[1] "ofn"      "-oTOV-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/OV-TP/22507289/OV-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/OV-TP/22534547/transformed.cor.cli.txt"

nPatients in clinical file=590, in cluster file=579, common to both=573
[1]  82 573
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              173               400 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              173               400 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              221               352 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              221               352 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              186               387 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              186               387 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              153               420 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              153               420 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              162               411 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              162               411 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              275               298 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              275               298 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               61               512 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               61               512 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               32               541 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               32               541 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              197               376 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              197               376 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               59               514 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               59               514 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              171               402 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              171               402 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              100               473 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              100               473 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              176               397 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              176               397 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              200               373 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              200               373 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              125               448 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              125               448 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              248               325 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              248               325 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               89               484 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               89               484 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               43               530 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               43               530 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               187                386 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               187                386 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               108                465 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               108                465 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                73                500 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                73                500 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
               112                461 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
               112                461 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               256                317 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               256                317 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               177                396 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               177                396 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                61                512 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                61                512 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                57                516 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                57                516 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                38                535 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                38                535 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                59                514 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                59                514 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                32                541 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                32                541 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                21                552 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                21                552 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                41                532 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                41                532 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               119                454 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               119                454 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                67                506 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                67                506 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               169                404 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               169                404 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               162                411 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               162                411 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               286                287 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               286                287 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               325                248 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               325                248 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               107                466 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               107                466 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                23                550 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                23                550 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               78               495 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               78               495 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              108               465 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              108               465 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               60               513 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               60               513 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               40               533 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               40               533 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               52               521 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               52               521 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               62               511 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               62               511 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               96               477 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               96               477 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               42               531 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               42               531 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              312               261 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              312               261 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              360               213 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              360               213 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              132               441 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              132               441 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              226               347 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              226               347 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              159               414 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              159               414 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              236               337 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              236               337 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
              121               452 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
              121               452 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               79               494 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               79               494 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              268               305 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              268               305 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               90               483 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               90               483 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              264               309 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              264               309 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              287               286 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              287               286 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                98                475 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                98                475 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               127                446 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               127                446 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               198                375 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               198                375 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               147                426 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               147                426 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                78                495 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                78                495 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               105                468 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               105                468 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               304                269 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               304                269 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               216                357 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               216                357 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               277                296 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               277                296 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               332                241 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               332                241 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               409                164 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               409                164 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               474                 99 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               474                 99 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               384                189 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               384                189 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               229                344 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               229                344 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               285                288 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               285                288 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               182                391 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               182                391 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               173                400 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               173                400 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                50                523 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                50                523 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                33                540 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                33                540 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               198                375 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               198                375 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               429                144 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               429                144 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              324               249 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              324               249 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              281               292 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              281               292 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "KARNOFSKY_PERFORMANCE_SCORE"         
[14] "HISTOLOGICAL_TYPE"                   
[15] "TUMOR_GRADE"                         
[16] "TUMOR_STAGE"                         
[17] "DAYS_TO_TUMOR_RECURRENCE"            
[18] "CHEMO_THERAPY"                       
[19] "RESIDUAL_TUMOR"                      
[20] "ETHNICITY"                           

Input Data has 20 rows and 573 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=302,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=211,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'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 7:'PATHOLOGY_T_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_T_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_N_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "GENDER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HISTOLOGICAL_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'TUMOR_GRADE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_GRADE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 16:'TUMOR_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 17:'DAYS_TO_TUMOR_RECURRENCE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DAYS_TO_TUMOR_RECURRENCE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 18:'CHEMO_THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "CHEMO_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 19:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 573 columns, 1 survival variables, and 6 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"              "TUMOR_TISSUE_SITE"          
[3] "RADIATION_THERAPY"           "KARNOFSKY_PERFORMANCE_SCORE"
[5] "RESIDUAL_TUMOR"              "ETHNICITY"                  
YEARS_TO_BIRTH, nv=55, binary=FALSE, numeric=TRUE
TUMOR_TISSUE_SITE, nv=3, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=6, binary=FALSE, numeric=TRUE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED    63 104
  1P GAIN WILD-TYPE 165 227
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              167               392 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              104               227 
$`1P GAIN MUTATED`
TCGA-5X-AA5U TCGA-04-1336 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 
       11.87        49.15        18.51        11.87        65.52        63.09 
TCGA-04-1364 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1649 TCGA-04-1655 
       33.67        38.37       119.08        29.10        64.64        45.37 
TCGA-09-1659 TCGA-09-1667 TCGA-09-1670 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 
        9.99        61.87        17.98        35.15         4.54       112.41 
TCGA-09-2051 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1495 TCGA-13-1496 
       63.09        83.31        55.23        81.01        90.38         4.24 
TCGA-13-1504 TCGA-13-1506 TCGA-13-2061 TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
       34.82        34.16        76.90         8.42        23.05        25.94 
TCGA-20-0991 TCGA-23-1031 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1124 
       26.20        18.90        33.30        86.01       129.96        58.13 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2079 TCGA-23-2084 TCGA-24-0982 
        0.53        24.95       115.89        91.66        49.84        22.32 
TCGA-24-1104 TCGA-24-1417 TCGA-24-1418 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 
       63.55         7.82         7.99        18.64        18.67         8.55 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
       12.46        45.14         9.11         1.18        22.22        26.96 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1564 
       16.21        56.58        39.88        19.53        44.09        25.87 
TCGA-24-1565 TCGA-24-1614 TCGA-24-1842 TCGA-24-1843 TCGA-24-1845 TCGA-24-1924 
       10.26        48.33         8.32         3.48         3.81        30.21 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2026 TCGA-24-2029 TCGA-24-2038 TCGA-24-2254 
       11.05        81.11        34.82        14.43        44.52        57.07 
TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2290 TCGA-24-2297 TCGA-25-1312 
       31.63        70.45        44.61        36.23        55.86         1.02 
TCGA-25-1313 TCGA-25-1317 TCGA-25-1321 TCGA-25-1323 TCGA-25-1329 TCGA-25-1626 
       26.96         2.01        33.96        12.99        15.02        17.03 
TCGA-25-1627 TCGA-25-1630 TCGA-25-1633 TCGA-25-1635 TCGA-25-1877 TCGA-25-2392 
       12.95        38.20        62.17        52.04        24.00         1.02 
TCGA-25-2400 TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 TCGA-29-1707 TCGA-29-1710 
       42.02        68.32        16.93        23.93        41.98        31.27 
TCGA-29-1761 TCGA-29-1763 TCGA-29-1764 TCGA-29-1769 TCGA-29-1770 TCGA-29-1775 
       17.36        66.81        62.93        22.98        24.36        12.36 
TCGA-29-1777 TCGA-29-1783 TCGA-29-1784 TCGA-29-2425 TCGA-29-2432 TCGA-30-1714 
       12.30         7.23         5.36        65.00        21.47        38.07 
TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 
       51.91         2.47        15.68         6.12        36.62         1.22 
TCGA-31-1959 TCGA-36-1569 TCGA-36-1577 TCGA-36-1581 TCGA-36-2529 TCGA-36-2551 
        2.20        29.10        25.74        24.69        35.05        16.18 
TCGA-42-2582 TCGA-42-2587 TCGA-57-1582 TCGA-57-1994 TCGA-59-2351 TCGA-59-2355 
       47.57        23.74        24.03        25.02       116.12         2.14 
TCGA-61-1722 TCGA-61-1730 TCGA-61-1733 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 
        8.09         4.34        31.79        35.80         2.43        33.67 
TCGA-61-1743 TCGA-61-1899 TCGA-61-1906 TCGA-61-1911 TCGA-61-1914 TCGA-61-1919 
       43.69         8.42        34.13        42.51        56.61        38.17 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2088 TCGA-61-2092 TCGA-61-2097 TCGA-61-2102 
       30.64        39.85         4.77        51.72        60.62         6.48 
TCGA-61-2104 TCGA-61-2109 TCGA-61-2111 TCGA-61-2614 TCGA-OY-A56P TCGA-09-0365 
       76.87        20.68       125.75         8.61        39.68         9.47 
TCGA-09-0366 TCGA-09-0369 TCGA-10-0930 TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 
       57.76        35.57        34.19        24.59        39.58         2.73 
TCGA-13-0726 TCGA-13-0751 TCGA-13-0757 TCGA-13-0760 TCGA-13-0795 TCGA-13-0885 
       31.20        55.17        11.18        11.54        20.35       111.39 
TCGA-13-0888 TCGA-13-0893 TCGA-13-0897 TCGA-13-0911 TCGA-13-0919 
       92.42        43.36        71.74        44.55        84.53 

$`1P GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 
       13.81        20.52        43.92        41.00         1.81         2.01 
TCGA-04-1338 TCGA-04-1341 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 
       46.62         1.08        48.76        21.57        63.98        65.46 
TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 
        0.53        49.28        32.52        44.32        76.57       103.40 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1542 
       82.39        56.55        41.59        19.99         0.79        84.20 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1651 TCGA-04-1652 
       55.43        48.89        27.88        28.64        36.23        31.86 
TCGA-04-1654 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 
       47.70        38.43        89.33        74.93        41.62        57.60 
TCGA-09-1668 TCGA-09-1669 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 
       55.36        30.51         5.85         3.02         8.55        97.55 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2050 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 
        6.18         6.12        71.11        39.75        20.94        26.93 
TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1409 TCGA-13-1411 
       12.46        77.10        81.17        28.54        57.27        17.46 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
       32.35        54.64        87.06        61.71        29.42       124.44 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
       20.68        22.39        70.82        83.93        52.44       125.56 
TCGA-13-1494 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 
       93.90       127.27        66.15       115.07        13.97        43.20 
TCGA-13-1505 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
       65.69        65.52        80.15        44.68        54.25        14.53 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2065 TCGA-13-A5FT TCGA-20-0996 
       80.02        78.48        77.88        65.52        70.45        72.20 
TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 
       27.52        25.38        19.10        16.70         2.93         2.66 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
       47.54        49.68        40.54        15.39        26.83        32.09 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 
       49.41         8.81        29.13         2.76        51.35        54.51 
TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1120 TCGA-23-1121 
        3.22        31.20        68.68        19.46         4.27         6.38 
TCGA-23-1122 TCGA-23-1123 TCGA-23-2078 TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 
       39.09        33.47        87.48        77.00         2.76         4.70 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        4.50         7.63        11.64        21.80        41.56         7.66 
TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1419 TCGA-24-1422 
       54.12        47.41         6.31         6.38         7.86         0.76 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        6.25         6.02         5.95         5.36         4.83        17.39 
TCGA-24-1430 TCGA-24-1435 TCGA-24-1463 TCGA-24-1467 TCGA-24-1470 TCGA-24-1545 
       28.37        43.53        72.92       105.99         3.45        57.40 
TCGA-24-1546 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       64.27        41.06        51.91        41.39        58.09        88.50 
TCGA-24-1556 TCGA-24-1562 TCGA-24-1563 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 
       70.62        45.50        47.70        17.23        90.15        88.37 
TCGA-24-1616 TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 
       38.24         3.72         4.37        11.28         5.79         5.52 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1927 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 
        9.80        22.68        16.44         4.87       152.02        44.84 
TCGA-24-2024 TCGA-24-2027 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 
       58.16       109.71        55.92        18.48        28.18        64.01 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2288 TCGA-24-2289 
       36.16         0.79         0.36        47.54         0.82        67.36 
TCGA-24-2293 TCGA-24-2295 TCGA-24-2298 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 
       16.64        33.11        53.26        33.01        52.04        42.05 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 TCGA-25-1623 TCGA-25-1625 
       34.98        65.00        37.97         2.99        18.58        27.62 
TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 
       20.61         0.30        59.15        35.87        14.96        24.99 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 
       85.05        13.02        49.05        38.04         3.02        12.00 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       45.01        19.99         2.96        29.03        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 
       78.90        47.61        48.33       101.79        39.02        40.41 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 TCGA-29-1703 TCGA-29-1705 TCGA-29-1711 
       33.93        31.20        36.36        59.67        18.25        34.62 
TCGA-29-1762 TCGA-29-1766 TCGA-29-1768 TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 
       86.60        39.42        31.30        22.55        17.33        11.84 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2428 
       14.93         8.38        36.30        86.17        62.47        45.11 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1853 
       13.84        42.25        11.47         9.76        35.77        36.26 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1880 TCGA-30-1887 
        0.26        48.10        44.91        34.78        57.57        24.26 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 
       30.05        48.79        45.57        30.18        18.77        22.49 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 
        6.71        42.51        44.12        28.77        21.53        22.85 
TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1578 TCGA-36-1580 TCGA-36-2530 
       22.55         8.55        30.08        27.85        24.23        33.01 
TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 
       29.49        29.82        25.91        25.08        23.80        21.60 
TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 
        2.24        20.98        18.31        20.52        14.17         6.05 
TCGA-36-2552 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 
       11.47        28.93        42.02        10.42        40.77         1.48 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 
       11.38        21.14         1.74        22.32        29.00        25.08 
TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 
      180.20        80.12        22.32         9.40        34.39         5.42 
TCGA-59-2372 TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 
       44.81        11.11        20.94        31.43        18.54        27.88 
TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1895 TCGA-61-1900 TCGA-61-1901 
       28.47        48.79        44.84         1.45         5.79        11.41 
TCGA-61-1903 TCGA-61-1904 TCGA-61-1907 TCGA-61-1910 TCGA-61-1913 TCGA-61-1915 
       13.02         9.07        31.30        37.05        48.92        67.76 
TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       43.43        15.75         2.01         5.52        14.50        17.98 
TCGA-61-2003 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
        4.01        30.64         1.18        45.96        45.40         4.80 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 TCGA-61-2101 TCGA-61-2110 
       71.74        61.64        58.39        65.52        55.50        44.52 
TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       22.22         6.35        31.07        18.94         0.79         9.99 
TCGA-09-0364 TCGA-09-0367 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       29.16        17.98        54.31        25.91        81.86        18.51 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 
       32.88        14.66         6.71        35.44        36.92        19.99 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 
       20.91         6.21        44.55        12.39        15.19        17.82 
TCGA-13-0755 TCGA-13-0758 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 
        2.50        11.38        38.01       111.78        61.84        56.71 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 
       58.65        40.24       118.42       107.28        63.09        69.73 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 
       83.34        87.48        45.99        51.02        43.86        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 TCGA-13-0887 
       35.31        13.61        68.94       107.18       153.37        66.67 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
       95.15       145.45       102.84        66.15       134.04        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
      127.79        50.37       123.16       118.98        60.59       116.65 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 
       37.64       109.32        58.68        48.79        48.76        83.74 
TCGA-13-0924 TCGA-13-2071 
       85.94        25.41 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.53              0.26 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           129.96            180.20 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            31.20             33.29 
[1] "0.5 - 130.0 (31.2)" "0.3 - 180.2 (33.3)"
[1] "hr=" "1.2"
D1V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  1P GAIN MUTATED         1   165                1
  1P GAIN WILD-TYPE       2   393                1
D1V3, multiclass
                  clus
vv                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  OMENTUM                        1                 2
  OVARY                        165               393
  PERITONEUM OVARY               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V4, binary
                   cls
clus                  0   1
  1P GAIN MUTATED   161   2
  1P GAIN WILD-TYPE 380   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED    161    2
  1P GAIN WILD-TYPE  380    3
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO              161               380
  YES               2                 3
[1] 2 2
[1] FALSE
D1V5, continuous
                   vv
clus                R0 R1 R2 RX
  1P GAIN MUTATED    2  7  2  0
  1P GAIN WILD-TYPE 13 19  3  3
D1V6, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0               2                13
  R1               7                19
  R2               2                 3
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     1  84
  1P GAIN WILD-TYPE   9 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1   84
  1P GAIN WILD-TYPE    9  243
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              84               243
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    84 129
  1Q GAIN WILD-TYPE 144 202
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              213               346 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              129               202 
$`1Q GAIN MUTATED`
TCGA-5X-AA5U TCGA-04-1336 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 
       11.87        49.15        18.51        11.87        65.52        63.09 
TCGA-04-1356 TCGA-04-1364 TCGA-04-1514 TCGA-04-1516 TCGA-04-1525 TCGA-04-1530 
       49.28        33.67        56.55        41.59        38.37       119.08 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1649 TCGA-04-1652 TCGA-04-1655 
       29.10        84.20        55.43        64.64        31.86        45.37 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1667 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 
        9.99        38.43        61.87        55.36        17.98         5.85 
TCGA-09-1674 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2051 
        8.55         6.12        35.15         4.54       112.41        63.09 
TCGA-09-2056 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1481 TCGA-13-1484 
       12.46        55.23        57.27        81.01        87.06       124.44 
TCGA-13-1495 TCGA-13-1504 TCGA-13-1506 TCGA-13-2061 TCGA-13-A5FU TCGA-20-0987 
       90.38        34.82        34.16        76.90         8.42        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-20-1683 TCGA-20-1684 TCGA-23-1031 TCGA-23-1114 
       25.94        26.20        25.38        19.10        18.90        68.68 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 
       86.01       129.96        58.13         0.53        24.95       115.89 
TCGA-24-0982 TCGA-24-1104 TCGA-24-1413 TCGA-24-1418 TCGA-24-1422 TCGA-24-1423 
       22.32        63.55         6.31         7.99         0.76         6.25 
TCGA-24-1431 TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1471 
       18.64         8.55        12.46        45.14         9.11         1.18 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1548 TCGA-24-1549 TCGA-24-1553 TCGA-24-1557 
       22.22        26.96        16.21        56.58        58.09        39.88 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1564 TCGA-24-1565 TCGA-24-1604 TCGA-24-1614 
       19.53        44.09        25.87        10.26        88.37        48.33 
TCGA-24-1842 TCGA-24-1843 TCGA-24-1845 TCGA-24-1850 TCGA-24-1924 TCGA-24-1930 
        8.32         3.48         3.81         5.52        30.21        81.11 
TCGA-24-2020 TCGA-24-2026 TCGA-24-2029 TCGA-24-2038 TCGA-24-2254 TCGA-24-2271 
      152.02        34.82        14.43        44.52        57.07        31.63 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2290 TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 
       70.45        44.61        36.23        55.86         1.02        26.96 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 
       42.05         2.01        34.98        65.00        37.97        33.96 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1626 TCGA-25-1627 TCGA-25-1630 TCGA-25-1633 
       12.99        15.02        17.03        12.95        38.20        62.17 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1871 TCGA-25-1877 TCGA-25-2392 TCGA-25-2396 
       35.87        52.04        24.99        24.00         1.02         3.02 
TCGA-25-2400 TCGA-29-1688 TCGA-29-1690 TCGA-29-1695 TCGA-29-1698 TCGA-29-1701 
       42.02        78.90        47.61        40.41        68.32        16.93 
TCGA-29-1702 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1763 TCGA-29-1764 
       23.93        41.98        31.27        34.62        66.81        62.93 
TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1777 
       39.42        22.98        24.36        17.33        12.36        12.30 
TCGA-29-1783 TCGA-29-1784 TCGA-29-2425 TCGA-29-2432 TCGA-29-2434 TCGA-29-A5NZ 
        7.23         5.36        65.00        21.47        11.47        35.77 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1862 TCGA-30-1866 
       38.07        51.91         2.47        15.68         6.12        36.62 
TCGA-30-1867 TCGA-31-1959 TCGA-36-1569 TCGA-36-1571 TCGA-36-1576 TCGA-36-1581 
        1.22         2.20        29.10        22.85        30.08        24.69 
TCGA-36-2529 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-57-1582 
       35.05        16.18        11.47        47.57        23.74        24.03 
TCGA-57-1586 TCGA-57-1994 TCGA-59-2351 TCGA-59-2355 TCGA-61-1722 TCGA-61-1730 
       22.32        25.02       116.12         2.14         8.09         4.34 
TCGA-61-1733 TCGA-61-1734 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 
       31.79        28.47        35.80         2.43        33.67        43.69 
TCGA-61-1899 TCGA-61-1904 TCGA-61-1906 TCGA-61-1911 TCGA-61-1914 TCGA-61-1919 
        8.42         9.07        34.13        42.51        56.61        38.17 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2088 TCGA-61-2092 TCGA-61-2097 
        4.01        30.64        39.85         4.77        51.72        60.62 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2111 
       65.52        55.50         6.48        76.87        20.68       125.75 
TCGA-61-2614 TCGA-OY-A56P TCGA-09-0365 TCGA-09-0366 TCGA-09-0369 TCGA-10-0930 
        8.61        39.68         9.47        57.76        35.57        34.19 
TCGA-10-0933 TCGA-10-0935 TCGA-10-0938 TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 
       14.66        35.44        20.91        24.59        39.58         2.73 
TCGA-13-0727 TCGA-13-0751 TCGA-13-0757 TCGA-13-0760 TCGA-13-0762 TCGA-13-0795 
       15.19        55.17        11.18        11.54       111.78        20.35 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0888 TCGA-13-0890 TCGA-13-0897 TCGA-13-0901 
       83.34        87.48        92.42       145.45        71.74        19.36 
TCGA-13-0911 TCGA-13-0919 TCGA-13-0921 
       44.55        84.53        48.76 

$`1Q GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 
       13.81        20.52        43.92        41.00         1.81         2.01 
TCGA-04-1338 TCGA-04-1341 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 
       46.62         1.08        48.76        21.57        63.98        65.46 
TCGA-04-1353 TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 
        0.53        32.52        44.32        76.57       103.40        82.39 
TCGA-04-1517 TCGA-04-1519 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1651 
       19.99         0.79        48.89        27.88        28.64        36.23 
TCGA-04-1654 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 
       47.70        89.33        74.93        41.62        57.60        30.51 
TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 TCGA-09-2050 TCGA-09-2053 TCGA-09-2054 
        3.02        97.55         6.18        71.11        39.75        20.94 
TCGA-09-2055 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1411 
       26.93        77.10        81.17        28.54        83.31        17.46 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 
       32.35        54.64        61.71        29.42        20.68        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1496 
       70.82        83.93        52.44       125.56        93.90         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1505 
      127.27        66.15       115.07        13.97        43.20        65.69 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 
       65.52        80.15        44.68        54.25        14.53        80.02 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2065 TCGA-13-A5FT TCGA-20-0996 TCGA-20-1682 
       78.48        77.88        65.52        70.45        72.20        27.52 
TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 
       16.70         2.93         2.66        47.54        49.68        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
       15.39        26.83        32.09        49.41         8.81        29.13 
TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 
        2.76        51.35        54.51         3.22        31.20        19.46 
TCGA-23-1117 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-2078 
       33.30         4.27         6.38        39.09        33.47        87.48 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 
       91.66        77.00        49.84         2.76         4.70         4.50 
TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 
        7.63        11.64        21.80        41.56         7.66        54.12 
TCGA-24-1105 TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 TCGA-24-1424 TCGA-24-1425 
       47.41         6.38         7.82         7.86         6.02         5.95 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1434 TCGA-24-1435 
        5.36         4.83        17.39        28.37        18.67        43.53 
TCGA-24-1463 TCGA-24-1467 TCGA-24-1470 TCGA-24-1545 TCGA-24-1546 TCGA-24-1550 
       72.92       105.99         3.45        57.40        64.27        41.06 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 TCGA-24-1556 TCGA-24-1562 TCGA-24-1563 
       51.91        41.39        88.50        70.62        45.50        47.70 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1616 TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 
       17.23        90.15        38.24         3.72         4.37        11.28 
TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 
        5.79         9.80        22.68        16.44        11.05         4.87 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 
       44.84        58.16       109.71        55.92        18.48        28.18 
TCGA-24-2036 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2288 
       64.01        36.16         0.79         0.36        47.54         0.82 
TCGA-24-2289 TCGA-24-2293 TCGA-24-2295 TCGA-24-2298 TCGA-25-1314 TCGA-25-1315 
       67.36        16.64        33.11        53.26        33.01        52.04 
TCGA-25-1322 TCGA-25-1623 TCGA-25-1625 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 
        2.99        18.58        27.62        20.61         0.30        59.15 
TCGA-25-1870 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2397 
       14.96        85.05        13.02        49.05        38.04        12.00 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       45.01        19.99         2.96        29.03        31.00        26.99 
TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 
       48.33       101.79        39.02        33.93        31.20        36.36 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1761 TCGA-29-1762 TCGA-29-1768 TCGA-29-1771 
       59.67        18.25        17.36        86.60        31.30        22.55 
TCGA-29-1776 TCGA-29-1778 TCGA-29-1781 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 
       11.84        14.93         8.38        36.30        86.17        62.47 
TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2436 TCGA-30-1853 TCGA-30-1857 
       45.11        13.84        42.25         9.76        36.26         0.26 
TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 
       48.10        44.91        34.78        57.57        24.26        30.05 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 
       48.79        45.57        30.18        18.77        22.49         6.71 
TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1570 TCGA-36-1574 TCGA-36-1575 
       42.51        44.12        28.77        21.53        22.55         8.55 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       25.74        27.85        24.23        33.01        29.49        29.82 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 
       25.91        25.08        23.80        21.60         2.24        20.98 
TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-42-2588 TCGA-42-2589 
       18.31        20.52        14.17         6.05        28.93        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 
       10.42        40.77         1.48        11.38        21.14         1.74 
TCGA-57-1992 TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2352 
       29.00        25.08       180.20        80.12        22.32         9.40 
TCGA-59-2354 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 
       34.39         5.42        44.81        11.11        20.94        31.43 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1736 TCGA-61-1737 TCGA-61-1895 TCGA-61-1900 
       18.54        27.88        48.79        44.84         1.45         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1907 TCGA-61-1910 TCGA-61-1913 TCGA-61-1915 
       11.41        13.02        31.30        37.05        48.92        67.76 
TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       43.43        15.75         2.01         5.52        14.50        17.98 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2094 
       30.64         1.18        45.96        45.40         4.80        71.74 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2110 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 
       61.64        58.39        44.52        22.22         6.35        31.07 
TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 TCGA-09-0367 TCGA-10-0925 
       18.94         0.79         9.99        29.16        17.98        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0934 TCGA-10-0936 
       25.91        81.86        18.51        32.88         6.71        36.92 
TCGA-10-0937 TCGA-13-0714 TCGA-13-0720 TCGA-13-0725 TCGA-13-0726 TCGA-13-0730 
       19.99         6.21        44.55        12.39        31.20        17.82 
TCGA-13-0755 TCGA-13-0758 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 
        2.50        11.38        38.01        61.84        56.71        58.65 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 TCGA-13-0801 
       40.24       118.42       107.28        63.09        69.73        45.99 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
       51.02        43.86        35.28        35.31        13.61        68.94 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0891 
      107.18       111.39       153.37        66.67        95.15       102.84 
TCGA-13-0893 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       43.36        66.15       134.04       127.79        50.37       123.16 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
      118.98        60.59       116.65        37.64       109.32        58.68 
TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       48.79        83.74        85.94        25.41 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.53              0.26 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           152.02            180.20 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            33.67             32.70 
[1] "0.5 - 152.0 (33.7)" "0.3 - 180.2 (32.7)"
[1] "hr=" "1.1"
D2V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  1Q GAIN MUTATED         2   210                2
  1Q GAIN WILD-TYPE       1   348                0
D2V3, multiclass
                  clus
vv                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  OMENTUM                        2                 1
  OVARY                        210               348
  PERITONEUM OVARY               2                 0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V4, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   210   0
  1Q GAIN WILD-TYPE 331   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    210    0
  1Q GAIN WILD-TYPE  331    5
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO              210               331
  YES               0                 5
[1] 2 2
[1] FALSE
D2V5, continuous
                   vv
clus                R0 R1 R2 RX
  1Q GAIN MUTATED    5  7  2  0
  1Q GAIN WILD-TYPE 10 19  3  3
D2V6, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0               5                10
  R1               7                19
  R2               2                 3
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     4 111
  1Q GAIN WILD-TYPE   6 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      4  111
  1Q GAIN WILD-TYPE    6  216
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 6
  NOT HISPANIC OR LATINO             111               216
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    74 106
  2P GAIN WILD-TYPE 154 225
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              180               379 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              106               225 
$`2P GAIN MUTATED`
TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1336 TCGA-04-1342 TCGA-04-1347 TCGA-04-1350 
       20.52        11.87        49.15        18.51        63.09        63.98 
TCGA-04-1356 TCGA-04-1364 TCGA-04-1371 TCGA-04-1525 TCGA-04-1542 TCGA-04-1646 
       49.28        33.67        82.39        38.37        84.20        27.88 
TCGA-04-1655 TCGA-09-1661 TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 TCGA-09-2043 
       45.37        38.43        17.98         5.85         8.55         6.18 
TCGA-09-2048 TCGA-09-2054 TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 TCGA-13-1412 
        4.54        20.94        83.31        57.27        81.01        32.35 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-2057 TCGA-13-2060 TCGA-13-A5FU 
       43.20        34.82        65.69        80.02        77.88         8.42 
TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1024 TCGA-23-1114 TCGA-23-1118 
        2.93         2.66        47.54        15.39        68.68        86.01 
TCGA-23-1119 TCGA-23-1121 TCGA-23-1122 TCGA-23-1809 TCGA-23-2072 TCGA-23-2078 
      129.96         6.38        39.09         0.53        24.95        87.48 
TCGA-23-2643 TCGA-24-0970 TCGA-24-0982 TCGA-24-1417 TCGA-24-1418 TCGA-24-1422 
        4.70        11.64        22.32         7.82         7.99         0.76 
TCGA-24-1424 TCGA-24-1434 TCGA-24-1436 TCGA-24-1467 TCGA-24-1469 TCGA-24-1471 
        6.02        18.67         8.55       105.99         9.11         1.18 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1552 TCGA-24-1553 TCGA-24-1558 TCGA-24-1560 
       22.22        26.96        41.39        58.09        19.53        44.09 
TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 TCGA-24-1850 
       88.37        38.24         8.32         3.72         3.81         5.52 
TCGA-24-1924 TCGA-24-1928 TCGA-24-2019 TCGA-24-2029 TCGA-24-2033 TCGA-24-2261 
       30.21        11.05         4.87        14.43        18.48         0.79 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2295 TCGA-25-1312 TCGA-25-1315 
       44.61         0.82        67.36        33.11         1.02        52.04 
TCGA-25-1317 TCGA-25-1319 TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1628 
        2.01        65.00        15.02        18.58        17.03        20.61 
TCGA-25-1631 TCGA-25-1634 TCGA-25-1870 TCGA-25-1877 TCGA-25-2391 TCGA-25-2393 
        0.30        35.87        14.96        24.00        49.05        38.04 
TCGA-25-2398 TCGA-25-2400 TCGA-25-2409 TCGA-29-1691 TCGA-29-1695 TCGA-29-1701 
       45.01        42.02        26.99        48.33        40.41        16.93 
TCGA-29-1702 TCGA-29-1763 TCGA-29-1764 TCGA-29-1769 TCGA-29-1774 TCGA-29-1775 
       23.93        66.81        62.93        22.98        17.33        12.36 
TCGA-29-1778 TCGA-29-2425 TCGA-29-2429 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 
       14.93        65.00        13.84        35.77        38.07        51.91 
TCGA-30-1859 TCGA-30-1862 TCGA-31-1950 TCGA-31-1953 TCGA-31-1959 TCGA-36-1568 
       48.10         6.12        18.77         6.71         2.20        28.77 
TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1578 TCGA-36-1581 TCGA-36-2543 
       22.85         8.55        30.08        27.85        24.69         2.24 
TCGA-36-2547 TCGA-36-2552 TCGA-42-2587 TCGA-42-2589 TCGA-57-1582 TCGA-57-1583 
       20.52        11.47        23.74        42.02        24.03        11.38 
TCGA-57-1585 TCGA-57-1586 TCGA-57-1994 TCGA-59-2348 TCGA-59-2352 TCGA-59-2372 
        1.74        22.32        25.02       180.20         9.40        44.81 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1741 TCGA-61-1899 TCGA-61-1900 
       27.88         4.34        31.79        33.67         8.42         5.79 
TCGA-61-1906 TCGA-61-1919 TCGA-61-2000 TCGA-61-2003 TCGA-61-2009 TCGA-61-2018 
       34.13        38.17        14.50         4.01        39.85        45.40 
TCGA-61-2088 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 
        4.77        60.62        65.52        55.50         6.48        76.87 
TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
      125.75        22.22         6.35         8.61        39.68        18.94 
TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0369 TCGA-10-0927 
        9.99        29.16         9.47        57.76        35.57        81.86 
TCGA-10-0933 TCGA-10-0935 TCGA-10-0938 TCGA-13-0724 TCGA-13-0730 TCGA-13-0757 
       14.66        35.44        20.91         2.73        17.82        11.18 
TCGA-13-0760 TCGA-13-0800 TCGA-13-0802 TCGA-13-0884 TCGA-13-0888 TCGA-13-0893 
       11.54        87.48        51.02       107.18        92.42        43.36 
TCGA-13-0899 TCGA-13-0901 TCGA-13-0906 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 
       66.15        19.36       118.98        84.53        48.79        48.76 

