-AP-A0LF TCGA-AX-A1CR TCGA-A5-A0G2 TCGA-A5-A1OH TCGA-A5-A2K3 
       10.19        93.99        23.05       149.56        36.33        66.15 
TCGA-AJ-A23M TCGA-AJ-A3TW TCGA-AP-A0L8 TCGA-AP-A0LI TCGA-AX-A1C8 TCGA-AX-A1CA 
       20.25        16.87        48.79        97.71        25.51        32.02 
TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-B5-A11P TCGA-D1-A1O0 TCGA-EO-A3AZ 
       76.83         4.77        30.12        52.04         2.07        27.16 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A2OO TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 
       19.27        18.84        45.76        28.93        30.67        59.28 
TCGA-FI-A3PX TCGA-PG-A915 TCGA-QS-A8F1 
       78.38         8.19         4.44 

$`1P LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06B 
       18.08        20.81       110.63        57.80        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN 
       12.26        36.39        61.18        27.88         1.38        80.38 
TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV 
       27.09        22.06        66.41        61.87        51.55        12.56 
TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP 
       14.27         1.81        19.79         4.44        47.84        16.93 
TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 
       33.30         6.21        22.78        17.88        10.19        14.40 
TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 
       18.87        17.92        19.89         5.88        66.77        13.84 
TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 
       73.32        36.00        23.74         0.43        39.52        10.29 
TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88        37.02        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP 
      105.37       123.68        74.10        65.75        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       73.87        36.82        28.27        54.02        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       37.91        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K4 
       15.95        31.99        31.99        33.07       118.19        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK 
       24.72        34.95        25.51        14.96        11.21        18.41 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       14.43        10.26        21.14        19.79        35.15        34.36 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
       34.16        18.12        18.90        33.90         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-A3QS 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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 
       12.82        20.78         2.70        35.11         0.13       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
       21.99        23.31        86.07        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        12.62        20.91       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
      110.37        66.25        36.36        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        90.97        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        60.23        45.86        27.85        51.12 
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        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       80.55        88.24        71.51        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       49.87        57.47        27.39        30.02        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       35.74        37.78        43.82        40.11        77.39        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI 
       32.91        34.65        26.37        25.91        34.09        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA 
       73.41        80.25        37.58        71.24        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       34.32        46.49        38.24        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-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       18.35        14.47         0.39        56.91        86.37        55.30 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       59.24        86.01        58.75        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       27.85        13.45        59.84       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        73.64        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       77.23        73.28        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       225.50       102.31        50.89        51.45 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       14.70        48.43        11.87        52.54        31.36       136.60 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 
       96.30        93.50        71.84        39.35        27.65        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-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        35.21        71.24        63.68        74.63        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        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       14.01        15.45        15.45         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        22.39        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD 
       35.08        31.00        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        24.33        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        92.88       114.90        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        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       83.64        86.99        66.48        16.83        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-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-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.95        48.79         8.48        58.95        15.88         4.27 
TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU 
       18.84        17.29         2.20        71.61       109.08       100.83 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU 
       89.33        10.92        27.16        25.91        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        79.10        58.95         2.37        45.57 
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        50.73        35.15        38.07 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       46.42        26.96        22.26        16.34        38.47        51.09 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99        54.15        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GS 
       23.34        23.90        33.34        32.71        17.62        22.03 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        32.78        15.81        11.08        37.05        19.33 
TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 
       12.59        22.82        20.05        31.04        29.10        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY 
       32.52        11.38        14.14        14.70        16.96        68.38 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       39.88        77.33         7.99        25.22        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 
        9.34        41.56         1.74        17.75        14.04        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        21.30        38.70 
TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       22.59        17.16         6.97        22.65        39.95        24.95 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       23.64        14.83        20.75        18.28         0.07         0.23 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             2.07              0.07 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           149.56            225.50 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            30.12             29.90 
[1] "2.1 - 149.6 (30.1)" "0.1 - 225.5 (29.9)"
[1] "hr=" "1.5"
D42V2, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    19   8
  1P LOSS WILD-TYPE 271 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     19    8
  1P LOSS WILD-TYPE  271  216
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               19               271
  YES               8               216
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  1P LOSS MUTATED                                         7
  1P LOSS WILD-TYPE                                     397
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  1P LOSS MUTATED                               3
  1P LOSS WILD-TYPE                            19
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  1P LOSS MUTATED                                  17
  1P LOSS WILD-TYPE                                96
D42V3, multiclass
                                         clus
vv                                        1P LOSS MUTATED 1P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               7               397
  MIXED SEROUS AND ENDOMETRIOID                         3                19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    17                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"
                   vv
clus                 R0  R1  R2  RX
  1P LOSS MUTATED    17   3   4   0
  1P LOSS WILD-TYPE 354  19  12  40
D42V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              17               354
  R1               3                19
  R2               4                12
  RX               0                40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    11   5
  1Q LOSS WILD-TYPE 436  85
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               16               521 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                5                85 
$`1Q LOSS MUTATED`
TCGA-AP-A0LF TCGA-AX-A1CR TCGA-A5-A0G2 TCGA-AJ-A23M TCGA-AJ-A3TW TCGA-AP-A0L8 
       93.99        23.05       149.56        20.25        16.87        48.79 
TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-B5-A11P TCGA-D1-A1O0 TCGA-EO-A3AZ 
       76.83         4.77        30.12        52.04         2.07        27.16 
TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-PG-A915 
       28.93        30.67        59.28         8.19 

$`1Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LS 
       18.08        20.81        10.19       110.63        57.80        95.47 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 
       67.66        12.26        36.39        61.18        27.88         1.38 
TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       80.38        27.09        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 
       12.56        14.27         1.81        19.79         4.44        47.84 
TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 
       16.93        33.30         6.21        22.78        17.88        10.19 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX 
       14.40        18.87        17.92        19.89         5.88        66.77 
TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C 
       13.84        73.32        36.00        23.74         0.43        39.52 
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
       10.29       106.88        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN 
      112.54       105.37       123.68        74.10        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        73.87        36.82        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ 
       42.35        15.95        31.99        31.99        36.33        33.07 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
      118.19        66.15        28.64        24.72        34.95        25.51 
TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
       14.96        11.21        18.41        14.43        10.26        21.14 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI 
       19.79        35.15        34.36        34.16        18.12        18.90 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
       33.90         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-A3QS 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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 
       35.11         0.13       129.80        21.99        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       48.03        63.91        45.53        36.89        23.87        12.62 
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        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        46.72        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       61.64        80.78        49.22        25.08        71.67        90.97 
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 
       60.23        45.86        27.85        51.12        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        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        61.08        35.74        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        77.39        13.28        32.91        34.65 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI 
       25.51        26.37        32.02        25.91        34.09        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA 
       73.41        80.25        37.58        71.24        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       34.32        46.49        38.24        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-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       18.35        14.47         0.39        56.91        86.37        55.30 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       59.24        86.01        58.75        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       27.85        13.45        59.84       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        73.64        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       77.23        73.28        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       225.50       102.31        50.89        51.45 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       14.70        48.43        11.87        52.54        31.36       136.60 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 
       96.30        93.50        71.84        39.35        27.65        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-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        35.21        71.24        63.68        74.63        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        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       14.01        15.45        15.45         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        22.39        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD 
       35.08        31.00        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        24.33        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        92.88       114.90        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        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       83.64        86.99        66.48        16.83        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-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-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.95        48.79         8.48        58.95        15.88         4.27 
TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU 
       18.84        17.29         2.20        71.61       109.08       100.83 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU 
       89.33        10.92        27.16        25.91        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        79.10        58.95         2.37        45.57 
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        50.73        35.15        38.07 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       46.42        26.96        22.26        16.34        38.47        51.09 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99        54.15        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.34        23.90        33.34        32.71        19.27        18.84 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       17.62        22.03        16.11        32.78        15.81        11.08 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       37.05        19.33        12.59        22.82        20.05        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        32.52        11.38        14.14 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
       14.70        16.96        68.38        39.88        77.33         7.99 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A3PV TCGA-FI-A3PX 
       25.22        96.69        59.01         9.34        41.56        78.38 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 
        1.74        17.75        14.04        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        21.30        38.70        22.59        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        22.65        39.95        24.95        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44        20.75        18.28         0.07         0.23 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             2.07              0.07 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           149.56            225.50 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           29.525            29.920 
[1] "2.1 - 149.6 (29.5)" "0.1 - 225.5 (29.9)"
[1] "hr=" "1.8"
D43V2, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    11   5
  1Q LOSS WILD-TYPE 279 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     11    5
  1Q LOSS WILD-TYPE  279  219
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO               11               279
  YES               5               219
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  1Q LOSS MUTATED                                         5
  1Q LOSS WILD-TYPE                                     399
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  1Q LOSS MUTATED                               2
  1Q LOSS WILD-TYPE                            20
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  1Q LOSS MUTATED                                   9
  1Q LOSS WILD-TYPE                               104
D43V3, multiclass
                                         clus
vv                                        1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               5               399
  MIXED SEROUS AND ENDOMETRIOID                         2                20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     9               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"
                   vv
clus                 R0  R1  R2  RX
  1Q LOSS MUTATED    10   1   3   0
  1Q LOSS WILD-TYPE 361  21  13  40
D43V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0              10               361
  R1               1                21
  R2               3                13
  RX               0                40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED     8   4
  2P LOSS WILD-TYPE 439  86
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               12               525 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                4                86 
$`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        92.88 
TCGA-D1-A16I TCGA-D1-A1O0 TCGA-EY-A1GW TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-PG-A915 
       11.51         2.07        11.08        59.28        41.56         8.19 

$`2P LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF 
       18.08        20.81        10.19       110.63        57.80        93.99 
TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 
       95.47        67.66        12.26        36.39        23.05        61.18 
TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 
       27.88         1.38        80.38        27.09        22.06        66.41 
TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       61.87        51.55        12.56        14.27         1.81        19.79 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK 
        4.44        47.84        16.93        33.30         6.21        22.78 
TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 
       17.88        10.19        14.40        18.87        17.92        19.89 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ 
        5.88        66.77        13.84        73.32        36.00        23.74 
TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
        0.43        39.52        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       123.68 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       74.10        65.75        60.53        46.55        73.87        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        54.02        23.21        68.65        37.91        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        31.99 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 
       31.99        36.33        33.07       118.19        66.15        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK 
       24.72        34.95        25.51        14.96        11.21        18.41 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       20.25        14.43        10.26        21.14        19.79        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
       34.36        18.12        18.90        33.90         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       22.49        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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 
       12.82        20.78         2.70        35.11         0.13       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
       21.99        23.31        86.07        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       36.89        23.87        12.62        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      117.99       110.37        66.25        36.36        97.71        46.72 
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-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        90.97        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        60.23        45.86 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T 
       27.85        51.12        21.90        36.13        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        80.55        88.24        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       79.46        49.87        57.47        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       61.08        35.74        37.78        43.82        40.11        77.39 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       13.28        32.91        34.65        25.51        26.37        32.02 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       25.91        34.09        76.83        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
       37.58         4.77        71.24        40.80        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       46.49        38.24        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-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
       20.52         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        86.37        55.30        59.24 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.01        58.75        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       13.45        59.84       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        73.64        61.68        85.78        52.04        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       77.23        73.28        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       225.50       102.31        50.89        51.45 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       14.70        48.43        11.87        52.54        31.36       136.60 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 
       96.30        93.50        71.84        39.35        27.65        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-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        35.21        71.24        63.68        74.63        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        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.01        15.45         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        22.39        35.90        34.98        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F 
       31.00        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        24.33        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       114.90        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        89.59        63.58        83.64        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        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-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-A2G6 
       18.02        15.06         1.05         3.95        48.79         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN 
       58.95        15.88         4.27        18.84        17.29         2.20 
TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
       71.61       109.08       100.83        89.33        10.92        27.16 
TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
       25.91        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        79.10 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       58.95         2.37        45.57        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 
       50.73        35.15        38.07        27.16        46.42        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC 
       22.26        16.34        38.47        51.09        14.99        54.15 
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-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS 
       33.34        32.71        19.27        18.84        17.62        22.03 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       16.11        32.78        15.81        37.05        19.33        12.59 
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-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY 
       32.52        11.38        14.14        14.70        16.96        68.38 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       39.88        77.33         7.99        25.22        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
        9.34        28.93        30.67        78.38         1.74        17.75 
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-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       21.30        38.70        22.59        17.16         6.97        22.65 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       39.95        24.95        23.64        14.83         4.44        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       18.28         0.07         0.23 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.56              0.07 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            92.88            225.50 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           18.855            29.950 
[1] "0.6 - 92.9 (18.9)"  "0.1 - 225.5 (29.9)"
[1] "hr=" "2.9"
D44V2, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     9   2
  2P LOSS WILD-TYPE 281 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      9    2
  2P LOSS WILD-TYPE  281  222
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                9               281
  YES               2               222
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  2P LOSS MUTATED                                         7
  2P LOSS WILD-TYPE                                     397
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  2P LOSS MUTATED                               0
  2P LOSS WILD-TYPE                            22
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  2P LOSS MUTATED                                   5
  2P LOSS WILD-TYPE                               108
D44V3, multiclass
                                         clus
vv                                        2P LOSS MUTATED 2P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               7               397
  MIXED SEROUS AND ENDOMETRIOID                         0                22
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     5               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"
                   vv
clus                 R0  R1  R2  RX
  2P LOSS MUTATED     8   1   1   2
  2P LOSS WILD-TYPE 363  21  15  38
D44V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0               8               363
  R1               1                21
  R2               1                15
  RX               2                38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    11   7
  2Q LOSS WILD-TYPE 436  83
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               18               519 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                7                83 
$`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-A16I TCGA-D1-A1O0 TCGA-D1-A3DG 
       20.52        15.45        92.88        11.51         2.07         4.27 
TCGA-EY-A1GC TCGA-EY-A1GW TCGA-EY-A2OQ TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-PG-A915 
       54.15        11.08        29.10        59.28        41.56         8.19 

$`2Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF 
       18.08        20.81        10.19       110.63        57.80        93.99 
TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 
       95.47        67.66        12.26        36.39        23.05        61.18 
TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 
       27.88         1.38        80.38        27.09        22.06        66.41 
TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       61.87        51.55        12.56        14.27         1.81        19.79 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK 
        4.44        47.84        16.93        33.30         6.21        22.78 
TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 
       17.88        10.19        14.40        18.87        17.92        19.89 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ 
        5.88        66.77        13.84        73.32        36.00        23.74 
TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
        0.43        39.52        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       123.68 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       74.10        65.75        60.53        46.55        73.87        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        54.02        23.21        68.65        37.91        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        31.99 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 
       31.99        36.33        33.07       118.19        66.15        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK 
       24.72        34.95        25.51        14.96        11.21        18.41 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       20.25        14.43        10.26        21.14        19.79        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
       34.36        18.12        18.90        33.90         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       22.49        17.06        36.99        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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       20.78         2.70        35.11         0.13       129.80        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07        48.03        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        12.62        20.91       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        90.97        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        60.23        45.86        27.85        51.12 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       21.90        36.13        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       57.47        27.39        30.02        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        77.39        13.28        32.91 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       34.65        25.51        26.37        32.02        25.91        34.09 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 
       76.83        85.48        73.41        80.25        37.58         4.77 
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        38.24 
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-A3G4 TCGA-AX-A3G6 
        0.20         0.56        43.82         0.20         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 
       86.37        55.30        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       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        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       85.78        52.04        32.09        77.23        73.28        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       225.50 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      102.31        50.89        51.45        14.70        48.43        11.87 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       52.54        31.36       136.60        96.30        93.50        71.84 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       39.35        27.65        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        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       63.68        74.63        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        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        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-A222 
       14.83        13.78        14.73        14.01        15.45         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        22.39        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       34.98        35.90        35.08        31.00        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 
       24.33        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       114.90        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        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       63.58        83.64        86.99        66.48        16.83        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-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-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-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH 
        3.95        48.79         8.48        58.95        15.88        18.84 
TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV 
       17.29         2.20        71.61       109.08       100.83        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       10.92        27.16        25.91        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-EC-A1NJ 
       23.38        79.10        58.95         2.37        45.57        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        50.73        35.15        38.07        27.16 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       46.42        26.96        22.26        16.34        38.47        51.09 
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-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR 
       23.90        33.34        32.71        19.27        18.84        17.62 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 
       22.03        16.11        32.78        15.81        37.05        19.33 
TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 
       12.59        22.82        20.05        45.76        31.04        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY 
       32.52        11.38        14.14        14.70        16.96        68.38 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       39.88        77.33         7.99        25.22        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
        9.34        28.93        30.67        78.38         1.74        17.75 
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-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       21.30        38.70        22.59        17.16         6.97        22.65 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       39.95        24.95        23.64        14.83         4.44        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       18.28         0.07         0.23 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.56              0.07 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            92.88            225.50 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            21.39             30.02 
[1] "0.6 - 92.9 (21.4)"  "0.1 - 225.5 (30.0)"
[1] "hr=" "3.3"
D45V2, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    13   4
  2Q LOSS WILD-TYPE 277 220
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     13    4
  2Q LOSS WILD-TYPE  277  220
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               13               277
  YES               4               220
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  2Q LOSS MUTATED                                        11
  2Q LOSS WILD-TYPE                                     393
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  2Q LOSS MUTATED                               0
  2Q LOSS WILD-TYPE                            22
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  2Q LOSS MUTATED                                   7
  2Q LOSS WILD-TYPE                               106
D45V3, multiclass
                                         clus
vv                                        2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              11               393
  MIXED SEROUS AND ENDOMETRIOID                         0                22
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     7               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"
                   vv
clus                 R0  R1  R2  RX
  2Q LOSS MUTATED    13   1   1   2
  2Q LOSS WILD-TYPE 358  21  15  38
D45V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0              13               358
  R1               1                21
  R2               1                15
  RX               2                38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    38  14
  3P LOSS WILD-TYPE 409  76
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               52               485 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               14                76 
$`3P LOSS MUTATED`
TCGA-2E-A9G8 TCGA-AP-A05D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-B5-A0JN 
       41.06        57.80        36.39        23.05        61.18        80.38 
TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0YV TCGA-A5-A1OG TCGA-A5-A2K3 TCGA-AJ-A23M 
       27.09        22.06        12.56        31.99        66.15        20.25 
TCGA-AJ-A3BF TCGA-AJ-A3EJ TCGA-AJ-A3TW TCGA-AP-A052 TCGA-AP-A0L9 TCGA-AP-A0LI 
       18.12         1.64        16.87        21.99       125.42        97.71 
TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A2HK TCGA-AX-A3G4 
       46.78        21.90         0.56        37.78         2.96         0.30 
TCGA-AX-A3GI TCGA-B5-A0K3 TCGA-B5-A11I TCGA-B5-A1N2 TCGA-BG-A18C TCGA-BK-A4ZD 
        0.39        27.29        75.72        31.36        15.45        16.64 
TCGA-BS-A0TI TCGA-D1-A0ZZ TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A1NW TCGA-D1-A1O0 
       61.87        22.55        31.07        18.67         0.72         2.07 
TCGA-DF-A2KR TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GO 
       71.61        25.91        35.38        16.34        23.90        19.27 
TCGA-EY-A1GP TCGA-EY-A1GV TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A54A 
       18.84        15.81        29.10        27.35        32.52        14.70 
TCGA-FI-A2D2 TCGA-FI-A2EY TCGA-KP-A3W3 TCGA-SL-A6J9 
       77.33        28.93        26.10         0.07 

$`3P LOSS WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B 
       20.81        10.19       110.63        93.99        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       12.26        27.88         1.38        66.41        61.87        51.55 
TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP 
       14.27         1.81        19.79         4.44        47.84        16.93 
TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 
       33.30         6.21        22.78        17.88        10.19        14.40 
TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 
       18.87        17.92        19.89         5.88        66.77        13.84 
TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 
       73.32        36.00        23.74         0.43        39.52        10.29 
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN 
      112.54       105.37       123.68        74.10        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        73.87        36.82        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 
       42.35        15.95        31.99        36.33        33.07       118.19 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ 
       28.64        24.72        34.95        25.51        14.96        11.21 
TCGA-A5-A7WK TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       18.41        14.43        10.26        21.14        19.79        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
       34.36        34.16        18.90        33.90        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-A5DV TCGA-AJ-A5DW 
       15.35        15.95        14.76        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 
       20.78         2.70        35.11         0.13       129.80        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07        48.03        63.91        45.53        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       12.62        20.91        48.79       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        46.72        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       61.64        80.78        49.22        25.08        71.67        90.97 
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        60.23 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T 
       45.86        27.85        51.12        36.13        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        80.55        88.24        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       79.46        49.87        57.47        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       61.08        35.74        43.82        40.11        77.39        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       32.91        34.65        25.51        26.37        32.02        25.91 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       34.09        76.83        85.48        73.41        80.25        37.58 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
        4.77        30.12        71.24        40.80        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO 
       46.49        38.24        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-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 
       86.37        55.30        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 
       71.44        48.59        36.49        72.62        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       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        73.64        61.68        85.78        52.04 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        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       225.50       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 
       51.45        14.70        48.43        11.87        52.54       136.60 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 
       96.30        93.50        71.84        39.35        27.65        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-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        35.21        71.24        63.68        74.63        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        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.01        15.45         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        22.39        35.90        34.98        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 
       31.00        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        24.33        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        92.88 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
      114.90        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        89.59        63.58        83.64        86.99        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       23.93         1.74        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-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V 
       11.51        29.92        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-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-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       18.25        16.87        18.02        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
       48.79         8.48        58.95        15.88         4.27        18.84 
TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY 
       17.29         2.20       109.08       100.83        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        79.10        58.95 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37        45.57        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        50.73 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU 
       35.15        38.07        27.16        46.42        26.96        22.26 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       38.47        51.09        14.99        54.15        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GR 
       27.16        23.34        23.34        33.34        32.71        17.62 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       22.03        16.11        32.78        11.08        37.05        19.33 
TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A4KR 
       12.59        22.82        20.05        45.76        31.04        11.38 
TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 
       14.14        16.96        68.38        39.88         7.99        25.22 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV 
       96.69        59.01         9.34        30.67        59.28        41.56 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 
       78.38         1.74        17.75        14.04        13.28         9.47 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       18.21        23.24        21.30        38.70        22.59         8.19 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       17.16         6.97        22.65        39.95        24.95        23.64 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       14.83         4.44        20.75        18.28         0.23 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.07              0.13 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           125.42            225.50 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           24.905            30.440 
[1] "0.1 - 125.4 (24.9)" "0.1 - 225.5 (30.4)"
[1] "hr=" "2.1"
D46V2, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    27  22
  3P LOSS WILD-TYPE 263 202
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     27   22
  3P LOSS WILD-TYPE  263  202
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               27               263
  YES              22               202
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  3P LOSS MUTATED                                        20
  3P LOSS WILD-TYPE                                     384
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  3P LOSS MUTATED                               6
  3P LOSS WILD-TYPE                            16
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  3P LOSS MUTATED                                  26
  3P LOSS WILD-TYPE                                87
D46V3, multiclass
                                         clus
vv                                        3P LOSS MUTATED 3P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              20               384
  MIXED SEROUS AND ENDOMETRIOID                         6                16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    26                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"
                   vv
clus                 R0  R1  R2  RX
  3P LOSS MUTATED    35   2   2   5
  3P LOSS WILD-TYPE 336  20  14  35
D46V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0              35               336
  R1               2                20
  R2               2                14
  RX               5                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"

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    25   6
  3Q LOSS WILD-TYPE 422  84
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               31               506 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                6                84 
$`3Q LOSS MUTATED`
TCGA-2E-A9G8 TCGA-AP-A05D TCGA-AX-A2H8 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-A5-A2K3 
       41.06        57.80        61.18        80.38        27.09        66.15 
TCGA-AJ-A3BF TCGA-AJ-A3TW TCGA-AP-A052 TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DQ 
       18.12        16.87        21.99       125.42        97.71        46.78 
TCGA-AP-A3K1 TCGA-AX-A0IW TCGA-AX-A2HK TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0K8 
       21.90        37.78         2.96         0.30         0.39        27.85 
TCGA-BG-A18C TCGA-BK-A4ZD TCGA-D1-A16S TCGA-D1-A1O0 TCGA-DF-A2L0 TCGA-EO-A3AZ 
       15.45        16.64        18.67         2.07        25.91        27.16 
TCGA-EY-A1GJ TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A54A 
       23.90        19.27        18.84        29.10        27.35        14.70 
TCGA-FI-A2D2 
       77.33 

$`3Q LOSS WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B 
       20.81        10.19       110.63        93.99        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-BG-A0M6 
       12.26        36.39        23.05        27.88         1.38        22.06 
TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 
       66.41        61.87        51.55        12.56        14.27         1.81 
TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 
       19.79         4.44        47.84        16.93        33.30         6.21 
TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 
       22.78        17.88        10.19        14.40        18.87        17.92 
TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 
       19.89         5.88        66.77        13.84        73.32        36.00 
TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 
       23.74         0.43        39.52        10.29       106.88       149.56 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
      123.68        74.10        65.75        60.53        46.55        73.87 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       36.82        28.27        54.02        23.21        68.65        37.91 
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-A2K2 TCGA-A5-A2K4 
       31.99        31.99        36.33        33.07       118.19        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK 
       24.72        34.95        25.51        14.96        11.21        18.41 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       20.25        14.43        10.26        21.14        19.79        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
       34.36        34.16        18.90        33.90         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-A3QS 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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 
       12.82        20.78         2.70        35.11         0.13       129.80 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07        48.03        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        12.62        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 
       66.25        36.36        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       33.40        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       90.97        55.89        31.30        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO 
       60.23        45.86        27.85        51.12        36.13         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        61.08        35.74        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       77.39        13.28        32.91        34.65        25.51        26.37 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       32.02        25.91        34.09        76.83        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       80.25        37.58         4.77        30.12        71.24        40.80 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       81.37        34.32        46.49        38.24        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-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.20        20.52         0.26         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       14.47        56.91        86.37        55.30        59.24        86.01 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       58.75        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E 
       27.29        57.76        64.21        63.55        13.45        59.84 
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        73.64 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       61.68        85.78        52.04        32.09        77.23        73.28 
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 
      225.50       102.31        50.89        51.45        14.70        48.43 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       11.87        52.54        31.36       136.60        96.30        93.50 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       71.84        39.35        27.65        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-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       71.24        63.68        74.63        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        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        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-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        22.39 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       35.90        34.98        35.90        35.08        31.00        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 
       24.33        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        92.88       114.90 
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 
       89.59        63.58        83.64        86.99        66.48        16.83 
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-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74        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-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-A1O5 
       13.22         0.72        18.25        16.87        18.02        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        1.05         3.95        48.79         8.48        58.95        15.88 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS 
        4.27        18.84        17.29         2.20        71.61       109.08 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
      100.83        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        79.10        58.95         2.37        45.57 
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        50.73        35.15        38.07 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       46.42        26.96        22.26        16.34        38.47        51.09 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99        54.15        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT 
       23.34        33.34        32.71        17.62        22.03        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       32.78        15.81        11.08        37.05        19.33        12.59 
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        32.52        11.38 
TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 
       14.14        16.96        68.38        39.88         7.99        25.22 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 
       96.69        59.01         9.34        28.93        30.67        59.28 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 
       41.56        78.38         1.74        17.75        14.04        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        21.30        38.70 
TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       22.59         8.19        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       24.95        23.64        14.83         4.44        20.75        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.30              0.07 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           125.42            225.50 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            25.91             30.15 
[1] "0.3 - 125.4 (25.9)" "0.1 - 225.5 (30.1)"
[1] "hr=" "1.3"
D47V2, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    19  10
  3Q LOSS WILD-TYPE 271 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     19   10
  3Q LOSS WILD-TYPE  271  214
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               19               271
  YES              10               214
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  3Q LOSS MUTATED                                        13
  3Q LOSS WILD-TYPE                                     391
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  3Q LOSS MUTATED                               2
  3Q LOSS WILD-TYPE                            20
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  3Q LOSS MUTATED                                  16
  3Q LOSS WILD-TYPE                                97
D47V3, multiclass
                                         clus
vv                                        3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              13               391
  MIXED SEROUS AND ENDOMETRIOID                         2                20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    16                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"
                   vv
clus                 R0  R1  R2  RX
  3Q LOSS MUTATED    21   0   2   3
  3Q LOSS WILD-TYPE 350  22  14  37
D47V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0              21               350
  R1               0                22
  R2               2                14
  RX               3                37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    77  28
  4P LOSS WILD-TYPE 370  62
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              105               432 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               28                62 
$`4P LOSS MUTATED`
TCGA-AJ-A2QM TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       29.39        10.19       110.63        57.80        93.99        67.66 
TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-BG-A0M8 TCGA-BG-A0YV 
       23.05        61.18        27.88         1.38        66.41        12.56 
TCGA-D1-A3JP TCGA-EY-A212 TCGA-EY-A214 TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0G2 
       16.93        10.19        14.40        23.74        39.52       149.56 
TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 
       60.53        36.82        37.91        36.33       118.19        28.64 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A2QK TCGA-AJ-A3BD 
       25.51        14.96        18.41        20.25        21.14        34.16 
TCGA-AJ-A3EJ TCGA-AJ-A3NF TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A05H TCGA-AP-A0L9 
        1.64        21.21        16.87        16.87        45.53       125.42 
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        32.02 
TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2HK TCGA-AX-A2IO 
       25.91        76.83         4.77        30.12         2.96        64.93 
TCGA-AX-A3FS TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-B5-A0JX TCGA-B5-A0K8 TCGA-B5-A11I 
        0.23        20.52         0.30        58.75        27.85        75.72 
TCGA-B5-A11P TCGA-B5-A1MY TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A3PP 
       52.04        11.87        29.65        34.13        34.95        22.39 
TCGA-BK-A0CC TCGA-BK-A26L TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A15V TCGA-D1-A169 
       35.08        24.13        92.88        83.64        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-A3JQ TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-DI-A2QT 
       17.29        71.61       109.08        25.91        35.38        12.39 
TCGA-DI-A2QY TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EY-A1GC TCGA-EY-A1GM TCGA-EY-A1GO 
      110.10        27.16        22.26        54.15        32.71        19.27 
TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A3L3 TCGA-EY-A3QX 
       18.84        17.62        20.05        45.76        27.35        32.52 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-JU-AAVI 
        9.34        28.93        30.67        41.56        78.38        17.75 
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-A7D5 TCGA-PG-A915 TCGA-QS-A8F1 
       38.70         8.19         4.44 

$`4P LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AJ-A3IA TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CP TCGA-B5-A0JN TCGA-B5-A0KB 
       20.81        95.47        12.26        36.39        80.38        27.09 
TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       22.06        61.87        51.55        14.27         1.81        19.79 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ 
        4.44        47.84        33.30         6.21        22.78        17.88 
TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 
       18.87        17.92        19.89         5.88        66.77        13.84 
TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 
       73.32        36.00         0.43        10.29       106.88        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       123.68 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        65.75        46.55        73.87        28.27        54.02 
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-A2K3 
       42.35        15.95        31.99        31.99        33.07        66.15 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A7WJ TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL 
       24.72        34.95        11.21        14.43        10.26        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK 
       35.15        34.36        18.12        18.90        33.90        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG 
       22.49        22.26        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-A6NU 
       15.35        15.95        14.76        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
        2.70        35.11         0.13       129.80        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       86.07        48.03        63.91        36.89        23.87        12.62 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       20.91        48.79       117.99       110.37        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP 
       97.71        46.72        83.97        27.12        82.52        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       80.78        49.22        25.08        71.67        90.97        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        60.23 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       45.86        27.85        51.12        13.58        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       80.55        88.24        71.51        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       49.87        57.47        27.39        30.02        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       35.74        43.82        40.11        77.39        13.28        32.91 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       34.65        25.51        26.37        34.09        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
       80.25        37.58        71.24        40.80        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FT 
       46.49        38.24        17.75        30.74        31.13         0.20 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.56        43.82         0.20         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        86.37        55.30 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       59.24        86.01        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       72.62        27.29        57.76        64.21        63.55        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
       59.84       185.79       113.36        88.34        54.44        73.64 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       61.68        85.78        32.09        77.23        73.28        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       225.50 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
      102.31        50.89        51.45        14.70        48.43        52.54 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       31.36       136.60        96.30        93.50        71.84        39.35 
TCGA-B5-A3FH TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       27.65        41.06        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        71.24        63.68        74.63        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       48.56        23.47        43.30        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       15.45        15.45         9.57        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B 
       11.31        35.90        34.98        35.90        31.00        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 
       24.33        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       114.90        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        89.59 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        86.99        66.48        16.83        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-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-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
       10.65         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-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-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       18.25        16.87        18.02        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
       48.79         8.48        58.95        15.88         4.27        18.84 
TCGA-DF-A2KN TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        2.20       100.83        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-EC-A1NJ TCGA-EC-A1QX 
       79.10        58.95         2.37        45.57        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-A3B0 TCGA-EO-A3B1 
       34.39        50.73        35.15        38.07        46.42        26.96 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       16.34        38.47        51.09        14.99        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GS 
       27.16        23.34        23.34        23.90        33.34        22.03 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        32.78        15.81        11.08        37.05        19.33 
TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A548 
       12.59        22.82        31.04        29.10        11.38        14.14 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
       14.70        16.96        68.38        39.88        77.33         7.99 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-PG-A6IB 
       25.22        96.69        59.01        59.28         1.74        21.30 
TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       22.59        17.16         6.97        22.65        39.95        24.95 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       23.64        14.83        20.75        18.28         0.07         0.23 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.23              0.07 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           149.56            225.50 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            27.16             30.74 
[1] "0.2 - 149.6 (27.2)" "0.1 - 225.5 (30.7)"
[1] "hr=" "2"  
D48V2, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    54  45
  4P LOSS WILD-TYPE 236 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     54   45
  4P LOSS WILD-TYPE  236  179
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               54               236
  YES              45               179
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  4P LOSS MUTATED                                        34
  4P LOSS WILD-TYPE                                     370
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  4P LOSS MUTATED                               8
  4P LOSS WILD-TYPE                            14
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  4P LOSS MUTATED                                  64
  4P LOSS WILD-TYPE                                49
D48V3, multiclass
                                         clus
vv                                        4P LOSS MUTATED 4P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              34               370
  MIXED SEROUS AND ENDOMETRIOID                         8                14
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    64                49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  4P LOSS MUTATED    67   5   5  10
  4P LOSS WILD-TYPE 304  17  11  30
D48V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0              67               304
  R1               5                17
  R2               5                11
  RX              10                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"

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    73  30
  4Q LOSS WILD-TYPE 374  60
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              103               434 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               30                60 
$`4Q LOSS MUTATED`
TCGA-AJ-A2QM TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A1CR TCGA-AX-A2H8 
       29.39        10.19        57.80        93.99        23.05        61.18 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-D1-A3JP TCGA-EY-A212 
       27.88        80.38        66.41        12.56        16.93        10.19 
TCGA-EY-A214 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0G2 TCGA-A5-A0GJ 
       14.40        36.00        23.74        39.52       149.56        65.75 
TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 
       60.53        36.82        37.91        31.99        36.33       118.19 
TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3BD 
       28.64        25.51        18.41        20.25        14.43        34.16 
TCGA-AJ-A3EJ TCGA-AJ-A3NF TCGA-AJ-A3QS TCGA-AP-A05H TCGA-AP-A0L9 TCGA-AP-A0LO 
        1.64        21.21        16.87        45.53       125.42        33.40 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1CA TCGA-AX-A1CC 
       21.90        36.13         0.56        37.78        32.02        25.91 
TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3G1 
       76.83         4.77        30.12        64.93         0.23        20.52 
TCGA-AX-A3G4 TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A1N2 
        0.30        75.72        52.04        50.89        11.87        31.36 
TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A3PP TCGA-BK-A0CC 
       39.35        29.65        34.13        34.95        22.39        35.08 
TCGA-BK-A26L TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16R 
       24.13        92.88        83.64        39.48        37.32         0.69 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A179 TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-D1-A3DG 
       18.67         3.95        14.73         0.72         2.07         4.27 
TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-DI-A1NO 
       18.84        17.29       109.08        25.91        35.38         9.37 
TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EY-A1GC TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       27.16        22.26        54.15        32.71        19.27        18.84 
TCGA-EY-A1GR TCGA-EY-A2OO TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-FI-A2EX TCGA-FI-A2EY 
       17.62        45.76        27.35        32.52         9.34        28.93 
TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 
       30.67        41.56        78.38        17.75        14.04        13.28 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       26.10        18.21        23.24        38.70        22.59         8.19 
TCGA-QS-A8F1 
        4.44 

$`4Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AJ-A3IA TCGA-AP-A053 TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP 
       20.81       110.63        95.47        67.66        12.26        36.39 
TCGA-AX-A3G3 TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A220 
        1.38        27.09        22.06        61.87        51.55        14.27 
TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1G7 
        1.81        19.79         4.44        47.84        33.30         6.21 
TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D 
       22.78        17.88        18.87        17.92        19.89         5.88 
TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 
       66.77        13.84        73.32         0.43        10.29       106.88 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
      123.68        74.10        46.55        73.87        28.27        54.02 
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-A2K3 TCGA-A5-A2K5 
       42.35        15.95        31.99        33.07        66.15        24.72 
TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       34.95        14.96        11.21        10.26        21.14        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK 
       35.15        34.36        18.12        18.90        33.90        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG 
       22.49        22.26        17.06        36.99        20.65        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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       20.78         2.70        35.11         0.13       129.80        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N 
       23.31        86.07        48.03        63.91        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       12.62        20.91        48.79       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       61.64        80.78        49.22        25.08        71.67        90.97 
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-AX-A05S TCGA-AX-A05T 
       60.23        45.86        27.85        51.12        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        80.55        88.24        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       79.46        49.87        57.47        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       61.08        35.74        43.82        40.11        77.39        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CI 
       32.91        34.65        25.51        26.37        34.09        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA 
       73.41        80.25        37.58        71.24        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       34.32        46.49        38.24        17.75        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G6 
       31.13         0.20         0.56        43.82         0.20         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 
       86.37        55.30        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       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        73.64        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        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       225.50       102.31        51.45 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       14.70        48.43        52.54       136.60        96.30        93.50 
TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       71.84        27.65        41.06        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        35.21        71.24        63.68        74.63        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        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       14.01        15.45        15.45         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        35.90        31.00 
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        24.33        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       114.90 
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-A0ZP 
       89.59        63.58        86.99        66.48        16.83        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-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        1.74        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-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-DF-A2KN 
        3.95        48.79         8.48        58.95        15.88         2.20 
TCGA-DF-A2KR TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
       71.61       100.83        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        79.10        58.95         2.37        45.57        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        50.73        35.15        38.07        46.42 
TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD 
       26.96        16.34        38.47        51.09        14.99        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        23.90        33.34 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       22.03        16.11        32.78        15.81        11.08        37.05 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A2OQ 
       19.33        12.59        22.82        20.05        31.04        29.10 
TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 
       11.38        14.14        14.70        16.96        68.38        39.88 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F9 
       77.33         7.99        25.22        96.69        59.01        59.28 
TCGA-H5-A2HR TCGA-KP-A3W1 TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
        1.74         9.47        21.30        17.16         6.97        22.65 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       39.95        24.95        23.64        14.83        20.75        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.23              0.07 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           149.56            225.50 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            27.88             30.15 
[1] "0.2 - 149.6 (27.9)" "0.1 - 225.5 (30.1)"
[1] "hr=" "2.3"
D49V2, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    55  44
  4Q LOSS WILD-TYPE 235 180
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     55   44
  4Q LOSS WILD-TYPE  235  180
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               55               235
  YES              44               180
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  4Q LOSS MUTATED                                        33
  4Q LOSS WILD-TYPE                                     371
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  4Q LOSS MUTATED                               8
  4Q LOSS WILD-TYPE                            14
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  4Q LOSS MUTATED                                  63
  4Q LOSS WILD-TYPE                                50
D49V3, multiclass
                                         clus
vv                                        4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              33               371
  MIXED SEROUS AND ENDOMETRIOID                         8                14
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    63                50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  4Q LOSS MUTATED    66   5   4   9
  4Q LOSS WILD-TYPE 305  17  12  31
D49V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0              66               305
  R1               5                17
  R2               4                12
  RX               9                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"

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    38  15
  5P LOSS WILD-TYPE 409  75
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               53               484 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               15                75 
$`5P LOSS MUTATED`
TCGA-AJ-A2QM TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A2HF TCGA-B5-A0KB TCGA-BG-A0M8 
       29.39        93.99        67.66        27.88        27.09        66.41 
TCGA-D1-A3JP TCGA-EY-A212 TCGA-KJ-A3U4 TCGA-A5-A0G2 TCGA-A5-A0R6 TCGA-A5-A0R7 
       16.93        10.19        36.00       149.56        37.91        17.59 
TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3QS TCGA-AP-A05H 
       25.51        20.25         1.64        22.26        16.87        45.53 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A3K1 TCGA-AX-A2H4 
       48.79       125.42        97.71        33.40        21.90        30.12 
TCGA-AX-A3FZ TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A1N2 TCGA-B5-A3FD TCGA-B5-A3S1 
        0.20        27.85        75.72        31.36        39.35        29.65 
TCGA-B5-A5OE TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0U9 
       34.95        22.39        35.08        24.13        16.64        92.88 
TCGA-D1-A15V TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A179 TCGA-D1-A1NU 
       39.48        11.51        18.67         3.95        14.73        13.22 
TCGA-DF-A2L0 TCGA-EO-A2CG TCGA-EO-A3KU TCGA-EY-A1GO TCGA-EY-A1GP TCGA-FI-A3PV 
       25.91        51.42        22.26        19.27        18.84        41.56 
TCGA-FI-A3PX TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A914 TCGA-QS-A8F1 
       78.38         9.47        26.10        22.59         4.44 

$`5P LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06D 
       20.81        10.19       110.63        57.80        95.47        12.26 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-BG-A0M6 
       36.39        23.05        61.18         1.38        80.38        22.06 
TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       61.87        51.55        12.56        14.27         1.81        19.79 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ 
        4.44        47.84        33.30         6.21        22.78        17.88 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX 
       14.40        18.87        17.92        19.89         5.88        66.77 
TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 
       13.84        73.32        23.74         0.43        39.52        10.29 
TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88        37.02        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP 
      105.37       123.68        74.10        65.75        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       73.87        36.82        28.27        54.02        23.21        68.65 
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        31.99 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 
       31.99        36.33        33.07       118.19        66.15        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23N 
       24.72        34.95        14.96        11.21        18.41        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
       10.26        21.14        19.79        35.15        34.36        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 
       18.12        18.90        33.90        14.66        22.49        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-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 
       35.11         0.13       129.80        21.99        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       48.03        63.91        36.89        23.87        12.62        20.91 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL 
      117.99       110.37        66.25        36.36        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       27.12        82.52        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        90.97        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        60.23        45.86        27.85        51.12 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       36.13         0.56        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       57.47        27.39        30.02        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        77.39        13.28        32.91 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       34.65        25.51        26.37        32.02        25.91        34.09 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 
       76.83        85.48        73.41        80.25        37.58         4.77 
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        38.24 
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-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 
        0.20         0.56        43.82        20.52         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 
       86.37        55.30        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       64.21        63.55        13.45        59.84       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        73.64        61.68        85.78        52.04 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        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       225.50       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 
       51.45        14.70        48.43        11.87        52.54       136.60 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD 
       96.30        93.50        71.84        27.65        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        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       63.68        74.63        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        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        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-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
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-A56F 
       34.98        35.90        31.00        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        24.33        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       114.90        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        89.59        63.58        83.64        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        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-A15W 
       28.67        23.93        22.55         1.74        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-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-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-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
       48.79         8.48        58.95        15.88         4.27        18.84 
TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV 
       17.29         2.20        71.61       109.08       100.83        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 
       79.10        58.95         2.37        45.57        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-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 
       50.73        35.15        38.07        27.16        46.42        26.96 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       16.34        38.47        51.09        14.99        54.15        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        23.90        33.34 
TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       32.71        17.62        22.03        16.11        32.78        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON 
       11.08        37.05        19.33        12.59        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        32.52        11.38 
TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
       14.14        14.70        16.96        68.38        39.88        77.33 
TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
        7.99        25.22        96.69        59.01         9.34        28.93 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 
       30.67        59.28         1.74        17.75        14.04        13.28 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A915 TCGA-PG-A916 
       18.21        23.24        21.30        38.70         8.19        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        22.65        39.95        24.95        23.64        14.83 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       20.75        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            225.50 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            27.09             30.15 
[1] "0.2 - 149.6 (27.1)" "0.1 - 225.5 (30.1)"
[1] "hr=" "1.9"
D50V2, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    26  25
  5P LOSS WILD-TYPE 264 199
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     26   25
  5P LOSS WILD-TYPE  264  199
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               26               264
  YES              25               199
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  5P LOSS MUTATED                                        17
  5P LOSS WILD-TYPE                                     387
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  5P LOSS MUTATED                               1
  5P LOSS WILD-TYPE                            21
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  5P LOSS MUTATED                                  35
  5P LOSS WILD-TYPE                                78
D50V3, multiclass
                                         clus
vv                                        5P LOSS MUTATED 5P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              17               387
  MIXED SEROUS AND ENDOMETRIOID                         1                21
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    35                78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  5P LOSS MUTATED    34   0   3   5
  5P LOSS WILD-TYPE 337  22  13  35
D50V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0              34               337
  R1               0                22
  R2               3                13
  RX               5                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"

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    50  23
  5Q LOSS WILD-TYPE 397  67
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               73               464 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               23                67 
$`5Q LOSS MUTATED`
TCGA-AJ-A2QM TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AX-A06B TCGA-AX-A2HF TCGA-B5-A0KB 
       29.39        20.81        10.19        67.66        27.88        27.09 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-D1-A3JP TCGA-EY-A212 TCGA-EY-A214 
       22.06        66.41        12.56        16.93        10.19        14.40 
TCGA-KJ-A3U4 TCGA-A5-A0G2 TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A1OH TCGA-A5-A3LO 
       36.00       149.56        37.91        17.59        36.33        25.51 
TCGA-AJ-A23M TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3QS TCGA-AP-A05H TCGA-AP-A0L8 
       20.25         1.64        22.26        16.87        45.53        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AX-A0IW TCGA-AX-A1CA TCGA-AX-A1CF 
      125.42        97.71        33.40        37.78        32.02        76.83 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A3FZ TCGA-AX-A3G6 TCGA-B5-A0K8 TCGA-B5-A11I 
        4.77        30.12         0.20         0.26        27.85        75.72 
TCGA-B5-A1MU TCGA-B5-A1N2 TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE 
       50.89        31.36        39.35        29.65        34.13        34.95 
TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0U9 
       22.39        35.08        31.00        24.13        16.64        92.88 
TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A179 TCGA-D1-A1NU 
       22.55        39.48        11.51        18.67        14.73        13.22 
TCGA-DF-A2L0 TCGA-DI-A1NO TCGA-DI-A2QY TCGA-EO-A2CG TCGA-EO-A3AZ TCGA-EO-A3KU 
       25.91         9.37       110.10        51.42        27.16        22.26 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GW TCGA-EY-A3QX TCGA-FI-A2D2 TCGA-FI-A2F8 
       19.27        18.84        11.08        32.52        77.33        30.67 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A914 TCGA-PG-A915 
       41.56        78.38         9.47        26.10        22.59         8.19 
TCGA-QS-A8F1 
        4.44 

$`5Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CP 
      110.63        57.80        93.99        95.47        12.26        36.39 
TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-BG-A0MS TCGA-BG-A0VT 
       23.05        61.18         1.38        80.38        61.87        51.55 
TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 
       14.27         1.81        19.79         4.44        47.84        33.30 
TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 
        6.21        22.78        17.88        18.87        17.92        19.89 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KP-A3VZ TCGA-4E-A92E 
        5.88        66.77        13.84        73.32        23.74         0.43 
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
       39.52        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-A0GJ 
       32.78       112.54       105.37       123.68        74.10        65.75 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        73.87        36.82        28.27        54.02 
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-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 
       15.95        31.99        31.99        33.07       118.19        66.15 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK 
       28.64        24.72        34.95        14.96        11.21        18.41 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       14.43        10.26        21.14        19.79        35.15        34.36 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
       34.16        18.12        18.90        33.90        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-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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
        2.70        35.11         0.13       129.80        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       86.07        48.03        63.91        36.89        23.87        12.62 
TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
       20.91       117.99       110.37        66.25        36.36        46.72 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       83.97        27.12        82.52        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        90.97        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        60.23        45.86        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       51.12        21.90        36.13         0.56        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        80.55        88.24        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       79.46        49.87        57.47        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       61.08        35.74        43.82        40.11        77.39        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE 
       32.91        34.65        25.51        26.37        25.91        34.09 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H5 TCGA-AX-A2H7 
       85.48        73.41        80.25        37.58        71.24        40.80 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       81.37        34.32        46.49        38.24        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-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
       43.82        20.52         0.30         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        86.37        55.30        59.24 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.01        58.75        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       72.62        27.29        57.76        64.21        63.55        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
       59.84       185.79       113.36        88.34        54.44        73.64 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       61.68        85.78        52.04        32.09        77.23        73.28 
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 
      225.50       102.31        51.45        14.70        48.43        11.87 
TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH 
       52.54       136.60        96.30        93.50        71.84        27.65 
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 
       71.24        63.68        74.63        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        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       15.45         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-A56F 
       35.90        34.98        35.90        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        24.33        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       114.90        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        89.59        63.58        83.64        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X 
       28.67        23.93         1.74        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-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
       48.79         8.48        58.95        15.88         4.27        18.84 
TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV 
       17.29         2.20        71.61       109.08       100.83        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-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
       35.38        12.39        31.10        23.38        79.10        58.95 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37        45.57        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        50.73        35.15 
TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       38.07        46.42        26.96        16.34        38.47        51.09 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99        54.15        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GS 
       23.34        23.90        33.34        32.71        17.62        22.03 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       16.11        32.78        15.81        37.05        19.33        12.59 
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-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 
       11.38        14.14        14.70        16.96        68.38        39.88 
TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
        7.99        25.22        96.69        59.01         9.34        28.93 
TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W4 
       59.28         1.74        17.75        14.04        13.28        18.21 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       23.24        21.30        38.70        17.16         6.97        22.65 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       39.95        24.95        23.64        14.83        20.75        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.20              0.07 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           149.56            225.50 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            27.16             30.15 
[1] "0.2 - 149.6 (27.2)" "0.1 - 225.5 (30.1)"
[1] "hr=" "2.4"
D51V2, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    37  33
  5Q LOSS WILD-TYPE 253 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     37   33
  5Q LOSS WILD-TYPE  253  191
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               37               253
  YES              33               191
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  5Q LOSS MUTATED                                        20
  5Q LOSS WILD-TYPE                                     384
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  5Q LOSS MUTATED                               4
  5Q LOSS WILD-TYPE                            18
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  5Q LOSS MUTATED                                  49
  5Q LOSS WILD-TYPE                                64
D51V3, multiclass
                                         clus
vv                                        5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              20               384
  MIXED SEROUS AND ENDOMETRIOID                         4                18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    49                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  5Q LOSS MUTATED    48   2   3   6
  5Q LOSS WILD-TYPE 323  20  13  34
D51V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0              48               323
  R1               2                20
  R2               3                13
  RX               6                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"

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    14   5
  6P LOSS WILD-TYPE 433  85
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               19               518 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                5                85 
$`6P LOSS MUTATED`
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A05D TCGA-E6-A8L9 TCGA-KJ-A3U4 TCGA-A5-A0G2 
       20.81        10.19        57.80        33.30        36.00       149.56 
TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-A5-A7WK TCGA-AP-A05J TCGA-AP-A0L9 TCGA-AX-A1C7 
       60.53        37.91        18.41        36.89       125.42        34.65 
TCGA-AX-A2H4 TCGA-B5-A11P TCGA-BG-A3PP TCGA-BK-A139 TCGA-EY-A2OQ TCGA-FI-A2D2 
       30.12        52.04        22.39        31.00        29.10        77.33 
TCGA-FI-A3PV 
       41.56 

$`6P LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AP-A053 TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D 
       18.08       110.63        93.99        95.47        67.66        12.26 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN 
       36.39        23.05        61.18        27.88         1.38        80.38 
TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV 
       27.09        22.06        66.41        61.87        51.55        12.56 
TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP 
       14.27         1.81        19.79         4.44        47.84        16.93 
TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 
        6.21        22.78        17.88        10.19        14.40        18.87 
TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 
       17.92        19.89         5.88        66.77        13.84        73.32 
TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 
       23.74         0.43        39.52        10.29       106.88        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       123.68 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       74.10        65.75        46.55        73.87        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       54.02        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        31.99        31.99        36.33 
TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
       33.07       118.19        66.15        28.64        24.72        34.95 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O 
       25.51        14.96        11.21        20.25        14.43        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF 
       21.14        19.79        35.15        34.36        34.16        18.12 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       18.90        33.90         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-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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       20.78         2.70        35.11         0.13       129.80        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05N 
       23.31        86.07        48.03        63.91        45.53        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       12.62        20.91        48.79       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       33.40        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       90.97        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        60.23        45.86        27.85        51.12        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        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       57.47        27.39        30.02        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        77.39        13.28        32.91 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       25.51        26.37        32.02        25.91        34.09        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H5 
       85.48        73.41        80.25        37.58         4.77        71.24 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       40.80        81.37        34.32        46.49        38.24        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-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 
       86.37        55.30        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       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        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       85.78        32.09        77.23        73.28        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       225.50       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        51.45        14.70        48.43        11.87        52.54 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       31.36       136.60        96.30        93.50        71.84        39.35 
TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW 
       27.65        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        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       74.63        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        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-A222 
       13.78        14.73        14.01        15.45        15.45         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-A26L TCGA-BK-A4ZD 
       35.90        35.08        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        24.33        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        92.88       114.90        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        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       83.64        86.99        66.48        16.83        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-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-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        1.05         3.95        48.79         8.48        58.95        15.88 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS 
        4.27        18.84        17.29         2.20        71.61       109.08 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH 
      100.83        89.33        10.92        27.16        25.91        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        79.10        58.95         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       45.57        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        50.73        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW 
       38.07        27.16        46.42        26.96        22.26        16.34 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       38.47        51.09        14.99        54.15        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM 
       27.16        23.34        23.34        23.90        33.34        32.71 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       19.27        18.84        17.62        22.03        16.11        32.78 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM 
       15.81        11.08        37.05        19.33        12.59        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        32.52        11.38 
TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
       14.14        14.70        16.96        68.38        39.88         7.99 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 
       25.22        96.69        59.01         9.34        28.93        30.67 
TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 
       59.28        78.38         1.74        17.75        14.04        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        21.30        38.70 
TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       22.59         8.19        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       24.95        23.64        14.83         4.44        20.75        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            10.19              0.07 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           149.56            225.50 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            36.00             29.36 
[1] "10.2 - 149.6 (36.0)" "0.1 - 225.5 (29.4)" 
[1] "hr=" "1.2"
D52V2, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    13   5
  6P LOSS WILD-TYPE 277 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     13    5
  6P LOSS WILD-TYPE  277  219
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               13               277
  YES               5               219
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  6P LOSS MUTATED                                         5
  6P LOSS WILD-TYPE                                     399
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  6P LOSS MUTATED                               2
  6P LOSS WILD-TYPE                            20
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  6P LOSS MUTATED                                  13
  6P LOSS WILD-TYPE                               100
D52V3, multiclass
                                         clus
vv                                        6P LOSS MUTATED 6P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               5               399
  MIXED SEROUS AND ENDOMETRIOID                         2                20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    13               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"
                   vv
clus                 R0  R1  R2  RX
  6P LOSS MUTATED    17   0   1   0
  6P LOSS WILD-TYPE 354  22  15  40
D52V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              17               354
  R1               0                22
  R2               1                15
  RX               0                40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    18   6
  6Q LOSS WILD-TYPE 429  84
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               24               513 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                6                84 
$`6Q LOSS MUTATED`
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A05D TCGA-E6-A8L9 TCGA-KJ-A3U4 TCGA-A5-A0G2 
       20.81        10.19        57.80        33.30        36.00       149.56 
TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-AJ-A3BF TCGA-AJ-A3QS TCGA-AP-A05J TCGA-AP-A0L9 
       60.53        37.91        18.12        16.87        36.89       125.42 
TCGA-AW-A1PO TCGA-AX-A1C7 TCGA-AX-A2H4 TCGA-B5-A11P TCGA-B5-A1MY TCGA-BG-A3PP 
        0.56        34.65        30.12        52.04        11.87        22.39 
TCGA-D1-A16I TCGA-EO-A3B1 TCGA-EY-A2OQ TCGA-FI-A2D2 TCGA-FI-A3PV TCGA-PG-A7D5 
       11.51        26.96        29.10        77.33        41.56        38.70 