$`2P GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1338 
       13.81        43.92        41.00         1.81         2.01        46.62 
TCGA-04-1341 TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 TCGA-04-1349 TCGA-04-1351 
        1.08        11.87        65.52        48.76        21.57        65.46 
TCGA-04-1353 TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 
        0.53        32.52        44.32        76.57       103.40        56.55 
TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1530 TCGA-04-1536 TCGA-04-1638 
       41.59        19.99         0.79       119.08        29.10        55.43 
TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 
       48.89        28.64        64.64        36.23        31.86        47.70 
TCGA-09-1659 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 
        9.99        89.33        74.93        41.62        57.60        61.87 
TCGA-09-1668 TCGA-09-1669 TCGA-09-1673 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 
       55.36        30.51         3.02        97.55         6.12        35.15 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2055 TCGA-09-2056 
      112.41        71.11        63.09        39.75        26.93        12.46 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1411 TCGA-13-1477 
       77.10        81.17        28.54        55.23        17.46        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 
       87.06        61.71        29.42       124.44        20.68        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       70.82        83.93        52.44       125.56        93.90        90.38 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1506 
        4.24       127.27        66.15       115.07        13.97        34.16 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 
       65.52        80.15        44.68        54.25        14.53        78.48 
TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
       76.90        65.52        70.45        23.05        25.94        26.20 
TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-23-1022 
       72.20        27.52        25.38        19.10        16.70        49.68 
TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
       40.54        26.83        32.09        49.41         8.81        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 
       18.90         2.76        51.35        54.51         3.22        31.20 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1120 TCGA-23-1123 TCGA-23-1124 TCGA-23-2077 
       19.46        33.30         4.27        33.47        58.13       115.89 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2645 TCGA-24-0966 
       91.66        77.00        49.84         2.76         4.50         7.63 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 
       21.80        41.56         7.66        54.12        63.55        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1419 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 
        6.31         6.38         7.86         6.25         5.95         5.36 
TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 TCGA-24-1463 
        4.83        17.39        28.37        18.64        43.53        72.92 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1470 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 
       12.46        45.14         3.45        57.40        64.27        16.21 
TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       56.58        41.06        51.91        88.50        70.62        39.88 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       45.50        47.70        25.87        10.26        17.23        90.15 
TCGA-24-1614 TCGA-24-1843 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1920 
       48.33         3.48         4.37        11.28         5.79         9.80 
TCGA-24-1923 TCGA-24-1927 TCGA-24-1930 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 
       22.68        16.44        81.11       152.02        44.84        58.16 
TCGA-24-2026 TCGA-24-2027 TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
       34.82       109.71        55.92        28.18        64.01        44.52 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       57.07        36.16         0.36        47.54        31.63        70.45 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1314 
       36.23        16.64        55.86        53.26        26.96        33.01 
TCGA-25-1316 TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 
       42.05        34.98        37.97        33.96         2.99        12.99 
TCGA-25-1625 TCGA-25-1627 TCGA-25-1630 TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 
       27.62        12.95        38.20        59.15        62.17        52.04 
TCGA-25-1871 TCGA-25-1878 TCGA-25-2042 TCGA-25-2392 TCGA-25-2396 TCGA-25-2397 
       24.99        85.05        13.02         1.02         3.02        12.00 
TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 
       19.99         2.96        29.03        31.00        78.90        47.61 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
      101.79        39.02        33.93        31.20        68.32        36.36 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 
       59.67        18.25        41.98        31.27        34.62        17.36 
TCGA-29-1762 TCGA-29-1766 TCGA-29-1768 TCGA-29-1770 TCGA-29-1771 TCGA-29-1776 
       86.60        39.42        31.30        24.36        22.55        11.84 
TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 
       12.30         8.38         7.23         5.36        36.30        86.17 
TCGA-29-2427 TCGA-29-2428 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 
       62.47        45.11        42.25        21.47        11.47         9.76 
TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1860 TCGA-30-1861 
       36.26         2.47        15.68         0.26        44.91        34.78 
TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 
       36.62         1.22        57.57        24.26        30.05        48.79 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1955 TCGA-31-1956 TCGA-36-1569 
       45.57        30.18        22.49        42.51        44.12        29.10 
TCGA-36-1570 TCGA-36-1574 TCGA-36-1577 TCGA-36-1580 TCGA-36-2529 TCGA-36-2530 
       21.53        22.55        25.74        24.23        35.05        33.01 
TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 
       29.49        29.82        25.91        25.08        23.80        21.60 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-42-2582 
       20.98        18.31        14.17         6.05        16.18        47.57 
TCGA-42-2588 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1584 TCGA-57-1992 
       28.93        10.42        40.77         1.48        21.14        29.00 
TCGA-57-1993 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2354 TCGA-59-2355 
       25.08        80.12        22.32       116.12        34.39         2.14 
TCGA-59-2363 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
        5.42        11.11         8.09        20.94        31.43        18.54 
TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1743 
       28.47        48.79        44.84        35.80         2.43        43.69 
TCGA-61-1895 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1907 TCGA-61-1910 
        1.45        11.41        13.02         9.07        31.30        37.05 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 
       42.51        48.92        56.61        67.76        43.43        15.75 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2002 TCGA-61-2008 TCGA-61-2012 TCGA-61-2016 
        2.01         5.52        17.98        30.64        30.64         1.18 
TCGA-61-2017 TCGA-61-2087 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 
       45.96         4.80        51.72        71.74        61.64        58.39 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2613 TCGA-VG-A8LO TCGA-09-0367 TCGA-10-0925 
       20.68        44.52        31.07         0.79        17.98        54.31 
TCGA-10-0926 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 TCGA-10-0936 
       25.91        18.51        34.19        32.88         6.71        36.92 
TCGA-10-0937 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 
       19.99         6.21        24.59        44.55        39.58        12.39 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0751 TCGA-13-0755 TCGA-13-0758 TCGA-13-0761 
       31.20        15.19        55.17         2.50        11.38        38.01 
TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 
      111.78        61.84        56.71        58.65        40.24       118.42 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 
      107.28        63.09        20.35        69.73        83.34        45.99 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0885 
       43.86        35.28        35.31        13.61        68.94       111.39 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0897 
      153.37        66.67        95.15       145.45       102.84        71.74 
TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0908 TCGA-13-0910 
      134.04       127.79        50.37       123.16        60.59       116.65 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0923 TCGA-13-0924 
       44.55        37.64       109.32        58.68        83.74        85.94 
TCGA-13-2071 
       25.41 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.30              0.26 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           180.20            153.37 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            24.82             34.98 
[1] "0.3 - 180.2 (24.8)" "0.3 - 153.4 (35.0)"
[1] "hr=" "1.2"
D3V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  2P GAIN MUTATED         1   180                0
  2P GAIN WILD-TYPE       2   378                2
D3V3, multiclass
                  clus
vv                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  OMENTUM                        1                 2
  OVARY                        180               378
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V4, binary
                   cls
clus                  0   1
  2P GAIN MUTATED   175   0
  2P GAIN WILD-TYPE 366   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED    175    0
  2P GAIN WILD-TYPE  366    5
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO              175               366
  YES               0                 5
[1] 2 2
[1] FALSE
D3V5, continuous
                   vv
clus                R0 R1 R2 RX
  2P GAIN MUTATED    5  7  2  1
  2P GAIN WILD-TYPE 10 19  3  2
D3V6, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0               5                10
  R1               7                19
  R2               2                 3
  RX               1                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     3  97
  2P GAIN WILD-TYPE   7 230
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      3   97
  2P GAIN WILD-TYPE    7  230
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 7
  NOT HISPANIC OR LATINO              97               230
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    60  88
  2Q GAIN WILD-TYPE 168 243
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              148               411 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               88               243 
$`2Q GAIN MUTATED`
TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1347 TCGA-04-1350 TCGA-04-1356 TCGA-04-1364 
       20.52        11.87        63.09        63.98        49.28        33.67 
TCGA-04-1516 TCGA-04-1536 TCGA-04-1542 TCGA-04-1646 TCGA-04-1649 TCGA-04-1655 
       41.59        29.10        84.20        27.88        64.64        45.37 
TCGA-09-1661 TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 TCGA-09-2043 TCGA-09-2048 
       38.43        17.98         5.85         8.55         6.18         4.54 
TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 TCGA-13-1412 TCGA-13-1488 TCGA-13-1496 
       83.31        57.27        81.01        32.35        70.82         4.24 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-2057 TCGA-13-2060 TCGA-20-1687 
       43.20        34.82        65.69        80.02        77.88         2.66 
TCGA-23-1021 TCGA-23-1024 TCGA-23-1111 TCGA-23-1114 TCGA-23-1118 TCGA-23-1119 
       47.54        15.39         3.22        68.68        86.01       129.96 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1809 TCGA-23-2072 TCGA-23-2643 TCGA-24-0982 
        6.38        39.09         0.53        24.95         4.70        22.32 
TCGA-24-1418 TCGA-24-1422 TCGA-24-1424 TCGA-24-1430 TCGA-24-1434 TCGA-24-1436 
        7.99         0.76         6.02        28.37        18.67         8.55 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1553 
      105.99         9.11         1.18        22.22        26.96        58.09 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 TCGA-24-1844 
       19.53        44.09        88.37        38.24         8.32         3.72 
TCGA-24-1850 TCGA-24-1924 TCGA-24-1928 TCGA-24-2033 TCGA-24-2261 TCGA-24-2288 
        5.52        30.21        11.05        18.48         0.79         0.82 
TCGA-24-2289 TCGA-24-2295 TCGA-25-1317 TCGA-25-1319 TCGA-25-1321 TCGA-25-1329 
       67.36        33.11         2.01        65.00        33.96        15.02 
TCGA-25-1623 TCGA-25-1626 TCGA-25-1634 TCGA-25-1870 TCGA-25-1877 TCGA-25-1878 
       18.58        17.03        35.87        14.96        24.00        85.05 
TCGA-29-1691 TCGA-29-1695 TCGA-29-1696 TCGA-29-1763 TCGA-29-1764 TCGA-29-1769 
       48.33        40.41        33.93        66.81        62.93        22.98 
TCGA-29-1775 TCGA-29-2425 TCGA-29-2429 TCGA-30-1714 TCGA-30-1718 TCGA-30-1859 
       12.36        65.00        13.84        38.07        51.91        48.10 
TCGA-30-1862 TCGA-31-1950 TCGA-31-1959 TCGA-36-1568 TCGA-36-1576 TCGA-36-1578 
        6.12        18.77         2.20        28.77        30.08        27.85 
TCGA-36-1581 TCGA-36-2547 TCGA-36-2552 TCGA-42-2587 TCGA-57-1582 TCGA-57-1583 
       24.69        20.52        11.47        23.74        24.03        11.38 
TCGA-57-1585 TCGA-57-1586 TCGA-57-1994 TCGA-59-2348 TCGA-59-2352 TCGA-61-1730 
        1.74        22.32        25.02       180.20         9.40         4.34 
TCGA-61-1733 TCGA-61-1741 TCGA-61-1743 TCGA-61-1899 TCGA-61-1906 TCGA-61-1919 
       31.79        33.67        43.69         8.42        34.13        38.17 
TCGA-61-2003 TCGA-61-2012 TCGA-61-2018 TCGA-61-2088 TCGA-61-2097 TCGA-61-2098 
        4.01        30.64        45.40         4.77        60.62        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2113 TCGA-61-2612 TCGA-61-2614 
       55.50         6.48        76.87        22.22         6.35         8.61 
TCGA-OY-A56P TCGA-OY-A56Q TCGA-09-0365 TCGA-09-0366 TCGA-09-0369 TCGA-10-0927 
       39.68        18.94         9.47        57.76        35.57        81.86 
TCGA-10-0933 TCGA-10-0935 TCGA-10-0938 TCGA-13-0724 TCGA-13-0730 TCGA-13-0757 
       14.66        35.44        20.91         2.73        17.82        11.18 
TCGA-13-0760 TCGA-13-0800 TCGA-13-0883 TCGA-13-0884 TCGA-13-0888 TCGA-13-0893 
       11.54        87.48        68.94       107.18        92.42        43.36 
TCGA-13-0901 TCGA-13-0906 TCGA-13-0919 TCGA-13-0920 
       19.36       118.98        84.53        48.79 

$`2Q GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 
       13.81        43.92        41.00         1.81        49.15         2.01 
TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 
       46.62         1.08        18.51        11.87        65.52        48.76 
TCGA-04-1349 TCGA-04-1351 TCGA-04-1353 TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 
       21.57        65.46         0.53        32.52        44.32        76.57 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 
      103.40        82.39        56.55        19.99         0.79        38.37 
TCGA-04-1530 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1651 TCGA-04-1652 
      119.08        55.43        48.89        28.64        36.23        31.86 
TCGA-04-1654 TCGA-09-1659 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 
       47.70         9.99        89.33        74.93        41.62        57.60 
TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1673 TCGA-09-1675 TCGA-09-2044 
       61.87        55.36        30.51         3.02        97.55         6.12 
TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 
       35.15       112.41        71.11        63.09        39.75        20.94 
TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 
       26.93        12.46        77.10        81.17        28.54        55.23 
TCGA-13-1411 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
       17.46        54.64        87.06        61.71        29.42       124.44 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       20.68        22.39        83.93        52.44       125.56        93.90 
TCGA-13-1495 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1506 
       90.38       127.27        66.15       115.07        13.97        34.16 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 
       65.52        80.15        44.68        54.25        14.53        78.48 
TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
       76.90        65.52        70.45         8.42        23.05        25.94 
TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 
       26.20        72.20        27.52        25.38        19.10        16.70 
TCGA-20-1686 TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
        2.93        49.68        40.54        26.83        32.09        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 
        8.81        29.13        18.90         2.76        51.35        54.51 
TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1120 TCGA-23-1123 TCGA-23-1124 
       31.20        19.46        33.30         4.27        33.47        58.13 
TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
      115.89        87.48        91.66        77.00        49.84         2.76 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        4.50         7.63        11.64        21.80        41.56         7.66 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 
       54.12        63.55        47.41         6.31         6.38         7.82 
TCGA-24-1419 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        7.86         6.25         5.95         5.36         4.83        17.39 
TCGA-24-1431 TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1470 
       18.64        43.53        72.92        12.46        45.14         3.45 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 
       57.40        64.27        16.21        56.58        41.06        51.91 
TCGA-24-1552 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1562 TCGA-24-1563 
       41.39        88.50        70.62        39.88        45.50        47.70 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1614 TCGA-24-1843 
       25.87        10.26        17.23        90.15        48.33         3.48 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 
        3.81         4.37        11.28         5.79         9.80        22.68 
TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 
       16.44        81.11         4.87       152.02        44.84        58.16 
TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 
       34.82       109.71        14.43        55.92        28.18        64.01 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 
       44.52        57.07        36.16         0.36        47.54        31.63 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 
       70.45        44.61        36.23        16.64        55.86        53.26 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1318 
        1.02        26.96        33.01        52.04        42.05        34.98 
TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 TCGA-25-1625 TCGA-25-1627 TCGA-25-1628 
       37.97         2.99        12.99        27.62        12.95        20.61 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 TCGA-25-1871 
       38.20         0.30        59.15        62.17        52.04        24.99 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 
       13.02        49.05         1.02        38.04         3.02        12.00 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 
       45.01        19.99        42.02         2.96        29.03        31.00 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1697 
       26.99        78.90        47.61       101.79        39.02        31.20 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 
       68.32        36.36        16.93        23.93        59.67        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1766 
       41.98        31.27        34.62        17.36        86.60        39.42 
TCGA-29-1768 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 TCGA-29-1777 
       31.30        24.36        22.55        17.33        11.84        12.30 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 
       14.93         8.38         7.23         5.36        36.30        86.17 
TCGA-29-2427 TCGA-29-2428 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 
       62.47        45.11        42.25        21.47        11.47         9.76 
TCGA-29-A5NZ TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1860 
       35.77        36.26         2.47        15.68         0.26        44.91 
TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 
       34.78        36.62         1.22        57.57        24.26        30.05 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 
       48.79        45.57        30.18        22.49         6.71        42.51 
TCGA-31-1956 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 
       44.12        29.10        21.53        22.85        22.55         8.55 
TCGA-36-1577 TCGA-36-1580 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       25.74        24.23        35.05        33.01        29.49        29.82 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 
       25.91        25.08        23.80        21.60         2.24        20.98 
TCGA-36-2545 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-42-2582 TCGA-42-2588 
       18.31        14.17         6.05        16.18        47.57        28.93 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1584 TCGA-57-1992 
       42.02        10.42        40.77         1.48        21.14        29.00 
TCGA-57-1993 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2354 TCGA-59-2355 
       25.08        80.12        22.32       116.12        34.39         2.14 
TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
        5.42        44.81        11.11         8.09        20.94        31.43 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
       18.54        27.88        28.47        48.79        44.84        35.80 
TCGA-61-1740 TCGA-61-1895 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 
        2.43         1.45         5.79        11.41        13.02         9.07 
TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 
       31.30        37.05        42.51        48.92        56.61        67.76 
TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       43.43        15.75         2.01         5.52        14.50        17.98 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2087 TCGA-61-2092 
       30.64        39.85         1.18        45.96         4.80        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       71.74        61.64        58.39        20.68        44.52       125.75 
TCGA-61-2613 TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 TCGA-09-0367 TCGA-10-0925 
       31.07         0.79         9.99        29.16        17.98        54.31 
TCGA-10-0926 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 TCGA-10-0936 
       25.91        18.51        34.19        32.88         6.71        36.92 
TCGA-10-0937 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 
       19.99         6.21        24.59        44.55        39.58        12.39 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0751 TCGA-13-0755 TCGA-13-0758 TCGA-13-0761 
       31.20        15.19        55.17         2.50        11.38        38.01 
TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 
      111.78        61.84        56.71        58.65        40.24       118.42 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 
      107.28        63.09        20.35        69.73        83.34        45.99 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0885 
       51.02        43.86        35.28        35.31        13.61       111.39 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0897 
      153.37        66.67        95.15       145.45       102.84        71.74 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0908 
       66.15       134.04       127.79        50.37       123.16        60.59 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0921 
      116.65        44.55        37.64       109.32        58.68        48.76 
TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       83.74        85.94        25.41 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.53              0.26 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           180.20            153.37 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           28.125            34.620 
[1] "0.5 - 180.2 (28.1)" "0.3 - 153.4 (34.6)"
[1] "hr=" "1.2"
D4V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  2Q GAIN MUTATED         0   149                0
  2Q GAIN WILD-TYPE       3   409                2
D4V3, multiclass
                  clus
vv                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  OMENTUM                        0                 3
  OVARY                        149               409
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V4, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED   142   1
  2Q GAIN WILD-TYPE 399   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED    142    1
  2Q GAIN WILD-TYPE  399    4
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO              142               399
  YES               1                 4
[1] 2 2
[1] FALSE
D4V5, continuous
                   vv
clus                R0 R1 R2 RX
  2Q GAIN MUTATED    4  6  1  1
  2Q GAIN WILD-TYPE 11 20  4  2
D4V6, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0               4                11
  R1               6                20
  R2               1                 4
  RX               1                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     3  77
  2Q GAIN WILD-TYPE   7 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      3   77
  2Q GAIN WILD-TYPE    7  250
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 7
  NOT HISPANIC OR LATINO              77               250
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    66  92
  3P GAIN WILD-TYPE 162 239
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              158               401 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               92               239 
$`3P GAIN MUTATED`
TCGA-59-A5PD TCGA-04-1332 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1343 
       20.52        41.00         2.01        46.62         1.08        11.87 
TCGA-04-1349 TCGA-04-1371 TCGA-04-1516 TCGA-04-1517 TCGA-04-1536 TCGA-04-1646 
       21.57        82.39        41.59        19.99        29.10        27.88 
TCGA-04-1652 TCGA-04-1655 TCGA-09-1659 TCGA-09-1665 TCGA-09-1668 TCGA-09-1669 
       31.86        45.37         9.99        41.62        55.36        30.51 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 TCGA-09-2043 TCGA-13-1403 TCGA-13-1410 
       17.98         5.85         8.55         6.18        77.10        81.01 
TCGA-13-1484 TCGA-13-1489 TCGA-13-1495 TCGA-13-1504 TCGA-13-1505 TCGA-13-1507 
      124.44        83.93        90.38        34.82        65.69        65.52 
TCGA-13-2061 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1686 
       76.90        26.20        27.52        25.38        19.10         2.93 
TCGA-20-1687 TCGA-23-1026 TCGA-23-1109 TCGA-23-1110 TCGA-23-1116 TCGA-23-1117 
        2.66        26.83        51.35        54.51        19.46        33.30 
TCGA-23-1119 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2643 
      129.96        24.95       115.89        87.48        91.66         4.70 
TCGA-24-0979 TCGA-24-0982 TCGA-24-1413 TCGA-24-1424 TCGA-24-1426 TCGA-24-1428 
       41.56        22.32         6.31         6.02         5.36        17.39 
TCGA-24-1434 TCGA-24-1436 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 
       18.67         8.55       105.99         3.45         1.18        22.22 
TCGA-24-1553 TCGA-24-1557 TCGA-24-1558 TCGA-24-1564 TCGA-24-1567 TCGA-24-1614 
       58.09        39.88        19.53        25.87        17.23        48.33 
TCGA-24-1842 TCGA-24-1844 TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 
        8.32         3.72        11.28         5.52         9.80        22.68 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 TCGA-24-2020 TCGA-24-2038 
       30.21        16.44        11.05         4.87       152.02        44.52 
TCGA-24-2261 TCGA-24-2267 TCGA-24-2295 TCGA-24-2298 TCGA-25-1318 TCGA-25-1319 
        0.79        47.54        33.11        53.26        34.98        65.00 
TCGA-25-1321 TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1634 TCGA-25-1635 
       33.96        15.02        18.58        17.03        35.87        52.04 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2398 TCGA-25-2400 TCGA-25-2404 TCGA-29-1694 
       24.00        85.05        45.01        42.02        29.03        39.02 
TCGA-29-1698 TCGA-29-1701 TCGA-29-1705 TCGA-29-1710 TCGA-29-1761 TCGA-29-1770 
       68.32        16.93        18.25        31.27        17.36        24.36 
TCGA-29-1778 TCGA-29-1783 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2431 
       14.93         7.23        86.17        65.00        45.11        42.25 
TCGA-30-1718 TCGA-30-1859 TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-30-1892 
       51.91        48.10        34.78        36.62         1.22        48.79 
TCGA-31-1950 TCGA-36-1578 TCGA-36-2529 TCGA-36-2543 TCGA-42-2587 TCGA-42-2590 
       18.77        27.85        35.05         2.24        23.74        10.42 
TCGA-57-1582 TCGA-57-1585 TCGA-57-1994 TCGA-59-2351 TCGA-59-2352 TCGA-61-1899 
       24.03         1.74        25.02       116.12         9.40         8.42 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1915 
       11.41        13.02         9.07        34.13        31.30        67.76 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2097 TCGA-61-2102 
       17.98         4.01        30.64        39.85        60.62         6.48 
TCGA-61-2111 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-09-0364 
      125.75         6.35         8.61        39.68        18.94        29.16 
TCGA-09-0367 TCGA-10-0930 TCGA-10-0935 TCGA-10-0936 TCGA-13-0724 TCGA-13-0751 
       17.98        34.19        35.44        36.92         2.73        55.17 
TCGA-13-0760 TCGA-13-0762 TCGA-13-0795 TCGA-13-0800 TCGA-13-0803 TCGA-13-0884 
       11.54       111.78        20.35        87.48        43.86       107.18 
TCGA-13-0911 TCGA-13-0921 
       44.55        48.76 