$`6Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AP-A053 TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D 
       18.08       110.63        93.99        95.47        67.66        12.26 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN 
       36.39        23.05        61.18        27.88         1.38        80.38 
TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV 
       27.09        22.06        66.41        61.87        51.55        12.56 
TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP 
       14.27         1.81        19.79         4.44        47.84        16.93 
TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 
        6.21        22.78        17.88        10.19        14.40        18.87 
TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 
       17.92        19.89         5.88        66.77        13.84        73.32 
TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 
       23.74         0.43        39.52        10.29       106.88        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       123.68 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       74.10        65.75        46.55        73.87        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       54.02        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        31.99        31.99        36.33 
TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
       33.07       118.19        66.15        28.64        24.72        34.95 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N 
       25.51        14.96        11.21        18.41        20.25        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
       10.26        21.14        19.79        35.15        34.36        34.16 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       18.90        33.90         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-A3OJ 
       17.06        36.99        20.65        21.21        15.62        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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
        2.70        35.11         0.13       129.80        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05O 
       86.07        48.03        63.91        45.53        23.87        12.62 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       20.91        48.79       117.99       110.37        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        46.72        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       61.64        80.78        49.22        25.08        71.67        90.97 
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 
       60.23        45.86        27.85        51.12        21.90        36.13 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        61.08        35.74        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 
       40.11        77.39        13.28        32.91        25.51        26.37 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       32.02        25.91        34.09        76.83        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA 
       80.25        37.58         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-A2HK 
       34.32        46.49        38.24        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-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       18.35        14.47         0.39        56.91        86.37        55.30 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       59.24        86.01        58.75        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       27.85        13.45        59.84       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        73.64        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       77.23        73.28        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       225.50       102.31        50.89        51.45 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       14.70        48.43        52.54        31.36       136.60        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       93.50        71.84        39.35        27.65        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-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       35.21        71.24        63.68        74.63        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       48.56        23.47        43.30        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       15.45        15.45         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        35.90        35.08        31.00 
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        24.33        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 
       92.88       114.90        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        89.59        63.58        83.64        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        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-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-A2G0 
       18.02         2.07        15.06         1.05         3.95        48.79 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ 
        8.48        58.95        15.88         4.27        18.84        17.29 
TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY 
        2.20        71.61       109.08       100.83        89.33        10.92 
TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       27.16        25.91        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 
       79.10        58.95         2.37        45.57        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        50.73        35.15        38.07        27.16        46.42 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC 
       22.26        16.34        38.47        51.09        14.99        54.15 
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-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS 
       33.34        32.71        19.27        18.84        17.62        22.03 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        32.78        15.81        11.08        37.05        19.33 
TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 
       12.59        22.82        20.05        45.76        31.04        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY 
       32.52        11.38        14.14        14.70        16.96        68.38 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
       39.88         7.99        25.22        96.69        59.01         9.34 
TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
       28.93        30.67        59.28        78.38         1.74        17.75 
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-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       21.30        22.59         8.19        17.16         6.97        22.65 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       39.95        24.95        23.64        14.83         4.44        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       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            225.50 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           33.975            29.690 
[1] "0.6 - 149.6 (34.0)" "0.1 - 225.5 (29.7)"
[1] "hr=" "1.3"
D53V2, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    12  11
  6Q LOSS WILD-TYPE 278 213
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     12   11
  6Q LOSS WILD-TYPE  278  213
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               12               278
  YES              11               213
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  6Q LOSS MUTATED                                         5
  6Q LOSS WILD-TYPE                                     399
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  6Q LOSS MUTATED                               1
  6Q LOSS WILD-TYPE                            21
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  6Q LOSS MUTATED                                  19
  6Q LOSS WILD-TYPE                                94
D53V3, multiclass
                                         clus
vv                                        6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               5               399
  MIXED SEROUS AND ENDOMETRIOID                         1                21
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    19                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"
                   vv
clus                 R0  R1  R2  RX
  6Q LOSS MUTATED    21   0   1   0
  6Q LOSS WILD-TYPE 350  22  15  40
D53V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              21               350
  R1               0                22
  R2               1                15
  RX               0                40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    32  13
  7P LOSS WILD-TYPE 415  77
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               45               492 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               13                77 
$`7P LOSS MUTATED`
TCGA-AX-A06B TCGA-AX-A1CR TCGA-B5-A0JN TCGA-B5-A0KB TCGA-EY-A212 TCGA-EY-A547 
       67.66        23.05        80.38        27.09        10.19        17.92 
TCGA-KP-A3VZ TCGA-A5-A0R6 TCGA-A5-A1OH TCGA-AJ-A23M TCGA-AP-A054 TCGA-AP-A0L8 
       23.74        37.91        36.33        20.25        23.31        48.79 
TCGA-AP-A1DQ TCGA-AX-A1CA TCGA-AX-A2H2 TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IO 
       46.78        32.02         4.77        30.74         2.96        64.93 
TCGA-B5-A0K8 TCGA-B5-A11I TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BS-A0U9 TCGA-D1-A16V 
       27.85        75.72        22.39        35.08        92.88         3.95 
TCGA-D1-A1O0 TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-DI-A2QY 
        2.07        58.95        18.84        25.91        35.38       110.10 
TCGA-E6-A1LZ TCGA-EC-A1NJ TCGA-EO-A1Y8 TCGA-EO-A2CH TCGA-EO-A3KU TCGA-EY-A1GC 
       79.10        16.04        37.71        19.40        22.26        54.15 
TCGA-EY-A2OO TCGA-FI-A2EW TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-KP-A3W0 
       45.76        59.01        30.67        59.28        41.56        13.28 
TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A915 
       23.24        38.70         8.19 

$`7P LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF 
       18.08        20.81        10.19       110.63        57.80        93.99 
TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 
       95.47        12.26        36.39        61.18        27.88         1.38 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 
       22.06        66.41        61.87        51.55        12.56        14.27 
TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 
        1.81        19.79         4.44        47.84        16.93        33.30 
TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A549 
        6.21        22.78        17.88        14.40        18.87        19.89 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E 
        5.88        66.77        13.84        73.32        36.00         0.43 
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       39.52        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       123.68        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       65.75        60.53        46.55        73.87        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       54.02        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-A1OJ 
       29.06        42.35        15.95        31.99        31.99        33.07 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
      118.19        66.15        28.64        24.72        34.95        25.51 
TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
       14.96        11.21        18.41        14.43        10.26        21.14 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI 
       19.79        35.15        34.36        34.16        18.12        18.90 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
       33.90         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-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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A056 
        2.70        35.11         0.13       129.80        21.99        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       48.03        63.91        45.53        36.89        23.87        12.62 
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        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        46.72        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       61.64        80.78        49.22        25.08        71.67        90.97 
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        60.23 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
       45.86        27.85        51.12        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        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        61.08        35.74        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        77.39        13.28        32.91        34.65        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       26.37        25.91        34.09        76.83        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA 
       80.25        37.58        30.12        71.24        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2IN TCGA-AX-A3FS 
       34.32        46.49        38.24        17.75        31.13         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-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-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        86.37        55.30        59.24        86.01        58.75 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       69.27        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       57.76        64.21        63.55        13.45        59.84       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        73.64        61.68        85.78 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       52.04        32.09        77.23        73.28        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       225.50       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        51.45        14.70        48.43        11.87        52.54 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       31.36       136.60        96.30        93.50        71.84        39.35 
TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW 
       27.65        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        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       74.63        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        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-A222 
       13.78        14.73        14.01        15.45        15.45         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-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD 
       35.90        31.00        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        24.33        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       114.90        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        89.59        63.58        83.64 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       86.99        66.48        16.83        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-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        48.79 
TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR 
        8.48        15.88         4.27        17.29         2.20        71.61 
TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
      109.08       100.83        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-EC-A1QX TCGA-EC-A24G 
       23.38        58.95         2.37        45.57         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        50.73        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EO-A3KX 
       38.07        27.16        46.42        26.96        16.34        38.47 
TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       51.09        14.99        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.34        23.90        33.34        32.71        19.27        18.84 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       17.62        22.03        16.11        32.78        15.81        11.08 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP 
       37.05        19.33        12.59        22.82        20.05        31.04 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A 
       29.10        27.35        32.52        11.38        14.14        14.70 
TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 
       16.96        68.38        39.88        77.33         7.99        25.22 
TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
       96.69         9.34        28.93        78.38         1.74        17.75 
TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A914 
       14.04         9.47        26.10        18.21        21.30        22.59 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       17.16         6.97        22.65        39.95        24.95        23.64 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83         4.44        20.75        18.28         0.07         0.23 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             2.07              0.07 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            110.1             225.5 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           30.740            29.785 
[1] "2.1 - 110.1 (30.7)" "0.1 - 225.5 (29.8)"
[1] "hr=" "1.9"
D54V2, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    24  19
  7P LOSS WILD-TYPE 266 205
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     24   19
  7P LOSS WILD-TYPE  266  205
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO               24               266
  YES              19               205
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  7P LOSS MUTATED                                        15
  7P LOSS WILD-TYPE                                     389
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  7P LOSS MUTATED                               2
  7P LOSS WILD-TYPE                            20
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  7P LOSS MUTATED                                  28
  7P LOSS WILD-TYPE                                85
D54V3, multiclass
                                         clus
vv                                        7P LOSS MUTATED 7P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              15               389
  MIXED SEROUS AND ENDOMETRIOID                         2                20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    28                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"
                   vv
clus                 R0  R1  R2  RX
  7P LOSS MUTATED    29   4   1   5
  7P LOSS WILD-TYPE 342  18  15  35
D54V4, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  R0              29               342
  R1               4                18
  R2               1                15
  RX               5                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"

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED    33  12
  7Q LOSS WILD-TYPE 414  78
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               45               492 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               12                78 
$`7Q LOSS MUTATED`
TCGA-AX-A1CR TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0YV TCGA-EY-A212 TCGA-EY-A547 
       23.05        80.38        22.06        12.56        10.19        17.92 
TCGA-A5-A0R6 TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AP-A0L8 
       37.91        36.33       118.19        20.25        34.16        48.79 
TCGA-AX-A1CA TCGA-AX-A2HK TCGA-B5-A0K8 TCGA-B5-A11I TCGA-BG-A3PP TCGA-BK-A0CC 
       32.02         2.96        27.85        75.72        22.39        35.08 
TCGA-BK-A139 TCGA-BK-A26L TCGA-BS-A0U9 TCGA-D1-A15V TCGA-D1-A16S TCGA-D1-A1O0 
       31.00        24.13        92.88        39.48        18.67         2.07 
TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-DI-A2QY TCGA-E6-A1LZ 
       58.95        18.84        25.91        35.38       110.10        79.10 
TCGA-EO-A2CH TCGA-EO-A3KU TCGA-EY-A1GC TCGA-EY-A2ON TCGA-EY-A2OO TCGA-FI-A2EU 
       19.40        22.26        54.15        20.05        45.76        96.69 
TCGA-FI-A2EW TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-KP-A3W0 
       59.01        30.67        59.28        41.56        78.38        13.28 
TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A915 
       23.24        38.70         8.19 

$`7Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF 
       18.08        20.81        10.19       110.63        57.80        93.99 
TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-AX-A2HF 
       95.47        67.66        12.26        36.39        61.18        27.88 
TCGA-AX-A3G3 TCGA-B5-A0KB TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A220 
        1.38        27.09        66.41        61.87        51.55        14.27 
TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 
        1.81        19.79         4.44        47.84        16.93        33.30 
TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A549 
        6.21        22.78        17.88        14.40        18.87        19.89 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ 
        5.88        66.77        13.84        73.32        36.00        23.74 
TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
        0.43        39.52        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       123.68 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       74.10        65.75        60.53        46.55        73.87        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 
       28.27        54.02        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        31.99        31.99 
TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
       33.07        66.15        28.64        24.72        34.95        25.51 
TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
       14.96        11.21        18.41        14.43        10.26        21.14 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK 
       19.79        35.15        34.36        18.12        18.90        33.90 
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-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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 
       35.11         0.13       129.80        21.99        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       48.03        63.91        45.53        36.89        23.87        12.62 
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        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        46.72        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       61.64        80.78        49.22        25.08        71.67        90.97 
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 
       60.23        45.86        27.85        51.12        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        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        61.08        35.74        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        77.39        13.28        32.91        34.65 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       25.51        26.37        25.91        34.09        76.83        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       73.41        80.25        37.58         4.77        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       40.80        81.37        34.32        46.49        38.24        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-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
       43.82         0.20        20.52         0.30         0.26         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS 
        1.18        18.35        14.47         0.39        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       55.30        59.24        86.01        58.75        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        13.45        59.84       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        73.64        61.68        85.78        52.04        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       77.23        73.28        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       225.50       102.31        50.89        51.45 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       14.70        48.43        11.87        52.54        31.36       136.60 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 
       96.30        93.50        71.84        39.35        27.65        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-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        35.21        71.24        63.68        74.63        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        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       14.01        15.45        15.45         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        35.90        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 
       24.33        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       114.90        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        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       63.58        83.64        86.99        66.48        16.83        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-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        1.74        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-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JQ TCGA-DF-A2KN 
       48.79         8.48        15.88         4.27        17.29         2.20 
TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
       71.61       109.08       100.83        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        58.95         2.37        45.57        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-A3AZ TCGA-EO-A3B0 
       34.39        50.73        35.15        38.07        27.16        46.42 
TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD 
       26.96        16.34        38.47        51.09        14.99        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        23.90        33.34 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT 
       32.71        19.27        18.84        17.62        22.03        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       32.78        15.81        11.08        37.05        19.33        12.59 
TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       22.82        31.04        29.10        27.35        32.52        11.38 
TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
       14.14        14.70        16.96        68.38        39.88        77.33 
TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EX TCGA-FI-A2EY TCGA-H5-A2HR TCGA-JU-AAVI 
        7.99        25.22         9.34        28.93         1.74        17.75 
TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A914 
       14.04         9.47        26.10        18.21        21.30        22.59 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       17.16         6.97        22.65        39.95        24.95        23.64 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83         4.44        20.75        18.28         0.07         0.23 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             2.07              0.07 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           118.19            225.50 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            32.02             29.67 
[1] "2.1 - 118.2 (32.0)" "0.1 - 225.5 (29.7)"
[1] "hr=" "1.5"
D55V2, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    23  21
  7Q LOSS WILD-TYPE 267 203
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     23   21
  7Q LOSS WILD-TYPE  267  203
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO               23               267
  YES              21               203
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  7Q LOSS MUTATED                                        10
  7Q LOSS WILD-TYPE                                     394
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  7Q LOSS MUTATED                               2
  7Q LOSS WILD-TYPE                            20
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  7Q LOSS MUTATED                                  33
  7Q LOSS WILD-TYPE                                80
D55V3, multiclass
                                         clus
vv                                        7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              10               394
  MIXED SEROUS AND ENDOMETRIOID                         2                20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    33                80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  7Q LOSS MUTATED    31   2   2   5
  7Q LOSS WILD-TYPE 340  20  14  35
D55V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0              31               340
  R1               2                20
  R2               2                14
  RX               5                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"

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    58  20
  8P LOSS WILD-TYPE 389  70
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               78               459 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               20                70 
$`8P LOSS MUTATED`
TCGA-2E-A9G8 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A1CP TCGA-AX-A2HF TCGA-AX-A3G3 
       41.06        57.80        93.99        36.39        27.88         1.38 
TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A547 
       80.38        22.06        66.41        10.19        14.40        17.92 
TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A1OH TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-AJ-A23M 
       23.74        39.52        36.33        66.15        28.64        20.25 
TCGA-AJ-A3NF TCGA-AJ-A3TW TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A1DQ 
       21.21        16.87        45.53        36.89        48.79        46.78 
TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1C8 TCGA-AX-A1CC TCGA-AX-A1CN TCGA-AX-A2H5 
        0.56        37.78        25.51        25.91        37.58        71.24 
TCGA-AX-A3GI TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A1N2 
        0.39        27.85        75.72       102.31        11.87        31.36 
TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A0MT TCGA-BG-A0YU TCGA-BG-A2AE TCGA-BG-A3PP 
       29.65        34.13        21.17        14.83        23.70        22.39 
TCGA-BK-A26L TCGA-D1-A0ZP TCGA-D1-A0ZZ TCGA-D1-A16G TCGA-D1-A1NU TCGA-D1-A1NW 
       24.13        29.95        22.55        27.42        13.22         0.72 
TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KS TCGA-DI-A1NN TCGA-DI-A2QT 
       58.95        18.84        17.29       109.08        35.38        12.39 
TCGA-DI-A2QY TCGA-EO-A1Y7 TCGA-EO-A2CG TCGA-EO-A3KU TCGA-EY-A1GJ TCGA-EY-A1GS 
      110.10        49.15        51.42        22.26        23.90        22.03 
TCGA-EY-A1GV TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-FI-A2D2 TCGA-FI-A2EU 
       15.81        27.35        32.52        11.38        77.33        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR 
       59.01         9.34        28.93        41.56        78.38         1.74 
TCGA-JU-AAVI TCGA-KP-A3W1 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       17.75         9.47        23.24        38.70        22.59         8.19 

$`8P LOSS WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D 
       20.81        10.19       110.63        95.47        67.66        12.26 
TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-B5-A0KB TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV 
       23.05        61.18        27.09        61.87        51.55        12.56 
TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP 
       14.27         1.81        19.79         4.44        47.84        16.93 
TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A215 TCGA-EY-A549 
       33.30         6.21        22.78        17.88        18.87        19.89 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E 
        5.88        66.77        13.84        73.32        36.00         0.43 
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-A0GJ 
       32.78       112.54       105.37       123.68        74.10        65.75 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        73.87        36.82        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ 
       29.06        42.35        15.95        31.99        31.99        33.07 
TCGA-A5-A2K2 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ 
      118.19        24.72        34.95        25.51        14.96        11.21 
TCGA-A5-A7WK TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       18.41        14.43        10.26        21.14        19.79        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       34.36        34.16        18.12        18.90        33.90         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-A5DV 
       15.62        15.35        15.95        14.76        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 
       12.82        20.78         2.70        35.11         0.13       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05N 
       21.99        23.31        86.07        48.03        63.91        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       12.62        20.91       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       33.40        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       90.97        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 
       60.23        45.86        27.85        51.12        21.90        36.13 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        61.08        35.74        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C9 TCGA-AX-A1CA 
       77.39        13.28        32.91        34.65        26.37        32.02 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A2H2 
       34.09        76.83        85.48        73.41        80.25         4.77 
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        38.24 
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-A3G4 
        0.20         0.56        43.82         0.20        20.52         0.30 
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 
       86.37        55.30        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       64.21        63.55        13.45        59.84       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        73.64        61.68        85.78        52.04 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        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       225.50        50.89        51.45 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       14.70        48.43        52.54       136.60        96.30        93.50 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW 
       71.84        39.35        27.65        41.06        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        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       74.63        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       43.04        59.74        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A186 TCGA-BG-A187 
       34.29        52.64        52.83        56.58        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 
       14.01        15.45        15.45         9.57        20.02        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        35.90        35.08        31.00 
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        24.33        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        92.88 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
      114.90        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        89.59        63.58        83.64        86.99        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       16.83         8.55         0.56         4.87        28.67        23.93 
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-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-A1NX 
       11.15        24.30         2.33        22.92         1.41        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-A3DA TCGA-D1-A3DG TCGA-DF-A2KN TCGA-DF-A2KR 
       48.79         8.48        15.88         4.27         2.20        71.61 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH 
      100.83        89.33        10.92        27.16        25.91        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-EC-A1NJ TCGA-EC-A1QX 
       79.10        58.95         2.37        45.57        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       16.80        10.92        37.71        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       46.26        57.60        51.52        19.40        34.39        50.73 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KW 
       35.15        38.07        27.16        46.42        26.96        16.34 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       38.47        51.09        14.99        54.15        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       27.16        23.34        23.34        33.34        32.71        19.27 
TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A1GX 
       18.84        17.62        16.11        32.78        11.08        37.05 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       19.33        12.59        22.82        20.05        45.76        31.04 
TCGA-EY-A2OQ TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 
       29.10        14.14        14.70        16.96        68.38        39.88 
TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-K6-A3WQ TCGA-KP-A3W0 
        7.99        25.22        30.67        59.28        14.04        13.28 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       26.10        18.21        21.30        17.16         6.97        22.65 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       39.95        24.95        23.64        14.83         4.44        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       18.28         0.07         0.23 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.39              0.07 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            110.1             225.5 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           27.635            30.150 
[1] "0.4 - 110.1 (27.6)" "0.1 - 225.5 (30.1)"
[1] "hr=" "1.8"
D56V2, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    31  41
  8P LOSS WILD-TYPE 259 183
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     31   41
  8P LOSS WILD-TYPE  259  183
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO               31               259
  YES              41               183
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  8P LOSS MUTATED                                        17
  8P LOSS WILD-TYPE                                     387
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  8P LOSS MUTATED                               4
  8P LOSS WILD-TYPE                            18
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  8P LOSS MUTATED                                  57
  8P LOSS WILD-TYPE                                56
D56V3, multiclass
                                         clus
vv                                        8P LOSS MUTATED 8P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              17               387
  MIXED SEROUS AND ENDOMETRIOID                         4                18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    57                56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  8P LOSS MUTATED    49   4   3   9
  8P LOSS WILD-TYPE 322  18  13  31
D56V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0              49               322
  R1               4                18
  R2               3                13
  RX               9                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"

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    18   4
  8Q LOSS WILD-TYPE 429  86
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               22               515 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4                86 
$`8Q LOSS MUTATED`
TCGA-AP-A05D TCGA-AX-A2HF TCGA-B5-A0JN TCGA-KP-A3VZ TCGA-A5-A2K3 TCGA-AJ-A23M 
       57.80        27.88        80.38        23.74        66.15        20.25 
TCGA-AX-A2H5 TCGA-AX-A3GI TCGA-B5-A3S1 TCGA-BG-A0YU TCGA-BG-A3PP TCGA-BK-A26L 
       71.24         0.39        29.65        14.83        22.39        24.13 
TCGA-D1-A3JQ TCGA-DI-A1NN TCGA-DI-A2QT TCGA-EO-A3KU TCGA-EY-A3L3 TCGA-EY-A3QX 
       17.29        35.38        12.39        22.26        27.35        32.52 
TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A3PX TCGA-PG-A7D5 
       77.33        96.69        78.38        38.70 

$`8Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A0LF TCGA-AP-A0LS 
       18.08        20.81        10.19       110.63        93.99        95.47 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A3G3 
       67.66        12.26        36.39        23.05        61.18         1.38 
TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV 
       27.09        22.06        66.41        61.87        51.55        12.56 
TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP 
       14.27         1.81        19.79         4.44        47.84        16.93 
TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 
       33.30         6.21        22.78        17.88        10.19        14.40 
TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 
       18.87        17.92        19.89         5.88        66.77        13.84 
TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 
       73.32        36.00         0.43        39.52        10.29       106.88 
TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      149.56        37.02        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP 
      105.37       123.68        74.10        65.75        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       73.87        36.82        28.27        54.02        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       37.91        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-A2K2 
       15.95        31.99        31.99        36.33        33.07       118.19 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ 
       28.64        24.72        34.95        25.51        14.96        11.21 
TCGA-A5-A7WK TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       18.41        14.43        10.26        21.14        19.79        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       34.36        34.16        18.12        18.90        33.90         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-A8CV 
       16.87        22.32        12.82        20.78         2.70        35.11 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        0.13       129.80        21.99        23.31        86.07        48.03 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       63.91        45.53        36.89        23.87        12.62        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        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        46.72        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       61.64        80.78        49.22        25.08        71.67        90.97 
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 
       60.23        45.86        27.85        51.12        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        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        61.08        35.74        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        77.39        13.28        32.91        34.65 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       25.51        26.37        32.02        25.91        34.09        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 
       85.48        73.41        80.25        37.58         4.77        30.12 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       40.80        81.37        34.32        46.49        38.24        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        86.37 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       55.30        59.24        86.01        58.75        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       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        73.64        61.68        85.78 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       52.04        32.09        77.23        73.28        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       225.50       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        51.45        14.70        48.43        11.87        52.54 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       31.36       136.60        96.30        93.50        71.84        39.35 
TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       27.65        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        71.24        63.68        74.63 
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-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A186 TCGA-BG-A187 
       34.29        52.64        52.83        56.58        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       14.01        15.45        15.45         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        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
       31.00        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        24.33        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 
       92.88       114.90        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        89.59        63.58        83.64        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        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-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-A3DH 
       48.79         8.48        58.95        15.88         4.27        18.84 
TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY 
        2.20        71.61       109.08       100.83        89.33        10.92 
TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       27.16        25.91        16.31        39.29        36.62        24.30 
TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
        9.37        31.10       110.10        23.38        79.10        58.95 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37        45.57        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        50.73 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KW 
       35.15        38.07        27.16        46.42        26.96        16.34 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       38.47        51.09        14.99        54.15        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM 
       27.16        23.34        23.34        23.90        33.34        32.71 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       19.27        18.84        17.62        22.03        16.11        32.78 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM 
       15.81        11.08        37.05        19.33        12.59        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A548 
       20.05        45.76        31.04        29.10        11.38        14.14 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 
       14.70        16.96        68.38        39.88         7.99        25.22 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV 
       59.01         9.34        28.93        30.67        59.28        41.56 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 
        1.74        17.75        14.04        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        21.30        22.59         8.19        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        22.65        39.95        24.95        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44        20.75        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            225.50 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           28.765            29.950 
[1] "0.4 - 96.7 (28.8)"  "0.1 - 225.5 (29.9)"
[1] "hr=" "1.1"
D57V2, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     9  10
  8Q LOSS WILD-TYPE 281 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      9   10
  8Q LOSS WILD-TYPE  281  214
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                9               281
  YES              10               214
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  8Q LOSS MUTATED                                         1
  8Q LOSS WILD-TYPE                                     403
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  8Q LOSS MUTATED                               1
  8Q LOSS WILD-TYPE                            21
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  8Q LOSS MUTATED                                  20
  8Q LOSS WILD-TYPE                                93
D57V3, multiclass
                                         clus
vv                                        8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               1               403
  MIXED SEROUS AND ENDOMETRIOID                         1                21
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    20                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"
                   vv
clus                 R0  R1  R2  RX
  8Q LOSS MUTATED    13   1   1   3
  8Q LOSS WILD-TYPE 358  21  15  37
D57V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              13               358
  R1               1                21
  R2               1                15
  RX               3                37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    67  32
  9P LOSS WILD-TYPE 380  58
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               99               438 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               32                58 
$`9P LOSS MUTATED`
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AX-A1CP TCGA-AX-A1CR 
       20.81        10.19       110.63        57.80        36.39        23.05 
TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-D1-A3JP TCGA-EY-A212 
       27.09        22.06        66.41        12.56        16.93        10.19 
TCGA-EY-A214 TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0G2 TCGA-A5-A0GG TCGA-A5-A0GR 
       14.40        23.74        39.52       149.56       123.68        36.82 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0VP TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO 
       37.91        17.59        42.35       118.19        28.64        25.51 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ 
       20.25        14.43        34.16        18.12        18.90         1.64 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A0L8 
       22.26        17.06        20.78        21.99        45.53        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
      125.42        97.71        46.78        21.90        36.13         0.56 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CF TCGA-AX-A2H4 TCGA-AX-A3FX 
       37.78        34.65        25.51        76.83        30.12        43.82 
TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0K8 TCGA-B5-A11P 
       20.52         0.30         0.26         0.39        27.85        52.04 
TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OE 
      102.31        11.87       136.60        39.35        29.65        34.95 
TCGA-BG-A18C TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L TCGA-BS-A0TI TCGA-BS-A0V8 
       15.45        35.08        31.00        24.13        61.87        83.64 
TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A1NU 
       22.55        39.48        37.32        31.07        18.67        13.22 
TCGA-D1-A1O0 TCGA-D1-A3JQ TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QU 
        2.07        17.29        25.91        35.38        12.39        31.10 
TCGA-DI-A2QY TCGA-EO-A1Y7 TCGA-EO-A2CG TCGA-EO-A3AZ TCGA-EO-A3KW TCGA-EY-A1GC 
      110.10        49.15        51.42        27.16        16.34        54.15 
TCGA-EY-A1GO TCGA-EY-A1GV TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2EX TCGA-FI-A2EY 
       19.27        15.81        14.70        77.33         9.34        28.93 
TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-KP-A3W3 
       30.67        41.56        17.75        14.04         9.47        26.10 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-QS-A8F1 
       18.21        23.24         4.44 