$`3P GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1342 
       13.81        11.87        43.92         1.81        49.15        18.51 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 
       65.52        63.09        48.76        63.98        65.46         0.53 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       49.28        32.52        44.32        33.67        76.57       103.40 
TCGA-04-1514 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 
       56.55         0.79        38.37       119.08        84.20        55.43 
TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-09-1661 
       48.89        28.64        64.64        36.23        47.70        38.43 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 TCGA-09-1673 TCGA-09-1675 
       89.33        74.93        57.60        61.87         3.02        97.55 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
        6.12        35.15         4.54       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1404 TCGA-13-1405 
       39.75        20.94        26.93        12.46        81.17        28.54 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 
       83.31        55.23        57.27        17.46        32.35        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 
       87.06        61.71        29.42        20.68        22.39        70.82 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
       52.44       125.56        93.90         4.24       127.27        66.15 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 
      115.07        13.97        43.20        34.16        80.15        44.68 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2065 
       54.25        14.53        80.02        78.48        77.88        65.52 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0996 TCGA-20-1685 
       70.45         8.42        23.05        25.94        72.20        16.70 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1027 TCGA-23-1028 
       47.54        49.68        40.54        15.39        32.09        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1111 TCGA-23-1113 
        8.81        29.13        18.90         2.76         3.22        31.20 
TCGA-23-1114 TCGA-23-1118 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 
       68.68        86.01         4.27         6.38        39.09        33.47 
TCGA-23-1124 TCGA-23-1809 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2645 
       58.13         0.53        77.00        49.84         2.76         4.50 
TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 
        7.63        11.64        21.80         7.66        54.12        63.55 
TCGA-24-1105 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 
       47.41         6.38         7.82         7.99         7.86         0.76 
TCGA-24-1423 TCGA-24-1425 TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 
        6.25         5.95         4.83        28.37        18.64        43.53 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1544 TCGA-24-1545 
       72.92        12.46        45.14         9.11        26.96        57.40 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
       64.27        16.21        56.58        41.06        51.91        41.39 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1565 
       88.50        70.62        44.09        45.50        47.70        10.26 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-1843 TCGA-24-1845 TCGA-24-1846 
       90.15        88.37        38.24         3.48         3.81         4.37 
TCGA-24-1849 TCGA-24-1930 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 
        5.79        81.11        44.84        58.16        34.82       109.71 
TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2254 
       14.43        55.92        18.48        28.18        64.01        57.07 
TCGA-24-2260 TCGA-24-2262 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
       36.16         0.36        31.63        70.45        44.61         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 
       67.36        36.23        16.64        55.86         1.02        26.96 
TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1320 TCGA-25-1322 
       33.01        52.04        42.05         2.01        37.97         2.99 
TCGA-25-1323 TCGA-25-1625 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
       12.99        27.62        12.95        20.61        38.20         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1870 TCGA-25-1871 TCGA-25-2042 TCGA-25-2391 
       59.15        62.17        14.96        24.99        13.02        49.05 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 TCGA-25-2401 
        1.02        38.04         3.02        12.00        19.99         2.96 
TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 
       31.00        26.99        78.90        47.61        48.33       101.79 
TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 TCGA-29-1702 TCGA-29-1703 
       40.41        33.93        31.20        36.36        23.93        59.67 
TCGA-29-1707 TCGA-29-1711 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 
       41.98        34.62        86.60        66.81        62.93        39.42 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 
       31.30        22.98        22.55        17.33        12.36        11.84 
TCGA-29-1777 TCGA-29-1781 TCGA-29-1784 TCGA-29-1785 TCGA-29-2427 TCGA-29-2429 
       12.30         8.38         5.36        36.30        62.47        13.84 
TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1853 
       21.47        11.47         9.76        35.77        38.07        36.26 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1860 TCGA-30-1862 TCGA-30-1880 
        2.47        15.68         0.26        44.91         6.12        57.57 
TCGA-30-1887 TCGA-30-1891 TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 
       24.26        30.05        45.57        30.18        22.49         6.71 
TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
       42.51        44.12         2.20        28.77        29.10        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1580 
       22.85        22.55         8.55        30.08        25.74        24.23 
TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
       24.69        33.01        29.49        29.82        25.91        25.08 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 
       23.80        21.60        20.98        18.31        20.52        14.17 
TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 
        6.05        16.18        11.47        47.57        28.93        42.02 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1992 
       40.77         1.48        11.38        21.14        22.32        29.00 
TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2354 TCGA-59-2355 
       25.08       180.20        80.12        22.32        34.39         2.14 
TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
        5.42        44.81        11.11         8.09        20.94        31.43 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 
       18.54        27.88         4.34        31.79        28.47        48.79 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 
       44.84        35.80         2.43        33.67        43.69         1.45 
TCGA-61-1900 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 
        5.79        37.05        42.51        48.92        56.61        43.43 
TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2012 
       15.75        38.17         2.01         5.52        14.50        30.64 
TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 
        1.18        45.96        45.40         4.80         4.77        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 
       71.74        61.64        58.39        65.52        55.50        76.87 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2113 TCGA-61-2613 TCGA-VG-A8LO TCGA-WR-A838 
       20.68        44.52        22.22        31.07         0.79         9.99 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0369 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 
        9.47        57.76        35.57        54.31        25.91        81.86 
TCGA-10-0928 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0937 TCGA-10-0938 
       18.51        32.88        14.66         6.71        19.99        20.91 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 
        6.21        24.59        44.55        39.58        12.39        31.20 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0761 
       15.19        17.82         2.50        11.18        11.38        38.01 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       61.84        56.71        58.65        40.24       118.42       107.28 
TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 
       63.09        69.73        83.34        45.99        51.02        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
       35.31        13.61        68.94       111.39       153.37        66.67 
TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 
       92.42        95.15       145.45       102.84        43.36        71.74 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       66.15       134.04        19.36       127.79        50.37       123.16 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
      118.98        60.59       116.65        37.64       109.32        58.68 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       84.53        48.79        83.74        85.94        25.41 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.79              0.26 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           152.02            180.20 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           28.455            34.620 
[1] "0.8 - 152.0 (28.5)" "0.3 - 180.2 (34.6)"
[1] "hr=" "1.1"
D5V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  3P GAIN MUTATED         0   158                1
  3P GAIN WILD-TYPE       3   400                1
D5V3, multiclass
                  clus
vv                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  OMENTUM                        0                 3
  OVARY                        158               400
  PERITONEUM OVARY               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V4, binary
                   cls
clus                  0   1
  3P GAIN MUTATED   154   1
  3P GAIN WILD-TYPE 387   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED    154    1
  3P GAIN WILD-TYPE  387    4
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO              154               387
  YES               1                 4
[1] 2 2
[1] FALSE
D5V5, continuous
                   vv
clus                R0 R1 R2 RX
  3P GAIN MUTATED    2 10  1  1
  3P GAIN WILD-TYPE 13 16  4  2
D5V6, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0               2                13
  R1              10                16
  R2               1                 4
  RX               1                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     2  87
  3P GAIN WILD-TYPE   8 240
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2   87
  3P GAIN WILD-TYPE    8  240
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 8
  NOT HISPANIC OR LATINO              87               240
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED   112 157
  3Q GAIN WILD-TYPE 116 174
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              269               290 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              157               174 
$`3Q GAIN MUTATED`
TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 
       20.52        11.87        41.00         1.81        49.15         2.01 
TCGA-04-1338 TCGA-04-1341 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 
       46.62         1.08        11.87        65.52        63.09        21.57 
TCGA-04-1350 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1371 
       63.98        32.52        44.32        33.67        76.57        82.39 
TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 
       41.59        19.99        38.37       119.08        29.10        84.20 
TCGA-04-1646 TCGA-04-1649 TCGA-04-1652 TCGA-04-1655 TCGA-09-1659 TCGA-09-1665 
       27.88        64.64        31.86        45.37         9.99        41.62 
TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 TCGA-09-2043 
       55.36        30.51        17.98         5.85         8.55         6.18 
TCGA-09-2044 TCGA-09-2048 TCGA-09-2049 TCGA-09-2053 TCGA-13-1403 TCGA-13-1409 
        6.12         4.54       112.41        39.75        77.10        57.27 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 TCGA-13-1484 TCGA-13-1487 TCGA-13-1489 
       81.01        17.46        87.06       124.44        22.39        83.93 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
       90.38         4.24        34.82        65.69        34.16        65.52 
TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FU TCGA-20-0990 
       80.02        77.88        76.90        65.52         8.42        25.94 
TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1686 TCGA-20-1687 
       26.20        27.52        25.38        19.10         2.93         2.66 
TCGA-23-1021 TCGA-23-1026 TCGA-23-1029 TCGA-23-1031 TCGA-23-1109 TCGA-23-1110 
       47.54        26.83         8.81        18.90        51.35        54.51 
TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1119 TCGA-23-1122 TCGA-23-1123 
       68.68        19.46        33.30       129.96        39.09        33.47 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2084 
        0.53        24.95       115.89        87.48        91.66        49.84 
TCGA-23-2643 TCGA-24-0970 TCGA-24-0979 TCGA-24-0982 TCGA-24-1413 TCGA-24-1417 
        4.70        11.64        41.56        22.32         6.31         7.82 
TCGA-24-1424 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1434 TCGA-24-1436 
        6.02         5.36         4.83        17.39        18.67         8.55 
TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1548 TCGA-24-1553 
      105.99         3.45         1.18        22.22        16.21        58.09 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1564 TCGA-24-1567 TCGA-24-1604 TCGA-24-1614 
       39.88        19.53        25.87        17.23        88.37        48.33 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1847 TCGA-24-1850 
       38.24         8.32         3.48         3.72        11.28         5.52 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 
        9.80        22.68        30.21        16.44        11.05        81.11 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2026 TCGA-24-2033 TCGA-24-2038 TCGA-24-2260 
        4.87       152.02        34.82        18.48        44.52        36.16 
TCGA-24-2261 TCGA-24-2267 TCGA-24-2280 TCGA-24-2295 TCGA-24-2298 TCGA-25-1312 
        0.79        47.54        70.45        33.11        53.26         1.02 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 TCGA-25-1323 TCGA-25-1329 
        2.01        34.98        65.00        33.96        12.99        15.02 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1630 TCGA-25-1634 
       18.58        27.62        17.03        12.95        38.20        35.87 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2396 
       52.04        14.96        24.99        24.00        85.05         3.02 
TCGA-25-2398 TCGA-25-2400 TCGA-25-2404 TCGA-29-1693 TCGA-29-1694 TCGA-29-1698 
       45.01        42.02        29.03       101.79        39.02        68.32 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1710 TCGA-29-1761 
       16.93        23.93        59.67        18.25        31.27        17.36 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1770 TCGA-29-1775 TCGA-29-1776 TCGA-29-1778 
       62.93        39.42        24.36        12.36        11.84        14.93 
TCGA-29-1783 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2431 TCGA-29-2432 
        7.23        86.17        65.00        45.11        42.25        21.47 
TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1853 TCGA-30-1857 TCGA-30-1859 
       11.47        35.77        51.91        36.26         0.26        48.10 
TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-30-1887 TCGA-30-1892 TCGA-31-1950 
       34.78        36.62         1.22        24.26        48.79        18.77 
TCGA-31-1956 TCGA-36-1569 TCGA-36-1574 TCGA-36-1576 TCGA-36-1578 TCGA-36-1581 
       44.12        29.10        22.55        30.08        27.85        24.69 
TCGA-36-2529 TCGA-36-2530 TCGA-36-2534 TCGA-36-2543 TCGA-36-2545 TCGA-36-2547 
       35.05        33.01        29.82         2.24        18.31        20.52 
TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 TCGA-42-2590 TCGA-42-2593 
       14.17        16.18        11.47        23.74        10.42         1.48 
TCGA-57-1582 TCGA-57-1585 TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2350 
       24.03         1.74        22.32        25.08        25.02        22.32 
TCGA-59-2351 TCGA-59-2352 TCGA-61-1722 TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 
      116.12         9.40         8.09        18.54        27.88        31.79 
TCGA-61-1899 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        8.42        11.41        13.02         9.07        34.13        31.30 
TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-2002 
       56.61        67.76        43.43        15.75        38.17        17.98 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2097 TCGA-61-2098 TCGA-61-2102 
        4.01        30.64        39.85        60.62        65.52         6.48 
TCGA-61-2104 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P 
       76.87       125.75        22.22         6.35         8.61        39.68 
TCGA-OY-A56Q TCGA-VG-A8LO TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 
       18.94         0.79        29.16         9.47        57.76        17.98 
TCGA-09-0369 TCGA-10-0930 TCGA-10-0933 TCGA-10-0935 TCGA-10-0936 TCGA-13-0724 
       35.57        34.19        14.66        35.44        36.92         2.73 
TCGA-13-0727 TCGA-13-0751 TCGA-13-0757 TCGA-13-0760 TCGA-13-0768 TCGA-13-0795 
       15.19        55.17        11.18        11.54        58.65        20.35 
TCGA-13-0800 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0884 TCGA-13-0888 
       87.48        51.02        43.86        35.28       107.18        92.42 
TCGA-13-0897 TCGA-13-0901 TCGA-13-0911 TCGA-13-0920 TCGA-13-0921 
       71.74        19.36        44.55        48.79        48.76 

$`3Q GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-04-1331 TCGA-04-1342 TCGA-04-1348 TCGA-04-1351 TCGA-04-1353 
       13.81        43.92        18.51        48.76        65.46         0.53 
TCGA-04-1356 TCGA-04-1367 TCGA-04-1514 TCGA-04-1519 TCGA-04-1638 TCGA-04-1644 
       49.28       103.40        56.55         0.79        55.43        48.89 
TCGA-04-1648 TCGA-04-1651 TCGA-04-1654 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       28.64        36.23        47.70        38.43        89.33        74.93 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1673 TCGA-09-1675 TCGA-09-2045 TCGA-09-2050 
       57.60        61.87         3.02        97.55        35.15        71.11 
TCGA-09-2051 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1404 TCGA-13-1405 
       63.09        20.94        26.93        12.46        81.17        28.54 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 
       83.31        55.23        32.35        54.64        61.71        29.42 
TCGA-13-1485 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1497 
       20.68        70.82        52.44       125.56        93.90       127.27 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1509 TCGA-13-1510 
       66.15       115.07        13.97        43.20        80.15        44.68 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0996 
       54.25        14.53        78.48        70.45        23.05        72.20 
TCGA-20-1685 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1027 TCGA-23-1028 
       16.70        49.68        40.54        15.39        32.09        49.41 
TCGA-23-1030 TCGA-23-1032 TCGA-23-1111 TCGA-23-1113 TCGA-23-1118 TCGA-23-1120 
       29.13         2.76         3.22        31.20        86.01         4.27 
TCGA-23-1121 TCGA-23-1124 TCGA-23-2081 TCGA-23-2641 TCGA-23-2645 TCGA-24-0966 
        6.38        58.13        77.00         2.76         4.50         7.63 
TCGA-24-0975 TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1416 
       21.80         7.66        54.12        63.55        47.41         6.38 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1430 
        7.99         7.86         0.76         6.25         5.95        28.37 
TCGA-24-1431 TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 
       18.64        43.53        72.92        12.46        45.14         9.11 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 
       26.96        57.40        64.27        56.58        41.06        51.91 
TCGA-24-1552 TCGA-24-1555 TCGA-24-1556 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       41.39        88.50        70.62        44.09        45.50        47.70 
TCGA-24-1565 TCGA-24-1603 TCGA-24-1845 TCGA-24-1846 TCGA-24-1849 TCGA-24-2023 
       10.26        90.15         3.81         4.37         5.79        44.84 
TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 
       58.16       109.71        14.43        55.92        28.18        64.01 
TCGA-24-2254 TCGA-24-2262 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 
       57.07         0.36        31.63        44.61         0.82        67.36 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 
       36.23        16.64        55.86        26.96        33.01        52.04 
TCGA-25-1316 TCGA-25-1320 TCGA-25-1322 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 
       42.05        37.97         2.99        20.61         0.30        59.15 
TCGA-25-1633 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2397 
       62.17        13.02        49.05         1.02        38.04        12.00 
TCGA-25-2399 TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 
       19.99         2.96        31.00        26.99        78.90        47.61 
TCGA-29-1691 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 TCGA-29-1707 
       48.33        40.41        33.93        31.20        36.36        41.98 
TCGA-29-1711 TCGA-29-1762 TCGA-29-1763 TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 
       34.62        86.60        66.81        31.30        22.98        22.55 
TCGA-29-1774 TCGA-29-1777 TCGA-29-1781 TCGA-29-1784 TCGA-29-1785 TCGA-29-2427 
       17.33        12.30         8.38         5.36        36.30        62.47 
TCGA-29-2429 TCGA-29-2436 TCGA-30-1714 TCGA-30-1855 TCGA-30-1856 TCGA-30-1860 
       13.84         9.76        38.07         2.47        15.68        44.91 
TCGA-30-1862 TCGA-30-1880 TCGA-30-1891 TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 
        6.12        57.57        30.05        45.57        30.18        22.49 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 
        6.71        42.51         2.20        28.77        21.53        22.85 
TCGA-36-1575 TCGA-36-1577 TCGA-36-1580 TCGA-36-2532 TCGA-36-2537 TCGA-36-2538 
        8.55        25.74        24.23        29.49        25.91        25.08 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-36-2549 TCGA-42-2582 TCGA-42-2588 
       23.80        21.60        20.98         6.05        47.57        28.93 
TCGA-42-2589 TCGA-42-2591 TCGA-57-1583 TCGA-57-1584 TCGA-57-1992 TCGA-59-2348 
       42.02        40.77        11.38        21.14        29.00       180.20 
TCGA-59-2349 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 
       80.12        34.39         2.14         5.42        44.81        11.11 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1730 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       20.94        31.43         4.34        28.47        48.79        44.84 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1900 
       35.80         2.43        33.67        43.69         1.45         5.79 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       37.05        42.51        48.92         2.01         5.52        14.50 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
       30.64         1.18        45.96        45.40         4.80         4.77 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2101 TCGA-61-2109 
       51.72        71.74        61.64        58.39        55.50        20.68 
TCGA-61-2110 TCGA-61-2613 TCGA-WR-A838 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 
       44.52        31.07         9.99        54.31        25.91        81.86 
TCGA-10-0928 TCGA-10-0931 TCGA-10-0934 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
       18.51        32.88         6.71        19.99        20.91         6.21 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 TCGA-13-0730 
       24.59        44.55        39.58        12.39        31.20        17.82 
TCGA-13-0755 TCGA-13-0758 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 
        2.50        11.38        38.01       111.78        61.84        56.71 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 
       40.24       118.42       107.28        63.09        69.73        83.34 
TCGA-13-0801 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0885 TCGA-13-0886 
       45.99        35.31        13.61        68.94       111.39       153.37 
TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 
       66.67        95.15       145.45       102.84        43.36        66.15 
TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 
      134.04       127.79        50.37       123.16       118.98        60.59 
TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0923 
      116.65        37.64       109.32        58.68        84.53        83.74 
TCGA-13-0924 TCGA-13-2071 
       85.94        25.41 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.26              0.30 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           152.02            180.20 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           29.030            37.345 
[1] "0.3 - 152.0 (29.0)" "0.3 - 180.2 (37.3)"
[1] "hr=" "1.2"
D6V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  3Q GAIN MUTATED         1   269                2
  3Q GAIN WILD-TYPE       2   289                0
D6V3, multiclass
                  clus
vv                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  OMENTUM                        1                 2
  OVARY                        269               289
  PERITONEUM OVARY               2                 0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V4, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED   265   1
  3Q GAIN WILD-TYPE 276   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED    265    1
  3Q GAIN WILD-TYPE  276    4
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO              265               276
  YES               1                 4
[1] 2 2
[1] FALSE
D6V5, continuous
                   vv
clus                R0 R1 R2 RX
  3Q GAIN MUTATED    8 16  4  1
  3Q GAIN WILD-TYPE  7 10  1  2
D6V6, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0               8                 7
  R1              16                10
  R2               4                 1
  RX               1                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     3 148
  3Q GAIN WILD-TYPE   7 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3  148
  3Q GAIN WILD-TYPE    7  179
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 7
  NOT HISPANIC OR LATINO             148               179
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    21  39
  4P GAIN WILD-TYPE 207 292
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               60               499 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               39               292 
$`4P GAIN MUTATED`
TCGA-5X-AA5U TCGA-04-1349 TCGA-04-1356 TCGA-04-1364 TCGA-04-1525 TCGA-04-1530 
       11.87        21.57        49.28        33.67        38.37       119.08 
TCGA-04-1646 TCGA-09-1668 TCGA-09-2048 TCGA-13-1496 TCGA-13-1499 TCGA-13-1505 
       27.88        55.36         4.54         4.24       115.07        65.69 
TCGA-13-2060 TCGA-13-A5FU TCGA-23-1026 TCGA-23-1114 TCGA-23-2645 TCGA-24-1427 
       77.88         8.42        26.83        68.68         4.50         4.83 
TCGA-24-1428 TCGA-24-1464 TCGA-24-1545 TCGA-24-1558 TCGA-24-1843 TCGA-24-1928 
       17.39        12.46        57.40        19.53         3.48        11.05 
TCGA-24-2026 TCGA-24-2033 TCGA-25-1313 TCGA-25-1635 TCGA-25-1877 TCGA-25-2392 
       34.82        18.48        26.96        52.04        24.00         1.02 
TCGA-25-2396 TCGA-25-2398 TCGA-29-1691 TCGA-29-1705 TCGA-29-1761 TCGA-29-1763 
        3.02        45.01        48.33        18.25        17.36        66.81 
TCGA-29-1770 TCGA-29-2432 TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1855 TCGA-36-1569 
       24.36        21.47        35.77        51.91         2.47        29.10 
TCGA-36-1570 TCGA-36-1575 TCGA-36-2529 TCGA-61-1728 TCGA-61-1733 TCGA-61-1740 
       21.53         8.55        35.05        27.88        31.79         2.43 
TCGA-61-1743 TCGA-61-1915 TCGA-61-1918 TCGA-61-2009 TCGA-61-2012 TCGA-61-2614 
       43.69        67.76        15.75        39.85        30.64         8.61 
TCGA-10-0926 TCGA-13-0714 TCGA-13-0794 TCGA-13-0802 TCGA-13-0883 TCGA-13-0920 
       25.91         6.21        63.09        51.02        68.94        48.79 

$`4P GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 
       13.81        20.52        43.92        41.00         1.81        49.15 
TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 
        2.01        46.62         1.08        18.51        11.87        65.52 
TCGA-04-1347 TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1361 
       63.09        48.76        63.98        65.46         0.53        32.52 
TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 
       44.32        76.57       103.40        82.39        56.55        41.59 
TCGA-04-1517 TCGA-04-1519 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 
       19.99         0.79        29.10        84.20        55.43        48.89 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 
       28.64        64.64        36.23        31.86        47.70        45.37 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 
        9.99        38.43        89.33        74.93        41.62        57.60 
TCGA-09-1667 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 
       61.87        30.51        17.98         5.85         3.02         8.55 
TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 
       97.55         6.18         6.12        35.15       112.41        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 
       63.09        39.75        20.94        26.93        12.46        77.10 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
       81.17        28.54        83.31        55.23        57.27        81.01 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
       17.46        32.35        54.64        87.06        61.71        29.42 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
      124.44        20.68        22.39        70.82        83.93        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 
      125.56        93.90        90.38       127.27        66.15        13.97 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 
       43.20        34.82        34.16        65.52        80.15        44.68 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 
       54.25        14.53        80.02        78.48        76.90        65.52 
TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 
       70.45        23.05        25.94        26.20        72.20        27.52 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 
       25.38        19.10        16.70         2.93         2.66        47.54 
TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 
       49.68        40.54        15.39        32.09        49.41         8.81 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
       29.13        18.90         2.76        51.35        54.51         3.22 
TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 
       31.20        19.46        33.30        86.01       129.96         4.27 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 
        6.38        39.09        33.47        58.13         0.53        24.95 
TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
      115.89        87.48        91.66        77.00        49.84         2.76 
TCGA-23-2643 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        4.70         7.63        11.64        21.80        41.56         7.66 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
       22.32        54.12        63.55        47.41         6.31         6.38 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
        7.82         7.99         7.86         0.76         6.25         6.02 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 
        5.95         5.36        28.37        18.64        18.67        43.53 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 
        8.55        72.92        45.14       105.99         9.11         3.45 
TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 
        1.18        22.22        26.96        64.27        16.21        56.58 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 
       41.06        51.91        41.39        58.09        88.50        70.62 
TCGA-24-1557 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 
       39.88        44.09        45.50        47.70        25.87        10.26 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 
       17.23        90.15        88.37        48.33        38.24         8.32 
TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 
        3.72         3.81         4.37        11.28         5.79         5.52 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 
        9.80        22.68        30.21        16.44        81.11         4.87 
TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 
      152.02        44.84        58.16       109.71        14.43        55.92 
TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 
       28.18        64.01        44.52        57.07        36.16         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
        0.36        47.54        31.63        70.45        44.61         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 
       67.36        36.23        16.64        33.11        55.86        53.26 
TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
        1.02        33.01        52.04        42.05         2.01        34.98 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 
       65.00        37.97        33.96         2.99        12.99        15.02 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 
       18.58        27.62        17.03        12.95        20.61        38.20 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 
        0.30        59.15        62.17        35.87        14.96        24.99 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2397 TCGA-25-2399 
       85.05        13.02        49.05        38.04        12.00        19.99 
TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 
       42.02         2.96        29.03        31.00        26.99        78.90 
TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 
       47.61       101.79        39.02        40.41        33.93        31.20 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 
       68.32        36.36        16.93        23.93        59.67        41.98 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 
       31.27        34.62        86.60        62.93        39.42        31.30 
TCGA-29-1769 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 
       22.98        22.55        17.33        12.36        11.84        12.30 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 
       14.93         8.38         7.23         5.36        36.30        86.17 
TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 
       65.00        62.47        45.11        13.84        42.25        11.47 
TCGA-29-2436 TCGA-30-1714 TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 
        9.76        38.07        36.26        15.68         0.26        48.10 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 
       44.91        34.78         6.12        36.62         1.22        57.57 
TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 
       24.26        30.05        48.79        45.57        30.18        18.77 
TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 
       22.49         6.71        42.51        44.12         2.20        28.77 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 
       22.85        22.55        30.08        25.74        27.85        24.23 
TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
       24.69        33.01        29.49        29.82        25.91        25.08 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 
       23.80        21.60         2.24        20.98        18.31        20.52 
TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 
       14.17         6.05        16.18        11.47        47.57        23.74 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 
       28.93        42.02        10.42        40.77         1.48        24.03 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 
       11.38        21.14         1.74        22.32        29.00        25.08 
TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       25.02       180.20        80.12        22.32       116.12         9.40 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 
       34.39         2.14         5.42        44.81        11.11         8.09 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1730 TCGA-61-1734 TCGA-61-1736 
       20.94        31.43        18.54         4.34        28.47        48.79 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
       44.84        35.80        33.67         1.45         8.42         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 
       11.41        13.02         9.07        34.13        31.30        37.05 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-1919 TCGA-61-1995 
       42.51        48.92        56.61        43.43        38.17         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2016 
        5.52        14.50        17.98         4.01        30.64         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 
       45.96        45.40         4.80         4.77        51.72        71.74 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 
       61.64        58.39        60.62        65.52        55.50         6.48 
TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 
       76.87        20.68        44.52       125.75        22.22         6.35 
TCGA-61-2613 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 
       31.07        39.68        18.94         0.79         9.99        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-10-0925 TCGA-10-0927 
        9.47        57.76        17.98        35.57        54.31        81.86 
TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 
       18.51        34.19        32.88        14.66         6.71        35.44 
TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 
       36.92        19.99        20.91        24.59        44.55        39.58 
TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
        2.73        12.39        31.20        15.19        17.82        55.17 
TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 
        2.50        11.18        11.38        11.54        38.01       111.78 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       61.84        56.71        58.65        40.24       118.42       107.28 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 
       20.35        69.73        83.34        87.48        45.99        43.86 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 
       35.28        35.31        13.61       107.18       111.39       153.37 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
       66.67        92.42        95.15       145.45       102.84        43.36 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 
       71.74        66.15       134.04        19.36       127.79        50.37 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
      123.16       118.98        60.59       116.65        44.55        37.64 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
      109.32        58.68        84.53        48.76        83.74        85.94 
TCGA-13-2071 
       25.41 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             1.02              0.26 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           119.08            180.20 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            27.42             33.47 
[1] "1.0 - 119.1 (27.4)" "0.3 - 180.2 (33.5)"
[1] "hr=" "1.4"
D7V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  4P GAIN MUTATED         1    58                1
  4P GAIN WILD-TYPE       2   500                1
D7V3, multiclass
                  clus
vv                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  OMENTUM                        1                 2
  OVARY                         58               500
  PERITONEUM OVARY               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V4, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    57   2
  4P GAIN WILD-TYPE 484   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     57    2
  4P GAIN WILD-TYPE  484    3
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               57               484
  YES               2                 3
[1] 2 2
[1] FALSE
D7V5, continuous
                   vv
clus                R0 R1 R2 RX
  4P GAIN MUTATED    1  4  1  0
  4P GAIN WILD-TYPE 14 22  4  3
D7V6, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0               1                14
  R1               4                22
  R2               1                 4
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     1  31
  4P GAIN WILD-TYPE   9 296
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1   31
  4P GAIN WILD-TYPE    9  296
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              31               296
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    10  22
  4Q GAIN WILD-TYPE 218 309
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               32               527 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               22               309 
$`4Q GAIN MUTATED`
TCGA-04-1349 TCGA-04-1356 TCGA-04-1525 TCGA-04-1530 TCGA-09-1668 TCGA-13-2060 
       21.57        49.28        38.37       119.08        55.36        77.88 
TCGA-13-A5FU TCGA-23-2645 TCGA-24-1427 TCGA-24-1558 TCGA-24-1843 TCGA-24-2026 
        8.42         4.50         4.83        19.53         3.48        34.82 
TCGA-25-1313 TCGA-25-1877 TCGA-25-2396 TCGA-29-1691 TCGA-29-1701 TCGA-29-1702 
       26.96        24.00         3.02        48.33        16.93        23.93 
TCGA-29-1770 TCGA-29-2432 TCGA-30-1855 TCGA-36-1575 TCGA-61-1728 TCGA-61-1743 
       24.36        21.47         2.47         8.55        27.88        43.69 
TCGA-61-1915 TCGA-61-2012 TCGA-10-0936 TCGA-13-0714 TCGA-13-0794 TCGA-13-0802 
       67.76        30.64        36.92         6.21        63.09        51.02 
TCGA-13-0883 TCGA-13-0920 
       68.94        48.79 

$`4Q GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 
       49.15         2.01        46.62         1.08        18.51        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 
       65.52        63.09        48.76        63.98        65.46         0.53 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 
       32.52        44.32        33.67        76.57       103.40        82.39 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1536 TCGA-04-1542 
       56.55        41.59        19.99         0.79        29.10        84.20 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 
       55.43        48.89        27.88        28.64        64.64        36.23 
TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       31.86        47.70        45.37         9.99        38.43        89.33 
TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 TCGA-09-1670 
       74.93        41.62        57.60        61.87        30.51        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 
        5.85         3.02         8.55        97.55         6.18         6.12 
TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 
       35.15         4.54       112.41        71.11        63.09        39.75 
TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
       20.94        26.93        12.46        77.10        81.17        28.54 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
       83.31        55.23        57.27        81.01        17.46        32.35 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 
       54.64        87.06        61.71        29.42       124.44        20.68 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       22.39        70.82        83.93        52.44       125.56        93.90 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 
       90.38         4.24       127.27        66.15       115.07        13.97 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       43.20        34.82        65.69        34.16        65.52        80.15 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2061 
       44.68        54.25        14.53        80.02        78.48        76.90 
TCGA-13-2065 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 
       65.52        70.45        23.05        25.94        26.20        72.20 
TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 
       27.52        25.38        19.10        16.70         2.93         2.66 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
       47.54        49.68        40.54        15.39        26.83        32.09 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 
       49.41         8.81        29.13        18.90         2.76        51.35 
TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 
       54.51         3.22        31.20        68.68        19.46        33.30 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 
       86.01       129.96         4.27         6.38        39.09        33.47 
TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 
       58.13         0.53        24.95       115.89        87.48        91.66 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-24-0966 TCGA-24-0970 
       77.00        49.84         2.76         4.70         7.63        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 
       21.80        41.56         7.66        22.32        54.12        63.55 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       47.41         6.31         6.38         7.82         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1428 
        0.76         6.25         6.02         5.95         5.36        17.39 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 
       28.37        18.64        18.67        43.53         8.55        72.92 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 
       12.46        45.14       105.99         9.11         3.45         1.18 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 
       22.22        26.96        57.40        64.27        16.21        56.58 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 
       41.06        51.91        41.39        58.09        88.50        70.62 
TCGA-24-1557 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 
       39.88        44.09        45.50        47.70        25.87        10.26 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 
       17.23        90.15        88.37        48.33        38.24         8.32 
TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 
        3.72         3.81         4.37        11.28         5.79         5.52 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 
        9.80        22.68        30.21        16.44        11.05        81.11 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 
        4.87       152.02        44.84        58.16       109.71        14.43 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 
       55.92        18.48        28.18        64.01        44.52        57.07 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       36.16         0.79         0.36        47.54        31.63        70.45 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 
       44.61         0.82        67.36        36.23        16.64        33.11 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 
       55.86        53.26         1.02        33.01        52.04        42.05 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 
        2.01        34.98        65.00        37.97        33.96         2.99 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 
       12.99        15.02        18.58        27.62        17.03        12.95 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
       20.61        38.20         0.30        59.15        62.17        35.87 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 
       52.04        14.96        24.99        85.05        13.02        49.05 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 
        1.02        38.04        12.00        45.01        19.99        42.02 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 
        2.96        29.03        31.00        26.99        78.90        47.61 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 
      101.79        39.02        40.41        33.93        31.20        68.32 
TCGA-29-1699 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 
       36.36        59.67        18.25        41.98        31.27        34.62 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 
       17.36        86.60        66.81        62.93        39.42        31.30 
TCGA-29-1769 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 
       22.98        22.55        17.33        12.36        11.84        12.30 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 
       14.93         8.38         7.23         5.36        36.30        86.17 
TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 
       65.00        62.47        45.11        13.84        42.25        11.47 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1856 
        9.76        35.77        38.07        51.91        36.26        15.68 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 
        0.26        48.10        44.91        34.78         6.12        36.62 
TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 
        1.22        57.57        24.26        30.05        48.79        45.57 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 
       30.18        18.77        22.49         6.71        42.51        44.12 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
        2.20        28.77        29.10        21.53        22.85        22.55 
TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 
       30.08        25.74        27.85        24.23        24.69        35.05 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       33.01        29.49        29.82        25.91        25.08        23.80 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 
       21.60         2.24        20.98        18.31        20.52        14.17 
TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
        6.05        16.18        11.47        47.57        23.74        28.93 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 
       42.02        10.42        40.77         1.48        24.03        11.38 
TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 
       21.14         1.74        22.32        29.00        25.08        25.02 
TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 
      180.20        80.12        22.32       116.12         9.40        34.39 
TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 
        2.14         5.42        44.81        11.11         8.09        20.94 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 
       31.43        18.54         4.34        31.79        28.47        48.79 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 
       44.84        35.80         2.43        33.67         1.45         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        5.79        11.41        13.02         9.07        34.13        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 
       37.05        42.51        48.92        56.61        43.43        15.75 
TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 
       38.17         2.01         5.52        14.50        17.98         4.01 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
       30.64        39.85         1.18        45.96        45.40         4.80 
TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 
        4.77        51.72        71.74        61.64        58.39        60.62 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       65.52        55.50         6.48        76.87        20.68        44.52 
TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P 
      125.75        22.22         6.35        31.07         8.61        39.68 
TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 
       18.94         0.79         9.99        29.16         9.47        57.76 
TCGA-09-0367 TCGA-09-0369 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       17.98        35.57        54.31        25.91        81.86        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 
       34.19        32.88        14.66         6.71        35.44        19.99 
TCGA-10-0938 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 
       20.91        24.59        44.55        39.58         2.73        12.39 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 
       31.20        15.19        17.82        55.17         2.50        11.18 
TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 
       11.38        11.54        38.01       111.78        61.84        56.71 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 
       58.65        40.24       118.42       107.28        20.35        69.73 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 
       83.34        87.48        45.99        43.86        35.28        35.31 
TCGA-13-0807 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 
       13.61       107.18       111.39       153.37        66.67        92.42 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 
       95.15       145.45       102.84        43.36        71.74        66.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
      134.04        19.36       127.79        50.37       123.16       118.98 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       60.59       116.65        44.55        37.64       109.32        58.68 
TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       84.53        48.76        83.74        85.94        25.41 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             2.47              0.26 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           119.08            180.20 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            27.42             33.01 
[1] "2.5 - 119.1 (27.4)" "0.3 - 180.2 (33.0)"
[1] "hr=" "1.4"
D8V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  4Q GAIN MUTATED         0    32                0
  4Q GAIN WILD-TYPE       3   526                2
D8V3, multiclass
                  clus
vv                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  OMENTUM                        0                 3
  OVARY                         32               526
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V4, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    30   1
  4Q GAIN WILD-TYPE 511   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     30    1
  4Q GAIN WILD-TYPE  511    4
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               30               511
  YES               1                 4
[1] 2 2
[1] FALSE
D8V5, continuous
                   vv
clus                R0 R1 R2 RX
  4Q GAIN MUTATED    0  1  1  0
  4Q GAIN WILD-TYPE 15 25  4  3
D8V6, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                47 
       TCGA-3P-A9WA        TCGA-5X-AA5U        TCGA-04-1516        TCGA-04-1644 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-13-A5FT        TCGA-24-2033        TCGA-29-2414        TCGA-29-2425 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-29-2427        TCGA-29-2428        TCGA-29-2429        TCGA-29-2431 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-29-2434        TCGA-29-2436        TCGA-36-2529        TCGA-36-2530 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-36-2532        TCGA-36-2534        TCGA-36-2537        TCGA-36-2538 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-36-2540        TCGA-36-2542        TCGA-36-2543        TCGA-36-2544 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-36-2545        TCGA-36-2547        TCGA-36-2548        TCGA-36-2549 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-36-2551        TCGA-36-2552        TCGA-42-2582        TCGA-42-2587 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-42-2588        TCGA-42-2589        TCGA-42-2590        TCGA-42-2593 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-57-1993        TCGA-59-2363        TCGA-59-2372        TCGA-61-2612 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-61-2613        TCGA-61-2614        TCGA-OY-A56P        TCGA-OY-A56Q 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-VG-A8LO        TCGA-13-0807        TCGA-13-0911 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1  18
  4Q GAIN WILD-TYPE   9 309
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1   18
  4Q GAIN WILD-TYPE    9  309
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              18               309
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    77 114
  5P GAIN WILD-TYPE 151 217
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              191               368 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              114               217 
$`5P GAIN MUTATED`
TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1337 TCGA-04-1341 TCGA-04-1342 TCGA-04-1346 
       20.52        11.87         2.01         1.08        18.51        65.52 
TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1353 TCGA-04-1364 TCGA-04-1530 
       63.09        21.57        63.98         0.53        33.67       119.08 
TCGA-04-1542 TCGA-04-1646 TCGA-04-1649 TCGA-04-1654 TCGA-09-1661 TCGA-09-1666 
       84.20        27.88        64.64        47.70        38.43        57.60 
TCGA-09-1670 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2054 TCGA-09-2056 
       17.98         8.55        97.55         6.18        20.94        12.46 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1411 
       77.10        81.17        83.31        55.23        57.27        17.46 
TCGA-13-1481 TCGA-13-1484 TCGA-13-1488 TCGA-13-1492 TCGA-13-1498 TCGA-13-1501 
       87.06       124.44        70.82       125.56        66.15        43.20 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1512 TCGA-13-2065 
       34.82        65.69        34.16        65.52        14.53        65.52 
TCGA-13-A5FU TCGA-20-0990 TCGA-20-1685 TCGA-20-1686 TCGA-23-1024 TCGA-23-1029 
        8.42        25.94        16.70         2.93        15.39         8.81 
TCGA-23-1032 TCGA-23-1111 TCGA-23-1116 TCGA-23-1119 TCGA-23-1121 TCGA-23-1809 
        2.76         3.22        19.46       129.96         6.38         0.53 
TCGA-23-2079 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0975 
       91.66        49.84         2.76         4.70         4.50        21.80 
TCGA-24-0979 TCGA-24-0982 TCGA-24-1104 TCGA-24-1417 TCGA-24-1418 TCGA-24-1423 
       41.56        22.32        63.55         7.82         7.99         6.25 
TCGA-24-1425 TCGA-24-1428 TCGA-24-1434 TCGA-24-1436 TCGA-24-1469 TCGA-24-1471 
        5.95        17.39        18.67         8.55         9.11         1.18 
TCGA-24-1474 TCGA-24-1549 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       22.22        56.58        58.09        88.50        70.62        39.88 
TCGA-24-1604 TCGA-24-1616 TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 TCGA-24-1850 
       88.37        38.24         3.72         3.81        11.28         5.52 
TCGA-24-1923 TCGA-24-1924 TCGA-24-1928 TCGA-24-2020 TCGA-24-2026 TCGA-24-2030 
       22.68        30.21        11.05       152.02        34.82        55.92 
TCGA-24-2260 TCGA-24-2267 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2295 
       36.16        47.54        44.61         0.82        67.36        33.11 
TCGA-24-2298 TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 TCGA-25-1322 TCGA-25-1329 
       53.26        34.98        65.00        33.96         2.99        15.02 
TCGA-25-1623 TCGA-25-1627 TCGA-25-1631 TCGA-25-1634 TCGA-25-1877 TCGA-25-1878 
       18.58        12.95         0.30        35.87        24.00        85.05 
TCGA-25-2392 TCGA-25-2396 TCGA-25-2404 TCGA-29-1688 TCGA-29-1691 TCGA-29-1695 
        1.02         3.02        29.03        78.90        48.33        40.41 
TCGA-29-1707 TCGA-29-1761 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 
       41.98        17.36        66.81        62.93        39.42        31.30 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1774 TCGA-29-2425 TCGA-29-2432 TCGA-30-1718 
       22.98        24.36        17.33        65.00        21.47        51.91 
TCGA-30-1853 TCGA-31-1950 TCGA-36-1568 TCGA-36-1569 TCGA-36-1576 TCGA-36-1578 
       36.26        18.77        28.77        29.10        30.08        27.85 
TCGA-36-1581 TCGA-36-2529 TCGA-36-2543 TCGA-36-2548 TCGA-42-2582 TCGA-42-2588 
       24.69        35.05         2.24        14.17        47.57        28.93 
TCGA-42-2593 TCGA-57-1582 TCGA-57-1585 TCGA-57-1993 TCGA-57-1994 TCGA-61-1725 
        1.48        24.03         1.74        25.08        25.02        31.43 
TCGA-61-1733 TCGA-61-1899 TCGA-61-1903 TCGA-61-1914 TCGA-61-1918 TCGA-61-1919 
       31.79         8.42        13.02        56.61        15.75        38.17 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2087 TCGA-61-2098 
        4.01        30.64        39.85        30.64         4.80        65.52 
TCGA-61-2101 TCGA-61-2111 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P TCGA-09-0366 
       55.50       125.75         6.35         8.61        39.68        57.76 
TCGA-09-0367 TCGA-09-0369 TCGA-10-0927 TCGA-10-0930 TCGA-10-0933 TCGA-10-0936 
       17.98        35.57        81.86        34.19        14.66        36.92 
TCGA-13-0717 TCGA-13-0723 TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
       24.59        39.58        12.39        15.19        17.82        55.17 
TCGA-13-0757 TCGA-13-0760 TCGA-13-0766 TCGA-13-0768 TCGA-13-0792 TCGA-13-0794 
       11.18        11.54        56.71        58.65       118.42        63.09 
TCGA-13-0801 TCGA-13-0804 TCGA-13-0883 TCGA-13-0886 TCGA-13-0889 TCGA-13-0899 
       45.99        35.28        68.94       153.37        95.15        66.15 
TCGA-13-0901 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0911 
       19.36        50.37       123.16       118.98        44.55 

$`5P GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 
       13.81        43.92        41.00         1.81        49.15        46.62 
TCGA-04-1343 TCGA-04-1348 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 
       11.87        48.76        65.46        49.28        32.52        44.32 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 
       76.57       103.40        82.39        56.55        41.59        19.99 
TCGA-04-1519 TCGA-04-1525 TCGA-04-1536 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 
        0.79        38.37        29.10        55.43        48.89        28.64 
TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-1659 TCGA-09-1662 TCGA-09-1664 
       36.23        31.86        45.37         9.99        89.33        74.93 
TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1672 TCGA-09-1673 
       41.62        61.87        55.36        30.51         5.85         3.02 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
        6.12        35.15         4.54       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2055 TCGA-13-1405 TCGA-13-1410 TCGA-13-1412 TCGA-13-1477 
       39.75        26.93        28.54        81.01        32.35        54.64 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 
       61.71        29.42        20.68        22.39        83.93        52.44 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1499 TCGA-13-1500 
       93.90        90.38         4.24       127.27       115.07        13.97 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
       80.15        44.68        54.25        80.02        78.48        77.88 
TCGA-13-2061 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 
       76.90        70.45        23.05        26.20        72.20        27.52 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 
       25.38        19.10         2.66        47.54        49.68        40.54 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 TCGA-23-1109 
       26.83        32.09        49.41        29.13        18.90        51.35 
TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 
       54.51        31.20        68.68        33.30        86.01         4.27 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 
       39.09        33.47        58.13        24.95       115.89        87.48 
TCGA-23-2081 TCGA-24-0966 TCGA-24-0970 TCGA-24-0980 TCGA-24-1103 TCGA-24-1105 
       77.00         7.63        11.64         7.66        54.12        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1419 TCGA-24-1422 TCGA-24-1424 TCGA-24-1426 
        6.31         6.38         7.86         0.76         6.02         5.36 
TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 
        4.83        28.37        18.64        43.53        72.92        12.46 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 
       45.14       105.99         3.45        26.96        57.40        64.27 
TCGA-24-1548 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1558 TCGA-24-1560 
       16.21        41.06        51.91        41.39        19.53        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       45.50        47.70        25.87        10.26        17.23        90.15 
TCGA-24-1614 TCGA-24-1842 TCGA-24-1843 TCGA-24-1846 TCGA-24-1849 TCGA-24-1920 
       48.33         8.32         3.48         4.37         5.79         9.80 
TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 
       16.44        81.11         4.87        44.84        58.16       109.71 
TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 
       14.43        18.48        28.18        64.01        44.52        57.07 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2271 TCGA-24-2280 TCGA-24-2290 TCGA-24-2293 
        0.79         0.36        31.63        70.45        36.23        16.64 
TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 
       55.86         1.02        26.96        33.01        52.04        42.05 
TCGA-25-1317 TCGA-25-1320 TCGA-25-1323 TCGA-25-1625 TCGA-25-1626 TCGA-25-1628 
        2.01        37.97        12.99        27.62        17.03        20.61 
TCGA-25-1630 TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 
       38.20        59.15        62.17        52.04        14.96        24.99 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 
       13.02        49.05        38.04        12.00        45.01        19.99 
TCGA-25-2400 TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 TCGA-29-1690 TCGA-29-1693 
       42.02         2.96        31.00        26.99        47.61       101.79 
TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 
       39.02        33.93        31.20        68.32        36.36        16.93 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 TCGA-29-1762 
       23.93        59.67        18.25        31.27        34.62        86.60 
TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 
       22.55        12.36        11.84        12.30        14.93         8.38 
TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2428 
        7.23         5.36        36.30        86.17        62.47        45.11 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 
       13.84        42.25        11.47         9.76        35.77        38.07 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 
        2.47        15.68         0.26        48.10        44.91        34.78 
TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 
        6.12        36.62         1.22        57.57        24.26        30.05 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 
       48.79        45.57        30.18        22.49         6.71        42.51 
TCGA-31-1956 TCGA-31-1959 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 
       44.12         2.20        21.53        22.85        22.55         8.55 
TCGA-36-1577 TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       25.74        24.23        33.01        29.49        29.82        25.91 
TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 
       25.08        23.80        21.60        20.98        18.31        20.52 
TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 TCGA-42-2589 TCGA-42-2590 
        6.05        16.18        11.47        23.74        42.02        10.42 
TCGA-42-2591 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1992 TCGA-59-2348 
       40.77        11.38        21.14        22.32        29.00       180.20 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 
       80.12        22.32       116.12         9.40        34.39         2.14 
TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1727 
        5.42        44.81        11.11         8.09        20.94        18.54 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
       27.88         4.34        28.47        48.79        44.84        35.80 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1900 TCGA-61-1901 
        2.43        33.67        43.69         1.45         5.79        11.41 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 
        9.07        34.13        31.30        37.05        42.51        48.92 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       67.76        43.43         2.01         5.52        14.50        17.98 
TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 
        1.18        45.96        45.40         4.77        51.72        71.74 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       61.64        58.39        60.62         6.48        76.87        20.68 
TCGA-61-2110 TCGA-61-2113 TCGA-61-2613 TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       44.52        22.22        31.07        18.94         0.79         9.99 
TCGA-09-0364 TCGA-09-0365 TCGA-10-0925 TCGA-10-0926 TCGA-10-0928 TCGA-10-0931 
       29.16         9.47        54.31        25.91        18.51        32.88 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 
        6.71        35.44        19.99        20.91         6.21        44.55 
TCGA-13-0724 TCGA-13-0726 TCGA-13-0755 TCGA-13-0758 TCGA-13-0761 TCGA-13-0762 
        2.73        31.20         2.50        11.38        38.01       111.78 
TCGA-13-0764 TCGA-13-0791 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 
       61.84        40.24       107.28        20.35        69.73        83.34 
TCGA-13-0800 TCGA-13-0802 TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 TCGA-13-0884 
       87.48        51.02        43.86        35.31        13.61       107.18 
TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
      111.39        66.67        92.42       145.45       102.84        43.36 
TCGA-13-0897 TCGA-13-0900 TCGA-13-0903 TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 
       71.74       134.04       127.79        60.59       116.65        37.64 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 
      109.32        58.68        84.53        48.79        48.76        83.74 
TCGA-13-0924 TCGA-13-2071 
       85.94        25.41 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.30              0.26 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           153.37            180.20 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           31.300            33.155 
[1] "0.3 - 153.4 (31.3)" "0.3 - 180.2 (33.2)"
[1] "hr=" "1"  
D9V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  5P GAIN MUTATED         0   191                2
  5P GAIN WILD-TYPE       3   367                0
D9V3, multiclass
                  clus
vv                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  OMENTUM                        0                 3
  OVARY                        191               367
  PERITONEUM OVARY               2                 0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V4, binary
                   cls
clus                  0   1
  5P GAIN MUTATED   189   1
  5P GAIN WILD-TYPE 352   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    189    1
  5P GAIN WILD-TYPE  352    4
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO              189               352
  YES               1                 4
[1] 2 2
[1] FALSE
D9V5, continuous
                   vv
clus                R0 R1 R2 RX
  5P GAIN MUTATED    3  8  4  0
  5P GAIN WILD-TYPE 12 18  1  3
D9V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0               3                12
  R1               8                18
  R2               4                 1
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     3 108
  5P GAIN WILD-TYPE   7 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      3  108
  5P GAIN WILD-TYPE    7  219
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 7
  NOT HISPANIC OR LATINO             108               219
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    22  34
  5Q GAIN WILD-TYPE 206 297
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               56               503 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               34               297 
$`5Q GAIN MUTATED`
TCGA-04-1337 TCGA-04-1347 TCGA-04-1349 TCGA-04-1353 TCGA-04-1364 TCGA-04-1530 
        2.01        63.09        21.57         0.53        33.67       119.08 
TCGA-04-1542 TCGA-09-1661 TCGA-09-1666 TCGA-09-1670 TCGA-13-1409 TCGA-13-1492 
       84.20        38.43        57.60        17.98        57.27       125.56 
TCGA-13-1498 TCGA-13-1504 TCGA-13-2065 TCGA-13-A5FU TCGA-23-1111 TCGA-23-1116 
       66.15        34.82        65.52         8.42         3.22        19.46 
TCGA-23-2079 TCGA-23-2645 TCGA-24-1104 TCGA-24-1417 TCGA-24-1428 TCGA-24-1434 
       91.66         4.50        63.55         7.82        17.39        18.67 
TCGA-24-1436 TCGA-24-1471 TCGA-24-1556 TCGA-24-1604 TCGA-24-1845 TCGA-24-1850 
        8.55         1.18        70.62        88.37         3.81         5.52 
TCGA-24-1923 TCGA-24-2288 TCGA-25-1329 TCGA-25-1631 TCGA-25-2392 TCGA-29-1688 
       22.68         0.82        15.02         0.30         1.02        78.90 
TCGA-29-1763 TCGA-29-1769 TCGA-29-1770 TCGA-29-2432 TCGA-30-1853 TCGA-36-1569 
       66.81        22.98        24.36        21.47        36.26        29.10 
TCGA-36-2529 TCGA-36-2543 TCGA-61-1725 TCGA-61-1733 TCGA-61-2009 TCGA-61-2612 
       35.05         2.24        31.43        31.79        39.85         6.35 
TCGA-61-2614 TCGA-09-0369 TCGA-10-0930 TCGA-10-0936 TCGA-13-0751 TCGA-13-0768 
        8.61        35.57        34.19        36.92        55.17        58.65 
TCGA-13-0792 TCGA-13-0911 
      118.42        44.55 