$`9P LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A2H8 
       18.08        93.99        95.47        67.66        12.26        61.18 
TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A220 
       27.88         1.38        80.38        61.87        51.55        14.27 
TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1G7 
        1.81        19.79         4.44        47.84        33.30         6.21 
TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D 
       22.78        17.88        18.87        17.92        19.89         5.88 
TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5S-A9Q8 
       66.77        13.84        73.32        36.00         0.43        10.29 
TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88        37.02        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
      105.37        74.10        65.75        60.53        46.55        73.87 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 
       28.27        54.02        23.21        68.65        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ 
       29.06        15.95        31.99        31.99        36.33        33.07 
TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK 
       66.15        24.72        34.95        14.96        11.21        18.41 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BK 
       10.26        21.14        19.79        35.15        34.36        33.90 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       14.66        22.49        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-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 
       12.82         2.70        35.11         0.13       129.80        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       86.07        48.03        63.91        36.89        23.87        12.62 
TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
       20.91       117.99       110.37        66.25        36.36        46.72 
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-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        90.97        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        60.23        45.86        27.85 
TCGA-AP-A1E4 TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       51.12        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ 
       27.39        30.02        60.66        61.08        35.74        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CA 
       40.11        77.39        13.28        32.91        26.37        32.02 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       25.91        34.09        85.48        73.41        80.25        37.58 
TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
        4.77        71.24        40.80        81.37        34.32        46.49 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       38.24        17.75        30.74         2.96        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.23         0.20         0.56         0.20         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        86.37        55.30        59.24 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.01        58.75        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       72.62        27.29        57.76        64.21        63.55        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       59.84       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 
       73.64        61.68        85.78        32.09        77.23        73.28 
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 
      225.50        50.89        51.45        14.70        48.43        52.54 
TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC 
       31.36        96.30        93.50        71.84        27.65        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-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       71.24        63.68        74.63        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        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        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-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        22.39 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD 
       35.90        34.98        35.90        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        24.33        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-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        92.88       114.90        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        89.59        63.58        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X 
       28.67        23.93         1.74        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        48.79 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KN 
        8.48        58.95        15.88         4.27        18.84         2.20 
TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
       71.61       109.08       100.83        89.33        10.92        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-E6-A1LX 
       16.31        39.29        36.62        24.30         9.37        23.38 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       79.10        58.95         2.37        45.57        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       16.80        10.92        37.71        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       46.26        57.60        51.52        19.40        34.39        50.73 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KX 
       35.15        38.07        46.42        26.96        22.26        38.47 
TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       51.09        14.99        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GR 
       23.34        23.90        33.34        32.71        18.84        17.62 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       22.03        16.11        32.78        11.08        37.05        19.33 
TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       12.59        22.82        20.05        45.76        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CY 
       27.35        32.52        11.38        14.14        16.96        68.38 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F9 
       39.88         7.99        25.22        96.69        59.01        59.28 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-KP-A3W0 TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 
       78.38         1.74        13.28        21.30        38.70        22.59 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        8.19        17.16         6.97        22.65        39.95        24.95 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       23.64        14.83        20.75        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            225.50 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           27.090            30.295 
[1] "0.3 - 149.6 (27.1)" "0.1 - 225.5 (30.3)"
[1] "hr=" "2.5"
D58V2, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    51  41
  9P LOSS WILD-TYPE 239 183
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     51   41
  9P LOSS WILD-TYPE  239  183
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               51               239
  YES              41               183
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  9P LOSS MUTATED                                        34
  9P LOSS WILD-TYPE                                     370
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  9P LOSS MUTATED                               7
  9P LOSS WILD-TYPE                            15
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  9P LOSS MUTATED                                  58
  9P LOSS WILD-TYPE                                55
D58V3, multiclass
                                         clus
vv                                        9P LOSS MUTATED 9P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              34               370
  MIXED SEROUS AND ENDOMETRIOID                         7                15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    58                55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  9P LOSS MUTATED    60   5   6  10
  9P LOSS WILD-TYPE 311  17  10  30
D58V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0              60               311
  R1               5                17
  R2               6                10
  RX              10                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"

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    83  34
  9Q LOSS WILD-TYPE 364  56
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              117               420 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               34                56 
$`9Q LOSS MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AX-A06B 
       41.06        20.81        10.19       110.63        57.80        67.66 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0KB 
       36.39        23.05        61.18        27.88        80.38        27.09 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-BG-A221 TCGA-D1-A3JP TCGA-EY-A212 
       22.06        66.41        12.56         1.81        16.93        10.19 
TCGA-EY-A214 TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0GG TCGA-A5-A0GR TCGA-A5-A0R6 
       14.40        23.74        39.52       123.68        36.82        37.91 
TCGA-A5-A0R7 TCGA-A5-A0VP TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M 
       17.59        42.35       118.19        28.64        25.51        20.25 
TCGA-AJ-A2QK TCGA-AJ-A2QN TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ 
       21.14        35.15        34.16        18.12        18.90         1.64 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A0L8 
       22.26        17.06        20.78        21.99        45.53        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A0IW 
      125.42        97.71        21.90        36.13         0.56        37.78 
TCGA-AX-A1C7 TCGA-AX-A1CF TCGA-AX-A2H4 TCGA-AX-A3FS TCGA-AX-A3FX TCGA-AX-A3G1 
       34.65        76.83        30.12         0.23        43.82        20.52 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A11P 
        0.30         0.26         0.39        27.85        75.72        52.04 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A3S1 
      102.31        50.89        11.87       136.60        39.35        29.65 
TCGA-B5-A5OE TCGA-BG-A18C TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L TCGA-BS-A0TI 
       34.95        15.45        35.08        31.00        24.13        61.87 
TCGA-BS-A0V8 TCGA-D1-A0ZQ TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16N 
       83.64         8.55        22.55        39.48        37.32        31.07 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A1NU TCGA-D1-A1O0 TCGA-D1-A2G7 TCGA-D1-A3DH 
       18.67         3.95        13.22         2.07        58.95        18.84 
TCGA-D1-A3JQ TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ 
       17.29        25.91        35.38        31.10       110.10        79.10 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AZ TCGA-EO-A3B1 
       49.15        37.71        51.42        19.40        27.16        26.96 
TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GV TCGA-EY-A210 TCGA-EY-A2ON 
       16.34        54.15        19.27        15.81        12.59        20.05 
TCGA-EY-A2OQ TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 
       29.10        68.38        77.33         9.34        28.93        30.67 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-KP-A3W3 
       41.56        78.38        17.75        14.04         9.47        26.10 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-QS-A8F1 
       18.21        23.24         4.44 

$`9Q LOSS WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A3G3 TCGA-BG-A0MS TCGA-BG-A0VT 
       93.99        95.47        12.26         1.38        61.87        51.55 
TCGA-BG-A220 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1G7 
       14.27        19.79         4.44        47.84        33.30         6.21 
TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D 
       22.78        17.88        18.87        17.92        19.89         5.88 
TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5S-A9Q8 
       66.77        13.84        73.32        36.00         0.43        10.29 
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP 
      112.54       105.37        74.10        65.75        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 
       73.87        28.27        54.02        23.21        68.65        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH 
       24.62        29.06        15.95        31.99        31.99        36.33 
TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-A5-A7WJ 
       33.07        66.15        24.72        34.95        14.96        11.21 
TCGA-A5-A7WK TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QO TCGA-AJ-A3BK 
       18.41        14.43        10.26        19.79        34.36        33.90 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       14.66        22.49        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-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 
       12.82         2.70        35.11         0.13       129.80        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       86.07        48.03        63.91        36.89        23.87        12.62 
TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
       20.91       117.99       110.37        66.25        36.36        46.72 
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-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        90.97        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        60.23        45.86 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       27.85        51.12        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       57.47        27.39        30.02        60.66        61.08        35.74 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 
       43.82        40.11        77.39        13.28        32.91        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       26.37        32.02        25.91        34.09        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA 
       80.25        37.58         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-A2HK 
       34.32        46.49        38.24        17.75        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G7 
       31.13        64.93         0.20         0.56         0.20         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        86.37        55.30 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       59.24        86.01        58.75        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J 
       13.45        59.84       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 
       73.64        61.68        85.78        32.09        77.23        73.28 
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 
      225.50        51.45        14.70        48.43        52.54        31.36 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD 
       96.30        93.50        71.84        27.65        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        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       63.68        74.63        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        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        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-A222 
       14.83        13.78        14.73        14.01        15.45         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        22.39        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F 
       34.98        35.90        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        24.33        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 
       92.88       114.90        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        89.59        63.58        86.99        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       16.83        29.95         0.56         4.87        28.67        23.93 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        1.74        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-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-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-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 
        1.41         0.72        18.25        16.87        18.02        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG 
        1.05         3.95        48.79         8.48        15.88         4.27 
TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY 
        2.20        71.61       109.08       100.83        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-EC-A1NJ 
       12.39        23.38        58.95         2.37        45.57        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
        7.36        16.80        10.92        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        50.73        35.15 
TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 
       38.07        46.42        22.26        38.47        51.09        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-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT 
       33.34        32.71        18.84        17.62        22.03        16.11 
TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2OO 
       32.78        11.08        37.05        19.33        22.82        45.76 
TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A 
       31.04        27.35        32.52        11.38        14.14        14.70 
TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       16.96        39.88         7.99        25.22        96.69        59.01 
TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-KP-A3W0 TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 
       59.28         1.74        13.28        21.30        38.70        22.59 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        8.19        17.16         6.97        22.65        39.95        24.95 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       23.64        14.83        20.75        18.28         0.07         0.23 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.23              0.07 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            136.6             225.5 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            27.88             30.15 
[1] "0.2 - 136.6 (27.9)" "0.1 - 225.5 (30.1)"
[1] "hr=" "2.2"
D59V2, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    64  46
  9Q LOSS WILD-TYPE 226 178
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     64   46
  9Q LOSS WILD-TYPE  226  178
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               64               226
  YES              46               178
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  9Q LOSS MUTATED                                        45
  9Q LOSS WILD-TYPE                                     359
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  9Q LOSS MUTATED                               9
  9Q LOSS WILD-TYPE                            13
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  9Q LOSS MUTATED                                  63
  9Q LOSS WILD-TYPE                                50
D59V3, multiclass
                                         clus
vv                                        9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              45               359
  MIXED SEROUS AND ENDOMETRIOID                         9                13
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    63                50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  9Q LOSS MUTATED    74   4   6  10
  9Q LOSS WILD-TYPE 297  18  10  30
D59V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              74               297
  R1               4                18
  R2               6                10
  RX              10                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"

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    32  12
  10P LOSS WILD-TYPE 415  78
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                44                493 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                12                 78 
$`10P LOSS MUTATED`
TCGA-AX-A06B TCGA-AX-A1CP TCGA-AX-A1CR TCGA-B5-A0KB TCGA-BG-A0M8 TCGA-D1-A3JP 
       67.66        36.39        23.05        27.09        66.41        16.93 
TCGA-E6-A8L9 TCGA-KP-A3VZ TCGA-A5-A1OH TCGA-A5-A7WK TCGA-AJ-A3BF TCGA-AJ-A3NF 
       33.30        23.74        36.33        18.41        18.12        21.21 
TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A5FX TCGA-AX-A2H2 
       21.99        45.53       125.42        97.71        36.13         4.77 
TCGA-AX-A2HK TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-BG-A18C TCGA-BG-A3PP 
        2.96        20.52         0.30         0.39        15.45        22.39 
TCGA-BK-A26L TCGA-BS-A0U9 TCGA-D1-A16I TCGA-D1-A3JQ TCGA-DI-A1NN TCGA-E6-A1LZ 
       24.13        92.88        11.51        17.29        35.38        79.10 
TCGA-EO-A3AZ TCGA-EO-A3KW TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A2OQ TCGA-FI-A2D2 
       27.16        16.34        17.62        22.03        29.10        77.33 
TCGA-FI-A2EW TCGA-FI-A2EY TCGA-FI-A3PV TCGA-FI-A3PX TCGA-JU-AAVI TCGA-KP-A3W3 
       59.01        28.93        41.56        78.38        17.75        26.10 
TCGA-KP-A3W4 TCGA-PG-A915 
       18.21         8.19 

$`10P LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF 
       18.08        20.81        10.19       110.63        57.80        93.99 
TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN 
       95.47        12.26        61.18        27.88         1.38        80.38 
TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 
       22.06        61.87        51.55        12.56        14.27         1.81 
TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ 
       19.79         4.44        47.84         6.21        22.78        17.88 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D 
       10.19        14.40        18.87        17.92        19.89         5.88 
TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5B-A90C 
       66.77        13.84        73.32        36.00         0.43        39.52 
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-A0GJ 
       32.78       112.54       105.37       123.68        74.10        65.75 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        73.87        36.82        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ 
       29.06        42.35        15.95        31.99        31.99        33.07 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
      118.19        66.15        28.64        24.72        34.95        25.51 
TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
       14.96        11.21        20.25        14.43        10.26        21.14 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3BK 
       19.79        35.15        34.36        34.16        18.90        33.90 
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-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-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV 
       16.87        22.32        12.82        20.78         2.70        35.11 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
        0.13       129.80        23.31        86.07        48.03        63.91 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD 
       36.89        23.87        12.62        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        66.25        36.36        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        90.97        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        60.23        45.86        27.85        51.12 
TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       21.90         0.56        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       57.47        27.39        30.02        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        77.39        13.28        32.91 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       34.65        25.51        26.37        32.02        25.91        34.09 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H4 
       76.83        85.48        73.41        80.25        37.58        30.12 
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        38.24 
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-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.56        43.82         0.20         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        86.37        55.30        59.24 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.01        58.75        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       13.45        59.84       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        73.64        61.68        85.78        52.04        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       77.23        73.28        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       225.50       102.31        50.89        51.45 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       14.70        48.43        11.87        52.54        31.36       136.60 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 
       96.30        93.50        71.84        39.35        27.65        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-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        35.21        71.24        63.68        74.63        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        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.01        15.45         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        35.90        35.08        31.00 
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        24.33        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       114.90 
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 
       89.59        63.58        83.64        86.99        66.48        16.83 
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-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74        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-A2G6 TCGA-D1-A2G7 
       15.06         1.05         3.95        48.79         8.48        58.95 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS 
       15.88         4.27        18.84         2.20        71.61       109.08 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH 
      100.83        89.33        10.92        27.16        25.91        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-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
      110.10        23.38        58.95         2.37        45.57        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        50.73        35.15        38.07        46.42 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC 
       26.96        22.26        38.47        51.09        14.99        54.15 
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-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU 
       33.34        32.71        19.27        18.84        16.11        32.78 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM 
       15.81        11.08        37.05        19.33        12.59        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        32.52        11.38 
TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
       14.14        14.70        16.96        68.38        39.88         7.99 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-H5-A2HR 
       25.22        96.69         9.34        30.67        59.28         1.74 
TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 
       14.04        13.28         9.47        23.24        21.30        38.70 
TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       22.59        17.16         6.97        22.65        39.95        24.95 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       23.64        14.83         4.44        20.75        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.30               0.07 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            125.42             225.50 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            23.935             30.150 
[1] "0.3 - 125.4 (23.9)" "0.1 - 225.5 (30.1)"
[1] "hr=" "1.9"
D60V2, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    25  15
  10P LOSS WILD-TYPE 265 209
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     25   15
  10P LOSS WILD-TYPE  265  209
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                25                265
  YES               15                209
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  10P LOSS MUTATED                                         9
  10P LOSS WILD-TYPE                                     395
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  10P LOSS MUTATED                               5
  10P LOSS WILD-TYPE                            17
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  10P LOSS MUTATED                                  30
  10P LOSS WILD-TYPE                                83
D60V3, multiclass
                                         clus
vv                                        10P LOSS MUTATED 10P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                9                395
  MIXED SEROUS AND ENDOMETRIOID                          5                 17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     30                 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"
                    vv
clus                  R0  R1  R2  RX
  10P LOSS MUTATED    30   2   3   5
  10P LOSS WILD-TYPE 341  20  13  35
D60V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               30                341
  R1                2                 20
  R2                3                 13
  RX                5                 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"

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    29  11
  10Q LOSS WILD-TYPE 418  79
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                40                497 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                11                 79 
$`10Q LOSS MUTATED`
TCGA-AX-A06B TCGA-AX-A1CR TCGA-B5-A0KB TCGA-BG-A0M8 TCGA-D1-A3JP TCGA-KJ-A3U4 
       67.66        23.05        27.09        66.41        16.93        36.00 
TCGA-A5-A1OH TCGA-A5-A7WK TCGA-AJ-A3BF TCGA-AJ-A3TW TCGA-AP-A05H TCGA-AP-A0L9 
       36.33        18.41        18.12        16.87        45.53       125.42 
TCGA-AP-A0LI TCGA-AP-A5FX TCGA-AX-A2H2 TCGA-AX-A2HK TCGA-AX-A3G1 TCGA-AX-A3G4 
       97.71        36.13         4.77         2.96        20.52         0.30 
TCGA-AX-A3GI TCGA-B5-A1MS TCGA-B5-A3FD TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A26L 
        0.39       102.31        39.35        15.45        22.39        24.13 
TCGA-BS-A0U9 TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A17K TCGA-D1-A3DH TCGA-DI-A1NN 
       92.88        11.51        29.92        28.08        18.84        35.38 
TCGA-EO-A3AZ TCGA-EO-A3KW TCGA-EY-A1GR TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A3PV 
       27.16        16.34        17.62        77.33        96.69        41.56 
TCGA-FI-A3PX TCGA-JU-AAVI TCGA-KP-A3W3 TCGA-KP-A3W4 
       78.38        17.75        26.10        18.21 

$`10Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF 
       18.08        20.81        10.19       110.63        57.80        93.99 
TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 
       95.47        12.26        36.39        61.18        27.88         1.38 
TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 
       80.38        22.06        61.87        51.55        12.56        14.27 
TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1G7 
        1.81        19.79         4.44        47.84        33.30         6.21 
TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 
       22.78        17.88        10.19        14.40        18.87        17.92 
TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KP-A3VZ 
       19.89         5.88        66.77        13.84        73.32        23.74 
TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
        0.43        39.52        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       123.68 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       74.10        65.75        60.53        46.55        73.87        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        54.02        23.21        68.65        37.91        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        31.99 
TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
       31.99        33.07       118.19        66.15        28.64        24.72 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-AJ-A23M TCGA-AJ-A23N 
       34.95        25.51        14.96        11.21        20.25        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
       10.26        21.14        19.79        35.15        34.36        34.16 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       18.90        33.90         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-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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
        2.70        35.11         0.13       129.80        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       86.07        48.03        63.91        36.89        23.87        12.62 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       20.91        48.79       117.99       110.37        66.25        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       46.72        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       80.78        49.22        25.08        71.67        90.97        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        60.23 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S 
       45.86        27.85        51.12        21.90         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       45.99        79.46        49.87        57.47        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       60.66        61.08        35.74        37.78        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       77.39        13.28        32.91        34.65        25.51        26.37 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       32.02        25.91        34.09        76.83        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA 
       80.25        37.58        30.12        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        38.24        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-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 
       86.37        55.30        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       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        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       85.78        52.04        32.09        77.23        73.28        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       225.50 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        51.45        14.70        48.43        11.87        52.54 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH 
       31.36       136.60        96.30        93.50        71.84        27.65 
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        71.24        63.68        74.63 
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-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
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-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       14.73        14.01        15.45         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        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
       31.00        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        24.33        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 
      114.90        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        89.59        63.58        83.64        86.99        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        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-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-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        1.05         3.95        48.79         8.48        58.95        15.88 
TCGA-D1-A3DG TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU 
        4.27        17.29         2.20        71.61       109.08       100.83 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU 
       89.33        10.92        27.16        25.91        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-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       23.38        79.10        58.95         2.37        45.57        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        50.73        35.15        38.07        46.42 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC 
       26.96        22.26        38.47        51.09        14.99        54.15 
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-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GT 
       33.34        32.71        19.27        18.84        22.03        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       32.78        15.81        11.08        37.05        19.33        12.59 
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-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY 
       32.52        11.38        14.14        14.70        16.96        68.38 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       39.88         7.99        25.22        59.01         9.34        28.93 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 
       30.67        59.28         1.74        14.04        13.28         9.47 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 
       23.24        21.30        38.70        22.59         8.19        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        22.65        39.95        24.95        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44        20.75        18.28         0.07         0.23 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.30               0.07 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            125.42             225.50 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            26.595             30.120 
[1] "0.3 - 125.4 (26.6)" "0.1 - 225.5 (30.1)"
[1] "hr=" "1.8"
D61V2, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    23  14
  10Q LOSS WILD-TYPE 267 210
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     23   14
  10Q LOSS WILD-TYPE  267  210
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                23                267
  YES               14                210
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  10Q LOSS MUTATED                                        12
  10Q LOSS WILD-TYPE                                     392
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  10Q LOSS MUTATED                               5
  10Q LOSS WILD-TYPE                            17
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  10Q LOSS MUTATED                                  23
  10Q LOSS WILD-TYPE                                90
D61V3, multiclass
                                         clus
vv                                        10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               12                392
  MIXED SEROUS AND ENDOMETRIOID                          5                 17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     23                 90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  10Q LOSS MUTATED    28   1   1   5
  10Q LOSS WILD-TYPE 343  21  15  35
D61V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               28                343
  R1                1                 21
  R2                1                 15
  RX                5                 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"

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    51  25
  11P LOSS WILD-TYPE 396  65
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                76                461 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                25                 65 
$`11P LOSS MUTATED`
TCGA-AJ-A3NH TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A1CR TCGA-AX-A3G3 TCGA-BG-A0YV 
       10.19        93.99        67.66        23.05         1.38        12.56 
TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A214 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-5B-A90C 
       16.93        33.30        14.40        36.00        23.74        39.52 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 
       65.75        60.53        36.82        31.99        36.33       118.19 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AJ-A3BF 
       66.15        28.64        18.41        20.25        34.16        18.12 
TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3NF TCGA-AJ-A3QS TCGA-AP-A05A TCGA-AP-A1DQ 
       18.90         1.64        21.21        16.87        63.91        46.78 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A1CA TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 
       21.90        36.13        32.02        20.52         0.30         0.26 
TCGA-AX-A3GI TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A1MS 
        0.39        27.29        27.85        52.04        32.09       102.31 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OD TCGA-BK-A139 TCGA-BK-A4ZD 
       31.36       136.60        39.35        34.13        31.00        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        18.84 
TCGA-DF-A2KS TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-EO-A1Y7 TCGA-EO-A1Y8 
      109.08         9.37        12.39        31.10        49.15        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        22.03 
TCGA-EY-A2OO TCGA-EY-A3L3 TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2EY TCGA-FI-A2F8 
       45.76        27.35        14.70        77.33        28.93        30.67 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-PG-A5BC 
       17.75        14.04         9.47        23.24 

$`11P LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06D 
       18.08        20.81       110.63        57.80        95.47        12.26 
TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 
       36.39        61.18        27.88        80.38        27.09        22.06 
TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       66.41        61.87        51.55        14.27         1.81        19.79 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 
        4.44        47.84         6.21        22.78        17.88        10.19 
TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 
       18.87        17.92        19.89         5.88        66.77        13.84 
TCGA-FI-A2F4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       73.32         0.43        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       123.68 
TCGA-A5-A0GH TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       74.10        46.55        73.87        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A2K5 TCGA-A5-A2K7 
       42.35        15.95        31.99        33.07        24.72        34.95 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
       25.51        14.96        11.21        14.43        10.26        21.14 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
       19.79        35.15        34.36        33.90        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       22.26        17.06        36.99        20.65        15.62        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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
        2.70        35.11         0.13       129.80        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       86.07        48.03        45.53        36.89        23.87        12.62 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       33.40        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       90.97        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 
       60.23        45.86        27.85        51.12         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       45.99        79.46        49.87        57.47        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       60.66        61.08        35.74        37.78        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       77.39        13.28        32.91        34.65        25.51        26.37 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       25.91        34.09        76.83        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA 
       37.58         4.77        30.12        71.24        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       34.32        46.49        38.24        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-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR 
        0.20         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 
       86.37        55.30        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 
       71.44        48.59        36.49        72.62        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        13.45        59.84       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        73.64        61.68        85.78        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       73.28        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       225.50        50.89        51.45        14.70        48.43 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH 
       11.87        52.54        96.30        93.50        71.84        27.65 
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-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        35.21        71.24        63.68        74.63        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        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       14.01        15.45        15.45         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        22.39        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 
       35.08        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        24.33        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 
       92.88       114.90        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        89.59        63.58        83.64        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       28.67        23.93         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-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-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        1.05         3.95        48.79         8.48        58.95        15.88 
TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY 
       17.29         2.20        71.61       100.83        89.33        10.92 
TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       27.16        25.91        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       35.38       110.10        23.38        79.10        58.95         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A22R 
       45.57        16.04         7.36        16.80        10.92        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-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 
       50.73        35.15        38.07        27.16        46.42        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC 
       22.26        16.34        38.47        51.09        14.99        54.15 
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-A1GL TCGA-EY-A1GM TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       33.34        32.71        16.11        32.78        15.81        11.08 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP 
       37.05        19.33        12.59        22.82        20.05        31.04 
TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CY 
       29.10        32.52        11.38        14.14        16.96        68.38 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
       39.88         7.99        25.22        96.69        59.01         9.34 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-KP-A3W0 TCGA-KP-A3W3 
       59.28        41.56        78.38         1.74        13.28        26.10 
TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 
       18.21        21.30        38.70        22.59         8.19        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        22.65        39.95        24.95        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44        20.75        18.28         0.07         0.23 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.26               0.07 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             136.6              225.5 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            25.515             30.150 
[1] "0.3 - 136.6 (25.5)" "0.1 - 225.5 (30.1)"
[1] "hr=" "2.7"
D62V2, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    40  29
  11P LOSS WILD-TYPE 250 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     40   29
  11P LOSS WILD-TYPE  250  195
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                40                250
  YES               29                195
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  11P LOSS MUTATED                                        28
  11P LOSS WILD-TYPE                                     376
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  11P LOSS MUTATED                               7
  11P LOSS WILD-TYPE                            15
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  11P LOSS MUTATED                                  41
  11P LOSS WILD-TYPE                                72
D62V3, multiclass
                                         clus
vv                                        11P LOSS MUTATED 11P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               28                376
  MIXED SEROUS AND ENDOMETRIOID                          7                 15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     41                 72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  11P LOSS MUTATED    44   3   4   7
  11P LOSS WILD-TYPE 327  19  12  33
D62V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0               44                327
  R1                3                 19
  R2                4                 12
  RX                7                 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"

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    51  22
  11Q LOSS WILD-TYPE 396  68
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                73                464 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                22                 68 
$`11Q LOSS MUTATED`
TCGA-AJ-A2QM TCGA-AJ-A3NH TCGA-AP-A0LF TCGA-AX-A1CR TCGA-AX-A3G3 TCGA-BG-A0YV 
       29.39        10.19        93.99        23.05         1.38        12.56 
TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A214 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-5B-A90C 
       16.93        33.30        14.40        36.00        23.74        39.52 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 
       65.75        60.53        36.82        31.99        36.33       118.19 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI 
       66.15        28.64        20.25        34.16        18.12        18.90 
TCGA-AJ-A3EJ TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A2IO 
        1.64        16.87        16.87        21.90        36.13        64.93 
TCGA-AX-A3G1 TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11P 
       20.52         0.26         0.39        27.29        27.85        52.04 
TCGA-B5-A11Q TCGA-B5-A1MS TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OD TCGA-BG-A3PP 
       32.09       102.31       136.60        39.35        34.13        22.39 
TCGA-BK-A4ZD TCGA-D1-A0ZZ TCGA-D1-A169 TCGA-D1-A16S TCGA-D1-A1NX TCGA-D1-A3DG 
       16.64        22.55        37.32        18.67        18.25         4.27 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       35.38         9.37        12.39        31.10        49.15        37.71 
TCGA-EO-A2CH TCGA-EO-A3KU TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS 
       19.40        22.26        19.27        18.84        17.62        22.03 
TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A2OO TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A54A 
       11.08        12.59        45.76        27.35        11.38        14.70 
TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-KP-A3W3 
       77.33        96.69        17.75        14.04         9.47        26.10 
TCGA-PG-A915 
        8.19 