$`5Q GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1336 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 
       49.15        46.62         1.08        18.51        11.87        65.52 
TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 
       48.76        63.98        65.46        49.28        32.52        44.32 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 
       76.57       103.40        82.39        56.55        41.59        19.99 
TCGA-04-1519 TCGA-04-1525 TCGA-04-1536 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
        0.79        38.37        29.10        55.43        48.89        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 
       28.64        64.64        36.23        31.86        47.70        45.37 
TCGA-09-1659 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 
        9.99        89.33        74.93        41.62        61.87        55.36 
TCGA-09-1669 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 
       30.51         5.85         3.02         8.55        97.55         6.18 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
        6.12        35.15         4.54       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 
       39.75        20.94        26.93        12.46        77.10        81.17 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
       28.54        83.31        55.23        81.01        17.46        32.35 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 
       54.64        87.06        61.71        29.42       124.44        20.68 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 
       22.39        70.82        83.93        52.44        93.90        90.38 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1505 
        4.24       127.27       115.07        13.97        43.20        65.69 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
       34.16        65.52        80.15        44.68        54.25        14.53 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-A5FT TCGA-20-0987 
       80.02        78.48        77.88        76.90        70.45        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 
       25.94        26.20        72.20        27.52        25.38        19.10 
TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 
       16.70         2.93         2.66        47.54        49.68        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
       15.39        26.83        32.09        49.41         8.81        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 
       18.90         2.76        51.35        54.51        31.20        68.68 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 
       33.30        86.01       129.96         4.27         6.38        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 
       33.47        58.13         0.53        24.95       115.89        87.48 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-24-0966 TCGA-24-0970 
       77.00        49.84         2.76         4.70         7.63        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1105 
       21.80        41.56         7.66        22.32        54.12        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 
        6.31         6.38         7.99         7.86         0.76         6.25 
TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 
        6.02         5.95         5.36         4.83        28.37        18.64 
TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 
       43.53        72.92        12.46        45.14       105.99         9.11 
TCGA-24-1470 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 
        3.45        22.22        26.96        57.40        64.27        16.21 
TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       56.58        41.06        51.91        41.39        58.09        88.50 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
       39.88        19.53        44.09        45.50        47.70        25.87 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 
       10.26        17.23        90.15        48.33        38.24         8.32 
TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1920 
        3.48         3.72         4.37        11.28         5.79         9.80 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 
       30.21        16.44        11.05        81.11         4.87       152.02 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 
       44.84        58.16        34.82       109.71        14.43        55.92 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 
       18.48        28.18        64.01        44.52        57.07        36.16 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 
        0.79         0.36        47.54        31.63        70.45        44.61 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 
       67.36        36.23        16.64        33.11        55.86        53.26 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
        1.02        26.96        33.01        52.04        42.05         2.01 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 
       34.98        65.00        37.97        33.96         2.99        12.99 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 
       18.58        27.62        17.03        12.95        20.61        38.20 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 
       59.15        62.17        35.87        52.04        14.96        24.99 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 
       24.00        85.05        13.02        49.05        38.04         3.02 
TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 
       12.00        45.01        19.99        42.02         2.96        29.03 
TCGA-25-2408 TCGA-25-2409 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 
       31.00        26.99        47.61        48.33       101.79        39.02 
TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 
       40.41        33.93        31.20        68.32        36.36        16.93 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 
       23.93        59.67        18.25        41.98        31.27        34.62 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1771 
       17.36        86.60        62.93        39.42        31.30        22.55 
TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 
       17.33        12.36        11.84        12.30        14.93         8.38 
TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 
        7.23         5.36        36.30        86.17        65.00        62.47 
TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ 
       45.11        13.84        42.25        11.47         9.76        35.77 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 
       38.07        51.91         2.47        15.68         0.26        48.10 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 
       44.91        34.78         6.12        36.62         1.22        57.57 
TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 
       24.26        30.05        48.79        45.57        30.18        18.77 
TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 
       22.49         6.71        42.51        44.12         2.20        28.77 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 
       21.53        22.85        22.55         8.55        30.08        25.74 
TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       27.85        24.23        24.69        33.01        29.49        29.82 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 
       25.91        25.08        23.80        21.60        20.98        18.31 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 
       20.52        14.17         6.05        16.18        11.47        47.57 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 
       23.74        28.93        42.02        10.42        40.77         1.48 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 
       24.03        11.38        21.14         1.74        22.32        29.00 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 
       25.08        25.02       180.20        80.12        22.32       116.12 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 
        9.40        34.39         2.14         5.42        44.81        11.11 
TCGA-61-1722 TCGA-61-1724 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1734 
        8.09        20.94        18.54        27.88         4.34        28.47 
TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 
       48.79        44.84        35.80         2.43        33.67        43.69 
TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 
        1.45         8.42         5.79        11.41        13.02         9.07 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 
       34.13        31.30        37.05        42.51        48.92        56.61 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
       67.76        43.43        15.75        38.17         2.01         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 TCGA-61-2016 
       14.50        17.98         4.01        30.64        30.64         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 
       45.96        45.40         4.80         4.77        51.72        71.74 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 
       61.64        58.39        60.62        65.52        55.50         6.48 
TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2613 
       76.87        20.68        44.52       125.75        22.22        31.07 
TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 
       39.68        18.94         0.79         9.99        29.16         9.47 
TCGA-09-0366 TCGA-09-0367 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       57.76        17.98        54.31        25.91        81.86        18.51 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 
       32.88        14.66         6.71        35.44        19.99        20.91 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 
        6.21        24.59        44.55        39.58         2.73        12.39 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 
       31.20        15.19        17.82         2.50        11.18        11.38 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 
       11.54        38.01       111.78        61.84        56.71        40.24 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 
      107.28        63.09        20.35        69.73        83.34        87.48 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
       45.99        51.02        43.86        35.28        35.31        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 
       68.94       107.18       111.39       153.37        66.67        92.42 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 
       95.15       145.45       102.84        43.36        71.74        66.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
      134.04        19.36       127.79        50.37       123.16       118.98 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
       60.59       116.65        37.64       109.32        58.68        84.53 
TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       48.79        48.76        83.74        85.94        25.41 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.30              0.26 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           125.56            180.20 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            31.61             33.01 
[1] "0.3 - 125.6 (31.6)" "0.3 - 180.2 (33.0)"
[1] "hr=" "1.1"
D10V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  5Q GAIN MUTATED         0    56                1
  5Q GAIN WILD-TYPE       3   502                1
D10V3, multiclass
                  clus
vv                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  OMENTUM                        0                 3
  OVARY                         56               502
  PERITONEUM OVARY               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V4, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    55   0
  5Q GAIN WILD-TYPE 486   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     55    0
  5Q GAIN WILD-TYPE  486    5
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               55               486
  YES               0                 5
[1] 2 2
[1] FALSE
D10V5, continuous
                   vv
clus                R0 R1 R2 RX
  5Q GAIN MUTATED    0  6  1  0
  5Q GAIN WILD-TYPE 15 20  4  3
D10V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0               0                15
  R1               6                20
  R2               1                 4
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     0  27
  5Q GAIN WILD-TYPE  10 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0   27
  5Q GAIN WILD-TYPE   10  300
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              27               300
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    75  91
  6P GAIN WILD-TYPE 153 240
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              166               393 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               91               240 
$`6P GAIN MUTATED`
TCGA-5X-AA5U TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 TCGA-04-1353 
       11.87        18.51        65.52        63.09        21.57         0.53 
TCGA-04-1362 TCGA-04-1364 TCGA-04-1516 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 
       44.32        33.67        41.59        38.37       119.08        29.10 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 
       38.43        89.33        41.62        57.60        61.87        55.36 
TCGA-09-1669 TCGA-09-1674 TCGA-09-2049 TCGA-09-2051 TCGA-09-2054 TCGA-13-1407 
       30.51         8.55       112.41        63.09        20.94        83.31 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1411 TCGA-13-1481 TCGA-13-1487 TCGA-13-1488 
       55.23        57.27        17.46        87.06        22.39        70.82 
TCGA-13-1489 TCGA-13-1496 TCGA-13-1499 TCGA-13-1510 TCGA-13-2057 TCGA-13-2060 
       83.93         4.24       115.07        44.68        80.02        77.88 
TCGA-13-2061 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1685 TCGA-20-1686 
       76.90        25.94        26.20        27.52        16.70         2.93 
TCGA-23-1023 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1114 
       40.54        18.90         2.76        51.35        54.51        68.68 
TCGA-23-1116 TCGA-23-1120 TCGA-23-1124 TCGA-23-1809 TCGA-23-2079 TCGA-24-0982 
       19.46         4.27        58.13         0.53        91.66        22.32 
TCGA-24-1417 TCGA-24-1423 TCGA-24-1424 TCGA-24-1469 TCGA-24-1474 TCGA-24-1558 
        7.82         6.25         6.02         9.11        22.22        19.53 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1604 TCGA-24-1614 TCGA-24-1850 TCGA-24-2020 
       47.70        25.87        88.37        48.33         5.52       152.02 
TCGA-24-2026 TCGA-24-2254 TCGA-24-2261 TCGA-24-2267 TCGA-24-2281 TCGA-24-2289 
       34.82        57.07         0.79        47.54        44.61        67.36 
TCGA-25-1317 TCGA-25-1319 TCGA-25-1321 TCGA-25-1323 TCGA-25-1634 TCGA-25-1870 
        2.01        65.00        33.96        12.99        35.87        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2392 TCGA-25-2398 TCGA-25-2400 
       24.99        24.00        85.05         1.02        45.01        42.02 
TCGA-25-2401 TCGA-25-2404 TCGA-29-1691 TCGA-29-1695 TCGA-29-1698 TCGA-29-1701 
        2.96        29.03        48.33        40.41        68.32        16.93 
TCGA-29-1702 TCGA-29-1710 TCGA-29-1764 TCGA-29-1770 TCGA-29-1774 TCGA-29-1778 
       23.93        31.27        62.93        24.36        17.33        14.93 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2432 TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1856 
       86.17        65.00        21.47        35.77        51.91        15.68 
TCGA-30-1861 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1571 TCGA-36-1575 
       34.78        42.51        44.12         2.20        22.85         8.55 
TCGA-36-1576 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2542 TCGA-36-2545 
       30.08        24.23        24.69        35.05        21.60        18.31 
TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 TCGA-42-2593 TCGA-57-1582 TCGA-57-1585 
       16.18        11.47        23.74         1.48        24.03         1.74 
TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-61-1722 TCGA-61-1730 TCGA-61-1737 
       22.32        25.08        25.02         8.09         4.34        44.84 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1899 TCGA-61-1907 TCGA-61-1915 TCGA-61-1918 
       33.67        43.69         8.42        31.30        67.76        15.75 
TCGA-61-1919 TCGA-61-1998 TCGA-61-2003 TCGA-61-2009 TCGA-61-2088 TCGA-61-2097 
       38.17         5.52         4.01        39.85         4.77        60.62 
TCGA-61-2098 TCGA-61-2102 TCGA-61-2104 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 
       65.52         6.48        76.87       125.75        22.22         6.35 
TCGA-61-2614 TCGA-OY-A56Q TCGA-WR-A838 TCGA-09-0364 TCGA-09-0366 TCGA-10-0925 
        8.61        18.94         9.99        29.16        57.76        54.31 
TCGA-10-0930 TCGA-10-0933 TCGA-13-0717 TCGA-13-0724 TCGA-13-0760 TCGA-13-0764 
       34.19        14.66        24.59         2.73        11.54        61.84 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0800 TCGA-13-0885 
      118.42       107.28        63.09        20.35        87.48       111.39 
TCGA-13-0886 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 
      153.37        48.79        83.74        85.94 

$`6P GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 
       13.81        20.52        43.92        41.00         1.81        49.15 
TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1343 TCGA-04-1348 TCGA-04-1350 
        2.01        46.62         1.08        11.87        48.76        63.98 
TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 
       65.46        49.28        32.52        76.57       103.40        82.39 
TCGA-04-1514 TCGA-04-1517 TCGA-04-1519 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 
       56.55        19.99         0.79        84.20        55.43        48.89 
TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 
       27.88        28.64        64.64        36.23        31.86        47.70 
TCGA-04-1655 TCGA-09-1659 TCGA-09-1664 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       45.37         9.99        74.93        17.98         5.85         3.02 
TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 
       97.55         6.18         6.12        35.15         4.54        71.11 
TCGA-09-2053 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
       39.75        26.93        12.46        77.10        81.17        28.54 
TCGA-13-1410 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
       81.01        32.35        54.64        61.71        29.42       124.44 
TCGA-13-1485 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1497 
       20.68        52.44       125.56        93.90        90.38       127.27 
TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       66.15        13.97        43.20        34.82        65.69        34.16 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2065 
       65.52        80.15        54.25        14.53        78.48        65.52 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 
       70.45         8.42        23.05        72.20        25.38        19.10 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
        2.66        47.54        49.68        15.39        26.83        32.09 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1111 TCGA-23-1113 TCGA-23-1117 
       49.41         8.81        29.13         3.22        31.20        33.30 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-2072 
       86.01       129.96         6.38        39.09        33.47        24.95 
TCGA-23-2077 TCGA-23-2078 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 
      115.89        87.48        77.00        49.84         2.76         4.70 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        4.50         7.63        11.64        21.80        41.56         7.66 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1418 
       54.12        63.55        47.41         6.31         6.38         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        7.86         0.76         5.95         5.36         4.83        17.39 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 
       28.37        18.64        18.67        43.53         8.55        72.92 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1544 
       12.46        45.14       105.99         3.45         1.18        26.96 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 
       57.40        64.27        16.21        56.58        41.06        51.91 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1560 
       41.39        58.09        88.50        70.62        39.88        44.09 
TCGA-24-1562 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1616 TCGA-24-1842 
       45.50        10.26        17.23        90.15        38.24         8.32 
TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 
        3.48         3.72         3.81         4.37        11.28         5.79 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 
        9.80        22.68        30.21        16.44        11.05        81.11 
TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 
        4.87        44.84        58.16       109.71        14.43        55.92 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2260 TCGA-24-2262 
       18.48        28.18        64.01        44.52        36.16         0.36 
TCGA-24-2271 TCGA-24-2280 TCGA-24-2288 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 
       31.63        70.45         0.82        36.23        16.64        33.11 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 
       55.86        53.26         1.02        26.96        33.01        52.04 
TCGA-25-1316 TCGA-25-1318 TCGA-25-1320 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 
       42.05        34.98        37.97         2.99        15.02        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
       27.62        17.03        12.95        20.61        38.20         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 
       59.15        62.17        52.04        13.02        49.05        38.04 
TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 
        3.02        12.00        19.99        31.00        26.99        78.90 
TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 
       47.61       101.79        39.02        33.93        31.20        36.36 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 
       59.67        18.25        41.98        34.62        17.36        86.60 
TCGA-29-1763 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 TCGA-29-1775 
       66.81        39.42        31.30        22.98        22.55        12.36 
TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 
       11.84        12.30         8.38         7.23         5.36        36.30 
TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 TCGA-29-2436 
       62.47        45.11        13.84        42.25        11.47         9.76 
TCGA-30-1714 TCGA-30-1853 TCGA-30-1855 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 
       38.07        36.26         2.47         0.26        48.10        44.91 
TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 
        6.12        36.62         1.22        57.57        24.26        30.05 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 
       48.79        45.57        30.18        18.77        22.49         6.71 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 TCGA-36-1577 TCGA-36-1578 
       28.77        29.10        21.53        22.55        25.74        27.85 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       33.01        29.49        29.82        25.91        25.08        23.80 
TCGA-36-2543 TCGA-36-2544 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-42-2582 
        2.24        20.98        20.52        14.17         6.05        47.57 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-57-1583 TCGA-57-1584 
       28.93        42.02        10.42        40.77        11.38        21.14 
TCGA-57-1992 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       29.00       180.20        80.12        22.32       116.12         9.40 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1724 
       34.39         2.14         5.42        44.81        11.11        20.94 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 
       31.43        18.54        27.88        31.79        28.47        48.79 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1895 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 
       35.80         2.43         1.45         5.79        11.41        13.02 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 
        9.07        34.13        37.05        42.51        48.92        56.61 
TCGA-61-1917 TCGA-61-1995 TCGA-61-2000 TCGA-61-2002 TCGA-61-2008 TCGA-61-2012 
       43.43         2.01        14.50        17.98        30.64        30.64 
TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 TCGA-61-2094 
        1.18        45.96        45.40         4.80        51.72        71.74 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2101 TCGA-61-2109 TCGA-61-2110 TCGA-61-2613 
       61.64        58.39        55.50        20.68        44.52        31.07 
TCGA-OY-A56P TCGA-VG-A8LO TCGA-09-0365 TCGA-09-0367 TCGA-09-0369 TCGA-10-0926 
       39.68         0.79         9.47        17.98        35.57        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 
       81.86        18.51        32.88         6.71        35.44        36.92 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 
       19.99        20.91         6.21        44.55        39.58        12.39 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 
       31.20        15.19        17.82        55.17         2.50        11.18 
TCGA-13-0758 TCGA-13-0761 TCGA-13-0762 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 
       11.38        38.01       111.78        56.71        58.65        40.24 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 
       69.73        83.34        45.99        51.02        43.86        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0887 TCGA-13-0888 
       35.31        13.61        68.94       107.18        66.67        92.42 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 
       95.15       145.45       102.84        43.36        71.74        66.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
      134.04        19.36       127.79        50.37       123.16       118.98 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       60.59       116.65        44.55        37.64       109.32        58.68 
TCGA-13-0919 TCGA-13-0921 TCGA-13-2071 
       84.53        48.76        25.41 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.53              0.26 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           153.37            180.20 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           31.285            33.010 
[1] "0.5 - 153.4 (31.3)" "0.3 - 180.2 (33.0)"
[1] "hr=" "1.2"
D11V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  6P GAIN MUTATED         1   166                1
  6P GAIN WILD-TYPE       2   392                1
D11V3, multiclass
                  clus
vv                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  OMENTUM                        1                 2
  OVARY                        166               392
  PERITONEUM OVARY               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V4, binary
                   cls
clus                  0   1
  6P GAIN MUTATED   164   1
  6P GAIN WILD-TYPE 377   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED    164    1
  6P GAIN WILD-TYPE  377    4
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO              164               377
  YES               1                 4
[1] 2 2
[1] FALSE
D11V5, continuous
                   vv
clus                R0 R1 R2 RX
  6P GAIN MUTATED    5  9  1  1
  6P GAIN WILD-TYPE 10 17  4  2
D11V6, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0               5                10
  R1               9                17
  R2               1                 4
  RX               1                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     2 101
  6P GAIN WILD-TYPE   8 226
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2  101
  6P GAIN WILD-TYPE    8  226
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 8
  NOT HISPANIC OR LATINO             101               226
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    44  52
  6Q GAIN WILD-TYPE 184 279
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               96               463 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               52               279 
$`6Q GAIN MUTATED`
TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 TCGA-04-1362 TCGA-04-1516 TCGA-04-1530 
       18.51        65.52        63.09        44.32        41.59       119.08 
TCGA-04-1536 TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1674 
       29.10        41.62        61.87        55.36        30.51         8.55 
TCGA-09-2051 TCGA-13-1408 TCGA-13-1409 TCGA-13-1487 TCGA-13-1488 TCGA-13-1496 
       63.09        55.23        57.27        22.39        70.82         4.24 
TCGA-13-1499 TCGA-13-2057 TCGA-13-2061 TCGA-20-0991 TCGA-20-1682 TCGA-23-1110 
      115.07        80.02        76.90        26.20        27.52        54.51 
TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 TCGA-23-1120 TCGA-23-1124 TCGA-23-1809 
        3.22        68.68        19.46         4.27        58.13         0.53 
TCGA-23-2079 TCGA-24-1424 TCGA-24-1469 TCGA-24-1474 TCGA-24-1558 TCGA-24-1563 
       91.66         6.02         9.11        22.22        19.53        47.70 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1850 TCGA-24-1920 TCGA-24-1928 TCGA-24-2267 
       88.37        48.33         5.52         9.80        11.05        47.54 
TCGA-24-2281 TCGA-24-2289 TCGA-25-1635 TCGA-25-1871 TCGA-25-1877 TCGA-25-2392 
       44.61        67.36        52.04        24.99        24.00         1.02 
TCGA-25-2400 TCGA-25-2404 TCGA-29-1691 TCGA-29-1695 TCGA-29-1698 TCGA-29-1702 
       42.02        29.03        48.33        40.41        68.32        23.93 
TCGA-29-1710 TCGA-29-1761 TCGA-29-1764 TCGA-29-1770 TCGA-29-1774 TCGA-29-1778 
       31.27        17.36        62.93        24.36        17.33        14.93 
TCGA-29-2425 TCGA-30-1861 TCGA-30-1862 TCGA-36-1575 TCGA-36-1576 TCGA-36-1581 
       65.00        34.78         6.12         8.55        30.08        24.69 
TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 TCGA-57-1582 TCGA-57-1993 TCGA-57-1994 
       16.18        11.47        23.74        24.03        25.08        25.02 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1915 TCGA-61-1919 TCGA-61-2003 TCGA-61-2088 
       33.67        43.69        67.76        38.17         4.01         4.77 
TCGA-61-2102 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-WR-A838 TCGA-09-0364 
        6.48       125.75        22.22         6.35         9.99        29.16 
TCGA-10-0930 TCGA-10-0933 TCGA-13-0723 TCGA-13-0724 TCGA-13-0760 TCGA-13-0764 
       34.19        14.66        39.58         2.73        11.54        61.84 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0800 TCGA-13-0885 TCGA-13-0920 TCGA-13-0924 
       63.09        20.35        87.48       111.39        48.79        85.94 