$`11Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AJ-A3IA TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D 
       20.81       110.63        57.80        95.47        67.66        12.26 
TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 
       36.39        61.18        27.88        80.38        27.09        22.06 
TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       66.41        61.87        51.55        14.27         1.81        19.79 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 
        4.44        47.84         6.21        22.78        17.88        10.19 
TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 
       18.87        17.92        19.89         5.88        66.77        13.84 
TCGA-FI-A2F4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       73.32         0.43        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       123.68 
TCGA-A5-A0GH TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       74.10        46.55        73.87        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A2K5 TCGA-A5-A2K7 
       42.35        15.95        31.99        33.07        24.72        34.95 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23N TCGA-AJ-A23O 
       25.51        14.96        11.21        18.41        14.43        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BK TCGA-AJ-A3EK 
       21.14        19.79        35.15        34.36        33.90        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-A5DV TCGA-AJ-A5DW 
       15.62        15.35        15.95        14.76        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       20.78         2.70        35.11         0.13       129.80        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07        48.03        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        12.62        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        90.97        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        60.23        45.86        27.85 
TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       51.12         0.56        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       57.47        27.39        30.02        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        77.39        13.28        32.91 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       34.65        25.51        26.37        32.02        25.91        34.09 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 
       76.83        85.48        73.41        80.25        37.58         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-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS 
       38.24        17.75        30.74         2.96        31.13         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G4 TCGA-AX-A3G7 
        0.20         0.56        43.82         0.20         0.30         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        86.37        55.30 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       59.24        86.01        58.75        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       36.49        72.62        57.76        64.21        63.55        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       59.84       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       73.64        61.68        85.78        77.23        73.28        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       225.50 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        51.45        14.70        48.43        11.87        52.54 
TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 
       31.36        96.30        93.50        71.84        27.65        29.65 
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        71.24        63.68        74.63        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       48.56        23.47        43.30        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       15.45        15.45         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        35.90        35.08        31.00 
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        24.33        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        92.88 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
      114.90        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        89.59        63.58        83.64        86.99        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       23.93         1.74        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-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-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-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
        0.72        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-A3DH 
        3.95        48.79         8.48        58.95        15.88        18.84 
TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV 
       17.29         2.20        71.61       109.08       100.83        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       10.92        27.16        25.91        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       24.30       110.10        23.38        79.10        58.95         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A22R 
       45.57        16.04         7.36        16.80        10.92        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-A3AZ TCGA-EO-A3B0 
       34.39        50.73        35.15        38.07        27.16        46.42 
TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC 
       26.96        16.34        38.47        51.09        14.99        54.15 
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-A1GL TCGA-EY-A1GM TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX 
       33.34        32.71        16.11        32.78        15.81        37.05 
TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX 
       19.33        22.82        20.05        31.04        29.10        32.52 
TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 
       14.14        16.96        68.38        39.88         7.99        25.22 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV 
       59.01         9.34        28.93        30.67        59.28        41.56 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       78.38         1.74        13.28        18.21        23.24        21.30 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       38.70        22.59        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       24.95        23.64        14.83         4.44        20.75        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.26               0.07 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             136.6              225.5 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            22.550             30.705 
[1] "0.3 - 136.6 (22.6)" "0.1 - 225.5 (30.7)"
[1] "hr=" "2.5"
D63V2, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    35  32
  11Q LOSS WILD-TYPE 255 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     35   32
  11Q LOSS WILD-TYPE  255  192
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                35                255
  YES               32                192
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  11Q LOSS MUTATED                                        24
  11Q LOSS WILD-TYPE                                     380
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  11Q LOSS MUTATED                               7
  11Q LOSS WILD-TYPE                            15
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  11Q LOSS MUTATED                                  42
  11Q LOSS WILD-TYPE                                71
D63V3, multiclass
                                         clus
vv                                        11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               24                380
  MIXED SEROUS AND ENDOMETRIOID                          7                 15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     42                 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"
                    vv
clus                  R0  R1  R2  RX
  11Q LOSS MUTATED    43   4   4   7
  11Q LOSS WILD-TYPE 328  18  12  33
D63V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0               43                328
  R1                4                 18
  R2                4                 12
  RX                7                 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"

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    29  16
  12P LOSS WILD-TYPE 418  74
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                45                492 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                16                 74 
$`12P LOSS MUTATED`
TCGA-AJ-A2QM TCGA-AX-A06B TCGA-BG-A0YV TCGA-EY-A212 TCGA-A5-A1OH TCGA-A5-A2K2 
       29.39        67.66        12.56        10.19        36.33       118.19 
TCGA-A5-A2K4 TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EM TCGA-AJ-A3NF TCGA-AP-A052 
       28.64        18.12        18.90        22.26        21.21        21.99 
TCGA-AP-A05H TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A3K1 TCGA-AX-A2H4 TCGA-AX-A3FX 
       45.53        97.71        33.40        21.90        30.12        43.82 
TCGA-B5-A0K3 TCGA-B5-A1MS TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BK-A139 TCGA-BK-A4ZD 
       27.29       102.31        29.65        34.95        31.00        16.64 
TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A16S TCGA-D1-A2G7 TCGA-D1-A3DH 
       83.64        22.55        39.48        18.67        58.95        18.84 
TCGA-DF-A2KR TCGA-DF-A2L0 TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1GS TCGA-EY-A1GW 
       71.61        25.91        26.96        16.34        22.03        11.08 
TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A3PV 
       29.10        11.38        14.70        96.69         9.34        41.56 
TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-PG-A915 
       13.28        26.10         8.19 

$`12P LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS 
       20.81        10.19       110.63        57.80        93.99        95.47 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 
       12.26        36.39        23.05        61.18        27.88         1.38 
TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       80.38        27.09        22.06        66.41        61.87        51.55 
TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP 
       14.27         1.81        19.79         4.44        47.84        16.93 
TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A214 TCGA-EY-A215 
       33.30         6.21        22.78        17.88        14.40        18.87 
TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 
       17.92        19.89         5.88        66.77        13.84        73.32 
TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 
       36.00        23.74         0.43        39.52        10.29       106.88 
TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      149.56        37.02        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP 
      105.37       123.68        74.10        65.75        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       73.87        36.82        28.27        54.02        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       37.91        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-A2K5 
       15.95        31.99        31.99        33.07        66.15        24.72 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M 
       34.95        25.51        14.96        11.21        18.41        20.25 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       14.43        10.26        21.14        19.79        35.15        34.36 
TCGA-AJ-A3BD TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 
       34.16        33.90         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-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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       35.11         0.13       129.80        23.31        86.07        48.03 
TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 
       63.91        36.89        23.87        12.62        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
      125.42       117.99       110.37        66.25        36.36        46.72 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       83.97        27.12        82.52        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        90.97        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        60.23        45.86        27.85 
TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       51.12        36.13         0.56        13.58        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       80.55        88.24        71.51        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       49.87        57.47        27.39        30.02        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       35.74        37.78        43.82        40.11        77.39        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       32.91        34.65        25.51        26.37        32.02        25.91 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       34.09        76.83        85.48        73.41        80.25        37.58 
TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
        4.77        71.24        40.80        81.37        34.32        46.49 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       38.24        17.75        30.74         2.96        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 
        0.23         0.20         0.56         0.20        20.52         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-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        86.37        55.30        59.24        86.01        58.75 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 
       69.27        71.44        48.59        36.49        72.62        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       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        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       85.78        52.04        32.09        77.23        73.28        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       225.50 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        51.45        14.70        48.43        11.87        52.54 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       31.36       136.60        96.30        93.50        71.84        39.35 
TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       27.65        41.06        34.13        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        35.21        71.24        63.68        74.63        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        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       14.01        15.45        15.45         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        22.39        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 
       35.08        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        24.33        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 
       92.88       114.90        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        89.59        63.58        86.99        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
       23.93         1.74        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-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-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-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-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG 
        1.05         3.95        48.79         8.48        15.88         4.27 
TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY 
       17.29         2.20       109.08       100.83        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        79.10 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       58.95         2.37        45.57        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-A3KU 
       50.73        35.15        38.07        27.16        46.42        22.26 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       38.47        51.09        14.99        54.15        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM 
       27.16        23.34        23.34        23.90        33.34        32.71 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       19.27        18.84        17.62        16.11        32.78        15.81 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       37.05        19.33        12.59        22.82        20.05        45.76 
TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CY 
       31.04        27.35        32.52        14.14        16.96        68.38 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EY 
       39.88        77.33         7.99        25.22        59.01        28.93 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ 
       30.67        59.28        78.38         1.74        17.75        14.04 
TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 
        9.47        18.21        23.24        21.30        38.70        22.59 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       17.16         6.97        22.65        39.95        24.95        23.64 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83         4.44        20.75        18.28         0.07         0.23 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              8.19               0.07 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            118.19             225.50 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            26.960             30.295 
[1] "8.2 - 118.2 (27.0)" "0.1 - 225.5 (30.3)"
[1] "hr=" "2.6"
D64V2, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    26  18
  12P LOSS WILD-TYPE 264 206
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     26   18
  12P LOSS WILD-TYPE  264  206
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                26                264
  YES               18                206
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  12P LOSS MUTATED                                        15
  12P LOSS WILD-TYPE                                     389
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  12P LOSS MUTATED                               1
  12P LOSS WILD-TYPE                            21
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  12P LOSS MUTATED                                  29
  12P LOSS WILD-TYPE                                84
D64V3, multiclass
                                         clus
vv                                        12P LOSS MUTATED 12P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               15                389
  MIXED SEROUS AND ENDOMETRIOID                          1                 21
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     29                 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"
                    vv
clus                  R0  R1  R2  RX
  12P LOSS MUTATED    28   3   4   5
  12P LOSS WILD-TYPE 343  19  12  35
D64V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               28                343
  R1                3                 19
  R2                4                 12
  RX                5                 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"

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    26  14
  12Q LOSS WILD-TYPE 421  76
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                40                497 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                14                 76 
$`12Q LOSS MUTATED`
TCGA-AJ-A3NH TCGA-BG-A0YV TCGA-EY-A212 TCGA-A5-A0R6 TCGA-A5-A1OH TCGA-A5-A2K2 
       10.19        12.56        10.19        37.91        36.33       118.19 
TCGA-A5-A2K4 TCGA-AJ-A3BF TCGA-AJ-A3NF TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A0LI 
       28.64        18.12        21.21        21.99        45.53        97.71 
TCGA-AP-A0LO TCGA-AP-A3K1 TCGA-B5-A0K3 TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BK-A139 
       33.40        21.90        27.29        29.65        34.95        31.00 
TCGA-BK-A4ZD TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A16S TCGA-D1-A2G7 TCGA-D1-A3DH 
       16.64        22.55        39.48        18.67        58.95        18.84 
TCGA-DF-A2KR TCGA-DF-A2L0 TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1GW 
       71.61        25.91        27.16        26.96        16.34        11.08 
TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A3PV 
       29.10        11.38        14.70        96.69         9.34        41.56 
TCGA-JU-AAVI TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-PG-A915 
       17.75        13.28        26.10         8.19 

$`12Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS 
       18.08        20.81       110.63        57.80        93.99        95.47 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF 
       67.66        12.26        36.39        23.05        61.18        27.88 
TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
        1.38        80.38        27.09        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 
       51.55        14.27         1.81        19.79         4.44        47.84 
TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A214 
       16.93        33.30         6.21        22.78        17.88        14.40 
TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 
       18.87        17.92        19.89         5.88        66.77        13.84 
TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 
       73.32        36.00        23.74         0.43        39.52        10.29 
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN 
      112.54       105.37       123.68        74.10        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        73.87        36.82        28.27        54.02        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-A1OG TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K5 
       15.95        31.99        31.99        33.07        66.15        24.72 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M 
       34.95        25.51        14.96        11.21        18.41        20.25 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       14.43        10.26        21.14        19.79        35.15        34.36 
TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
       34.16        18.90        33.90         1.64        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       22.26        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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 
       20.78         2.70        35.11         0.13       129.80        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       86.07        48.03        63.91        36.89        23.87        12.62 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP 
       36.36        46.72        83.97        27.12        82.52        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       80.78        49.22        25.08        71.67        90.97        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        60.23 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       45.86        27.85        51.12        36.13         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       45.99        79.46        49.87        57.47        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       60.66        61.08        35.74        37.78        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       77.39        13.28        32.91        34.65        25.51        26.37 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       32.02        25.91        34.09        76.83        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       80.25        37.58         4.77        30.12        71.24        40.80 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       81.37        34.32        46.49        38.24        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-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
       43.82         0.20        20.52         0.30         0.26         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS 
        1.18        18.35        14.47         0.39        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       55.30        59.24        86.01        58.75        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       48.59        36.49        72.62        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       27.85        13.45        59.84       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        73.64        61.68        85.78        52.04 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        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       225.50       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 
       51.45        14.70        48.43        11.87        52.54        31.36 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH 
      136.60        96.30        93.50        71.84        39.35        27.65 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       41.06        34.13        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        71.24        63.68        74.63        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       48.56        23.47        43.30        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       15.45        15.45         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        22.39        35.90        34.98        35.90        35.08 
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        24.33        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        92.88 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
      114.90        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        89.59        63.58        83.64        86.99        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
       23.93         1.74        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-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-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-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-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG 
        1.05         3.95        48.79         8.48        15.88         4.27 
TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY 
       17.29         2.20       109.08       100.83        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        79.10 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       58.95         2.37        45.57        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-A3B0 TCGA-EO-A3KU TCGA-EO-A3KX 
       50.73        35.15        38.07        46.42        22.26        38.47 
TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       51.09        14.99        54.15        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       23.34        23.34        23.90        33.34        32.71        19.27 
TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       18.84        17.62        22.03        16.11        32.78        15.81 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       37.05        19.33        12.59        22.82        20.05        45.76 
TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CY 
       31.04        27.35        32.52        14.14        16.96        68.38 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EY 
       39.88        77.33         7.99        25.22        59.01        28.93 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KP-A3W1 
       30.67        59.28        78.38         1.74        14.04         9.47 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 
       18.21        23.24        21.30        38.70        22.59        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        22.65        39.95        24.95        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44        20.75        18.28         0.07         0.23 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              8.19               0.07 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            118.19             225.50 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            26.005             30.440 
[1] "8.2 - 118.2 (26.0)" "0.1 - 225.5 (30.4)"
[1] "hr=" "2.8"
D65V2, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    21  18
  12Q LOSS WILD-TYPE 269 206
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     21   18
  12Q LOSS WILD-TYPE  269  206
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                21                269
  YES               18                206
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  12Q LOSS MUTATED                                        10
  12Q LOSS WILD-TYPE                                     394
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  12Q LOSS MUTATED                               2
  12Q LOSS WILD-TYPE                            20
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  12Q LOSS MUTATED                                  28
  12Q LOSS WILD-TYPE                                85
D65V3, multiclass
                                         clus
vv                                        12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               10                394
  MIXED SEROUS AND ENDOMETRIOID                          2                 20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     28                 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"
                    vv
clus                  R0  R1  R2  RX
  12Q LOSS MUTATED    29   2   2   4
  12Q LOSS WILD-TYPE 342  20  14  36
D65V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               29                342
  R1                2                 20
  R2                2                 14
  RX                4                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    67  25
  13Q LOSS WILD-TYPE 380  65
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                92                445 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                25                 65 
$`13Q LOSS MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A2QM TCGA-AJ-A3NH TCGA-AX-A06B TCGA-AX-A1CP TCGA-AX-A3G3 
       41.06        29.39        10.19        67.66        36.39         1.38 
TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0YV TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A547 
       27.09        22.06        12.56        16.93        33.30        17.92 
TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-5S-A9Q8 TCGA-A5-A0G2 TCGA-A5-A0GN TCGA-A5-A0R7 
       36.00        23.74        10.29       149.56        60.53        17.59 
TCGA-A5-A0VP TCGA-A5-A2K2 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WK TCGA-AJ-A2QK 
       42.35       118.19        25.51        14.96        18.41        21.14 
TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3TW TCGA-AJ-A6NU 
       18.90         1.64        22.26        17.06        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-A1C9 TCGA-AX-A1CF TCGA-AX-A1CK TCGA-AX-A2H4 TCGA-AX-A2HK TCGA-AX-A2IO 
       26.37        76.83        80.25        30.12         2.96        64.93 
TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0K3 
       43.82        20.52         0.30         0.26         0.39        27.29 
TCGA-B5-A11P TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A5OE TCGA-BG-A18C 
       52.04        11.87        31.36       136.60        34.95        15.45 
TCGA-BG-A2AE TCGA-BG-A3PP TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0U9 
       23.70        22.39        31.00        16.64        61.87        92.88 
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-DF-A2KR TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-EO-A1Y7 
        4.27        71.61        25.91        35.38         9.37        49.15 
TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EY-A1GC TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GV 
       34.39        27.16        54.15        18.84        17.62        15.81 
TCGA-EY-A1GW TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-FI-A2EX 
       11.08        20.05        45.76        29.10        32.52         9.34 
TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-KP-A3W0 
       28.93        30.67        41.56        78.38        14.04        13.28 
TCGA-KP-A3W1 TCGA-PG-A7D5 
        9.47        38.70 

$`13Q LOSS WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG TCGA-AJ-A3IA 
       88.18        60.53        30.15        16.83        18.08        20.81 
TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CR 
      110.63        57.80        93.99        95.47        12.26        23.05 
TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       61.18        27.88        80.38        66.41        61.87        51.55 
TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-EY-A1G7 
       14.27         1.81        19.79         4.44        47.84         6.21 
TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A549 
       22.78        17.88        10.19        14.40        18.87        19.89 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-4E-A92E TCGA-5B-A90C 
        5.88        66.77        13.84        73.32         0.43        39.52 
TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88        37.02        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GP TCGA-A5-A0GQ 
      105.37       123.68        74.10        65.75        46.55        73.87 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       36.82        28.27        54.02        23.21        68.65        37.91 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       19.59        24.62        29.06        15.95        31.99        31.99 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
       36.33        33.07        66.15        28.64        24.72        34.95 
TCGA-A5-A7WJ TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN 
       11.21        20.25        14.43        10.26        19.79        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
       34.36        34.16        18.12        33.90        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-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CV 
       14.76        16.87        22.32        12.82         2.70        35.11 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        0.13       129.80        21.99        23.31        86.07        48.03 
TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A0L8 TCGA-AP-A0L9 
       63.91        36.89        23.87        12.62        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL 
      117.99       110.37        66.25        36.36        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       27.12        82.52        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        90.97        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        60.23        45.86        27.85        51.12 
TCGA-AP-A3K1 TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       21.90        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        61.08        35.74        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        77.39        13.28        32.91        34.65 
TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       25.51        32.02        25.91        34.09        85.48        73.41 
TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
       37.58         4.77        71.24        40.80        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS 
       46.49        38.24        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-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       14.47        56.91        86.37        55.30        59.24        86.01 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       58.75        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       57.76        64.21        63.55        27.85        13.45        59.84 
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        73.64 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       61.68        85.78        32.09        77.23        73.28        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       225.50 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
      102.31        50.89        51.45        14.70        48.43        52.54 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 
       96.30        93.50        71.84        39.35        27.65        29.65 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       41.06        34.13        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        71.24        63.68        74.63        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       48.56        23.47        43.30        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 
       15.45         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        35.90        35.08        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        24.33        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       114.90        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        89.59        63.58        83.64        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        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-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-A16S 
       27.42        11.51        29.92        33.63        10.65        18.67 
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-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-D1-A3JQ 
       48.79         8.48        58.95        15.88        18.84        17.29 
TCGA-DF-A2KN TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        2.20       109.08       100.83        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-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
      110.10        23.38        79.10        58.95         2.37        45.57 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22R 
       16.04         7.36        16.80        10.92        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-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 
       19.40        50.73        35.15        38.07        46.42        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD 
       22.26        16.34        38.47        51.09        14.99        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        23.90        33.34 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GX 
       32.71        19.27        22.03        16.11        32.78        37.05 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A4KR 
       19.33        12.59        22.82        31.04        27.35        11.38 
TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
       14.14        14.70        16.96        68.38        39.88        77.33 
TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F9 TCGA-H5-A2HR 
        7.99        25.22        96.69        59.01        59.28         1.74 
TCGA-JU-AAVI TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 
       17.75        26.10        18.21        23.24        21.30        22.59 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        8.19        17.16         6.97        22.65        39.95        24.95 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       23.64        14.83         4.44        20.75        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.26               0.07 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            149.56             225.50 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             25.71              30.74 
[1] "0.3 - 149.6 (25.7)" "0.1 - 225.5 (30.7)"
[1] "hr=" "2.2"
D66V2, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    53  33
  13Q LOSS WILD-TYPE 237 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     53   33
  13Q LOSS WILD-TYPE  237  191
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                53                237
  YES               33                191
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  13Q LOSS MUTATED                                        48
  13Q LOSS WILD-TYPE                                     356
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  13Q LOSS MUTATED                               6
  13Q LOSS WILD-TYPE                            16
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  13Q LOSS MUTATED                                  39
  13Q LOSS WILD-TYPE                                74
D66V3, multiclass
                                         clus
vv                                        13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               48                356
  MIXED SEROUS AND ENDOMETRIOID                          6                 16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     39                 74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  13Q LOSS MUTATED    61   3   4   7
  13Q LOSS WILD-TYPE 310  19  12  33
D66V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0               61                310
  R1                3                 19
  R2                4                 12
  RX                7                 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"

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    44  18
  14Q LOSS WILD-TYPE 403  72
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                62                475 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                18                 72 
$`14Q LOSS MUTATED`
TCGA-AJ-A3NH TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-E6-A8L9 TCGA-EY-A214 
       10.19        80.38        27.09        22.06        33.30        14.40 
TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A2K4 TCGA-AJ-A23M 
       60.53        37.91        17.59        31.99        28.64        20.25 
TCGA-AJ-A3BD TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI 
       34.16        45.53        36.89        48.79       125.42        97.71 
TCGA-AP-A0LO TCGA-AX-A0IW TCGA-AX-A1CA TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 
       33.40        37.78        32.02        20.52         0.30         0.26 
TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A11P 
        0.30         0.39        27.29        27.85        75.72        52.04 
TCGA-B5-A1MY TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A18C TCGA-BK-A0CC TCGA-BK-A139 
       11.87        29.65        34.13        15.45        35.08        31.00 
TCGA-D1-A16I TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A3JQ TCGA-DF-A2KS 
       11.51        14.73        13.22         0.72        17.29       109.08 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3KU 
       35.38         9.37        12.39        51.42        34.39        22.26 
TCGA-EO-A3KW TCGA-EY-A1GO TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A2OO TCGA-EY-A2OQ 
       16.34        19.27        17.62        22.03        45.76        29.10 
TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
       14.70        68.38        59.28        78.38         1.74        17.75 
TCGA-PG-A915 TCGA-QS-A8F1 
        8.19         4.44 

$`14Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS 
       18.08        20.81       110.63        57.80        93.99        95.47 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF 
       67.66        12.26        36.39        23.05        61.18        27.88 
TCGA-AX-A3G3 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 
        1.38        66.41        61.87        51.55        12.56        14.27 
TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-EY-A1G7 
        1.81        19.79         4.44        47.84        16.93         6.21 
TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 
       22.78        17.88        10.19        18.87        17.92        19.89 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ 
        5.88        66.77        13.84        73.32        36.00        23.74 
TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
        0.43        39.52        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       123.68 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       74.10        65.75        46.55        73.87        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       54.02        23.21        68.65        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 
       42.35        15.95        31.99        36.33        33.07       118.19 
TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ 
       66.15        24.72        34.95        25.51        14.96        11.21 
TCGA-A5-A7WK TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       18.41        14.43        10.26        21.14        19.79        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
       34.36        18.12        18.90        33.90         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-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-A8CV TCGA-AJ-A8CW 
       22.32        12.82        20.78         2.70        35.11         0.13 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
      129.80        21.99        23.31        86.07        48.03        63.91 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       23.87        12.62        20.91       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP 
       36.36        46.72        83.97        27.12        82.52        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       80.78        49.22        25.08        71.67        90.97        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        60.23 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
       45.86        27.85        51.12        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        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        61.08        35.74        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       77.39        13.28        32.91        34.65        25.51        26.37 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       25.91        34.09        76.83        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA 
       37.58         4.77        30.12        71.24        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       34.32        46.49        38.24        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-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS 
        0.20         1.18        18.35        14.47        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       55.30        59.24        86.01        58.75        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       48.59        36.49        72.62        57.76        64.21        63.55 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J 
       13.45        59.84       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 
       73.64        61.68        85.78        32.09        77.23        73.28 
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 
      225.50       102.31        50.89        51.45        14.70        48.43 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       52.54        31.36       136.60        96.30        93.50        71.84 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       39.35        27.65        41.06        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        71.24        63.68        74.63 
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-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
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-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       14.73        14.01        15.45         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        22.39        35.90        34.98        35.90 
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        24.33        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 
       92.88       114.90        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        89.59        63.58        83.64        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        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-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-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-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-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        1.05         3.95        48.79         8.48        58.95        15.88 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KU TCGA-DF-A2KV 
        4.27        18.84         2.20        71.61       100.83        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       10.92        27.16        25.91        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
       24.30        31.10       110.10        23.38        79.10        58.95 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37        45.57        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-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       57.60        51.52        19.40        50.73        35.15        38.07 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 
       27.16        46.42        26.96        38.47        51.09        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       54.15        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU 
       23.90        33.34        32.71        18.84        16.11        32.78 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM 
       15.81        11.08        37.05        19.33        12.59        22.82 
TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 
       20.05        31.04        27.35        32.52        11.38        14.14 
TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU 
       16.96        39.88        77.33         7.99        25.22        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-K6-A3WQ 
       59.01         9.34        28.93        30.67        41.56        14.04 
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        21.30 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       38.70        22.59        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       24.95        23.64        14.83        20.75        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.26               0.07 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            125.42             225.50 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             27.57              30.12 
[1] "0.3 - 125.4 (27.6)" "0.1 - 225.5 (30.1)"
[1] "hr=" "2.2"
D67V2, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    30  26
  14Q LOSS WILD-TYPE 260 198
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     30   26
  14Q LOSS WILD-TYPE  260  198
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                30                260
  YES               26                198
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  14Q LOSS MUTATED                                        20
  14Q LOSS WILD-TYPE                                     384
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  14Q LOSS MUTATED                               3
  14Q LOSS WILD-TYPE                            19
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  14Q LOSS MUTATED                                  39
  14Q LOSS WILD-TYPE                                74
D67V3, multiclass
                                         clus
vv                                        14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               20                384
  MIXED SEROUS AND ENDOMETRIOID                          3                 19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     39                 74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  14Q LOSS MUTATED    36   2   3   4
  14Q LOSS WILD-TYPE 335  20  13  36
D67V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0               36                335
  R1                2                 20
  R2                3                 13
  RX                4                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    81  28
  15Q LOSS WILD-TYPE 366  62
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               109                428 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                28                 62 
$`15Q LOSS MUTATED`
TCGA-AJ-A2QM TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AX-A06B TCGA-AX-A1CR TCGA-AX-A2H8 
       29.39        10.19       110.63        67.66        23.05        61.18 
TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A547 
        1.38        80.38        27.09        10.19        14.40        17.92 
TCGA-KP-A3VZ TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A1OG 
       23.74        65.75        60.53        37.91        17.59        31.99 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WK 
      118.19        66.15        28.64        25.51        14.96        18.41 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3EJ 
       20.25        14.43        21.14        34.16        18.90         1.64 
TCGA-AJ-A3EM TCGA-AJ-A3NF TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A052 
       22.26        21.21        16.87        16.87        20.78        21.99 
TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A0IW 
       45.53        48.79       125.42        21.90        36.13        37.78 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2HK 
       26.37        32.02        25.91         4.77        30.12         2.96 
TCGA-AX-A3FS TCGA-AX-A3FZ TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0K3 
        0.23         0.20         0.26         0.30         0.39        27.29 
TCGA-B5-A0K8 TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3S1 
       27.85        52.04       102.31        31.36       136.60        29.65 
TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-BS-A0V8 
       15.45        22.39        24.13        16.64        92.88        83.64 
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-D1-A3JQ TCGA-DF-A2KS TCGA-DI-A2QY 
       14.73        13.22        18.84        17.29       109.08       110.10 
TCGA-E6-A1LZ TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AZ 
       79.10        37.71        51.42        19.40        34.39        27.16 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A210 
       26.96        22.26        54.15        19.27        18.84        12.59 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-FI-A2D2 
       20.05        45.76        29.10        27.35        11.38        77.33 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-K6-A3WQ 
       96.69        59.01        30.67        59.28        78.38        14.04 
TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A8F1 
       13.28        26.10        38.70        22.59         8.19         4.44 
TCGA-SJ-A6ZI 
       20.75 

$`15Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AJ-A3IA TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CP 
       20.81        57.80        93.99        95.47        12.26        36.39 
TCGA-AX-A2HF TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV 
       27.88        22.06        66.41        61.87        51.55        12.56 
TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP 
       14.27         1.81        19.79         4.44        47.84        16.93 
TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A215 TCGA-EY-A549 
       33.30         6.21        22.78        17.88        18.87        19.89 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E 
        5.88        66.77        13.84        73.32        36.00         0.43 
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       39.52        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       123.68        74.10 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        73.87        36.82        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       68.65        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A7WJ 
       31.99        36.33        33.07        24.72        34.95        11.21 
TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BK 
       10.26        19.79        35.15        34.36        18.12        33.90 
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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       35.11         0.13       129.80        23.31        86.07        48.03 
TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD 
       63.91        36.89        23.87        12.62        20.91       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        90.97        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        60.23        45.86        27.85 
TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       51.12         0.56        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       57.47        27.39        30.02        60.66        61.08        35.74 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        77.39        13.28        32.91        34.65 
TCGA-AX-A1C8 TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       25.51        34.09        76.83        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       37.58        71.24        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-A3FT 
       38.24        17.75        30.74        31.13        64.93         0.20 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.56        43.82        20.52         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       14.47        56.91        86.37        55.30        59.24        86.01 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       58.75        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       57.76        64.21        63.55        13.45        59.84       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        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       85.78        32.09        77.23        73.28        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       225.50        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3FA 
       51.45        14.70        48.43        11.87        52.54        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD 
       93.50        71.84        39.35        27.65        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-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       71.24        63.68        74.63        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        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        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-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        35.90        35.08        31.00        31.76        24.99 
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        24.33        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       114.90        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        89.59        63.58        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       66.48        16.83        29.95         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       23.93         1.74        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-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y 
       29.92        33.63        10.65         0.69         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       19.53         6.64        30.15        18.02         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-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
       22.92         1.41         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        48.79         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KU 
       58.95        15.88         4.27         2.20        71.61       100.83 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU 
       89.33        10.92        27.16        25.91        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-EC-A1NJ TCGA-EC-A1QX 
       23.38        58.95         2.37        45.57        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-A22X TCGA-EO-A22Y TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       46.26        57.60        51.52        50.73        35.15        38.07 
TCGA-EO-A3B0 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD 
       46.42        16.34        38.47        51.09        14.99        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        23.90        33.34 
TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       32.71        17.62        22.03        16.11        32.78        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A3QX 
       11.08        37.05        19.33        22.82        31.04        32.52 
TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
       14.14        14.70        16.96        68.38        39.88         7.99 
TCGA-FI-A2D6 TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI 
       25.22         9.34        28.93        41.56         1.74        17.75 
TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 
        9.47        18.21        23.24        21.30        17.16         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZJ 
       22.65        39.95        24.95        23.64        14.83        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.20               0.07 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             136.6              225.5 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            24.130             31.875 
[1] "0.2 - 136.6 (24.1)" "0.1 - 225.5 (31.9)"
[1] "hr=" "2"  
D68V2, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    57  45
  15Q LOSS WILD-TYPE 233 179
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     57   45
  15Q LOSS WILD-TYPE  233  179
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                57                233
  YES               45                179
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  15Q LOSS MUTATED                                        37
  15Q LOSS WILD-TYPE                                     367
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  15Q LOSS MUTATED                               9
  15Q LOSS WILD-TYPE                            13
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  15Q LOSS MUTATED                                  63
  15Q LOSS WILD-TYPE                                50
D68V3, multiclass
                                         clus
vv                                        15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               37                367
  MIXED SEROUS AND ENDOMETRIOID                          9                 13
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     63                 50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  15Q LOSS MUTATED    71   4   5  10
  15Q LOSS WILD-TYPE 300  18  11  30
D68V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0               71                300
  R1                4                 18
  R2                5                 11
  RX               10                 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"

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    68  30
  16P LOSS WILD-TYPE 379  60
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                98                439 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                30                 60 
$`16P LOSS MUTATED`
TCGA-AJ-A2QM TCGA-AJ-A3NH TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A1CR TCGA-AX-A3G3 
       29.39        10.19        93.99        67.66        23.05         1.38 
TCGA-B5-A0KB TCGA-BG-A0VT TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       27.09        51.55        16.93        33.30        36.00        23.74 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K4 TCGA-A5-A3LO 
       65.75        60.53        31.99        36.33        28.64        25.51 
TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AJ-A3EM TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A052 
       20.25        34.16        22.26        16.87        20.78        21.99 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 
       45.53        36.89        48.79        97.71        46.78        21.90 
TCGA-AX-A0IU TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A2H4 TCGA-AX-A2H5 
       35.74        26.37        25.91        76.83        30.12        71.24 
TCGA-AX-A2IO TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3GI 
       64.93        43.82         0.20         0.30         0.26         0.39 
TCGA-B5-A0JT TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MY 
       55.30        27.85        75.72        52.04       102.31        11.87 
TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BG-A0MU TCGA-BG-A18C TCGA-BG-A3PP 
       39.35        29.65        34.95        20.28        15.45        22.39 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A16G 
       35.08        31.00        16.64        83.64        22.55        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A17R 
       11.51        29.92        31.07        14.73        28.08        11.15 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2L0 
       13.22         0.72         2.07         4.27        18.84        25.91 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QY TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A2CG 
       35.38         9.37       110.10        10.92        37.71        51.42 
TCGA-EO-A2CH TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1GC TCGA-EY-A1GM TCGA-EY-A1GR 
       19.40        27.16        26.96        54.15        32.71        17.62 
TCGA-EY-A210 TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-FI-A2EU 
       12.59        29.10        27.35        32.52        11.38        96.69 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-JU-AAVI TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
       41.56        78.38        17.75        26.10        18.21        23.24 
TCGA-PG-A7D5 TCGA-QS-A8F1 
       38.70         4.44 

$`16P LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AJ-A3IA TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CP 
       20.81       110.63        57.80        95.47        12.26        36.39 
TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       61.18        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 
       12.56        14.27         1.81        19.79         4.44        47.84 
TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 
        6.21        22.78        17.88        10.19        14.40        18.87 
TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 
       17.92        19.89         5.88        66.77        13.84        73.32 
TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
        0.43        39.52        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       123.68 
TCGA-A5-A0GH TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        46.55        73.87        36.82        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A2K2 
       29.06        42.35        15.95        31.99        33.07       118.19 
TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK 
       66.15        24.72        34.95        14.96        11.21        18.41 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       14.43        10.26        21.14        19.79        35.15        34.36 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
       18.12        18.90        33.90         1.64        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-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT 
       15.95        14.76        16.87        22.32        12.82         2.70 
TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       35.11         0.13       129.80        23.31        86.07        48.03 
TCGA-AP-A05A TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD 
       63.91        23.87        12.62        20.91       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
      110.37        66.25        36.36        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR 
       71.67        90.97        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-A5FX 
        6.71        60.23        45.86        27.85        51.12        36.13 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IW TCGA-AX-A0IZ 
       27.39        30.02        60.66        61.08        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        77.39        13.28        32.91        34.65        25.51 
TCGA-AX-A1CA TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       32.02        34.09        85.48        73.41        80.25        37.58 
TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG 
        4.77        40.80        81.37        34.32        46.49        38.24 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT 
       17.75        30.74         2.96        31.13         0.23         0.20 
TCGA-AX-A3FW TCGA-AX-A3G1 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.56        20.52         0.30         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        86.37        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       64.21        63.55        13.45        59.84       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        73.64        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       77.23        73.28        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       225.50        50.89        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       48.43        52.54        31.36       136.60        96.30        93.50 
TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX 
       71.84        27.65        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        71.24        63.68        74.63 
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-A0MT TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       59.74        21.17        15.42        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.01        15.45         9.57        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C 
       11.31        35.90        34.98        35.90        31.76        24.99 
TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       24.13        13.18        10.03         9.86        46.95        24.33 
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        92.88       114.90        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        89.59 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        86.99        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 
        0.56         4.87        28.67        23.93         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-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-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       37.51        36.79        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-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-A17S 
       28.01        26.37        10.22         1.51         1.78        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-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 
       15.06         1.05         3.95        48.79         8.48        58.95 
TCGA-D1-A3DA TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU 
       15.88        17.29         2.20        71.61       109.08       100.83 
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-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
       24.30        12.39        31.10        23.38        79.10        58.95 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 
        2.37        45.57        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-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KU 
       34.39        50.73        35.15        38.07        46.42        22.26 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       16.34        38.47        51.09        14.99        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GO 
       27.16        23.34        23.34        23.90        33.34        19.27 
TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       18.84        22.03        16.11        32.78        15.81        11.08 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       37.05        19.33        22.82        20.05        45.76        31.04 
TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
       14.14        14.70        16.96        68.38        39.88        77.33 
TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 
        7.99        25.22        59.01         9.34        28.93        30.67 
TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-PG-A6IB 
       59.28         1.74        14.04        13.28         9.47        21.30 
TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       22.59         8.19        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       24.95        23.64        14.83        20.75        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.20               0.07 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             110.1              225.5 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            27.635             30.670 
[1] "0.2 - 110.1 (27.6)" "0.1 - 225.5 (30.7)"
[1] "hr=" "2.6"
D69V2, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    53  38
  16P LOSS WILD-TYPE 237 186
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     53   38
  16P LOSS WILD-TYPE  237  186
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                53                237
  YES               38                186
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  16P LOSS MUTATED                                        35
  16P LOSS WILD-TYPE                                     369
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  16P LOSS MUTATED                               6
  16P LOSS WILD-TYPE                            16
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  16P LOSS MUTATED                                  58
  16P LOSS WILD-TYPE                                55
D69V3, multiclass
                                         clus
vv                                        16P LOSS MUTATED 16P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               35                369
  MIXED SEROUS AND ENDOMETRIOID                          6                 16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     58                 55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  16P LOSS MUTATED    58   5   6  10
  16P LOSS WILD-TYPE 313  17  10  30
D69V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0               58                313
  R1                5                 17
  R2                6                 10
  RX               10                 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"

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED   105  34
  16Q LOSS WILD-TYPE 342  56
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               139                398 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                34                 56 
$`16Q LOSS MUTATED`
TCGA-AJ-A2QM TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A1CP 
       29.39        10.19        57.80        93.99        67.66        36.39 
TCGA-AX-A1CR TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0KB TCGA-BG-A0M8 TCGA-BG-A0VT 
       23.05        27.88         1.38        27.09        66.41        51.55 
TCGA-BG-A0YV TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A214 TCGA-EY-A547 TCGA-KJ-A3U4 
       12.56        16.93        33.30        14.40        17.92        36.00 
TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0GG TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R7 
       23.74        39.52       123.68        65.75        60.53        17.59 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M 
       31.99        36.33       118.19        28.64        25.51        20.25 
TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3EM TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A052 
       14.43        34.16        22.26        16.87        20.78        21.99 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 
       45.53        36.89        48.79        97.71        46.78        21.90 
TCGA-AX-A05U TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C9 TCGA-AX-A1CA 
       29.69        35.74        37.78        34.65        26.37        32.02 
TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CN TCGA-AX-A2H4 TCGA-AX-A2H5 
       25.91        76.83        85.48        37.58        30.12        71.24 
TCGA-AX-A2HD TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       46.49         2.96        64.93         0.56        43.82         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0JT TCGA-B5-A0K6 
       20.52         0.30         0.26         0.39        55.30        64.21 
TCGA-B5-A0K8 TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MY 
       27.85       113.36        75.72        52.04       102.31        11.87 
TCGA-B5-A1N2 TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BG-A0MU TCGA-BG-A0VW 
       31.36        39.35        29.65        34.95        20.28        52.01 
TCGA-BG-A186 TCGA-BG-A18C TCGA-BG-A2AE TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A4ZD 
       13.78        15.45        23.70        22.39        35.08        16.64 
TCGA-BS-A0TI TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       61.87        83.64        22.55        27.42        11.51        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-A3JQ TCGA-DF-A2L0 
       18.25         2.07         4.27        18.84        17.29        25.91 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y5 
       35.38         9.37        31.10       110.10        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3B1 
       37.71        51.42        19.40        34.39        27.16        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A210 
       22.26        16.34        54.15        32.71        17.62        12.59 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-FI-A2CY TCGA-FI-A2EU 
       29.10        27.35        32.52        11.38        68.38        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A3PV TCGA-FI-A3PX TCGA-KP-A3W3 
       59.01         9.34        28.93        41.56        78.38        26.10 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A915 TCGA-QS-A8F1 TCGA-SL-A6J9 
       18.21        23.24        38.70         8.19         4.44         0.07 
TCGA-SL-A6JA 
        0.23 

$`16Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AJ-A3IA TCGA-AP-A053 TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A2H8 TCGA-B5-A0JN 
       20.81       110.63        95.47        12.26        61.18        80.38 
TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 
       22.06        61.87        14.27         1.81        19.79         4.44 
TCGA-D1-A2G5 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A215 
       47.84         6.21        22.78        17.88        10.19        18.87 
TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-4E-A92E 
       19.89         5.88        66.77        13.84        73.32         0.43 
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-A0GP TCGA-A5-A0GQ 
       32.78       112.54       105.37        74.10        46.55        73.87 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       36.82        28.27        54.02        23.21        68.65        37.91 
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        31.99 
TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-A5-A7WJ 
       33.07        66.15        24.72        34.95        14.96        11.21 
TCGA-A5-A7WK TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       18.41        10.26        21.14        19.79        35.15        34.36 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
       18.12        18.90        33.90         1.64        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-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT 
       15.95        14.76        16.87        22.32        12.82         2.70 
TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       35.11         0.13       129.80        23.31        86.07        48.03 
TCGA-AP-A05A TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD 
       63.91        23.87        12.62        20.91       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
      110.37        66.25        36.36        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR 
       71.67        90.97        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-A5FX 
        6.71        60.23        45.86        27.85        51.12        36.13 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
        0.56        13.58        33.21        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       30.02        60.66        61.08        43.82        40.11        77.39 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1CE TCGA-AX-A1CJ TCGA-AX-A1CK 
       13.28        32.91        25.51        34.09        73.41        80.25 
TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HG TCGA-AX-A2HH 
        4.77        40.80        81.37        34.32        38.24        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-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV 
       18.35        14.47        56.91        86.37        59.24        86.01 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       58.75        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       27.29        57.76        63.55        13.45        59.84       185.79 
TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       88.34        54.44        73.64        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       77.23        73.28        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       225.50        50.89        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       48.43        52.54       136.60        96.30        93.50        71.84 
TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       27.65        41.06        34.13        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        35.21        71.24        63.68        74.63        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        59.74 
TCGA-BG-A0MT TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       21.17        15.42        51.06        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 
       56.58        14.83        14.73        14.01        15.45         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        35.90 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 
       31.00        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        24.33        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        92.88 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
      114.90        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        89.59        63.58        86.99        66.48        16.83 
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-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-A16O TCGA-D1-A16Q 
       37.32        36.36        37.51        36.79        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-A17L TCGA-D1-A17M TCGA-D1-A17N 
       30.44         1.28        28.01        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NY 
        1.78        24.30         2.33        22.92         1.41        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        48.79         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU 
       58.95        15.88         2.20        71.61       109.08       100.83 
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-A2QT TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       24.30        12.39        23.38        58.95         2.37        45.57 
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        50.73        35.15 
TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD 
       38.07        46.42        38.47        51.09        14.99        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        23.90        33.34 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       19.27        18.84        22.03        16.11        32.78        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       11.08        37.05        19.33        22.82        20.05        45.76 
TCGA-EY-A2OP TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D2 
       31.04        14.14        14.70        16.96        39.88        77.33 
TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-JU-AAVI 
        7.99        25.22        30.67        59.28         1.74        17.75 
TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 
       14.04        13.28         9.47        21.30        22.59        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        22.65        39.95        24.95        23.64        14.83 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       20.75        18.28 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.07               0.13 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            123.68             225.50 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            28.640             30.555 
[1] "0.1 - 123.7 (28.6)" "0.1 - 225.5 (30.6)"
[1] "hr=" "1.9"
D70V2, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    76  53
  16Q LOSS WILD-TYPE 214 171
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     76   53
  16Q LOSS WILD-TYPE  214  171
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                76                214
  YES               53                171
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  16Q LOSS MUTATED                                        57
  16Q LOSS WILD-TYPE                                     347
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  16Q LOSS MUTATED                               7
  16Q LOSS WILD-TYPE                            15
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  16Q LOSS MUTATED                                  76
  16Q LOSS WILD-TYPE                                37
D70V3, multiclass
                                         clus
vv                                        16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               57                347
  MIXED SEROUS AND ENDOMETRIOID                          7                 15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     76                 37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  16Q LOSS MUTATED    83   8   7  13
  16Q LOSS WILD-TYPE 288  14   9  27
D70V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0               83                288
  R1                8                 14
  R2                7                  9
  RX               13                 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"

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    91  37
  17P LOSS WILD-TYPE 356  53
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               128                409 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                37                 53 
$`17P LOSS MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AX-A06B TCGA-AX-A1CR 
       41.06        10.19       110.63        57.80        67.66        23.05 
TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 
       61.18        27.88         1.38        27.09        22.06        66.41 
TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A212 TCGA-EY-A547 TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       16.93        33.30        10.19        17.92        36.00        23.74 
TCGA-5B-A90C TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A1OG 
       39.52        65.75        60.53        36.82        37.91        31.99 
TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A7WK TCGA-AJ-A23M 
       36.33       118.19        28.64        25.51        18.41        20.25 
TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EM 
       14.43        21.14        34.16        18.12        18.90        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3NF TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A05A TCGA-AP-A05H 
       17.06        21.21        16.87        16.87        63.91        45.53 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A5FX 
       48.79       125.42        36.36        97.71        46.78        36.13 
TCGA-AW-A1PO TCGA-AX-A0IU TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CF TCGA-AX-A2H2 
        0.56        35.74        34.65        25.51        76.83         4.77 
TCGA-AX-A2H5 TCGA-AX-A2HH TCGA-AX-A2IO TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       71.24        17.75        64.93         0.56        43.82         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-B5-A0K8 TCGA-B5-A11I 
       20.52         0.30         0.26         0.30        27.85        75.72 
TCGA-B5-A11N TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD 
       61.68       102.31        11.87        31.36       136.60        39.35 
TCGA-B5-A3S1 TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A139 TCGA-BK-A26L TCGA-BS-A0U9 
       29.65        15.45        22.39        31.00        24.13        92.88 
TCGA-BS-A0V8 TCGA-D1-A0ZP TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16I 
       83.64        29.95        22.55        39.48        37.32        11.51 
TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A3DH 
       31.07        18.67        13.22         0.72        18.25        18.84 
TCGA-D1-A3JQ TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-DI-A1NO 
       17.29        71.61       109.08        25.91        35.38         9.37 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       12.39        31.10        79.10        10.92        49.15        37.71 
TCGA-EO-A2CH TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GM 
       19.40        22.26        16.34        54.15        23.90        32.71 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A2OQ TCGA-EY-A4KR 
       17.62        22.03        11.08        12.59        29.10        11.38 
TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV 
       14.70        68.38        77.33        28.93        30.67        41.56 
TCGA-FI-A3PX TCGA-JU-AAVI TCGA-KP-A3W0 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A914 
       78.38        17.75        13.28        23.24        38.70        22.59 
TCGA-PG-A915 TCGA-QS-A8F1 
        8.19         4.44 

$`17P LOSS WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AJ-A3IA TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CP TCGA-B5-A0JN 
       20.81        93.99        95.47        12.26        36.39        80.38 
TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       61.87        51.55        12.56        14.27         1.81        19.79 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A214 
        4.44        47.84         6.21        22.78        17.88        14.40 
TCGA-EY-A215 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 
       18.87        19.89         5.88        66.77        13.84        73.32 
TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
        0.43        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       123.68        74.10 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        73.87        28.27        54.02        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-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP 
       31.99        33.07        66.15        24.72        34.95        14.96 
TCGA-A5-A7WJ TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BK 
       11.21        10.26        19.79        35.15        34.36        33.90 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG 
        1.64        14.66        22.49        36.99        20.65        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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
        2.70        35.11         0.13       129.80        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       86.07        48.03        36.89        23.87        12.62        20.91 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
      117.99       110.37        66.25        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR 
       71.67        90.97        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        60.23        45.86        27.85        51.12        21.90 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        61.08        37.78        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       77.39        13.28        32.91        26.37        32.02        25.91 
TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H4 
       34.09        85.48        73.41        80.25        37.58        30.12 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HJ 
       40.80        81.37        34.32        46.49        38.24        30.74 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3G8 TCGA-AX-A3G9 
        2.96        31.13         0.23         0.20         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        86.37        55.30        59.24 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.01        58.75        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       72.62        27.29        57.76        64.21        63.55        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
       59.84       185.79       113.36        88.34        54.44        73.64 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       85.78        52.04        32.09        77.23        73.28        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       225.50 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3FA 
       50.89        51.45        14.70        48.43        52.54        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       93.50        71.84        27.65        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        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       63.68        74.63        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        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        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-A222 
       14.83        13.78        14.73        14.01        15.45         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 
       35.90        35.08        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        24.33        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       114.90        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        89.59        63.58        86.99        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       16.83         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        1.74        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-A16J TCGA-D1-A16O TCGA-D1-A16Q 
       37.51        36.79        27.42        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-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
        1.41        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        48.79         8.48        58.95        15.88         4.27 
TCGA-DF-A2KN TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        2.20       100.83        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-A1M0 
       39.29        36.62        24.30       110.10        23.38        58.95 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R 
        2.37        45.57        16.04         7.36        16.80        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-A3AZ TCGA-EO-A3B0 
       34.39        50.73        35.15        38.07        27.16        46.42 
TCGA-EO-A3B1 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       26.96        38.47        51.09        14.99        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP 
       27.16        23.34        23.34        33.34        19.27        18.84 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM 
       16.11        32.78        15.81        37.05        19.33        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 
       20.05        45.76        31.04        27.35        32.52        14.14 
TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       16.96        39.88         7.99        25.22        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-KP-A3W3 
        9.34        59.28         1.74        14.04         9.47        26.10 
TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       18.21        21.30        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       24.95        23.64        14.83        20.75        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.20               0.07 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             136.6              225.5 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            27.865             30.150 
[1] "0.2 - 136.6 (27.9)" "0.1 - 225.5 (30.1)"
[1] "hr=" "2.4"
D71V2, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    58  60
  17P LOSS WILD-TYPE 232 164
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     58   60
  17P LOSS WILD-TYPE  232  164
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                58                232
  YES               60                164
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  17P LOSS MUTATED                                        47
  17P LOSS WILD-TYPE                                     357
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  17P LOSS MUTATED                              10
  17P LOSS WILD-TYPE                            12
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  17P LOSS MUTATED                                  72
  17P LOSS WILD-TYPE                                41
D71V3, multiclass
                                         clus
vv                                        17P LOSS MUTATED 17P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               47                357
  MIXED SEROUS AND ENDOMETRIOID                         10                 12
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     72                 41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  17P LOSS MUTATED    80   8   6  13
  17P LOSS WILD-TYPE 291  14  10  27
D71V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0               80                291
  R1                8                 14
  R2                6                 10
  RX               13                 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"

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    65  27
  17Q LOSS WILD-TYPE 382  63
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                92                445 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                27                 63 
$`17Q LOSS MUTATED`
TCGA-AJ-A2QM TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AX-A1CR TCGA-AX-A2H8 
       29.39        10.19       110.63        57.80        23.05        61.18 
TCGA-BG-A0M8 TCGA-E6-A8L9 TCGA-EY-A212 TCGA-EY-A547 TCGA-KJ-A3U4 TCGA-5B-A90C 
       66.41        33.30        10.19        17.92        36.00        39.52 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 
       65.75        60.53        37.91        31.99        36.33       118.19 
TCGA-A5-A3LO TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A3BD 
       25.51        18.41        20.25        14.43        21.14        34.16 
TCGA-AJ-A3BI TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NF TCGA-AJ-A3TW TCGA-AP-A05A 
       18.90        22.26        17.06        21.21        16.87        63.91 
TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A5FX 
       45.53        48.79       125.42        97.71        46.78        36.13 
TCGA-AW-A1PO TCGA-AX-A2H5 TCGA-AX-A2HH TCGA-AX-A2IO TCGA-AX-A3FX TCGA-AX-A3FZ 
        0.56        71.24        17.75        64.93        43.82         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-B5-A11N TCGA-B5-A1MS 
       20.52         0.30         0.26         0.30        61.68       102.31 
TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-BG-A18C TCGA-BK-A139 TCGA-BK-A26L 
      136.60        39.35        29.65        15.45        31.00        24.13 
TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16N 
       92.88        83.64        22.55        37.32        11.51        31.07 
TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A3DH TCGA-DF-A2KR 
       14.73        13.22         0.72        18.25        18.84        71.61 
TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LZ 
      109.08        25.91         9.37        12.39        31.10        79.10 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC 
       10.92        49.15        37.71        22.26        16.34        54.15 
TCGA-EY-A1GJ TCGA-EY-A1GR TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A2OQ TCGA-FI-A2CY 
       23.90        17.62        11.08        12.59        29.10        68.38 
TCGA-FI-A2D2 TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-JU-AAVI TCGA-KP-A3W0 TCGA-PG-A7D5 
       77.33        28.93        30.67        17.75        13.28        38.70 
TCGA-PG-A914 TCGA-QS-A8F1 
       22.59         4.44 

$`17Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AJ-A3IA TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP 
       20.81        93.99        95.47        67.66        12.26        36.39 
TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0MS 
       27.88         1.38        80.38        27.09        22.06        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 
       51.55        12.56        14.27         1.81        19.79         4.44 
TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A214 
       47.84        16.93         6.21        22.78        17.88        14.40 
TCGA-EY-A215 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 
       18.87        19.89         5.88        66.77        13.84        73.32 
TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       23.74         0.43        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       123.68 
TCGA-A5-A0GH TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        46.55        73.87        36.82        28.27        54.02 
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-A2K3 TCGA-A5-A2K4 
       42.35        15.95        31.99        33.07        66.15        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-AJ-A23O TCGA-AJ-A2QL 
       24.72        34.95        14.96        11.21        10.26        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
       35.15        34.36        18.12        33.90         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       22.49        36.99        20.65        15.62        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS 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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 
       35.11         0.13       129.80        21.99        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD 
       48.03        36.89        23.87        12.62        20.91       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
      110.37        66.25        36.36        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR 
       71.67        90.97        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        60.23        45.86        27.85        51.12        21.90 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        61.08        35.74        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        77.39        13.28        32.91        34.65        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       26.37        32.02        25.91        34.09        76.83        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H7 
       73.41        80.25        37.58         4.77        30.12        40.80 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK 
       81.37        34.32        46.49        38.24        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3G8 TCGA-AX-A3G9 
       31.13         0.23         0.20         0.56         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        86.37        55.30        59.24 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.01        58.75        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       13.45        59.84       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        73.64        85.78        52.04        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       73.28        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       225.50        50.89        51.45        14.70        48.43 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       11.87        52.54        31.36        96.30        93.50        71.84 
TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       27.65        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        71.24        63.68        74.63 
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-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
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-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       14.73        14.01        15.45         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        22.39        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
       35.08        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        24.33        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 
      114.90        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        89.59        63.58        86.99        66.48        16.83 
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-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-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16O 
       36.36        37.51        36.79        27.42        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-A17A TCGA-D1-A17B 
       19.53         6.64        30.15        18.02         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-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
       22.92         1.41        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        1.05         3.95        48.79         8.48        58.95        15.88 
TCGA-D1-A3DG TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY 
        4.27        17.29         2.20       100.83        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-A2QY TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
      110.10        23.38        58.95         2.37        45.57        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-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       57.60        51.52        51.42        19.40        34.39        50.73 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KX 
       35.15        38.07        27.16        46.42        26.96        38.47 
TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       51.09        14.99        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GS 
       23.34        33.34        32.71        19.27        18.84        22.03 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM 
       16.11        32.78        15.81        37.05        19.33        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        32.52        11.38 
TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 
       14.14        14.70        16.96        39.88         7.99        25.22 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
       96.69        59.01         9.34        59.28        41.56        78.38 
TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
        1.74        14.04         9.47        26.10        18.21        23.24 
TCGA-PG-A6IB TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       21.30         8.19        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       24.95        23.64        14.83        20.75        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.20               0.07 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             136.6              225.5 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            29.245             30.020 
[1] "0.2 - 136.6 (29.2)" "0.1 - 225.5 (30.0)"
[1] "hr=" "2"  
D72V2, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    43  43
  17Q LOSS WILD-TYPE 247 181
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     43   43
  17Q LOSS WILD-TYPE  247  181
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                43                247
  YES               43                181
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  17Q LOSS MUTATED                                        39
  17Q LOSS WILD-TYPE                                     365
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  17Q LOSS MUTATED                               8
  17Q LOSS WILD-TYPE                            14
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  17Q LOSS MUTATED                                  46
  17Q LOSS WILD-TYPE                                67
D72V3, multiclass
                                         clus
vv                                        17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               39                365
  MIXED SEROUS AND ENDOMETRIOID                          8                 14
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     46                 67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS MUTATED    59   6   3  10
  17Q LOSS WILD-TYPE 312  16  13  30
D72V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0               59                312
  R1                6                 16
  R2                3                 13
  RX               10                 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"