$`6Q GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1343 TCGA-04-1348 
       49.15         2.01        46.62         1.08        11.87        48.76 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 
       21.57        63.98        65.46         0.53        49.28        32.52 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 
       33.67        76.57       103.40        82.39        56.55        19.99 
TCGA-04-1519 TCGA-04-1525 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
        0.79        38.37        84.20        55.43        48.89        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 
       28.64        64.64        36.23        31.86        47.70        45.37 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1670 
        9.99        38.43        89.33        74.93        57.60        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 
        5.85         3.02        97.55         6.18         6.12        35.15 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 
        4.54       112.41        71.11        39.75        20.94        26.93 
TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1410 
       12.46        77.10        81.17        28.54        83.31        81.01 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
       17.46        32.35        54.64        87.06        61.71        29.42 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
      124.44        20.68        83.93        52.44       125.56        93.90 
TCGA-13-1495 TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 
       90.38       127.27        66.15        13.97        43.20        34.82 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
       65.69        34.16        65.52        80.15        44.68        54.25 
TCGA-13-1512 TCGA-13-2059 TCGA-13-2060 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU 
       14.53        78.48        77.88        65.52        70.45         8.42 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 
       23.05        25.94        72.20        25.38        19.10        16.70 
TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 
        2.93         2.66        47.54        49.68        40.54        15.39 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 
       26.83        32.09        49.41         8.81        29.13        18.90 
TCGA-23-1032 TCGA-23-1109 TCGA-23-1113 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 
        2.76        51.35        31.20        33.30        86.01       129.96 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 
        6.38        39.09        33.47        24.95       115.89        87.48 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 
       77.00        49.84         2.76         4.70         4.50         7.63 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 
       11.64        21.80        41.56         7.66        22.32        54.12 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 
       63.55        47.41         6.31         6.38         7.82         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        7.86         0.76         6.25         5.95         5.36         4.83 
TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
       17.39        28.37        18.64        18.67        43.53         8.55 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 
       72.92        12.46        45.14       105.99         3.45         1.18 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 
       26.96        57.40        64.27        16.21        56.58        41.06 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       51.91        41.39        58.09        88.50        70.62        39.88 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       44.09        45.50        25.87        10.26        17.23        90.15 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 
       38.24         8.32         3.48         3.72         3.81         4.37 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 
       11.28         5.79        22.68        30.21        16.44        81.11 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 
        4.87       152.02        44.84        58.16        34.82       109.71 
TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
       14.43        55.92        18.48        28.18        64.01        44.52 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2271 TCGA-24-2280 
       57.07        36.16         0.79         0.36        31.63        70.45 
TCGA-24-2288 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 
        0.82        36.23        16.64        33.11        55.86        53.26 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
        1.02        26.96        33.01        52.04        42.05         2.01 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 
       34.98        65.00        37.97        33.96         2.99        12.99 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 
       15.02        18.58        27.62        17.03        12.95        20.61 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 
       38.20         0.30        59.15        62.17        35.87        14.96 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 
       85.05        13.02        49.05        38.04         3.02        12.00 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 
       45.01        19.99         2.96        31.00        26.99        78.90 
TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 
       47.61       101.79        39.02        33.93        31.20        36.36 
TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 TCGA-29-1762 
       16.93        59.67        18.25        41.98        34.62        86.60 
TCGA-29-1763 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 TCGA-29-1775 
       66.81        39.42        31.30        22.98        22.55        12.36 
TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 
       11.84        12.30         8.38         7.23         5.36        36.30 
TCGA-29-2414 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 
       86.17        62.47        45.11        13.84        42.25        21.47 
TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 
       11.47         9.76        35.77        38.07        51.91        36.26 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1866 
        2.47        15.68         0.26        48.10        44.91        36.62 
TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 
        1.22        57.57        24.26        30.05        48.79        45.57 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 
       30.18        18.77        22.49         6.71        42.51        44.12 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
        2.20        28.77        29.10        21.53        22.85        22.55 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 
       25.74        27.85        24.23        35.05        33.01        29.49 
TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 
       29.82        25.91        25.08        23.80        21.60         2.24 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-42-2582 
       20.98        18.31        20.52        14.17         6.05        47.57 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1583 
       28.93        42.02        10.42        40.77         1.48        11.38 
TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-59-2348 TCGA-59-2349 
       21.14         1.74        22.32        29.00       180.20        80.12 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       22.32       116.12         9.40        34.39         2.14         5.42 
TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
       44.81        11.11         8.09        20.94        31.43        18.54 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       27.88         4.34        31.79        28.47        48.79        44.84 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 
       35.80         2.43         1.45         8.42         5.79        11.41 
TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 
       13.02         9.07        34.13        31.30        37.05        42.51 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 
       48.92        56.61        43.43        15.75         2.01         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 
       14.50        17.98        30.64        39.85        30.64         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       45.96        45.40         4.80        51.72        71.74        61.64 
TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 TCGA-61-2109 
       58.39        60.62        65.52        55.50        76.87        20.68 
TCGA-61-2110 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
       44.52        31.07         8.61        39.68        18.94         0.79 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-10-0925 TCGA-10-0926 
        9.47        57.76        17.98        35.57        54.31        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 
       81.86        18.51        32.88         6.71        35.44        36.92 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0725 
       19.99        20.91         6.21        24.59        44.55        12.39 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 
       31.20        15.19        17.82        55.17         2.50        11.18 
TCGA-13-0758 TCGA-13-0761 TCGA-13-0762 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 
       11.38        38.01       111.78        56.71        58.65        40.24 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 
      118.42       107.28        69.73        83.34        45.99        51.02 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
       43.86        35.28        35.31        13.61        68.94       107.18 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 
      153.37        66.67        92.42        95.15       145.45       102.84 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       43.36        71.74        66.15       134.04        19.36       127.79 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       50.37       123.16       118.98        60.59       116.65        44.55 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 
       37.64       109.32        58.68        84.53        48.76        83.74 
TCGA-13-2071 
       25.41 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.53              0.26 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           125.75            180.20 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           30.295            33.010 
[1] "0.5 - 125.8 (30.3)" "0.3 - 180.2 (33.0)"
[1] "hr=" "1.1"
D12V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  6Q GAIN MUTATED         0    97                0
  6Q GAIN WILD-TYPE       3   461                2
D12V3, multiclass
                  clus
vv                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  OMENTUM                        0                 3
  OVARY                         97               461
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V4, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    95   0
  6Q GAIN WILD-TYPE 446   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     95    0
  6Q GAIN WILD-TYPE  446    5
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               95               446
  YES               0                 5
[1] 2 2
[1] FALSE
D12V5, continuous
                   vv
clus                R0 R1 R2 RX
  6Q GAIN MUTATED    3  4  0  0
  6Q GAIN WILD-TYPE 12 22  5  3
D12V6, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0               3                12
  R1               4                22
  R2               0                 5
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     2  54
  6Q GAIN WILD-TYPE   8 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      2   54
  6Q GAIN WILD-TYPE    8  273
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 8
  NOT HISPANIC OR LATINO              54               273
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    68 104
  7P GAIN WILD-TYPE 160 227
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              172               387 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              104               227 
$`7P GAIN MUTATED`
TCGA-04-1337 TCGA-04-1342 TCGA-04-1346 TCGA-04-1351 TCGA-04-1353 TCGA-04-1364 
        2.01        18.51        65.52        65.46         0.53        33.67 
TCGA-04-1367 TCGA-04-1514 TCGA-04-1517 TCGA-04-1542 TCGA-04-1646 TCGA-04-1649 
      103.40        56.55        19.99        84.20        27.88        64.64 
TCGA-04-1652 TCGA-09-1661 TCGA-09-1665 TCGA-09-1667 TCGA-09-1670 TCGA-09-1672 
       31.86        38.43        41.62        61.87        17.98         5.85 
TCGA-09-1674 TCGA-09-2043 TCGA-09-2045 TCGA-09-2049 TCGA-09-2051 TCGA-09-2053 
        8.55         6.18        35.15       112.41        63.09        39.75 
TCGA-09-2054 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 
       20.94        83.31        55.23        81.01        17.46        87.06 
TCGA-13-1482 TCGA-13-1484 TCGA-13-1485 TCGA-13-1488 TCGA-13-1489 TCGA-13-1495 
       61.71       124.44        20.68        70.82        83.93        90.38 
TCGA-13-1496 TCGA-13-1500 TCGA-13-1504 TCGA-13-1509 TCGA-13-2059 TCGA-13-2060 
        4.24        13.97        34.82        80.15        78.48        77.88 
TCGA-13-A5FU TCGA-20-0987 TCGA-20-0991 TCGA-20-1682 TCGA-20-1686 TCGA-20-1687 
        8.42        23.05        26.20        27.52         2.93         2.66 
TCGA-23-1021 TCGA-23-1024 TCGA-23-1032 TCGA-23-1111 TCGA-23-1116 TCGA-23-1117 
       47.54        15.39         2.76         3.22        19.46        33.30 
TCGA-23-1121 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2079 
        6.38        58.13         0.53        24.95       115.89        91.66 
TCGA-23-2081 TCGA-24-0980 TCGA-24-1413 TCGA-24-1418 TCGA-24-1424 TCGA-24-1428 
       77.00         7.66         6.31         7.99         6.02        17.39 
TCGA-24-1431 TCGA-24-1471 TCGA-24-1474 TCGA-24-1557 TCGA-24-1558 TCGA-24-1564 
       18.64         1.18        22.22        39.88        19.53        25.87 
TCGA-24-1614 TCGA-24-1845 TCGA-24-1928 TCGA-24-2020 TCGA-24-2026 TCGA-24-2030 
       48.33         3.81        11.05       152.02        34.82        55.92 
TCGA-24-2038 TCGA-24-2261 TCGA-24-2267 TCGA-24-2280 TCGA-24-2288 TCGA-24-2293 
       44.52         0.79        47.54        70.45         0.82        16.64 
TCGA-24-2295 TCGA-25-1312 TCGA-25-1313 TCGA-25-1318 TCGA-25-1320 TCGA-25-1323 
       33.11         1.02        26.96        34.98        37.97        12.99 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1870 TCGA-25-1871 TCGA-25-2397 
       17.03        12.95        20.61        14.96        24.99        12.00 
TCGA-25-2400 TCGA-29-1693 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
       42.02       101.79        40.41        31.20        68.32        36.36 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1763 TCGA-29-1764 TCGA-29-1775 TCGA-29-1778 
       41.98        31.27        66.81        62.93        12.36        14.93 
TCGA-29-1783 TCGA-29-2428 TCGA-29-2429 TCGA-29-2432 TCGA-29-2434 TCGA-29-A5NZ 
        7.23        45.11        13.84        21.47        11.47        35.77 
TCGA-30-1853 TCGA-30-1856 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-31-1950 
       36.26        15.68         6.12        36.62         1.22        18.77 
TCGA-31-1959 TCGA-36-1580 TCGA-36-2547 TCGA-36-2548 TCGA-42-2587 TCGA-57-1993 
        2.20        24.23        20.52        14.17        23.74        25.08 
TCGA-59-2349 TCGA-59-2351 TCGA-59-2355 TCGA-59-2372 TCGA-61-1730 TCGA-61-1733 
       80.12       116.12         2.14        44.81         4.34        31.79 
TCGA-61-1734 TCGA-61-1737 TCGA-61-1743 TCGA-61-1899 TCGA-61-1904 TCGA-61-1907 
       28.47        44.84        43.69         8.42         9.07        31.30 
TCGA-61-1911 TCGA-61-1914 TCGA-61-1918 TCGA-61-1919 TCGA-61-2003 TCGA-61-2088 
       42.51        56.61        15.75        38.17         4.01         4.77 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2110 TCGA-61-2113 
       65.52        55.50         6.48        76.87        44.52        22.22 
TCGA-61-2614 TCGA-OY-A56Q TCGA-09-0365 TCGA-09-0367 TCGA-10-0926 TCGA-13-0717 
        8.61        18.94         9.47        17.98        25.91        24.59 
TCGA-13-0730 TCGA-13-0757 TCGA-13-0760 TCGA-13-0768 TCGA-13-0795 TCGA-13-0803 
       17.82        11.18        11.54        58.65        20.35        43.86 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0888 TCGA-13-0899 TCGA-13-0901 TCGA-13-0903 
       13.61        68.94        92.42        66.15        19.36       127.79 
TCGA-13-0904 TCGA-13-0912 TCGA-13-0921 TCGA-13-0923 
       50.37        37.64        48.76        83.74 

$`7P GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1336 TCGA-04-1338 TCGA-04-1341 TCGA-04-1343 TCGA-04-1347 TCGA-04-1348 
       49.15        46.62         1.08        11.87        63.09        48.76 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 
       21.57        63.98        49.28        32.52        44.32        76.57 
TCGA-04-1371 TCGA-04-1516 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 
       82.39        41.59         0.79        38.37       119.08        29.10 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 
       55.43        48.89        28.64        36.23        47.70        45.37 
TCGA-09-1659 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 
        9.99        89.33        74.93        57.60        55.36        30.51 
TCGA-09-1673 TCGA-09-1675 TCGA-09-2044 TCGA-09-2048 TCGA-09-2050 TCGA-09-2055 
        3.02        97.55         6.12         4.54        71.11        26.93 
TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1409 TCGA-13-1412 
       12.46        77.10        81.17        28.54        57.27        32.35 
TCGA-13-1477 TCGA-13-1483 TCGA-13-1487 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       54.64        29.42        22.39        52.44       125.56        93.90 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 
      127.27        66.15       115.07        43.20        65.69        34.16 
TCGA-13-1507 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2061 
       65.52        44.68        54.25        14.53        80.02        76.90 
TCGA-13-2065 TCGA-13-A5FT TCGA-20-0990 TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 
       65.52        70.45        25.94        72.20        25.38        19.10 
TCGA-20-1685 TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       16.70        49.68        40.54        26.83        32.09        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 
        8.81        29.13        18.90        51.35        54.51        31.20 
TCGA-23-1114 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 
       68.68        86.01       129.96         4.27        39.09        33.47 
TCGA-23-2078 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 
       87.48        49.84         2.76         4.70         4.50         7.63 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 
       11.64        21.80        41.56        22.32        54.12        63.55 
TCGA-24-1105 TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 
       47.41         6.38         7.82         7.86         0.76         6.25 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1430 TCGA-24-1434 TCGA-24-1435 
        5.95         5.36         4.83        28.37        18.67        43.53 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 
        8.55        72.92        12.46        45.14       105.99         9.11 
TCGA-24-1470 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 
        3.45        26.96        57.40        64.27        16.21        56.58 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 
       41.06        51.91        41.39        58.09        88.50        70.62 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       44.09        45.50        47.70        10.26        17.23        90.15 
TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 
       88.37        38.24         8.32         3.48         3.72         4.37 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 
       11.28         5.79         5.52         9.80        22.68        30.21 
TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 
       16.44        81.11         4.87        44.84        58.16       109.71 
TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2254 TCGA-24-2260 
       14.43        18.48        28.18        64.01        57.07        36.16 
TCGA-24-2262 TCGA-24-2271 TCGA-24-2281 TCGA-24-2289 TCGA-24-2290 TCGA-24-2297 
        0.36        31.63        44.61        67.36        36.23        55.86 
TCGA-24-2298 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1319 
       53.26        33.01        52.04        42.05         2.01        65.00 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1630 
       33.96         2.99        15.02        18.58        27.62        38.20 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1877 
        0.30        59.15        62.17        35.87        52.04        24.00 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 
       85.05        13.02        49.05         1.02        38.04         3.02 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       45.01        19.99         2.96        29.03        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1694 TCGA-29-1696 TCGA-29-1701 
       78.90        47.61        48.33        39.02        33.93        16.93 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 
       23.93        59.67        18.25        34.62        17.36        86.60 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
       39.42        31.30        22.98        24.36        22.55        17.33 
TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 
       11.84        12.30         8.38         5.36        36.30        86.17 
TCGA-29-2425 TCGA-29-2427 TCGA-29-2431 TCGA-29-2436 TCGA-30-1714 TCGA-30-1718 
       65.00        62.47        42.25         9.76        38.07        51.91 
TCGA-30-1855 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1880 
        2.47         0.26        48.10        44.91        34.78        57.57 
TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 
       24.26        30.05        48.79        45.57        30.18        22.49 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
        6.71        42.51        44.12        28.77        29.10        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 
       22.85        22.55         8.55        30.08        25.74        27.85 
TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       24.69        35.05        33.01        29.49        29.82        25.91 
TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 
       25.08        23.80        21.60         2.24        20.98        18.31 
TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 
        6.05        16.18        11.47        47.57        28.93        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 
       10.42        40.77         1.48        24.03        11.38        21.14 
TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1994 TCGA-59-2348 TCGA-59-2350 
        1.74        22.32        29.00        25.02       180.20        22.32 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 
        9.40        34.39         5.42        11.11         8.09        20.94 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1736 TCGA-61-1738 TCGA-61-1740 
       31.43        18.54        27.88        48.79        35.80         2.43 
TCGA-61-1741 TCGA-61-1895 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1906 
       33.67         1.45         5.79        11.41        13.02        34.13 
TCGA-61-1910 TCGA-61-1913 TCGA-61-1915 TCGA-61-1917 TCGA-61-1995 TCGA-61-1998 
       37.05        48.92        67.76        43.43         2.01         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 
       14.50        17.98        30.64        39.85        30.64         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       45.96        45.40         4.80        51.72        71.74        61.64 
TCGA-61-2096 TCGA-61-2097 TCGA-61-2109 TCGA-61-2111 TCGA-61-2612 TCGA-61-2613 
       58.39        60.62        20.68       125.75         6.35        31.07 
TCGA-OY-A56P TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 TCGA-09-0366 TCGA-09-0369 
       39.68         0.79         9.99        29.16        57.76        35.57 
TCGA-10-0925 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 
       54.31        81.86        18.51        34.19        32.88        14.66 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
        6.71        35.44        36.92        19.99        20.91         6.21 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 
       44.55        39.58         2.73        12.39        31.20        15.19 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0758 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 
       55.17         2.50        11.38        38.01       111.78        61.84 
TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 
       56.71        40.24       118.42       107.28        63.09        69.73 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 
       83.34        87.48        45.99        51.02        35.28        35.31 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 
      107.18       111.39       153.37        66.67        95.15       145.45 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0905 TCGA-13-0906 
      102.84        43.36        71.74       134.04       123.16       118.98 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
       60.59       116.65        44.55       109.32        58.68        84.53 
TCGA-13-0920 TCGA-13-0924 TCGA-13-2071 
       48.79        85.94        25.41 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.53              0.26 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           152.02            180.20 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            27.24             34.16 
[1] "0.5 - 152.0 (27.2)" "0.3 - 180.2 (34.2)"
[1] "hr=" "1.1"
D13V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  7P GAIN MUTATED         2   171                0
  7P GAIN WILD-TYPE       1   387                2
D13V3, multiclass
                  clus
vv                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  OMENTUM                        2                 1
  OVARY                        171               387
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V4, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   163   2
  7P GAIN WILD-TYPE 378   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    163    2
  7P GAIN WILD-TYPE  378    3
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO              163               378
  YES               2                 3
[1] 2 2
[1] FALSE
D13V5, continuous
                   vv
clus                R0 R1 R2 RX
  7P GAIN MUTATED    4  7  1  1
  7P GAIN WILD-TYPE 11 19  4  2
D13V6, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0               4                11
  R1               7                19
  R2               1                 4
  RX               1                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     1 106
  7P GAIN WILD-TYPE   9 221
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      1  106
  7P GAIN WILD-TYPE    9  221
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO             106               221
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    75 118
  7Q GAIN WILD-TYPE 153 213
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              193               366 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              118               213 
$`7Q GAIN MUTATED`
TCGA-04-1337 TCGA-04-1341 TCGA-04-1342 TCGA-04-1347 TCGA-04-1349 TCGA-04-1351 
        2.01         1.08        18.51        63.09        21.57        65.46 
TCGA-04-1353 TCGA-04-1364 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1536 
        0.53        33.67        56.55        41.59        19.99        29.10 
TCGA-04-1542 TCGA-04-1646 TCGA-04-1649 TCGA-04-1652 TCGA-04-1655 TCGA-09-1661 
       84.20        27.88        64.64        31.86        45.37        38.43 
TCGA-09-1665 TCGA-09-1667 TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 TCGA-09-2043 
       41.62        61.87        17.98         5.85         8.55         6.18 
TCGA-09-2045 TCGA-09-2051 TCGA-09-2053 TCGA-13-1407 TCGA-13-1410 TCGA-13-1411 
       35.15        63.09        39.75        83.31        81.01        17.46 
TCGA-13-1412 TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 TCGA-13-1485 TCGA-13-1488 
       32.35        87.06        61.71       124.44        20.68        70.82 
TCGA-13-1489 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1500 TCGA-13-1504 
       83.93        90.38         4.24       127.27        13.97        34.82 
TCGA-13-1509 TCGA-13-2059 TCGA-13-2060 TCGA-13-A5FU TCGA-20-0987 TCGA-20-0991 
       80.15        78.48        77.88         8.42        23.05        26.20 
TCGA-20-1682 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1024 TCGA-23-1031 
       27.52         2.93         2.66        47.54        15.39        18.90 
TCGA-23-1032 TCGA-23-1111 TCGA-23-1119 TCGA-23-1121 TCGA-23-1122 TCGA-23-1124 
        2.76         3.22       129.96         6.38        39.09        58.13 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-24-1104 
        0.53        24.95       115.89        91.66        77.00        63.55 
TCGA-24-1413 TCGA-24-1418 TCGA-24-1424 TCGA-24-1428 TCGA-24-1431 TCGA-24-1436 
        6.31         7.99         6.02        17.39        18.64         8.55 
TCGA-24-1471 TCGA-24-1474 TCGA-24-1546 TCGA-24-1548 TCGA-24-1557 TCGA-24-1558 
        1.18        22.22        64.27        16.21        39.88        19.53 
TCGA-24-1614 TCGA-24-1844 TCGA-24-1845 TCGA-24-1850 TCGA-24-1928 TCGA-24-2019 
       48.33         3.72         3.81         5.52        11.05         4.87 
TCGA-24-2020 TCGA-24-2026 TCGA-24-2030 TCGA-24-2033 TCGA-24-2038 TCGA-24-2261 
      152.02        34.82        55.92        18.48        44.52         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2280 TCGA-24-2295 TCGA-25-1312 TCGA-25-1313 
        0.36        47.54        70.45        33.11         1.02        26.96 
TCGA-25-1314 TCGA-25-1318 TCGA-25-1320 TCGA-25-1323 TCGA-25-1623 TCGA-25-1626 
       33.01        34.98        37.97        12.99        18.58        17.03 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 TCGA-25-2397 
       12.95        20.61        14.96        24.99        85.05        12.00 
TCGA-25-2400 TCGA-25-2401 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
       42.02         2.96        40.41        31.20        68.32        36.36 
TCGA-29-1707 TCGA-29-1764 TCGA-29-1775 TCGA-29-1778 TCGA-29-1783 TCGA-29-2428 
       41.98        62.93        12.36        14.93         7.23        45.11 
TCGA-29-2429 TCGA-29-2432 TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1853 TCGA-30-1862 
       13.84        21.47        11.47        35.77        36.26         6.12 
TCGA-30-1866 TCGA-30-1867 TCGA-31-1950 TCGA-36-1580 TCGA-36-2529 TCGA-36-2545 
       36.62         1.22        18.77        24.23        35.05        18.31 
TCGA-36-2547 TCGA-36-2548 TCGA-42-2582 TCGA-42-2587 TCGA-42-2590 TCGA-57-1586 
       20.52        14.17        47.57        23.74        10.42        22.32 
TCGA-57-1993 TCGA-59-2349 TCGA-59-2351 TCGA-59-2355 TCGA-59-2372 TCGA-61-1725 
       25.08        80.12       116.12         2.14        44.81        31.43 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1737 TCGA-61-1740 TCGA-61-1743 
        4.34        31.79        28.47        44.84         2.43        43.69 
TCGA-61-1899 TCGA-61-1901 TCGA-61-1904 TCGA-61-1906 TCGA-61-1911 TCGA-61-1914 
        8.42        11.41         9.07        34.13        42.51        56.61 
TCGA-61-1918 TCGA-61-1919 TCGA-61-2003 TCGA-61-2088 TCGA-61-2101 TCGA-61-2102 
       15.75        38.17         4.01         4.77        55.50         6.48 
TCGA-61-2104 TCGA-61-2110 TCGA-61-2113 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
       76.87        44.52        22.22         8.61        39.68        18.94 
TCGA-WR-A838 TCGA-09-0365 TCGA-09-0367 TCGA-10-0926 TCGA-10-0927 TCGA-13-0717 
        9.99         9.47        17.98        25.91        81.86        24.59 
TCGA-13-0724 TCGA-13-0757 TCGA-13-0760 TCGA-13-0762 TCGA-13-0768 TCGA-13-0795 
        2.73        11.18        11.54       111.78        58.65        20.35 
TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0885 TCGA-13-0888 
       43.86        35.31        13.61        68.94       111.39        92.42 
TCGA-13-0899 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0912 TCGA-13-0921 
       66.15        19.36       127.79        50.37        37.64        48.76 
TCGA-13-0923 
       83.74 

$`7Q GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1336 TCGA-04-1338 TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 TCGA-04-1350 
       49.15        46.62        11.87        65.52        48.76        63.98 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 
       49.28        32.52        44.32        76.57       103.40        82.39 
TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 
        0.79        38.37       119.08        55.43        48.89        28.64 
TCGA-04-1651 TCGA-04-1654 TCGA-09-1659 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 
       36.23        47.70         9.99        89.33        74.93        57.60 
TCGA-09-1668 TCGA-09-1669 TCGA-09-1673 TCGA-09-1675 TCGA-09-2044 TCGA-09-2048 
       55.36        30.51         3.02        97.55         6.12         4.54 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 
      112.41        71.11        20.94        26.93        12.46        77.10 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1409 TCGA-13-1477 TCGA-13-1483 
       81.17        28.54        55.23        57.27        54.64        29.42 
TCGA-13-1487 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1498 TCGA-13-1499 
       22.39        52.44       125.56        93.90        66.15       115.07 
TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1510 TCGA-13-1511 
       43.20        65.69        34.16        65.52        44.68        54.25 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-20-0990 
       14.53        80.02        76.90        65.52        70.45        25.94 
TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-23-1022 TCGA-23-1023 
       72.20        25.38        19.10        16.70        49.68        40.54 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1109 
       26.83        32.09        49.41         8.81        29.13        51.35 
TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
       54.51        31.20        68.68        19.46        33.30        86.01 
TCGA-23-1120 TCGA-23-1123 TCGA-23-2078 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 
        4.27        33.47        87.48        49.84         2.76         4.70 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        4.50         7.63        11.64        21.80        41.56         7.66 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1105 TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 
       22.32        54.12        47.41         6.38         7.82         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1430 
        0.76         6.25         5.95         5.36         4.83        28.37 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 
       18.67        43.53        72.92        12.46        45.14       105.99 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1544 TCGA-24-1545 TCGA-24-1549 TCGA-24-1550 
        9.11         3.45        26.96        57.40        56.58        41.06 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1560 
       51.91        41.39        58.09        88.50        70.62        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       45.50        47.70        25.87        10.26        17.23        90.15 
TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1846 TCGA-24-1847 
       88.37        38.24         8.32         3.48         4.37        11.28 
TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 
        5.79         9.80        22.68        30.21        16.44        81.11 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2035 TCGA-24-2036 
       44.84        58.16       109.71        14.43        28.18        64.01 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 
       57.07        36.16        31.63        44.61         0.82        67.36 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 TCGA-25-1315 TCGA-25-1316 
       36.23        16.64        55.86        53.26        52.04        42.05 
TCGA-25-1317 TCGA-25-1319 TCGA-25-1321 TCGA-25-1322 TCGA-25-1329 TCGA-25-1625 
        2.01        65.00        33.96         2.99        15.02        27.62 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 
       38.20         0.30        59.15        62.17        35.87        52.04 
TCGA-25-1877 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 
       24.00        13.02        49.05         1.02        38.04         3.02 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 
       45.01        19.99        29.03        31.00        26.99        78.90 
TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1701 
       47.61        48.33       101.79        39.02        33.93        16.93 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 
       23.93        59.67        18.25        31.27        34.62        17.36 
TCGA-29-1762 TCGA-29-1763 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 
       86.60        66.81        39.42        31.30        22.98        24.36 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1784 
       22.55        17.33        11.84        12.30         8.38         5.36 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2431 TCGA-29-2436 
       36.30        86.17        65.00        62.47        42.25         9.76 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 
       38.07        51.91         2.47        15.68         0.26        48.10 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 
       44.91        34.78        57.57        24.26        30.05        48.79 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 
       45.57        30.18        22.49         6.71        42.51        44.12 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
        2.20        28.77        29.10        21.53        22.85        22.55 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 TCGA-36-2530 
        8.55        30.08        25.74        27.85        24.69        33.01 
TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 
       29.49        29.82        25.91        25.08        23.80        21.60 
TCGA-36-2543 TCGA-36-2544 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2588 
        2.24        20.98         6.05        16.18        11.47        28.93 
TCGA-42-2589 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 
       42.02        40.77         1.48        24.03        11.38        21.14 
TCGA-57-1585 TCGA-57-1992 TCGA-57-1994 TCGA-59-2348 TCGA-59-2350 TCGA-59-2352 
        1.74        29.00        25.02       180.20        22.32         9.40 
TCGA-59-2354 TCGA-59-2363 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1727 
       34.39         5.42        11.11         8.09        20.94        18.54 
TCGA-61-1728 TCGA-61-1736 TCGA-61-1738 TCGA-61-1741 TCGA-61-1895 TCGA-61-1900 
       27.88        48.79        35.80        33.67         1.45         5.79 
TCGA-61-1903 TCGA-61-1907 TCGA-61-1910 TCGA-61-1913 TCGA-61-1915 TCGA-61-1917 
       13.02        31.30        37.05        48.92        67.76        43.43 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2008 TCGA-61-2009 
        2.01         5.52        14.50        17.98        30.64        39.85 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 
       30.64         1.18        45.96        45.40         4.80        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2109 
       71.74        61.64        58.39        60.62        65.52        20.68 
TCGA-61-2111 TCGA-61-2612 TCGA-61-2613 TCGA-VG-A8LO TCGA-09-0364 TCGA-09-0366 
      125.75         6.35        31.07         0.79        29.16        57.76 
TCGA-09-0369 TCGA-10-0925 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 
       35.57        54.31        18.51        34.19        32.88        14.66 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
        6.71        35.44        36.92        19.99        20.91         6.21 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 
       44.55        39.58        12.39        31.20        15.19        17.82 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0758 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 
       55.17         2.50        11.38        38.01        61.84        56.71 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 
       40.24       118.42       107.28        63.09        69.73        83.34 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0884 TCGA-13-0886 
       87.48        45.99        51.02        35.28       107.18       153.37 
TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 
       66.67        95.15       145.45       102.84        43.36        71.74 
TCGA-13-0900 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
      134.04       123.16       118.98        60.59       116.65        44.55 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0924 TCGA-13-2071 
      109.32        58.68        84.53        48.79        85.94        25.41 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.36              0.26 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           152.02            180.20 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            27.52             34.29 
[1] "0.4 - 152.0 (27.5)" "0.3 - 180.2 (34.3)"
[1] "hr=" "1.2"
D14V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  7Q GAIN MUTATED         1   194                1
  7Q GAIN WILD-TYPE       2   364                1
D14V3, multiclass
                  clus
vv                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  OMENTUM                        1                 2
  OVARY                        194               364
  PERITONEUM OVARY               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V4, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   186   1
  7Q GAIN WILD-TYPE 355   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    186    1
  7Q GAIN WILD-TYPE  355    4
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO              186               355
  YES               1                 4
[1] 2 2
[1] FALSE
D14V5, continuous
                   vv
clus                R0 R1 R2 RX
  7Q GAIN MUTATED    7 10  2  1
  7Q GAIN WILD-TYPE  8 16  3  2
D14V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0               7                 8
  R1              10                16
  R2               2                 3
  RX               1                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     3 118
  7Q GAIN WILD-TYPE   7 209
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      3  118
  7Q GAIN WILD-TYPE    7  209
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 7
  NOT HISPANIC OR LATINO             118               209
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    44  79
  8P GAIN WILD-TYPE 184 252
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              123               436 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               79               252 
$`8P GAIN MUTATED`
TCGA-5X-AA5U TCGA-04-1335 TCGA-04-1342 TCGA-04-1343 TCGA-04-1347 TCGA-04-1349 
       11.87         1.81        18.51        11.87        63.09        21.57 
TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 TCGA-04-1542 
       63.98        65.46        49.28        44.32        33.67        84.20 
TCGA-09-1659 TCGA-09-1665 TCGA-09-1667 TCGA-09-1669 TCGA-09-1672 TCGA-09-2043 
        9.99        41.62        61.87        30.51         5.85         6.18 
TCGA-13-1404 TCGA-13-1408 TCGA-13-1409 TCGA-13-1485 TCGA-13-1488 TCGA-13-1497 
       81.17        55.23        57.27        20.68        70.82       127.27 
TCGA-13-1506 TCGA-13-2057 TCGA-13-2060 TCGA-20-0987 TCGA-20-1683 TCGA-20-1687 
       34.16        80.02        77.88        23.05        25.38         2.66 
TCGA-23-1023 TCGA-23-1029 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1119 
       40.54         8.81        51.35        54.51         3.22       129.96 
TCGA-23-2079 TCGA-24-0979 TCGA-24-1103 TCGA-24-1105 TCGA-24-1418 TCGA-24-1435 
       91.66        41.56        54.12        47.41         7.99        43.53 
TCGA-24-1471 TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 TCGA-24-1563 TCGA-24-1849 
        1.18        58.09        70.62        39.88        47.70         5.79 
TCGA-24-1923 TCGA-24-2019 TCGA-24-2020 TCGA-24-2027 TCGA-24-2262 TCGA-24-2271 
       22.68         4.87       152.02       109.71         0.36        31.63 
TCGA-25-1312 TCGA-25-1317 TCGA-25-1320 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 
        1.02         2.01        37.97         2.99        15.02        18.58 
TCGA-25-1625 TCGA-25-1628 TCGA-25-1632 TCGA-25-1877 TCGA-25-2392 TCGA-25-2398 
       27.62        20.61        59.15        24.00         1.02        45.01 
TCGA-25-2401 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1696 TCGA-29-1702 
        2.96        47.61        48.33       101.79        33.93        23.93 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1785 
       66.81        62.93        11.84        12.30        14.93        36.30 
TCGA-29-2425 TCGA-29-2431 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1861 
       65.00        42.25        38.07        51.91        36.26        34.78 
TCGA-30-1892 TCGA-31-1946 TCGA-31-1956 TCGA-31-1959 TCGA-36-1576 TCGA-36-2529 
       48.79        30.18        44.12         2.20        30.08        35.05 
TCGA-36-2548 TCGA-36-2551 TCGA-42-2582 TCGA-57-1582 TCGA-59-2354 TCGA-61-1743 
       14.17        16.18        47.57        24.03        34.39        43.69 
TCGA-61-1899 TCGA-61-1906 TCGA-61-2009 TCGA-61-2612 TCGA-OY-A56Q TCGA-09-0365 
        8.42        34.13        39.85         6.35        18.94         9.47 
TCGA-09-0369 TCGA-10-0935 TCGA-10-0937 TCGA-13-0717 TCGA-13-0724 TCGA-13-0726 
       35.57        35.44        19.99        24.59         2.73        31.20 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0768 TCGA-13-0794 TCGA-13-0800 
       55.17         2.50        11.54        58.65        63.09        87.48 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0893 TCGA-13-0897 TCGA-13-0903 TCGA-13-0908 
       68.94       107.18        43.36        71.74       127.79        60.59 
TCGA-13-0911 TCGA-13-0923 TCGA-13-2071 
       44.55        83.74        25.41 