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    38  12
  18P LOSS WILD-TYPE 409  78
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                50                487 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                12                 78 
$`18P LOSS MUTATED`
TCGA-AJ-A2QM TCGA-AX-A1CR TCGA-AX-A3G3 TCGA-EY-A214 TCGA-KP-A3VZ TCGA-A5-A0GJ 
       29.39        23.05         1.38        14.40        23.74        65.75 
TCGA-A5-A0GN TCGA-A5-A0R7 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP 
       60.53        17.59        66.15        28.64        25.51        14.96 
TCGA-AJ-A23M TCGA-AJ-A3BF TCGA-AP-A05H TCGA-AP-A0LH TCGA-AX-A2H2 TCGA-AX-A2H5 
       20.25        18.12        45.53        36.36         4.77        71.24 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-B5-A11P TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-BG-A18C 
        0.20        20.52        52.04       136.60        39.35        15.45 
TCGA-BG-A3PP TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0V8 TCGA-D1-A0ZZ 
       22.39        31.00        16.64        61.87        83.64        22.55 
TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A17K TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-DF-A2KS 
       11.51        18.67        28.08         0.72         2.07       109.08 
TCGA-DF-A2L0 TCGA-DI-A2QU TCGA-EO-A2CG TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GO 
       25.91        31.10        51.42        16.34        54.15        19.27 
TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A2OO TCGA-FI-A2EW TCGA-FI-A2EX 
       18.84        22.03        11.08        45.76        59.01         9.34 
TCGA-KP-A3W0 TCGA-SL-A6J9 
       13.28         0.07 

$`18P LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS 
       20.81        10.19       110.63        57.80        93.99        95.47 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-B5-A0JN 
       67.66        12.26        36.39        61.18        27.88        80.38 
TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV 
       27.09        22.06        66.41        61.87        51.55        12.56 
TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP 
       14.27         1.81        19.79         4.44        47.84        16.93 
TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A215 
       33.30         6.21        22.78        17.88        10.19        18.87 
TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 
       17.92        19.89         5.88        66.77        13.84        73.32 
TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 
       36.00         0.43        39.52        10.29       106.88       149.56 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
      123.68        74.10        46.55        73.87        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 
       54.02        23.21        68.65        37.91        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        31.99        31.99        36.33 
TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A7WJ TCGA-A5-A7WK 
       33.07       118.19        24.72        34.95        11.21        18.41 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       14.43        10.26        21.14        19.79        35.15        34.36 
TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
       34.16        18.90        33.90         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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 
       12.82        20.78         2.70        35.11         0.13       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J 
       21.99        23.31        86.07        48.03        63.91        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       23.87        12.62        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
      110.37        66.25        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        90.97        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        60.23        45.86        27.85        51.12 
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        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       80.55        88.24        71.51        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       49.87        57.47        27.39        30.02        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       35.74        37.78        43.82        40.11        77.39        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       32.91        34.65        25.51        26.37        32.02        25.91 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       34.09        76.83        85.48        73.41        80.25        37.58 
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        38.24 
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-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
        0.20         0.56        43.82         0.30         0.26         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS 
        1.18        18.35        14.47         0.39        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       55.30        59.24        86.01        58.75        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       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        73.64        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        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       225.50       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 
       51.45        14.70        48.43        11.87        52.54        31.36 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       96.30        93.50        71.84        27.65        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-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       35.21        71.24        63.68        74.63        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       48.56        23.47        43.30        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       15.45         9.57        20.02        23.70        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        31.76        24.99 
TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       24.13        13.18        10.03         9.86        46.95        24.33 
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        92.88       114.90        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        89.59        63.58 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       86.99        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
        4.87        28.67        23.93         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-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-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-A17L TCGA-D1-A17M TCGA-D1-A17N 
       30.44         1.28        28.01        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-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.95        48.79         8.48        58.95        15.88         4.27 
TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KU TCGA-DF-A2KV 
       18.84        17.29         2.20        71.61       100.83        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-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ 
       35.38         9.37        12.39       110.10        23.38        79.10 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       58.95         2.37        45.57        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-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       46.26        57.60        51.52        19.40        34.39        50.73 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU 
       35.15        38.07        27.16        46.42        26.96        22.26 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       38.47        51.09        14.99        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GR 
       23.34        23.34        23.90        33.34        32.71        17.62 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       16.11        32.78        15.81        37.05        19.33        12.59 
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        32.52 
TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 
       11.38        14.14        14.70        16.96        68.38        39.88 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A2F8 
       77.33         7.99        25.22        96.69        28.93        30.67 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ 
       59.28        41.56        78.38         1.74        17.75        14.04 
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        21.30        38.70 
TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       22.59         8.19        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       24.95        23.64        14.83         4.44        20.75        18.28 
TCGA-SL-A6JA 
        0.23 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.07               0.13 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             136.6              225.5 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             22.80              30.44 
[1] "0.1 - 136.6 (22.8)" "0.1 - 225.5 (30.4)"
[1] "hr=" "1.7"
D73V2, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    27  18
  18P LOSS WILD-TYPE 263 206
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     27   18
  18P LOSS WILD-TYPE  263  206
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                27                263
  YES               18                206
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  18P LOSS MUTATED                                        26
  18P LOSS WILD-TYPE                                     378
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  18P LOSS MUTATED                               5
  18P LOSS WILD-TYPE                            17
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  18P LOSS MUTATED                                  20
  18P LOSS WILD-TYPE                                93
D73V3, multiclass
                                         clus
vv                                        18P LOSS MUTATED 18P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               26                378
  MIXED SEROUS AND ENDOMETRIOID                          5                 17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     20                 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"
                    vv
clus                  R0  R1  R2  RX
  18P LOSS MUTATED    30   5   1   6
  18P LOSS WILD-TYPE 341  17  15  34
D73V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0               30                341
  R1                5                 17
  R2                1                 15
  RX                6                 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"

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    48  14
  18Q LOSS WILD-TYPE 399  76
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                62                475 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                14                 76 
$`18Q LOSS MUTATED`
TCGA-AX-A1CR TCGA-AX-A3G3 TCGA-D1-A3JP TCGA-EY-A214 TCGA-KP-A3VZ TCGA-A5-A0GJ 
       23.05         1.38        16.93        14.40        23.74        65.75 
TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A2K3 TCGA-A5-A2K4 
       60.53        36.82        17.59        31.99        66.15        28.64 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AP-A05H 
       25.51        14.96        20.25        34.16        18.12        45.53 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AX-A1CA TCGA-AX-A2H2 TCGA-AX-A3FZ TCGA-AX-A3G1 
       36.36        97.71        32.02         4.77         0.20        20.52 
TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A11P TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OE 
        0.30         0.39        52.04       136.60        39.35        34.95 
TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0V8 TCGA-D1-A0ZZ 
       15.45        22.39        16.64        61.87        83.64        22.55 
TCGA-D1-A169 TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A17K TCGA-D1-A1NW TCGA-D1-A1O0 
       37.32        18.67         3.95        28.08         0.72         2.07 
TCGA-D1-A3DH TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ 
       18.84       109.08        25.91        31.10       110.10        79.10 
TCGA-EO-A2CG TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GW 
       51.42        54.15        19.27        18.84        22.03        11.08 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-FI-A2CY TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A3PX 
       20.05        45.76        68.38        59.01         9.34        78.38 
TCGA-KP-A3W0 TCGA-SL-A6J9 
       13.28         0.07 

$`18Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF 
       18.08        20.81        10.19       110.63        57.80        93.99 
TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-AX-A2HF 
       95.47        67.66        12.26        36.39        61.18        27.88 
TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       80.38        27.09        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 
       12.56        14.27         1.81        19.79         4.44        47.84 
TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A215 
       33.30         6.21        22.78        17.88        10.19        18.87 
TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 
       17.92        19.89         5.88        66.77        13.84        73.32 
TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 
       36.00         0.43        39.52        10.29       106.88       149.56 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
      123.68        74.10        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       23.21        68.65        37.91        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 
       42.35        15.95        31.99        36.33        33.07       118.19 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23N TCGA-AJ-A23O 
       24.72        34.95        11.21        18.41        14.43        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BI TCGA-AJ-A3BK 
       21.14        19.79        35.15        34.36        18.90        33.90 
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-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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 
       35.11         0.13       129.80        21.99        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       48.03        63.91        36.89        23.87        12.62        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LJ 
       48.79       125.42       117.99       110.37        66.25        46.72 
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-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        90.97        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        60.23        45.86 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       27.85        51.12        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 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       45.99        79.46        49.87        57.47        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       60.66        61.08        35.74        37.78        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       77.39        13.28        32.91        34.65        25.51        26.37 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       25.91        34.09        76.83        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
       37.58        30.12        71.24        40.80        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       46.49        38.24        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-A0JR TCGA-B5-A0JS 
        0.30         1.18        18.35        14.47        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       55.30        59.24        86.01        58.75        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       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        73.64        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        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       225.50       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 
       51.45        14.70        48.43        11.87        52.54        31.36 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       96.30        93.50        71.84        27.65        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-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       71.24        63.68        74.63        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        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        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-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        35.90        35.08        31.00        31.76        24.99 
TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       24.13        13.18        10.03         9.86        46.95        24.33 
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        92.88       114.90        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        89.59        63.58 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       86.99        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
        4.87        28.67        23.93         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-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-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-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-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-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JQ 
       48.79         8.48        58.95        15.88         4.27        17.29 
TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        2.20        71.61       100.83        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-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       12.39        23.38        58.95         2.37        45.57        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        50.73        35.15        38.07        27.16        46.42 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 
       26.96        22.26        16.34        38.47        51.09        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-A1GL TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       33.34        32.71        17.62        16.11        32.78        15.81 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A2OQ 
       37.05        19.33        12.59        22.82        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 
       27.35        32.52        11.38        14.14        14.70        16.96 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EY 
       39.88        77.33         7.99        25.22        96.69        28.93 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ 
       30.67        59.28        41.56         1.74        17.75        14.04 
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        21.30        38.70 
TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       22.59         8.19        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       24.95        23.64        14.83         4.44        20.75        18.28 
TCGA-SL-A6JA 
        0.23 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.07               0.13 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             136.6              225.5 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            24.625             30.120 
[1] "0.1 - 136.6 (24.6)" "0.1 - 225.5 (30.1)"
[1] "hr=" "1.5"
D74V2, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    35  20
  18Q LOSS WILD-TYPE 255 204
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     35   20
  18Q LOSS WILD-TYPE  255  204
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                35                255
  YES               20                204
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  18Q LOSS MUTATED                                        29
  18Q LOSS WILD-TYPE                                     375
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  18Q LOSS MUTATED                               6
  18Q LOSS WILD-TYPE                            16
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  18Q LOSS MUTATED                                  28
  18Q LOSS WILD-TYPE                                85
D74V3, multiclass
                                         clus
vv                                        18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               29                375
  MIXED SEROUS AND ENDOMETRIOID                          6                 16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     28                 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"
                    vv
clus                  R0  R1  R2  RX
  18Q LOSS MUTATED    37   5   3   7
  18Q LOSS WILD-TYPE 334  17  13  33
D74V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0               37                334
  R1                5                 17
  R2                3                 13
  RX                7                 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"

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    41  16
  19P LOSS WILD-TYPE 406  74
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                57                480 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                16                 74 
$`19P LOSS MUTATED`
TCGA-2E-A9G8 TCGA-AX-A3G3 TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-D1-A3JP 
       41.06         1.38        27.09        22.06        66.41        16.93 
TCGA-E6-A8L9 TCGA-EY-A214 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-A5-A0GJ TCGA-A5-A0GN 
       33.30        14.40        36.00        23.74        65.75        60.53 
TCGA-A5-A1OG TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N 
       31.99        66.15        28.64        25.51        14.96        14.43 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3EJ TCGA-AJ-A3TW TCGA-AP-A05H TCGA-AP-A3K1 
       34.16        18.12         1.64        16.87        45.53        21.90 
TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A2H5 TCGA-AX-A2HK TCGA-AX-A3FZ TCGA-AX-A3G6 
       32.02        76.83        71.24         2.96         0.20         0.26 
TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MU TCGA-B5-A1MY 
        0.30         0.39        75.72        52.04        50.89        11.87 
TCGA-B5-A3F9 TCGA-BG-A18C TCGA-BS-A0U9 TCGA-D1-A15V TCGA-D1-A16N TCGA-DI-A2QT 
      136.60        15.45        92.88        39.48        31.07        12.39 
TCGA-EO-A1Y8 TCGA-EO-A2CH TCGA-EY-A1GP TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A3L3 
       37.71        19.40        18.84        15.81        11.08        27.35 
TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY TCGA-JU-AAVI 
       68.38        77.33        96.69         9.34        28.93        17.75 
TCGA-KP-A3W0 TCGA-PG-A914 TCGA-QS-A8F1 
       13.28        22.59         4.44 

$`19P LOSS WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS 
       20.81        10.19       110.63        57.80        93.99        95.47 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF 
       67.66        12.26        36.39        23.05        61.18        27.88 
TCGA-B5-A0JN TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 
       80.38        61.87        51.55        12.56        14.27         1.81 
TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ 
       19.79         4.44        47.84         6.21        22.78        17.88 
TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX 
       10.19        18.87        17.92        19.89         5.88        66.77 
TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 
       13.84        73.32         0.43        39.52        10.29       106.88 
TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      149.56        37.02        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
      105.37       123.68        74.10        46.55        73.87        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        54.02        23.21        68.65        37.91        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        31.99 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A7WJ 
       36.33        33.07       118.19        24.72        34.95        11.21 
TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       18.41        20.25        10.26        21.14        19.79        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       34.36        18.90        33.90        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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
        2.70        35.11         0.13       129.80        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       86.07        48.03        63.91        36.89        23.87        12.62 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       33.40        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       90.97        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        60.23        45.86        27.85        51.12        36.13 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        61.08        35.74        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        77.39        13.28        32.91        34.65 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       25.51        26.37        25.91        34.09        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA 
       80.25        37.58         4.77        30.12        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        38.24        17.75        30.74        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-A3G4 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        86.37 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       55.30        59.24        86.01        58.75        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       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        73.64        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       77.23        73.28        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       225.50       102.31        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       48.43        52.54        31.36        96.30        93.50        71.84 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       39.35        27.65        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        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       63.68        74.63        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        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        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-A222 
       14.83        13.78        14.73        14.01        15.45         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        22.39        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       34.98        35.90        35.08        31.00        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 
       24.33        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       114.90        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        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       63.58        83.64        86.99        66.48        16.83        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-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        1.74        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-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-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.95        48.79         8.48        58.95        15.88         4.27 
TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU 
       18.84        17.29         2.20        71.61       109.08       100.83 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU 
       89.33        10.92        27.16        25.91        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        79.10        58.95         2.37        45.57        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 
       50.73        35.15        38.07        27.16        46.42        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC 
       22.26        16.34        38.47        51.09        14.99        54.15 
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-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT 
       33.34        32.71        19.27        17.62        22.03        16.11 
TCGA-EY-A1GU TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON 
       32.78        37.05        19.33        12.59        22.82        20.05 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 
       45.76        31.04        29.10        32.52        11.38        14.14 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EW 
       14.70        16.96        39.88         7.99        25.22        59.01 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ 
       30.67        59.28        41.56        78.38         1.74        14.04 
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        21.30        38.70 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        8.19        17.16         6.97        22.65        39.95        24.95 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       23.64        14.83        20.75        18.28         0.07         0.23 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.20               0.07 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             136.6              225.5 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            25.510             30.135 
[1] "0.2 - 136.6 (25.5)" "0.1 - 225.5 (30.1)"
[1] "hr=" "2.1"
D75V2, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    27  23
  19P LOSS WILD-TYPE 263 201
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     27   23
  19P LOSS WILD-TYPE  263  201
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                27                263
  YES               23                201
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  19P LOSS MUTATED                                        18
  19P LOSS WILD-TYPE                                     386
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  19P LOSS MUTATED                               4
  19P LOSS WILD-TYPE                            18
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  19P LOSS MUTATED                                  35
  19P LOSS WILD-TYPE                                78
D75V3, multiclass
                                         clus
vv                                        19P LOSS MUTATED 19P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               18                386
  MIXED SEROUS AND ENDOMETRIOID                          4                 18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     35                 78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  19P LOSS MUTATED    33   4   4   4
  19P LOSS WILD-TYPE 338  18  12  36
D75V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0               33                338
  R1                4                 18
  R2                4                 12
  RX                4                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    40  14
  19Q LOSS WILD-TYPE 407  76
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                54                483 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                14                 76 
$`19Q LOSS MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A2QM TCGA-AX-A3G3 TCGA-BG-A0M8 TCGA-D1-A3JP TCGA-E6-A8L9 
       41.06        29.39         1.38        66.41        16.93        33.30 
TCGA-EY-A214 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A2K4 
       14.40        36.00        23.74        65.75        60.53        28.64 
TCGA-A5-A3LO TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ 
       25.51        14.43        34.16        18.12        18.90         1.64 
TCGA-AJ-A3NF TCGA-AJ-A3TW TCGA-AP-A05H TCGA-AP-A0L9 TCGA-AP-A0LH TCGA-AP-A3K1 
       21.21        16.87        45.53       125.42        36.36        21.90 
TCGA-AX-A2H5 TCGA-AX-A2HK TCGA-AX-A3FZ TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3GI 
       71.24         2.96         0.20         0.26         0.30         0.39 
TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A3F9 
       75.72        52.04       102.31        50.89        11.87       136.60 
TCGA-BG-A18C TCGA-BG-A3PP TCGA-BS-A0U9 TCGA-D1-A16N TCGA-DI-A2QT TCGA-EO-A1Y7 
       15.45        22.39        92.88        31.07        12.39        49.15 
TCGA-EO-A1Y8 TCGA-EO-A2CH TCGA-EY-A1GJ TCGA-EY-A1GW TCGA-EY-A3L3 TCGA-FI-A2CY 
       37.71        19.40        23.90        11.08        27.35        68.38 
TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-KP-A3W0 TCGA-PG-A914 TCGA-QS-A8F1 
       77.33        96.69         9.34        13.28        22.59         4.44 

$`19Q LOSS WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG TCGA-AJ-A3IA 
       88.18        60.53        30.15        16.83        18.08        20.81 
TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B 
       10.19       110.63        57.80        93.99        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-B5-A0JN 
       12.26        36.39        23.05        61.18        27.88        80.38 
TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 
       27.09        22.06        61.87        51.55        12.56        14.27 
TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-EY-A1G7 TCGA-EY-A1GK 
        1.81        19.79         4.44        47.84         6.21        22.78 
TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D 
       17.88        10.19        18.87        17.92        19.89         5.88 
TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 
       66.77        13.84        73.32         0.43        39.52        10.29 
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GP TCGA-A5-A0GQ 
      112.54       105.37       123.68        74.10        46.55        73.87 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       36.82        28.27        54.02        23.21        68.65        37.91 
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-A2K2 TCGA-A5-A2K3 
       31.99        31.99        36.33        33.07       118.19        66.15 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M 
       24.72        34.95        14.96        11.21        18.41        20.25 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BK 
       10.26        21.14        19.79        35.15        34.36        33.90 
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-A5DV 
       15.62        15.35        15.95        14.76        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 
       12.82        20.78         2.70        35.11         0.13       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J 
       21.99        23.31        86.07        48.03        63.91        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        12.62        20.91        48.79       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       66.25        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       33.40        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       90.97        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        60.23        45.86        27.85        51.12        36.13 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        61.08        35.74        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        77.39        13.28        32.91        34.65 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       25.51        26.37        32.02        25.91        34.09        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 
       85.48        73.41        80.25        37.58         4.77        30.12 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       40.80        81.37        34.32        46.49        38.24        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-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
       43.82        20.52         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        86.37        55.30        59.24        86.01        58.75 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       69.27        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       57.76        64.21        63.55        27.85        13.45        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      185.79       113.36        88.34        54.44        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       85.78        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MV 
       19.50        18.41        17.36        16.57       225.50        51.45 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB 
       14.70        48.43        52.54        31.36        96.30        93.50 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       71.84        39.35        27.65        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-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       71.24        63.68        74.63        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        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        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-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        35.90        35.08        31.00        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 
       24.33        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       114.90        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        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       63.58        83.64        86.99        66.48        16.83        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-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-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-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        1.05         3.95        48.79         8.48        58.95        15.88 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS 
        4.27        18.84        17.29         2.20        71.61       109.08 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH 
      100.83        89.33        10.92        27.16        25.91        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        79.10        58.95         2.37        45.57 
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 
       50.73        35.15        38.07        27.16        46.42        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC 
       22.26        16.34        38.47        51.09        14.99        54.15 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL 
       53.88        24.36        27.16        23.34        23.34        33.34 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT 
       32.71        19.27        18.84        17.62        22.03        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM 
       32.78        15.81        37.05        19.33        12.59        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A4KR 
       20.05        45.76        31.04        29.10        32.52        11.38 
TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 
       14.14        14.70        16.96        39.88         7.99        25.22 
TCGA-FI-A2EW TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
       59.01        28.93        30.67        59.28        41.56        78.38 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 
        1.74        17.75        14.04         9.47        26.10        18.21 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 
       23.24        21.30        38.70         8.19        17.16         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI 
       22.65        39.95        24.95        23.64        14.83        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       18.28         0.07         0.23 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.20               0.07 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             136.6              225.5 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            24.705             30.120 
[1] "0.2 - 136.6 (24.7)" "0.1 - 225.5 (30.1)"
[1] "hr=" "1.7"
D76V2, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    25  22
  19Q LOSS WILD-TYPE 265 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     25   22
  19Q LOSS WILD-TYPE  265  202
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                25                265
  YES               22                202
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  19Q LOSS MUTATED                                        18
  19Q LOSS WILD-TYPE                                     386
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  19Q LOSS MUTATED                               4
  19Q LOSS WILD-TYPE                            18
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  19Q LOSS MUTATED                                  32
  19Q LOSS WILD-TYPE                                81
D76V3, multiclass
                                         clus
vv                                        19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               18                386
  MIXED SEROUS AND ENDOMETRIOID                          4                 18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     32                 81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  19Q LOSS MUTATED    31   3   3   5
  19Q LOSS WILD-TYPE 340  19  13  35
D76V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0               31                340
  R1                3                 19
  R2                3                 13
  RX                5                 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"

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    17   5
  20P LOSS WILD-TYPE 430  85
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                22                515 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 5                 85 
$`20P LOSS MUTATED`
TCGA-2E-A9G8 TCGA-AP-A05D TCGA-BG-A0M6 TCGA-D1-A3JP TCGA-EY-A547 TCGA-A5-A0G2 
       41.06        57.80        22.06        16.93        17.92       149.56 
TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-AJ-A3BD TCGA-AP-A05H TCGA-AP-A0LI TCGA-AW-A1PO 
       60.53        37.91        34.16        45.53        97.71         0.56 
TCGA-AX-A1CF TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-B5-A0K8 TCGA-BG-A0MO TCGA-D1-A3JQ 
       76.83        20.52         0.30        27.85        43.04        17.29 
TCGA-EY-A1GJ TCGA-EY-A1GW TCGA-EY-A3QX TCGA-FI-A2D2 
       23.90        11.08        32.52        77.33 

$`20P LOSS WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B 
       20.81        10.19       110.63        93.99        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 
       12.26        36.39        23.05        61.18        27.88         1.38 
TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV 
       80.38        27.09        66.41        61.87        51.55        12.56 
TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 
       14.27         1.81        19.79         4.44        47.84        33.30 
TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 
        6.21        22.78        17.88        10.19        14.40        18.87 
TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 
       19.89         5.88        66.77        13.84        73.32        36.00 
TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 
       23.74         0.43        39.52        10.29       106.88        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       123.68 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       74.10        65.75        46.55        73.87        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       54.02        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        31.99        31.99        36.33 
TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
       33.07       118.19        66.15        28.64        24.72        34.95 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N 
       25.51        14.96        11.21        18.41        20.25        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF 
       10.26        21.14        19.79        35.15        34.36        18.12 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       18.90        33.90         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-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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       20.78         2.70        35.11         0.13       129.80        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N 
       23.31        86.07        48.03        63.91        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       12.62        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       66.25        36.36        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       33.40        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       90.97        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        60.23        45.86        27.85        51.12        21.90 
TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       36.13        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        61.08        35.74        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        77.39        13.28        32.91        34.65 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI 
       25.51        26.37        32.02        25.91        34.09        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       73.41        80.25        37.58         4.77        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       40.80        81.37        34.32        46.49        38.24        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-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.56        43.82         0.20         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        86.37        55.30 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       59.24        86.01        58.75        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       13.45        59.84       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        73.64        61.68        85.78        52.04        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       77.23        73.28        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       225.50       102.31        50.89        51.45 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       14.70        48.43        11.87        52.54        31.36       136.60 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 
       96.30        93.50        71.84        39.35        27.65        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-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        35.21        71.24        63.68        74.63        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        48.56        23.47        43.30        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       15.45        15.45         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        22.39        35.90        34.98        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F 
       31.00        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        24.33        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        92.88       114.90        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        89.59        63.58        83.64 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       86.99        66.48        16.83        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-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-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.95        48.79         8.48        58.95        15.88         4.27 
TCGA-D1-A3DH TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV 
       18.84         2.20        71.61       109.08       100.83        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       10.92        27.16        25.91        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-EC-A1NJ 
       23.38        79.10        58.95         2.37        45.57        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        50.73        35.15        38.07        27.16 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       46.42        26.96        22.26        16.34        38.47        51.09 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99        54.15        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR 
       23.34        33.34        32.71        19.27        18.84        17.62 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 
       22.03        16.11        32.78        15.81        37.05        19.33 
TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       12.59        22.82        20.05        45.76        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY 
       27.35        11.38        14.14        14.70        16.96        68.38 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
       39.88         7.99        25.22        96.69        59.01         9.34 
TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR 
       28.93        30.67        59.28        41.56        78.38         1.74 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 
       17.75        14.04        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        21.30        38.70        22.59         8.19        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        22.65        39.95        24.95        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44        20.75        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             225.50 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             33.34              29.88 
[1] "0.3 - 149.6 (33.3)" "0.1 - 225.5 (29.9)"
[1] "hr=" "1.3"
D77V2, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     9  12
  20P LOSS WILD-TYPE 281 212
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      9   12
  20P LOSS WILD-TYPE  281  212
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 9                281
  YES               12                212
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  20P LOSS MUTATED                                         9
  20P LOSS WILD-TYPE                                     395
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  20P LOSS MUTATED                               1
  20P LOSS WILD-TYPE                            21
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  20P LOSS MUTATED                                  12
  20P LOSS WILD-TYPE                               101
D77V3, multiclass
                                         clus
vv                                        20P LOSS MUTATED 20P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                9                395
  MIXED SEROUS AND ENDOMETRIOID                          1                 21
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     12                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"
                    vv
clus                  R0  R1  R2  RX
  20P LOSS MUTATED    16   1   2   0
  20P LOSS WILD-TYPE 355  21  14  40
D77V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0               16                355
  R1                1                 21
  R2                2                 14
  RX                0                 40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     9   2
  20Q LOSS WILD-TYPE 438  88
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                11                526 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                 88 
$`20Q LOSS MUTATED`
TCGA-AP-A05D TCGA-D1-A3JP TCGA-A5-A0G2 TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-AJ-A3BD 
       57.80        16.93       149.56        60.53        37.91        34.16 
TCGA-AW-A1PO TCGA-D1-A0ZZ TCGA-EY-A1GJ TCGA-EY-A3QX TCGA-FI-A2D2 
        0.56        22.55        23.90        32.52        77.33 

$`20Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A0LF TCGA-AP-A0LS 
       18.08        20.81        10.19       110.63        93.99        95.47 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF 
       67.66        12.26        36.39        23.05        61.18        27.88 
TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
        1.38        80.38        27.09        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 
       51.55        12.56        14.27         1.81        19.79         4.44 
TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 
       47.84        33.30         6.21        22.78        17.88        10.19 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX 
       14.40        18.87        17.92        19.89         5.88        66.77 
TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C 
       13.84        73.32        36.00        23.74         0.43        39.52 
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
       10.29       106.88        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GP 
      112.54       105.37       123.68        74.10        65.75        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       73.87        36.82        28.27        54.02        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-A2K2 TCGA-A5-A2K3 
       31.99        31.99        36.33        33.07       118.19        66.15 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ 
       28.64        24.72        34.95        25.51        14.96        11.21 
TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       18.41        20.25        14.43        10.26        21.14        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       35.15        34.36        18.12        18.90        33.90         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-A8CV 
       16.87        22.32        12.82        20.78         2.70        35.11 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        0.13       129.80        21.99        23.31        86.07        48.03 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       63.91        45.53        36.89        23.87        12.62        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        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        46.72        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       61.64        80.78        49.22        25.08        71.67        90.97 
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 
       60.23        45.86        27.85        51.12        21.90        36.13 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        61.08        35.74        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        77.39        13.28        32.91        34.65        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       26.37        32.02        25.91        34.09        76.83        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       73.41        80.25        37.58         4.77        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       40.80        81.37        34.32        46.49        38.24        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-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 
       86.37        55.30        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       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        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       85.78        52.04        32.09        77.23        73.28        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       225.50 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      102.31        50.89        51.45        14.70        48.43        11.87 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       52.54        31.36       136.60        96.30        93.50        71.84 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       39.35        27.65        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        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       63.68        74.63        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        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        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-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
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        22.39 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       35.90        34.98        35.90        35.08        31.00        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        24.33        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        92.88 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
      114.90        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        89.59        63.58        83.64        86.99        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       23.93         1.74        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-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        48.79         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN 
       58.95        15.88         4.27        18.84        17.29         2.20 
TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
       71.61       109.08       100.83        89.33        10.92        27.16 
TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
       25.91        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        79.10 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       58.95         2.37        45.57        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 
       50.73        35.15        38.07        27.16        46.42        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC 
       22.26        16.34        38.47        51.09        14.99        54.15 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL 
       53.88        24.36        27.16        23.34        23.34        33.34 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT 
       32.71        19.27        18.84        17.62        22.03        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       32.78        15.81        11.08        37.05        19.33        12.59 
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-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 
       11.38        14.14        14.70        16.96        68.38        39.88 
TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
        7.99        25.22        96.69        59.01         9.34        28.93 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
       30.67        59.28        41.56        78.38         1.74        17.75 
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-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 
       21.30        38.70        22.59         8.19        17.16         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 
       22.65        39.95        24.95        23.64        14.83         4.44 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       20.75        18.28         0.07         0.23 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              0.56               0.07 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            149.56             225.50 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            34.160             29.785 
[1] "0.6 - 149.6 (34.2)" "0.1 - 225.5 (29.8)"
[1] "hr=" "1.2"
D78V2, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     4   7
  20Q LOSS WILD-TYPE 286 217
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      4    7
  20Q LOSS WILD-TYPE  286  217
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 4                286
  YES                7                217
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  20Q LOSS MUTATED                                         3
  20Q LOSS WILD-TYPE                                     401
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  20Q LOSS MUTATED                               2
  20Q LOSS WILD-TYPE                            20
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  20Q LOSS MUTATED                                   6
  20Q LOSS WILD-TYPE                               107
D78V3, multiclass
                                         clus
vv                                        20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                3                401
  MIXED SEROUS AND ENDOMETRIOID                          2                 20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                      6                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"
                    vv
clus                  R0  R1  R2  RX
  20Q LOSS MUTATED    11   0   0   0
  20Q LOSS WILD-TYPE 360  22  16  40
D78V4, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0               11                360
  R1                0                 22
  R2                0                 16
  RX                0                 40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    37  17
  21Q LOSS WILD-TYPE 410  73
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                54                483 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                17                 73 
$`21Q LOSS MUTATED`
TCGA-AJ-A3BG TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A2HF TCGA-BG-A0M6 
       18.08        57.80        93.99        67.66        27.88        22.06 
TCGA-BG-A0M8 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A72D TCGA-A5-A0GN TCGA-A5-A1OH 
       66.41        10.19        14.40         5.88        60.53        36.33 
TCGA-A5-A2K3 TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AP-A052 TCGA-AP-A0L9 TCGA-AP-A0LI 
       66.15        20.25        10.26        21.99       125.42        97.71 
TCGA-AP-A3K1 TCGA-AX-A1CA TCGA-AX-A2IO TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-B5-A1N2 
       21.90        32.02        64.93         0.30         0.26        31.36 
TCGA-B5-A3FD TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A139 TCGA-D1-A0ZZ TCGA-D1-A15V 
       39.35        15.45        22.39        31.00        22.55        39.48 
TCGA-D1-A179 TCGA-D1-A3DG TCGA-DF-A2KR TCGA-DI-A1NN TCGA-DI-A1NO TCGA-E6-A1LX 
       14.73         4.27        71.61        35.38         9.37        23.38 
TCGA-EO-A2CH TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP 
       19.40        16.34        54.15        33.34        19.27        18.84 
TCGA-EY-A2OO TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2EY TCGA-FI-A2F8 
       45.76        11.38        14.70        77.33        28.93        30.67 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KP-A3W1 TCGA-PG-A5BC TCGA-PG-A915 
       78.38         1.74        17.75         9.47        23.24         8.19 

$`21Q LOSS WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CP 
       20.81        10.19       110.63        95.47        12.26        36.39 
TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0MS 
       23.05        61.18         1.38        80.38        27.09        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 
       51.55        12.56        14.27         1.81        19.79         4.44 
TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ 
       47.84        16.93        33.30         6.21        22.78        17.88 
TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 
       18.87        17.92        19.89        66.77        13.84        73.32 
TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 
       36.00        23.74         0.43        39.52        10.29       106.88 
TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      149.56        37.02        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GP TCGA-A5-A0GQ 
      105.37       123.68        74.10        65.75        46.55        73.87 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       36.82        28.27        54.02        23.21        68.65        37.91 
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-A2K2 TCGA-A5-A2K4 TCGA-A5-A2K5 
       31.99        31.99        33.07       118.19        28.64        24.72 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23N 
       34.95        25.51        14.96        11.21        18.41        14.43 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF 
       21.14        19.79        35.15        34.36        34.16        18.12 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       18.90        33.90         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-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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 
       20.78         2.70        35.11         0.13       129.80        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07        48.03        63.91        45.53        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       12.62        20.91        48.79       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        46.72        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       61.64        80.78        49.22        25.08        71.67        90.97 
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 
       60.23        45.86        27.85        51.12        36.13         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        61.08        35.74        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        77.39        13.28        32.91        34.65        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       26.37        25.91        34.09        76.83        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       80.25        37.58         4.77        30.12        71.24        40.80 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       81.37        34.32        46.49        38.24        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-A3G1 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.20        20.52         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        86.37        55.30        59.24        86.01 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       58.75        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       59.84       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 
       73.64        61.68        85.78        52.04        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       73.28        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       225.50       102.31        50.89        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       48.43        11.87        52.54       136.60        96.30        93.50 
TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       71.84        27.65        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        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       63.68        74.63        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        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        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-A222 
       14.83        13.78        14.73        14.01        15.45         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-A26L TCGA-BK-A4ZD 
       35.90        35.08        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        24.33        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        92.88       114.90        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        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       83.64        86.99        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 
        0.56         4.87        28.67        23.93         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-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-A17A TCGA-D1-A17B 
       19.53         6.64        30.15        18.02         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        48.79 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN 
        8.48        58.95        15.88        18.84        17.29         2.20 
TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 
      109.08       100.83        89.33        10.92        27.16        25.91 
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-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
      110.10        79.10        58.95         2.37        45.57        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-A3AZ TCGA-EO-A3B0 
       34.39        50.73        35.15        38.07        27.16        46.42 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD 
       26.96        22.26        38.47        51.09        14.99        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GM 
       24.36        27.16        23.34        23.34        23.90        32.71 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       17.62        22.03        16.11        32.78        15.81        11.08 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP 
       37.05        19.33        12.59        22.82        20.05        31.04 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CY 
       29.10        27.35        32.52        14.14        16.96        68.38 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
       39.88         7.99        25.22        96.69        59.01         9.34 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 
       59.28        41.56        14.04        13.28        26.10        18.21 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       21.30        38.70        22.59        17.16         6.97        22.65 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       39.95        24.95        23.64        14.83         4.44        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       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             225.50 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            22.895             30.120 
[1] "0.3 - 125.4 (22.9)" "0.1 - 225.5 (30.1)"
[1] "hr=" "2.4"
D79V2, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    29  22
  21Q LOSS WILD-TYPE 261 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     29   22
  21Q LOSS WILD-TYPE  261  202
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                29                261
  YES               22                202
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  21Q LOSS MUTATED                                        20
  21Q LOSS WILD-TYPE                                     384
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  21Q LOSS MUTATED                               4
  21Q LOSS WILD-TYPE                            18
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  21Q LOSS MUTATED                                  30
  21Q LOSS WILD-TYPE                                83
D79V3, multiclass
                                         clus
vv                                        21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               20                384
  MIXED SEROUS AND ENDOMETRIOID                          4                 18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     30                 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"
                    vv
clus                  R0  R1  R2  RX
  21Q LOSS MUTATED    37   2   4   5
  21Q LOSS WILD-TYPE 334  20  12  35
D79V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0               37                334
  R1                2                 20
  R2                4                 12
  RX                5                 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"

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    80  29
  22Q LOSS WILD-TYPE 367  61
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               109                428 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                29                 61 
$`22Q LOSS MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AX-A06B TCGA-AX-A1CP 
       41.06        20.81        10.19        57.80        67.66        36.39 
TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0KB TCGA-BG-A0M8 
       23.05        61.18        27.88         1.38        27.09        66.41 
TCGA-BG-A0YV TCGA-E6-A8L9 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A547 TCGA-KJ-A3U4 
       12.56        33.30        10.19        14.40        17.92        36.00 
TCGA-KP-A3VZ TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R7 TCGA-A5-A1OH 
       23.74        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 
      118.19        25.51        14.96        14.43        21.14        19.79 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3I9 TCGA-AJ-A3QS 
       34.16        18.12        18.90         1.64        17.06        16.87 
TCGA-AJ-A3TW TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A1DQ TCGA-AP-A5FX TCGA-AX-A0IW 
       16.87        45.53        48.79        46.78        36.13        37.78 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HK 
       34.65        25.51        32.02        30.12        71.24         2.96 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
        0.56        43.82        20.52         0.30         0.26         0.30 
TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A1N2 
       75.72        52.04       102.31        50.89        11.87        31.36 
TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OD TCGA-BG-A0VZ TCGA-BG-A18C TCGA-BG-A2AD 
      136.60        39.35        34.13        52.64        15.45        20.02 
TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BS-A0U9 TCGA-D1-A0ZP TCGA-D1-A0ZZ TCGA-D1-A16I 
       22.39        35.08        92.88        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-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-DI-A2QT 
        4.27        71.61       109.08        25.91        35.38        12.39 
TCGA-DI-A2QU TCGA-EO-A1Y7 TCGA-EO-A2CG TCGA-EO-A3AZ TCGA-EO-A3KW TCGA-EY-A1GC 
       31.10        49.15        51.42        27.16        16.34        54.15 
TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GW TCGA-EY-A210 
       23.90        32.71        18.84        17.62        11.08        12.59 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-FI-A2D2 TCGA-FI-A2F9 TCGA-FI-A3PX 
       20.05        45.76        29.10        77.33        59.28        78.38 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-PG-A914 
        1.74        17.75        14.04        26.10        38.70        22.59 
TCGA-SL-A6J9 
        0.07 

$`22Q LOSS WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AP-A053 TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06D TCGA-B5-A0JN TCGA-BG-A0M6 
      110.63        93.99        95.47        12.26        80.38        22.06 
TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 
       61.87        51.55        14.27         1.81        19.79         4.44 
TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A215 
       47.84        16.93         6.21        22.78        17.88        18.87 
TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-4E-A92E 
       19.89         5.88        66.77        13.84        73.32         0.43 
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       39.52        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       123.68        74.10 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        73.87        28.27        54.02        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       37.91        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
       31.99        31.99        33.07        66.15        28.64        24.72 
TCGA-A5-A2K7 TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QN 
       34.95        11.21        18.41        20.25        10.26        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3NC 
       34.36        33.90        14.66        22.49        22.26        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-A8CV TCGA-AJ-A8CW 
       22.32        12.82        20.78         2.70        35.11         0.13 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
      129.80        21.99        23.31        86.07        48.03        63.91 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        12.62        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        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        90.97        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        60.23        45.86        27.85        51.12 
TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       21.90         0.56        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       57.47        27.39        30.02        60.66        61.08        35.74 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 
       43.82        40.11        77.39        13.28        32.91        26.37 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       25.91        34.09        76.83        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       37.58         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 
       38.24        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-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        86.37        55.30        59.24        86.01        58.75 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       69.27        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       57.76        64.21        63.55        27.85        13.45        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      185.79       113.36        88.34        54.44        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       85.78        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MV 
       19.50        18.41        17.36        16.57       225.50        51.45 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       14.70        48.43        52.54        96.30        93.50        71.84 
TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       27.65        29.65        41.06        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        71.24        63.68        74.63 
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-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       34.29        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       14.01        15.45         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        35.90        31.00        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 
       24.33        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       114.90        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        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ 
       63.58        83.64        86.99        66.48        16.83         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 
        0.56         4.87        28.67        23.93         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-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-A16J TCGA-D1-A16O TCGA-D1-A16Q 
       37.51        36.79        27.42        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-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-A1NX 
       11.15        24.30         2.33        22.92         1.41        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-A3DH TCGA-D1-A3JQ 
       48.79         8.48        58.95        15.88        18.84        17.29 
TCGA-DF-A2KN TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        2.20       100.83        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QY TCGA-E6-A1LX 
       39.29        36.62        24.30         9.37       110.10        23.38 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       79.10        58.95         2.37        45.57        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       16.80        10.92        37.71        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       46.26        57.60        51.52        19.40        34.39        50.73 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KX 
       35.15        38.07        46.42        26.96        22.26        38.47 
TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       51.09        14.99        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       23.34        33.34        19.27        22.03        16.11        32.78 
TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A3L3 
       15.81        37.05        19.33        22.82        31.04        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY 
       32.52        11.38        14.14        14.70        16.96        68.38 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
       39.88         7.99        25.22        96.69        59.01         9.34 
TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W4 
       28.93        30.67        41.56        13.28         9.47        18.21 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       23.24        21.30         8.19        17.16         6.97        22.65 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       39.95        24.95        23.64        14.83         4.44        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.07               0.13 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             136.6              225.5 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            27.090             30.295 
[1] "0.1 - 136.6 (27.1)" "0.1 - 225.5 (30.3)"
[1] "hr=" "2.1"
D80V2, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    55  44
  22Q LOSS WILD-TYPE 235 180
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     55   44
  22Q LOSS WILD-TYPE  235  180
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                55                235
  YES               44                180
[1] 2 2
[1] FALSE
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  22Q LOSS MUTATED                                        47
  22Q LOSS WILD-TYPE                                     357
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  22Q LOSS MUTATED                              10
  22Q LOSS WILD-TYPE                            12
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  22Q LOSS MUTATED                                  53
  22Q LOSS WILD-TYPE                                60
D80V3, multiclass
                                         clus
vv                                        22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               47                357
  MIXED SEROUS AND ENDOMETRIOID                         10                 12
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     53                 60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  22Q LOSS MUTATED    68   6   4  12
  22Q LOSS WILD-TYPE 303  16  12  28
D80V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               68                303
  R1                6                 16
  R2                4                 12
  RX               12                 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"

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    57  28
  XP LOSS WILD-TYPE 390  62
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               85               452 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               28                62 
$`XP LOSS MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A2QM TCGA-AP-A053 TCGA-AP-A05D TCGA-AX-A06B TCGA-AX-A1CR 
       41.06        29.39       110.63        57.80        67.66        23.05 
TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0YV 
       27.88         1.38        80.38        22.06        66.41        12.56 
TCGA-EY-A547 TCGA-KJ-A3U4 TCGA-5B-A90C TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R6 
       17.92        36.00        39.52        65.75        60.53        37.91 
TCGA-A5-A0R7 TCGA-A5-A2K2 TCGA-A5-A3LP TCGA-A5-A7WK TCGA-AJ-A23N TCGA-AJ-A3BD 
       17.59       118.19        14.96        18.41        14.43        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3I9 TCGA-AP-A052 TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0LI 
       18.12        17.06        21.99        36.89        48.79        97.71 
TCGA-AP-A1DQ TCGA-AW-A1PO TCGA-AX-A1C7 TCGA-AX-A1CF TCGA-AX-A1CK TCGA-AX-A2H2 
       46.78         0.56        34.65        76.83        80.25         4.77 
TCGA-AX-A3G4 TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1N2 
        0.30        27.29        27.85        52.04       102.31        31.36 
TCGA-B5-A3FD TCGA-B5-A5OE TCGA-BG-A18C TCGA-BK-A0CC TCGA-BK-A4ZD TCGA-D1-A0ZZ 
       39.35        34.95        15.45        35.08        16.64        22.55 
TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A1NU 
       31.07        18.67         3.95        14.73        28.08        13.22 
TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KR TCGA-DF-A2KS 
        2.07         4.27        18.84        17.29        71.61       109.08 
TCGA-DF-A2L0 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY TCGA-EO-A2CG TCGA-EO-A2CH 
       25.91         9.37        12.39       110.10        51.42        19.40 
TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GP TCGA-EY-A1GR 
       27.16        22.26        16.34        23.90        18.84        17.62 
TCGA-EY-A1GW TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-FI-A2D2 
       11.08        29.10        27.35        32.52        11.38        77.33 
TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A3PV TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
       96.69        28.93        41.56        26.10        18.21        23.24 
TCGA-QS-A8F1 
        4.44 

$`XP LOSS WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG TCGA-AJ-A3IA 
       88.18        60.53        30.15        16.83        18.08        20.81 
TCGA-AJ-A3NH TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2H8 
       10.19        93.99        95.47        12.26        36.39        61.18 
TCGA-B5-A0KB TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       27.09        61.87        51.55        14.27         1.81        19.79 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK 
        4.44        47.84        16.93        33.30         6.21        22.78 
TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A549 TCGA-EY-A72D 
       17.88        10.19        14.40        18.87        19.89         5.88 
TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5S-A9Q8 
       66.77        13.84        73.32        23.74         0.43        10.29 
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GP TCGA-A5-A0GQ 
      112.54       105.37       123.68        74.10        46.55        73.87 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 
       36.82        28.27        54.02        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        31.99        31.99 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
       36.33        33.07        66.15        28.64        24.72        34.95 
TCGA-A5-A3LO TCGA-A5-A7WJ TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       25.51        11.21        20.25        10.26        21.14        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
       35.15        34.36        18.90        33.90         1.64        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-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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 
       12.82        20.78         2.70        35.11         0.13       129.80 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05N 
       23.31        86.07        48.03        63.91        45.53        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       12.62        20.91       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        46.72        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       61.64        80.78        49.22        25.08        71.67        90.97 
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        60.23 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S 
       45.86        27.85        51.12        21.90        36.13        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       45.99        79.46        49.87        57.47        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       60.66        61.08        35.74        37.78        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       77.39        13.28        32.91        25.51        26.37        32.02 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CN TCGA-AX-A2H4 
       25.91        34.09        85.48        73.41        37.58        30.12 
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        38.24 
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-A3G6 
        0.20         0.56        43.82         0.20        20.52         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 
       86.37        55.30        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 
       71.44        48.59        36.49        72.62        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        13.45        59.84       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        73.64        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       77.23        73.28        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       225.50        50.89        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       48.43        11.87        52.54       136.60        96.30        93.50 
TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW 
       71.84        27.65        29.65        41.06        34.13        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        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       74.63        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD 
       13.78        14.73        14.01        15.45         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        22.39        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F 
       35.90        31.00        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        24.33        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        92.88       114.90        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        89.59        63.58        83.64 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       86.99        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
        4.87        28.67        23.93         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-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        48.79 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-DF-A2KN TCGA-DF-A2KU TCGA-DF-A2KV 
        8.48        58.95        15.88         2.20       100.83        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        79.10        58.95         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       45.57        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-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 
       51.52        34.39        50.73        35.15        38.07        46.42 
TCGA-EO-A3B1 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       26.96        38.47        51.09        14.99        54.15        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM 
       24.36        27.16        23.34        23.34        33.34        32.71 
TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX 
       19.27        22.03        16.11        32.78        15.81        37.05 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       19.33        12.59        22.82        20.05        45.76        31.04 
TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
       14.14        14.70        16.96        68.38        39.88         7.99 
TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX 
       25.22        59.01         9.34        30.67        59.28        78.38 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-PG-A6IB 
        1.74        17.75        14.04        13.28         9.47        21.30 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       38.70        22.59         8.19        17.16         6.97        22.65 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       39.95        24.95        23.64        14.83        20.75        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.30              0.07 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           118.19            225.50 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           27.290            30.555 
[1] "0.3 - 118.2 (27.3)" "0.1 - 225.5 (30.6)"
[1] "hr=" "2.6"
D81V2, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    47  34
  XP LOSS WILD-TYPE 243 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     47   34
  XP LOSS WILD-TYPE  243  190
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               47               243
  YES              34               190
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  XP LOSS MUTATED                                        34
  XP LOSS WILD-TYPE                                     370
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  XP LOSS MUTATED                               5
  XP LOSS WILD-TYPE                            17
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  XP LOSS MUTATED                                  47
  XP LOSS WILD-TYPE                                66
D81V3, multiclass
                                         clus
vv                                        XP LOSS MUTATED XP LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              34               370
  MIXED SEROUS AND ENDOMETRIOID                         5                17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    47                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  XP LOSS MUTATED    55   2   6   9
  XP LOSS WILD-TYPE 316  20  10  31
D81V4, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  R0              55               316
  R1               2                20
  R2               6                10
  RX               9                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"

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    47  22
  XQ LOSS WILD-TYPE 400  68
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               69               468 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               22                68 
$`XQ LOSS MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A2QM TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       41.06        29.39       110.63        57.80        93.99        67.66 
TCGA-AX-A1CR TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-BG-A0M8 TCGA-BG-A0YV 
       23.05        27.88         1.38        80.38        66.41        12.56 
TCGA-KJ-A3U4 TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-A5-A2K2 TCGA-A5-A7WK 
       36.00        65.75        60.53        37.91       118.19        18.41 
TCGA-AJ-A3BF TCGA-AJ-A3I9 TCGA-AP-A052 TCGA-AP-A05J TCGA-AP-A1DQ TCGA-AW-A1PO 
       18.12        17.06        21.99        36.89        46.78         0.56 
TCGA-AX-A1C7 TCGA-AX-A1CF TCGA-AX-A1CK TCGA-AX-A3G4 TCGA-B5-A0K3 TCGA-B5-A0K8 
       34.65        76.83        80.25         0.30        27.29        27.85 
TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1N2 TCGA-B5-A3FD TCGA-B5-A5OE TCGA-BG-A18C 
       52.04       102.31        31.36        39.35        34.95        15.45 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-D1-A0ZZ TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A16V 
       35.08        31.00        22.55        31.07        18.67         3.95 
TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-D1-A3DH 
       14.73        28.08        13.22         2.07         4.27        18.84 
TCGA-DF-A2KR TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY TCGA-EO-A3AS TCGA-EO-A3KW 
       71.61         9.37        12.39       110.10        34.39        16.34 
TCGA-EY-A1GJ TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A2OQ 
       23.90        18.84        17.62        22.03        11.08        29.10 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-FI-A2D2 TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A3PV 
       32.52        11.38        77.33         9.34        28.93        41.56 
TCGA-KP-A3W3 TCGA-PG-A5BC TCGA-PG-A7D5 
       26.10        23.24        38.70 

$`XQ LOSS WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG TCGA-AJ-A3IA 
       88.18        60.53        30.15        16.83        18.08        20.81 
TCGA-AJ-A3NH TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-B5-A0KB 
       10.19        95.47        12.26        36.39        61.18        27.09 
TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       22.06        61.87        51.55        14.27         1.81        19.79 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK 
        4.44        47.84        16.93        33.30         6.21        22.78 
TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 
       17.88        10.19        14.40        18.87        17.92        19.89 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KP-A3VZ TCGA-4E-A92E 
        5.88        66.77        13.84        73.32        23.74         0.43 
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       39.52        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       123.68        74.10 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        73.87        36.82        28.27        54.02        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-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K3 
       15.95        31.99        31.99        36.33        33.07        66.15 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ 
       28.64        24.72        34.95        25.51        14.96        11.21 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       20.25        14.43        10.26        21.14        19.79        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
       34.36        34.16        18.90        33.90         1.64        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-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-A8CV TCGA-AJ-A8CW TCGA-AP-A051 
       12.82        20.78         2.70        35.11         0.13       129.80 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05N 
       23.31        86.07        48.03        63.91        45.53        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       12.62        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR 
       71.67        90.97        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        60.23        45.86        27.85        51.12        21.90 
TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       36.13        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        61.08        35.74        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 
       43.82        40.11        77.39        13.28        32.91        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       26.37        32.02        25.91        34.09        85.48        73.41 
TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA 
       37.58         4.77        30.12        71.24        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       34.32        46.49        38.24        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-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.20        20.52         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        86.37        55.30        59.24 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.01        58.75        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E 
       72.62        57.76        64.21        63.55        13.45        59.84 
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        73.64 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       61.68        85.78        32.09        77.23        73.28        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       225.50 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        51.45        14.70        48.43        11.87        52.54 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 
      136.60        96.30        93.50        71.84        27.65        29.65 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       41.06        34.13        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        71.24        63.68        74.63        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       48.56        23.47        43.30        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        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-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       15.45         9.57        20.02        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C 
       22.39        35.90        34.98        35.90        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 
       24.33        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        92.88       114.90 
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 
       89.59        63.58        83.64        86.99        66.48        16.83 
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-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-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y 
       29.92        33.63        10.65         0.69         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       19.53         6.64        30.15        18.02         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-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 
        1.41         0.72        18.25        16.87        18.02        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        1.05         3.95        48.79         8.48        58.95        15.88 
TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY 
       17.29         2.20       109.08       100.83        89.33        10.92 
TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       27.16        25.91        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        79.10        58.95         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       45.57        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-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       51.52        51.42        19.40        50.73        35.15        38.07 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KX TCGA-EO-A3L0 
       27.16        46.42        26.96        22.26        38.47        51.09 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99        54.15        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GT TCGA-EY-A1GU 
       23.34        33.34        32.71        19.27        16.11        32.78 
TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON 
       15.81        37.05        19.33        12.59        22.82        20.05 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 
       45.76        31.04        27.35        14.14        14.70        16.96 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       68.38        39.88         7.99        25.22        96.69        59.01 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ 
       30.67        59.28        78.38         1.74        17.75        14.04 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A915 
       13.28         9.47        18.21        21.30        22.59         8.19 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       17.16         6.97        22.65        39.95        24.95        23.64 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83         4.44        20.75        18.28         0.07         0.23 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.30              0.07 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           118.19            225.50 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            28.93             30.05 
[1] "0.3 - 118.2 (28.9)" "0.1 - 225.5 (30.0)"
[1] "hr=" "2.2"
D82V2, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    42  23
  XQ LOSS WILD-TYPE 248 201
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     42   23
  XQ LOSS WILD-TYPE  248  201
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               42               248
  YES              23               201
[1] 2 2
[1] FALSE
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  XQ LOSS MUTATED                                        31
  XQ LOSS WILD-TYPE                                     373
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  XQ LOSS MUTATED                               4
  XQ LOSS WILD-TYPE                            18
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  XQ LOSS MUTATED                                  35
  XQ LOSS WILD-TYPE                                78
D82V3, multiclass
                                         clus
vv                                        XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              31               373
  MIXED SEROUS AND ENDOMETRIOID                         4                18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    35                78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  XQ LOSS MUTATED    43   2   5   7
  XQ LOSS WILD-TYPE 328  20  11  33
D82V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              43               328
  R1               2                20
  R2               5                11
  RX               7                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"