$`8P GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 
       13.81        20.52        43.92        41.00        49.15         2.01 
TCGA-04-1338 TCGA-04-1341 TCGA-04-1346 TCGA-04-1348 TCGA-04-1353 TCGA-04-1361 
       46.62         1.08        65.52        48.76         0.53        32.52 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 
       76.57       103.40        82.39        56.55        41.59        19.99 
TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1638 TCGA-04-1644 
        0.79        38.37       119.08        29.10        55.43        48.89 
TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 
       27.88        28.64        64.64        36.23        31.86        47.70 
TCGA-04-1655 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1668 
       45.37        38.43        89.33        74.93        57.60        55.36 
TCGA-09-1670 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 
       17.98         3.02         8.55        97.55         6.12        35.15 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 
        4.54       112.41        71.11        63.09        39.75        20.94 
TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1405 TCGA-13-1407 TCGA-13-1410 
       26.93        12.46        77.10        28.54        83.31        81.01 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
       17.46        32.35        54.64        87.06        61.71        29.42 
TCGA-13-1484 TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
      124.44        22.39        83.93        52.44       125.56        93.90 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 
       90.38         4.24        66.15       115.07        13.97        43.20 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
       34.82        65.69        65.52        80.15        44.68        54.25 
TCGA-13-1512 TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU 
       14.53        78.48        76.90        65.52        70.45         8.42 
TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 
       25.94        26.20        72.20        27.52        19.10        16.70 
TCGA-20-1686 TCGA-23-1021 TCGA-23-1022 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
        2.93        47.54        49.68        15.39        26.83        32.09 
TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1113 TCGA-23-1114 
       49.41        29.13        18.90         2.76        31.20        68.68 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 
       19.46        33.30        86.01         4.27         6.38        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 
       33.47        58.13         0.53        24.95       115.89        87.48 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 
       77.00        49.84         2.76         4.70         4.50         7.63 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-0982 TCGA-24-1104 TCGA-24-1413 
       11.64        21.80         7.66        22.32        63.55         6.31 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
        6.38         7.82         7.86         0.76         6.25         6.02 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 
        5.95         5.36         4.83        17.39        28.37        18.64 
TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 
       18.67         8.55        72.92        12.46        45.14       105.99 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 
        9.11         3.45        22.22        26.96        57.40        64.27 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 
       16.21        56.58        41.06        51.91        41.39        88.50 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 
       19.53        44.09        45.50        25.87        10.26        17.23 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 
       90.15        88.37        48.33        38.24         8.32         3.48 
TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 
        3.72         3.81         4.37        11.28         5.52         9.80 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2023 TCGA-24-2024 
       30.21        16.44        11.05        81.11        44.84        58.16 
TCGA-24-2026 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 
       34.82        14.43        55.92        18.48        28.18        64.01 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 TCGA-24-2280 
       44.52        57.07        36.16         0.79        47.54        70.45 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 
       44.61         0.82        67.36        36.23        16.64        33.11 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 
       55.86        53.26        26.96        33.01        52.04        42.05 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 TCGA-25-1323 TCGA-25-1626 TCGA-25-1627 
       34.98        65.00        33.96        12.99        17.03        12.95 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 
       38.20         0.30        62.17        35.87        52.04        14.96 
TCGA-25-1871 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 
       24.99        85.05        13.02        49.05        38.04         3.02 
TCGA-25-2397 TCGA-25-2399 TCGA-25-2400 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       12.00        19.99        42.02        29.03        31.00        26.99 
TCGA-29-1688 TCGA-29-1694 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
       78.90        39.02        40.41        31.20        68.32        36.36 
TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 
       16.93        59.67        18.25        41.98        31.27        34.62 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 
       17.36        86.60        39.42        31.30        22.98        24.36 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
       22.55        17.33        12.36         8.38         7.23         5.36 
TCGA-29-2414 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2432 TCGA-29-2434 
       86.17        62.47        45.11        13.84        21.47        11.47 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 
        9.76        35.77         2.47        15.68         0.26        48.10 
TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 
       44.91         6.12        36.62         1.22        57.57        24.26 
TCGA-30-1891 TCGA-31-1944 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 
       30.05        45.57        18.77        22.49         6.71        42.51 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 
       28.77        29.10        21.53        22.85        22.55         8.55 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 
       25.74        27.85        24.23        24.69        33.01        29.49 
TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 
       29.82        25.91        25.08        23.80        21.60         2.24 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 TCGA-36-2552 TCGA-42-2587 
       20.98        18.31        20.52         6.05        11.47        23.74 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1583 
       28.93        42.02        10.42        40.77         1.48        11.38 
TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 
       21.14         1.74        22.32        29.00        25.08        25.02 
TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 
      180.20        80.12        22.32       116.12         9.40         2.14 
TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
        5.42        44.81        11.11         8.09        20.94        31.43 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 
       18.54        27.88         4.34        31.79        28.47        48.79 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 TCGA-61-1900 
       44.84        35.80         2.43        33.67         1.45         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 
       11.41        13.02         9.07        31.30        37.05        42.51 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 
       48.92        56.61        67.76        43.43        15.75        38.17 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 
        2.01         5.52        14.50        17.98         4.01        30.64 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
       30.64         1.18        45.96        45.40         4.80         4.77 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 
       51.72        71.74        61.64        58.39        60.62        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       55.50         6.48        76.87        20.68        44.52       125.75 
TCGA-61-2113 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-VG-A8LO TCGA-WR-A838 
       22.22        31.07         8.61        39.68         0.79         9.99 
TCGA-09-0364 TCGA-09-0366 TCGA-09-0367 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 
       29.16        57.76        17.98        54.31        25.91        81.86 
TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0936 
       18.51        34.19        32.88        14.66         6.71        36.92 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0727 
       20.91         6.21        44.55        39.58        12.39        15.19 
TCGA-13-0730 TCGA-13-0757 TCGA-13-0758 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 
       17.82        11.18        11.38        38.01       111.78        61.84 
TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 
       56.71        40.24       118.42       107.28        20.35        69.73 
TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 
       83.34        45.99        51.02        43.86        35.28        35.31 
TCGA-13-0807 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 
       13.61       111.39       153.37        66.67        92.42        95.15 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0904 
      145.45       102.84        66.15       134.04        19.36        50.37 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
      123.16       118.98       116.65        37.64       109.32        58.68 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0924 
       84.53        48.79        48.76        85.94 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.36              0.26 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           152.02            180.20 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           35.570            31.285 
[1] "0.4 - 152.0 (35.6)" "0.3 - 180.2 (31.3)"
[1] "hr=" "1"  
D15V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  8P GAIN MUTATED         0   123                1
  8P GAIN WILD-TYPE       3   435                1
D15V3, multiclass
                  clus
vv                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  OMENTUM                        0                 3
  OVARY                        123               435
  PERITONEUM OVARY               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V4, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   121   0
  8P GAIN WILD-TYPE 420   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    121    0
  8P GAIN WILD-TYPE  420    5
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO              121               420
  YES               0                 5
[1] 2 2
[1] FALSE
D15V5, continuous
                   vv
clus                R0 R1 R2 RX
  8P GAIN MUTATED    3  6  0  1
  8P GAIN WILD-TYPE 12 20  5  2
D15V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0               3                12
  R1               6                20
  R2               0                 5
  RX               1                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     3  74
  8P GAIN WILD-TYPE   7 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      3   74
  8P GAIN WILD-TYPE    7  253
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 7
  NOT HISPANIC OR LATINO              74               253
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED    89 153
  8Q GAIN WILD-TYPE 139 178
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              242               317 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              153               178 
$`8Q GAIN MUTATED`
TCGA-3P-A9WA TCGA-5X-AA5U TCGA-04-1335 TCGA-04-1338 TCGA-04-1342 TCGA-04-1343 
       13.81        11.87         1.81        46.62        18.51        11.87 
TCGA-04-1347 TCGA-04-1349 TCGA-04-1351 TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 
       63.09        21.57        65.46        49.28        44.32        33.67 
TCGA-04-1365 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1646 TCGA-04-1652 
       76.57       119.08        29.10        84.20        27.88        31.86 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 
        9.99        38.43        41.62        61.87        55.36        30.51 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 TCGA-09-2043 TCGA-13-1403 TCGA-13-1404 
       17.98         5.85         8.55         6.18        77.10        81.17 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1484 TCGA-13-1485 
       55.23        57.27        81.01        17.46       124.44        20.68 
TCGA-13-1488 TCGA-13-1497 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 
       70.82       127.27        13.97        43.20        34.82        65.69 
TCGA-13-1506 TCGA-13-1507 TCGA-13-2059 TCGA-13-2060 TCGA-20-0987 TCGA-20-0991 
       34.16        65.52        78.48        77.88        23.05        26.20 
TCGA-20-1683 TCGA-20-1686 TCGA-20-1687 TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 
       25.38         2.93         2.66        49.68        40.54        26.83 
TCGA-23-1029 TCGA-23-1031 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1116 
        8.81        18.90        51.35        54.51         3.22        19.46 
TCGA-23-1117 TCGA-23-1119 TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 
       33.30       129.96         6.38        33.47        58.13        24.95 
TCGA-23-2077 TCGA-23-2079 TCGA-23-2084 TCGA-23-2643 TCGA-23-2645 TCGA-24-0975 
      115.89        91.66        49.84         4.70         4.50        21.80 
TCGA-24-0979 TCGA-24-1103 TCGA-24-1105 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       41.56        54.12        47.41         7.82         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1464 
        0.76         6.25        18.67        43.53         8.55        12.46 
TCGA-24-1467 TCGA-24-1471 TCGA-24-1546 TCGA-24-1549 TCGA-24-1552 TCGA-24-1553 
      105.99         1.18        64.27        56.58        41.39        58.09 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1563 TCGA-24-1564 
       88.50        70.62        39.88        19.53        47.70        25.87 
TCGA-24-1844 TCGA-24-1847 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-2019 
        3.72        11.28        22.68        30.21        16.44         4.87 
TCGA-24-2020 TCGA-24-2027 TCGA-24-2033 TCGA-24-2035 TCGA-24-2262 TCGA-24-2271 
      152.02       109.71        18.48        28.18         0.36        31.63 
TCGA-24-2290 TCGA-24-2295 TCGA-25-1312 TCGA-25-1317 TCGA-25-1320 TCGA-25-1321 
       36.23        33.11         1.02         2.01        37.97        33.96 
TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1627 TCGA-25-1628 
        2.99        15.02        18.58        27.62        12.95        20.61 
TCGA-25-1632 TCGA-25-1877 TCGA-25-1878 TCGA-25-2392 TCGA-25-2396 TCGA-25-2398 
       59.15        24.00        85.05         1.02         3.02        45.01 
TCGA-25-2399 TCGA-25-2401 TCGA-25-2409 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 
       19.99         2.96        26.99        47.61        48.33       101.79 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
       39.02        40.41        33.93        31.20        68.32        36.36 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1776 
       23.93        59.67        66.81        62.93        39.42        11.84 
TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 
       12.30        14.93         8.38         7.23         5.36        36.30 
TCGA-29-2425 TCGA-29-2427 TCGA-29-2431 TCGA-29-2432 TCGA-30-1714 TCGA-30-1718 
       65.00        62.47        42.25        21.47        38.07        51.91 
TCGA-30-1853 TCGA-30-1857 TCGA-30-1859 TCGA-30-1861 TCGA-30-1887 TCGA-30-1892 
       36.26         0.26        48.10        34.78        24.26        48.79 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1956 TCGA-31-1959 
       45.57        30.18        18.77        22.49        44.12         2.20 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 TCGA-36-1576 TCGA-36-1580 TCGA-36-2529 
       29.10        21.53        22.55        30.08        24.23        35.05 
TCGA-36-2543 TCGA-36-2548 TCGA-36-2551 TCGA-42-2582 TCGA-42-2588 TCGA-57-1582 
        2.24        14.17        16.18        47.57        28.93        24.03 
TCGA-57-1585 TCGA-57-1586 TCGA-59-2348 TCGA-59-2354 TCGA-61-1724 TCGA-61-1725 
        1.74        22.32       180.20        34.39        20.94        31.43 
TCGA-61-1728 TCGA-61-1736 TCGA-61-1741 TCGA-61-1743 TCGA-61-1899 TCGA-61-1906 
       27.88        48.79        33.67        43.69         8.42        34.13 
TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1914 TCGA-61-1919 TCGA-61-1998 
       31.30        37.05        42.51        56.61        38.17         5.52 
TCGA-61-2009 TCGA-61-2016 TCGA-61-2088 TCGA-61-2109 TCGA-61-2612 TCGA-61-2614 
       39.85         1.18         4.77        20.68         6.35         8.61 
TCGA-OY-A56Q TCGA-VG-A8LO TCGA-09-0365 TCGA-10-0925 TCGA-10-0927 TCGA-10-0930 
       18.94         0.79         9.47        54.31        81.86        34.19 
TCGA-10-0933 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0717 
       14.66        35.44        36.92        19.99        20.91        24.59 
TCGA-13-0724 TCGA-13-0726 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 
        2.73        31.20        55.17         2.50        11.54        38.01 
TCGA-13-0768 TCGA-13-0792 TCGA-13-0794 TCGA-13-0800 TCGA-13-0802 TCGA-13-0807 
       58.65       118.42        63.09        87.48        51.02        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 
       68.94       107.18       145.45        43.36        71.74        66.15 
TCGA-13-0900 TCGA-13-0903 TCGA-13-0911 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 
      134.04       127.79        44.55        84.53        48.76        83.74 
TCGA-13-0924 TCGA-13-2071 
       85.94        25.41 

$`8Q GAIN WILD-TYPE`
TCGA-59-A5PD TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1341 
       20.52        43.92        41.00        49.15         2.01         1.08 
TCGA-04-1346 TCGA-04-1348 TCGA-04-1350 TCGA-04-1353 TCGA-04-1361 TCGA-04-1367 
       65.52        48.76        63.98         0.53        32.52       103.40 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 
       82.39        56.55        41.59        19.99         0.79        38.37 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 
       55.43        48.89        28.64        64.64        36.23        47.70 
TCGA-04-1655 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1673 TCGA-09-1675 
       45.37        89.33        74.93        57.60         3.02        97.55 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
        6.12        35.15         4.54       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1405 TCGA-13-1407 
       39.75        20.94        26.93        12.46        28.54        83.31 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1487 
       32.35        54.64        87.06        61.71        29.42        22.39 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
       83.93        52.44       125.56        93.90        90.38         4.24 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
       66.15       115.07        80.15        44.68        54.25        14.53 
TCGA-13-2057 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 
       80.02        76.90        65.52        70.45         8.42        25.94 
TCGA-20-0996 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 TCGA-23-1021 TCGA-23-1024 
       72.20        27.52        19.10        16.70        47.54        15.39 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1030 TCGA-23-1032 TCGA-23-1113 TCGA-23-1114 
       32.09        49.41        29.13         2.76        31.20        68.68 
TCGA-23-1118 TCGA-23-1120 TCGA-23-1122 TCGA-23-1809 TCGA-23-2078 TCGA-23-2081 
       86.01         4.27        39.09         0.53        87.48        77.00 
TCGA-23-2641 TCGA-24-0966 TCGA-24-0970 TCGA-24-0980 TCGA-24-0982 TCGA-24-1104 
        2.76         7.63        11.64         7.66        22.32        63.55 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        6.31         6.38         6.02         5.95         5.36         4.83 
TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1463 TCGA-24-1466 TCGA-24-1469 
       17.39        28.37        18.64        72.92        45.14         9.11 
TCGA-24-1470 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 TCGA-24-1550 
        3.45        22.22        26.96        57.40        16.21        41.06 
TCGA-24-1551 TCGA-24-1560 TCGA-24-1562 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       51.91        44.09        45.50        10.26        17.23        90.15 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1845 
       88.37        48.33        38.24         8.32         3.48         3.81 
TCGA-24-1846 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1928 TCGA-24-1930 
        4.37         5.79         5.52         9.80        11.05        81.11 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2029 TCGA-24-2030 TCGA-24-2036 
       44.84        58.16        34.82        14.43        55.92        64.01 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 TCGA-24-2280 
       44.52        57.07        36.16         0.79        47.54        70.45 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 
       44.61         0.82        67.36        16.64        55.86        53.26 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1318 TCGA-25-1319 
       26.96        33.01        52.04        42.05        34.98        65.00 
TCGA-25-1323 TCGA-25-1626 TCGA-25-1630 TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 
       12.99        17.03        38.20         0.30        62.17        35.87 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 
       52.04        14.96        24.99        13.02        49.05        38.04 
TCGA-25-2397 TCGA-25-2400 TCGA-25-2404 TCGA-25-2408 TCGA-29-1688 TCGA-29-1701 
       12.00        42.02        29.03        31.00        78.90        16.93 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 
       18.25        41.98        31.27        34.62        17.36        86.60 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 
       31.30        22.98        24.36        22.55        17.33        12.36 
TCGA-29-2414 TCGA-29-2428 TCGA-29-2429 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ 
       86.17        45.11        13.84        11.47         9.76        35.77 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 
        2.47        15.68        44.91         6.12        36.62         1.22 
TCGA-30-1880 TCGA-30-1891 TCGA-31-1953 TCGA-31-1955 TCGA-36-1568 TCGA-36-1571 
       57.57        30.05         6.71        42.51        28.77        22.85 
TCGA-36-1575 TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 
        8.55        25.74        27.85        24.69        33.01        29.49 
TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 
       29.82        25.91        25.08        23.80        21.60        20.98 
TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 TCGA-36-2552 TCGA-42-2587 TCGA-42-2589 
       18.31        20.52         6.05        11.47        23.74        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 TCGA-57-1992 
       10.42        40.77         1.48        11.38        21.14        29.00 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       25.08        25.02        80.12        22.32       116.12         9.40 
TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1727 
        2.14         5.42        44.81        11.11         8.09        18.54 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 
        4.34        31.79        28.47        44.84        35.80         2.43 
TCGA-61-1895 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1913 
        1.45         5.79        11.41        13.02         9.07        48.92 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 TCGA-61-2000 TCGA-61-2002 
       67.76        43.43        15.75         2.01        14.50        17.98 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
        4.01        30.64        30.64        45.96        45.40         4.80 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 
       51.72        71.74        61.64        58.39        60.62        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
       55.50         6.48        76.87        44.52       125.75        22.22 
TCGA-61-2613 TCGA-OY-A56P TCGA-WR-A838 TCGA-09-0364 TCGA-09-0366 TCGA-09-0367 
       31.07        39.68         9.99        29.16        57.76        17.98 
TCGA-09-0369 TCGA-10-0926 TCGA-10-0928 TCGA-10-0931 TCGA-10-0934 TCGA-13-0714 
       35.57        25.91        18.51        32.88         6.71         6.21 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 TCGA-13-0757 
       44.55        39.58        12.39        15.19        17.82        11.18 
TCGA-13-0758 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0793 
       11.38       111.78        61.84        56.71        40.24       107.28 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 
       20.35        69.73        83.34        45.99        43.86        35.28 
TCGA-13-0805 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 
       35.31       111.39       153.37        66.67        92.42        95.15 
TCGA-13-0891 TCGA-13-0901 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 
      102.84        19.36        50.37       123.16       118.98        60.59 
TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 
      116.65        37.64       109.32        58.68        48.79 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.26              0.30 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           180.20            153.37 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           33.385            32.350 
[1] "0.3 - 180.2 (33.4)" "0.3 - 153.4 (32.4)"
[1] "hr=" "1.1"
D16V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  8Q GAIN MUTATED         1   242                2
  8Q GAIN WILD-TYPE       2   316                0
D16V3, multiclass
                  clus
vv                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  OMENTUM                        1                 2
  OVARY                        242               316
  PERITONEUM OVARY               2                 0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V4, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   237   1
  8Q GAIN WILD-TYPE 304   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    237    1
  8Q GAIN WILD-TYPE  304    4
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO              237               304
  YES               1                 4
[1] 2 2
[1] FALSE
D16V5, continuous
                   vv
clus                R0 R1 R2 RX
  8Q GAIN MUTATED    3 12  2  2
  8Q GAIN WILD-TYPE 12 14  3  1
D16V6, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0               3                12
  R1              12                14
  R2               2                 3
  RX               2                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     4 144
  8Q GAIN WILD-TYPE   6 183
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      4  144
  8Q GAIN WILD-TYPE    6  183
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 6
  NOT HISPANIC OR LATINO             144               183
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    34  52
  9P GAIN WILD-TYPE 194 279
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               86               473 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               52               279 
$`9P GAIN MUTATED`
TCGA-5X-AA5U TCGA-04-1362 TCGA-04-1516 TCGA-09-1668 TCGA-09-2045 TCGA-09-2051 
       11.87        44.32        41.59        55.36        35.15        63.09 
TCGA-13-1488 TCGA-13-1504 TCGA-13-1505 TCGA-13-1507 TCGA-13-1511 TCGA-20-0990 
       70.82        34.82        65.69        65.52        54.25        25.94 
TCGA-20-1683 TCGA-20-1686 TCGA-20-1687 TCGA-23-1024 TCGA-23-1026 TCGA-23-1032 
       25.38         2.93         2.66        15.39        26.83         2.76 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1809 TCGA-23-2077 TCGA-23-2084 TCGA-24-0980 
        6.38        39.09         0.53       115.89        49.84         7.66 
TCGA-24-1424 TCGA-24-1428 TCGA-24-1434 TCGA-24-1436 TCGA-24-1466 TCGA-24-1469 
        6.02        17.39        18.67         8.55        45.14         9.11 
TCGA-24-1471 TCGA-24-1544 TCGA-24-1548 TCGA-24-1552 TCGA-24-1553 TCGA-24-1556 
        1.18        26.96        16.21        41.39        58.09        70.62 
TCGA-24-1842 TCGA-24-1844 TCGA-24-1847 TCGA-24-1850 TCGA-24-1924 TCGA-24-1928 
        8.32         3.72        11.28         5.52        30.21        11.05 
TCGA-24-2020 TCGA-24-2026 TCGA-24-2288 TCGA-24-2298 TCGA-25-1319 TCGA-25-1320 
      152.02        34.82         0.82        53.26        65.00        37.97 
TCGA-25-1329 TCGA-25-1628 TCGA-25-1635 TCGA-25-1878 TCGA-25-2396 TCGA-25-2404 
       15.02        20.61        52.04        85.05         3.02        29.03 
TCGA-29-1762 TCGA-29-1763 TCGA-29-1777 TCGA-29-1784 TCGA-30-1855 TCGA-30-1859 
       86.60        66.81        12.30         5.36         2.47        48.10 
TCGA-30-1862 TCGA-30-1867 TCGA-36-1577 TCGA-36-1581 TCGA-36-2532 TCGA-36-2543 
        6.12         1.22        25.74        24.69        29.49         2.24 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1906 TCGA-61-2087 TCGA-61-2094 
       33.67        43.69         1.45        34.13         4.80        71.74 
TCGA-61-2111 TCGA-10-0933 TCGA-10-0935 TCGA-10-0936 TCGA-13-0723 TCGA-13-0730 
      125.75        14.66        35.44        36.92        39.58        17.82 
TCGA-13-0751 TCGA-13-0803 TCGA-13-0807 TCGA-13-0884 TCGA-13-0893 TCGA-13-0911 
       55.17        43.86        13.61       107.18        43.36        44.55 
TCGA-13-0919 TCGA-13-0923 
       84.53        83.74 

$`9P GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 
       13.81        20.52        43.92        41.00         1.81        49.15 
TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 
        2.01        46.62         1.08        18.51        11.87        65.52 
TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 
       63.09        48.76        21.57        63.98        65.46         0.53 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 
       49.28        32.52        33.67        76.57       103.40        82.39 
TCGA-04-1514 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 
       56.55        19.99         0.79        38.37       119.08        29.10 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 
       84.20        55.43        48.89        27.88        28.64        64.64 
TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 
       36.23        31.86        47.70        45.37         9.99        38.43 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 
       89.33        74.93        41.62        57.60        61.87        30.51 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 
       17.98         5.85         3.02         8.55        97.55         6.18 
TCGA-09-2044 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2053 TCGA-09-2054 
        6.12         4.54       112.41        71.11        39.75        20.94 
TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 
       26.93        12.46        77.10        81.17        28.54        83.31 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 
       55.23        57.27        81.01        17.46        32.35        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 
       87.06        61.71        29.42       124.44        20.68        22.39 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
       83.93        52.44       125.56        93.90        90.38         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1506 
      127.27        66.15       115.07        13.97        43.20        34.16 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
       80.15        44.68        14.53        80.02        78.48        77.88 
TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0991 
       76.90        65.52        70.45         8.42        23.05        26.20 
TCGA-20-0996 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 TCGA-23-1021 TCGA-23-1022 
       72.20        27.52        19.10        16.70        47.54        49.68 
TCGA-23-1023 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 
       40.54        32.09        49.41         8.81        29.13        18.90 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 
       51.35        54.51         3.22        31.20        68.68        19.46 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1123 TCGA-23-1124 
       33.30        86.01       129.96         4.27        33.47        58.13 
TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 
       24.95        87.48        91.66        77.00         2.76         4.70 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0982 
        4.50         7.63        11.64        21.80        41.56        22.32 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 
       54.12        63.55        47.41         6.31         6.38         7.82 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 
        7.99         7.86         0.76         6.25         5.95         5.36 
TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 
        4.83        28.37        18.64        43.53        72.92        12.46 
TCGA-24-1467 TCGA-24-1470 TCGA-24-1474 TCGA-24-1545 TCGA-24-1546 TCGA-24-1549 
      105.99         3.45        22.22        57.40        64.27        56.58 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1555 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 
       41.06        51.91        88.50        39.88        19.53        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       45.50        47.70        25.87        10.26        17.23        90.15 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1843 TCGA-24-1845 TCGA-24-1846 
       88.37        48.33        38.24         3.48         3.81         4.37 
TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 
        5.79         9.80        22.68        16.44        81.11         4.87 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 
       44.84        58.16       109.71        14.43        55.92        18.48 
TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 
       28.18        64.01        44.52        57.07        36.16         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2289 
        0.36        47.54        31.63        70.45        44.61        67.36 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 
       36.23        16.64        33.11        55.86         1.02        26.96 
TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1321 
       33.01        52.04        42.05         2.01        34.98        33.96 
TCGA-25-1322 TCGA-25-1323 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 
        2.99        12.99        18.58        27.62        17.03        12.95 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 
       38.20         0.30        59.15        62.17        35.87        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 
       24.99        24.00        13.02        49.05         1.02        38.04 
TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2408 
       12.00        45.01        19.99        42.02         2.96        31.00 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 
       26.99        78.90        47.61        48.33       101.79        39.02 
TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 
       40.41        33.93        31.20        68.32        36.36        16.93 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 
       23.93        59.67        18.25        41.98        31.27        34.62 
TCGA-29-1761 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 
       17.36        62.93        39.42        31.30        22.98        24.36 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1778 TCGA-29-1781 
       22.55        17.33        12.36        11.84        14.93         8.38 
TCGA-29-1783 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 
        7.23        36.30        86.17        65.00        62.47        45.11 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ 
       13.84        42.25        21.47        11.47         9.76        35.77 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 TCGA-30-1860 
       38.07        51.91        36.26        15.68         0.26        44.91 
TCGA-30-1861 TCGA-30-1866 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 
       34.78        36.62        57.57        24.26        30.05        48.79 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 
       45.57        30.18        18.77        22.49         6.71        42.51 
TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 
       44.12         2.20        28.77        29.10        21.53        22.85 
TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1578 TCGA-36-1580 TCGA-36-2529 
       22.55         8.55        30.08        27.85        24.23        35.05 
TCGA-36-2530 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 
       33.01        29.82        25.91        25.08        23.80        21.60 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 
       20.98        18.31        20.52        14.17         6.05        16.18 
TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
       11.47        47.57        23.74        28.93        42.02        10.42 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 
       40.77         1.48        24.03        11.38        21.14         1.74 
TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 
       22.32        29.00        25.08        25.02       180.20        80.12 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       22.32       116.12         9.40        34.39         2.14         5.42 
TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
       44.81        11.11         8.09        20.94        31.43        18.54 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       27.88         4.34        31.79        28.47        48.79        44.84 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 
       35.80         2.43         8.42         5.79        11.41        13.02 
TCGA-61-1904 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 
        9.07        31.30        37.05        42.51        48.92        56.61 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
       67.76        43.43        15.75        38.17         2.01         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 
       14.50        17.98         4.01        30.64        39.85        30.64 
TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2088 TCGA-61-2092 TCGA-61-2095 
        1.18        45.96        45.40         4.77        51.72        61.64 
TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 
       58.39        60.62        65.52        55.50         6.48        76.87 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       20.68        44.52        22.22         6.35        31.07         8.61 
TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 
       39.68        18.94         0.79         9.99        29.16         9.47 
TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 
       57.76        17.98        35.57        54.31        25.91        81.86 
TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 TCGA-10-0937 TCGA-10-0938 
       18.51        34.19        32.88         6.71        19.99        20.91 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 
        6.21        24.59        44.55         2.73        12.39        31.20 
TCGA-13-0727 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 
       15.19         2.50        11.18        11.38        11.54        38.01 
TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 
      111.78        61.84        56.71        58.65        40.24       118.42 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 
      107.28        63.09        20.35        69.73        83.34        87.48 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0883 TCGA-13-0885 
       45.99        51.02        35.28        35.31        68.94       111.39 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 
      153.37        66.67        92.42        95.15       145.45       102.84 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 
       71.74        66.15       134.04        19.36       127.79        50.37 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 
      123.16       118.98        60.59       116.65        37.64       109.32 
TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0924 TCGA-13-2071 
       58.68        48.79        48.76        85.94        25.41 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.53              0.26 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           152.02            180.20 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            29.85             33.01 
[1] "0.5 - 152.0 (29.9)" "0.3 - 180.2 (33.0)"
[1] "hr=" "1.1"
D17V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  9P GAIN MUTATED         0    88                0
  9P GAIN WILD-TYPE       3   470                2
D17V3, multiclass
                  clus
vv                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  OMENTUM                        0                 3
  OVARY                         88               470
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V4, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    84   1
  9P GAIN WILD-TYPE 457   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     84    1
  9P GAIN WILD-TYPE  457    4
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               84               457
  YES               1                 4
[1] 2 2
[1] FALSE
D17V5, continuous
                   vv
clus                R0 R1 R2 RX
  9P GAIN MUTATED    3  3  0  0
  9P GAIN WILD-TYPE 12 23  5  3
D17V6, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0               3                12
  R1               3                23
  R2               0                 5
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     0  51
  9P GAIN WILD-TYPE  10 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0   51
  9P GAIN WILD-TYPE   10  276
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              51               276
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    18  24
  9Q GAIN WILD-TYPE 210 307
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               42               517 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               24               307 
$`9Q GAIN MUTATED`
TCGA-04-1362 TCGA-04-1516 TCGA-09-1668 TCGA-13-1505 TCGA-20-1683 TCGA-20-1687 
       44.32        41.59        55.36        65.69        25.38         2.66 
TCGA-23-1122 TCGA-23-1809 TCGA-23-2084 TCGA-24-0980 TCGA-24-1434 TCGA-24-1436 
       39.09         0.53        49.84         7.66        18.67         8.55 
TCGA-24-1466 TCGA-24-1552 TCGA-24-1842 TCGA-24-1844 TCGA-24-1847 TCGA-24-1850 
       45.14        41.39         8.32         3.72        11.28         5.52 
TCGA-24-2020 TCGA-24-2298 TCGA-25-1329 TCGA-25-1628 TCGA-25-1635 TCGA-25-1878 
      152.02        53.26        15.02        20.61        52.04        85.05 
TCGA-25-2404 TCGA-29-1762 TCGA-29-1784 TCGA-30-1855 TCGA-30-1862 TCGA-31-1959 
       29.03        86.60         5.36         2.47         6.12         2.20 
TCGA-36-1577 TCGA-36-2542 TCGA-42-2591 TCGA-61-1740 TCGA-61-1907 TCGA-61-2008 
       25.74        21.60        40.77         2.43        31.30        30.64 
TCGA-13-0723 TCGA-13-0761 TCGA-13-0887 TCGA-13-0893 TCGA-13-0911 TCGA-13-0919 
       39.58        38.01        66.67        43.36        44.55        84.53 

$`9Q GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 
       49.15         2.01        46.62         1.08        18.51        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 
       65.52        63.09        48.76        21.57        63.98        65.46 
TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
        0.53        49.28        32.52        33.67        76.57       103.40 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 
       82.39        56.55        19.99         0.79        38.37       119.08 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 
       29.10        84.20        55.43        48.89        27.88        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 
       64.64        36.23        31.86        47.70        45.37         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 
       38.43        89.33        74.93        41.62        57.60        61.87 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 
       30.51        17.98         5.85         3.02         8.55        97.55 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 
        6.18         6.12        35.15         4.54       112.41        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 
       63.09        39.75        20.94        26.93        12.46        77.10 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
       81.17        28.54        83.31        55.23        57.27        81.01 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
       17.46        32.35        54.64        87.06        61.71        29.42 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
      124.44        20.68        22.39        70.82        83.93        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
      125.56        93.90        90.38         4.24       127.27        66.15 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 
      115.07        13.97        43.20        34.82        34.16        65.52 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 
       80.15        44.68        54.25        14.53        80.02        78.48 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
       77.88        76.90        65.52        70.45         8.42        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 
       25.94        26.20        72.20        27.52        19.10        16.70 
TCGA-20-1686 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
        2.93        47.54        49.68        40.54        15.39        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       32.09        49.41         8.81        29.13        18.90         2.76 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 
       51.35        54.51         3.22        31.20        68.68        19.46 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1123 
       33.30        86.01       129.96         4.27         6.38        33.47 
TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
       58.13        24.95       115.89        87.48        91.66        77.00 
TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 
        2.76         4.70         4.50         7.63        11.64        21.80 
TCGA-24-0979 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 
       41.56        22.32        54.12        63.55        47.41         6.31 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 
        6.38         7.82         7.99         7.86         0.76         6.25 
TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 
        6.02         5.95         5.36         4.83        17.39        28.37 
TCGA-24-1431 TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 TCGA-24-1467 TCGA-24-1469 
       18.64        43.53        72.92        12.46       105.99         9.11 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 
        3.45         1.18        22.22        26.96        57.40        64.27 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1553 TCGA-24-1555 
       16.21        56.58        41.06        51.91        58.09        88.50 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       70.62        39.88        19.53        44.09        45.50        47.70 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 
       25.87        10.26        17.23        90.15        88.37        48.33 
TCGA-24-1616 TCGA-24-1843 TCGA-24-1845 TCGA-24-1846 TCGA-24-1849 TCGA-24-1920 
       38.24         3.48         3.81         4.37         5.79         9.80 
TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 
       22.68        30.21        16.44        11.05        81.11         4.87 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 
       44.84        58.16        34.82       109.71        14.43        55.92 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 
       18.48        28.18        64.01        44.52        57.07        36.16 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 
        0.79         0.36        47.54        31.63        70.45        44.61 
TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 
        0.82        67.36        36.23        16.64        33.11        55.86 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
        1.02        26.96        33.01        52.04        42.05         2.01 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 
       34.98        65.00        37.97        33.96         2.99        12.99 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 
       18.58        27.62        17.03        12.95        38.20         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
       59.15        62.17        35.87        14.96        24.99        24.00 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 
       13.02        49.05         1.02        38.04         3.02        12.00 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 
       45.01        19.99        42.02         2.96        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 
       78.90        47.61        48.33       101.79        39.02        40.41 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 
       33.93        31.20        68.32        36.36        16.93        23.93 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 
       59.67        18.25        41.98        31.27        34.62        17.36 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 
       66.81        62.93        39.42        31.30        22.98        24.36 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 
       22.55        17.33        12.36        11.84        12.30        14.93 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 
        8.38         7.23        36.30        86.17        65.00        62.47 
TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 
       45.11        13.84        42.25        21.47        11.47         9.76 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 
       35.77        38.07        51.91        36.26        15.68         0.26 
TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 
       48.10        44.91        34.78        36.62         1.22        57.57 
TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 
       24.26        30.05        48.79        45.57        30.18        18.77 
TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 
       22.49         6.71        42.51        44.12        28.77        29.10 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1578 
       21.53        22.85        22.55         8.55        30.08        27.85 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       24.23        24.69        35.05        33.01        29.49        29.82 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 
       25.91        25.08        23.80         2.24        20.98        18.31 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 
       20.52        14.17         6.05        16.18        11.47        47.57 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2593 TCGA-57-1582 
       23.74        28.93        42.02        10.42         1.48        24.03 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 
       11.38        21.14         1.74        22.32        29.00        25.08 
TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       25.02       180.20        80.12        22.32       116.12         9.40 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 
       34.39         2.14         5.42        44.81        11.11         8.09 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 
       20.94        31.43        18.54        27.88         4.34        31.79 
TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1741 TCGA-61-1743 
       28.47        48.79        44.84        35.80        33.67        43.69 
TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 
        1.45         8.42         5.79        11.41        13.02         9.07 
TCGA-61-1906 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 
       34.13        37.05        42.51        48.92        56.61        67.76 
TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       43.43        15.75        38.17         2.01         5.52        14.50 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 
       17.98         4.01        39.85        30.64         1.18        45.96 
TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       45.40         4.80         4.77        51.72        71.74        61.64 
TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 
       58.39        60.62        65.52        55.50         6.48        76.87 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 
       20.68        44.52       125.75        22.22         6.35        31.07 
TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 
        8.61        39.68        18.94         0.79         9.99        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-10-0925 TCGA-10-0926 
        9.47        57.76        17.98        35.57        54.31        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       81.86        18.51        34.19        32.88        14.66         6.71 
TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
       35.44        36.92        19.99        20.91         6.21        24.59 
TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 
       44.55         2.73        12.39        31.20        15.19        17.82 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0762 
       55.17         2.50        11.18        11.38        11.54       111.78 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       61.84        56.71        58.65        40.24       118.42       107.28 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
       63.09        20.35        69.73        83.34        87.48        45.99 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
       51.02        43.86        35.28        35.31        13.61        68.94 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 
      107.18       111.39       153.37        92.42        95.15       145.45 
TCGA-13-0891 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
      102.84        71.74        66.15       134.04        19.36       127.79 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 
       50.37       123.16       118.98        60.59       116.65        37.64 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
      109.32        58.68        48.79        48.76        83.74        85.94 
TCGA-13-2071 
       25.41 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.53              0.26 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           152.02            180.20 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            30.97             33.01 
[1] "0.5 - 152.0 (31.0)" "0.3 - 180.2 (33.0)"
[1] "hr=" "1.1"
D18V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  9Q GAIN MUTATED         0    42                0
  9Q GAIN WILD-TYPE       3   516                2
D18V3, multiclass
                  clus
vv                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  OMENTUM                        0                 3
  OVARY                         42               516
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V4, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    40   1
  9Q GAIN WILD-TYPE 501   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     40    1
  9Q GAIN WILD-TYPE  501    4
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               40               501
  YES               1                 4
[1] 2 2
[1] FALSE
D18V5, continuous
                   vv
clus                R0 R1 R2 RX
  9Q GAIN MUTATED    1  2  0  0
  9Q GAIN WILD-TYPE 14 24  5  3
D18V6, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0               1                14
  R1               2                24
  R2               0                 5
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     0  26
  9Q GAIN WILD-TYPE  10 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0   26
  9Q GAIN WILD-TYPE   10  301
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              26               301
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    76 107
  10P GAIN WILD-TYPE 152 224
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               183                376 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               107                224 
$`10P GAIN MUTATED`
TCGA-04-1332 TCGA-04-1338 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 
       41.00        46.62        11.87        65.52        63.09        21.57 
TCGA-04-1350 TCGA-04-1353 TCGA-04-1356 TCGA-04-1362 TCGA-04-1517 TCGA-04-1530 
       63.98         0.53        49.28        44.32        19.99       119.08 
TCGA-04-1542 TCGA-04-1646 TCGA-04-1649 TCGA-04-1652 TCGA-04-1655 TCGA-09-1659 
       84.20        27.88        64.64        31.86        45.37         9.99 
TCGA-09-1661 TCGA-09-1667 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       38.43        61.87        55.36        17.98         5.85         3.02 
TCGA-09-1674 TCGA-09-2050 TCGA-09-2051 TCGA-13-1407 TCGA-13-1409 TCGA-13-1411 
        8.55        71.11        63.09        83.31        57.27        17.46 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1492 TCGA-13-1495 TCGA-13-1496 
       32.35        54.64        87.06       125.56        90.38         4.24 
TCGA-13-1499 TCGA-13-1504 TCGA-13-2060 TCGA-13-2061 TCGA-20-0987 TCGA-20-1682 
      115.07        34.82        77.88        76.90        23.05        27.52 
TCGA-20-1683 TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 TCGA-23-1022 TCGA-23-1024 
       25.38        16.70         2.93        47.54        49.68        15.39 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1116 TCGA-23-1122 TCGA-23-1123 
       18.90         2.76        54.51        19.46        39.09        33.47 
TCGA-23-1124 TCGA-23-2077 TCGA-23-2643 TCGA-24-0982 TCGA-24-1417 TCGA-24-1418 
       58.13       115.89         4.70        22.32         7.82         7.99 
TCGA-24-1424 TCGA-24-1427 TCGA-24-1428 TCGA-24-1434 TCGA-24-1436 TCGA-24-1469 
        6.02         4.83        17.39        18.67         8.55         9.11 
TCGA-24-1544 TCGA-24-1548 TCGA-24-1564 TCGA-24-1565 TCGA-24-1616 TCGA-24-1843 
       26.96        16.21        25.87        10.26        38.24         3.48 
TCGA-24-1850 TCGA-24-1928 TCGA-24-2020 TCGA-24-2260 TCGA-24-2261 TCGA-24-2281 
        5.52        11.05       152.02        36.16         0.79        44.61 
TCGA-24-2293 TCGA-25-1312 TCGA-25-1317 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 
       16.64         1.02         2.01        37.97        33.96         2.99 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 
       15.02        18.58        17.03        12.95        20.61         0.30 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1871 TCGA-25-1877 TCGA-25-2392 TCGA-29-1691 
       35.87        52.04        24.99        24.00         1.02        48.33 
TCGA-29-1693 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1710 TCGA-29-1763 
      101.79        16.93        23.93        59.67        31.27        66.81 
TCGA-29-1766 TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 TCGA-29-1783 TCGA-29-1785 
       39.42        12.36        12.30        14.93         7.23        36.30 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2432 TCGA-29-2436 TCGA-29-A5NZ 
       86.17        65.00        45.11        21.47         9.76        35.77 
TCGA-30-1853 TCGA-30-1856 TCGA-30-1861 TCGA-30-1866 TCGA-30-1887 TCGA-31-1950 
       36.26        15.68        34.78        36.62        24.26        18.77 
TCGA-31-1953 TCGA-36-1569 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 
        6.71        29.10        25.74        27.85        24.23        24.69 
TCGA-36-2529 TCGA-36-2543 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2588 
       35.05         2.24        14.17        16.18        11.47        28.93 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 
       24.03        11.38        22.32        25.08        25.02       180.20 
TCGA-59-2352 TCGA-59-2372 TCGA-61-1722 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 
        9.40        44.81         8.09        27.88         4.34        31.79 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1904 TCGA-61-1907 TCGA-61-1911 TCGA-61-1917 
        2.43        33.67         9.07        31.30        42.51        43.43 
TCGA-61-1918 TCGA-61-1919 TCGA-61-2003 TCGA-61-2012 TCGA-61-2018 TCGA-61-2098 
       15.75        38.17         4.01        30.64        45.40        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2111 TCGA-61-2612 TCGA-OY-A56P TCGA-OY-A56Q 
       55.50         6.48       125.75         6.35        39.68        18.94 
TCGA-WR-A838 TCGA-09-0365 TCGA-09-0369 TCGA-10-0930 TCGA-10-0933 TCGA-13-0727 
        9.99         9.47        35.57        34.19        14.66        15.19 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0762 TCGA-13-0768 TCGA-13-0802 
       17.82        55.17        11.18       111.78        58.65        51.02 
TCGA-13-0807 TCGA-13-0884 TCGA-13-0885 TCGA-13-0888 TCGA-13-0890 TCGA-13-0901 
       13.61       107.18       111.39        92.42       145.45        19.36 
TCGA-13-0911 TCGA-13-0919 TCGA-13-0923 
       44.55        84.53        83.74 

$`10P GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 
       13.81        20.52        11.87        43.92         1.81        49.15 
TCGA-04-1337 TCGA-04-1341 TCGA-04-1342 TCGA-04-1348 TCGA-04-1351 TCGA-04-1361 
        2.01         1.08        18.51        48.76        65.46        32.52 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 
       33.67        76.57       103.40        82.39        56.55        41.59 
TCGA-04-1519 TCGA-04-1525 TCGA-04-1536 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 
        0.79        38.37        29.10        55.43        48.89        28.64 
TCGA-04-1651 TCGA-04-1654 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 
       36.23        47.70        89.33        74.93        41.62        57.60 
TCGA-09-1669 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 
       30.51        97.55         6.18         6.12        35.15         4.54 
TCGA-09-2049 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 
      112.41        39.75        20.94        26.93        12.46        77.10 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1410 TCGA-13-1482 TCGA-13-1483 
       81.17        28.54        55.23        81.01        61.71        29.42 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
      124.44        20.68        22.39        70.82        83.93        52.44 
TCGA-13-1494 TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1505 
       93.90       127.27        66.15        13.97        43.20        65.69 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
       34.16        65.52        80.15        44.68        54.25        14.53 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 
       80.02        78.48        65.52        70.45         8.42        25.94 
TCGA-20-0991 TCGA-20-0996 TCGA-20-1684 TCGA-20-1687 TCGA-23-1023 TCGA-23-1026 
       26.20        72.20        19.10         2.66        40.54        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1109 TCGA-23-1111 
       32.09        49.41         8.81        29.13        51.35         3.22 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 
       31.20        68.68        33.30        86.01       129.96         4.27 
TCGA-23-1121 TCGA-23-1809 TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
        6.38         0.53        24.95        87.48        91.66        77.00 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 
       49.84         2.76         4.50         7.63        11.64        21.80 
TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 
       41.56         7.66        54.12        63.55        47.41         6.31 
TCGA-24-1416 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 
        6.38         7.86         0.76         6.25         5.95         5.36 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 
       28.37        18.64        43.53        72.92        12.46        45.14 
TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1545 TCGA-24-1546 
      105.99         3.45         1.18        22.22        57.40        64.27 
TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       56.58        41.06        51.91        41.39        58.09        88.50 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       70.62        39.88        19.53        44.09        45.50        47.70 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1842 TCGA-24-1844 
       17.23        90.15        88.37        48.33         8.32         3.72 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 
        3.81         4.37        11.28         5.79         9.80        22.68 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 
       30.21        16.44        81.11         4.87        44.84        58.16 
TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 
       34.82       109.71        14.43        55.92        18.48        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 
       64.01        44.52        57.07         0.36        47.54        31.63 
TCGA-24-2280 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2295 TCGA-24-2297 
       70.45         0.82        67.36        36.23        33.11        55.86 
TCGA-24-2298 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1318 
       53.26        26.96        33.01        52.04        42.05        34.98 
TCGA-25-1319 TCGA-25-1323 TCGA-25-1625 TCGA-25-1630 TCGA-25-1632 TCGA-25-1633 
       65.00        12.99        27.62        38.20        59.15        62.17 
TCGA-25-1870 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 
       14.96        85.05        13.02        49.05        38.04         3.02 
TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 
       12.00        45.01        19.99        42.02         2.96        29.03 
TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1694 TCGA-29-1695 
       31.00        26.99        78.90        47.61        39.02        40.41 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1705 TCGA-29-1707 
       33.93        31.20        68.32        36.36        18.25        41.98 
TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 
       34.62        17.36        86.60        62.93        31.30        22.98 
TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 TCGA-29-1781 TCGA-29-1784 
       24.36        22.55        17.33        11.84         8.38         5.36 
TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 TCGA-30-1714 TCGA-30-1718 
       62.47        13.84        42.25        11.47        38.07        51.91 
TCGA-30-1855 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1867 
        2.47         0.26        48.10        44.91         6.12         1.22 
TCGA-30-1880 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 
       57.57        30.05        48.79        45.57        30.18        22.49 
TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 
       42.51        44.12         2.20        28.77        21.53        22.85 
TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       22.55         8.55        30.08        33.01        29.49        29.82 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 
       25.91        25.08        23.80        21.60        20.98        18.31 
TCGA-36-2547 TCGA-36-2549 TCGA-42-2582 TCGA-42-2587 TCGA-42-2589 TCGA-42-2590 
       20.52         6.05        47.57        23.74        42.02        10.42 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 TCGA-59-2349 
       40.77         1.48        21.14         1.74        29.00        80.12 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-61-1721 
       22.32       116.12        34.39         2.14         5.42        11.11 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       20.94        31.43        18.54        28.47        48.79        44.84 
TCGA-61-1738 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 
       35.80        43.69         1.45         8.42         5.79        11.41 
TCGA-61-1903 TCGA-61-1906 TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 
       13.02        34.13        37.05        48.92        56.61        67.76 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2008 TCGA-61-2009 
        2.01         5.52        14.50        17.98        30.64        39.85 
TCGA-61-2016 TCGA-61-2017 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 
        1.18        45.96         4.80         4.77        51.72        71.74 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       61.64        58.39        60.62        76.87        20.68        44.52 
TCGA-61-2113 TCGA-61-2613 TCGA-61-2614 TCGA-VG-A8LO TCGA-09-0364 TCGA-09-0366 
       22.22        31.07         8.61         0.79        29.16        57.76 
TCGA-09-0367 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 
       17.98        54.31        25.91        81.86        18.51        32.88 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
        6.71        35.44        36.92        19.99        20.91         6.21 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 
       24.59        44.55        39.58         2.73        12.39        31.20 
TCGA-13-0755 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 
        2.50        11.38        11.54        38.01        61.84        56.71 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 
       40.24       118.42       107.28        63.09        20.35        69.73 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 
       83.34        87.48        45.99        43.86        35.28        35.31 
TCGA-13-0883 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 
       68.94       153.37        66.67        95.15       102.84        43.36 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       71.74        66.15       134.04       127.79        50.37       123.16 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
      118.98        60.59       116.65        37.64       109.32        58.68 
TCGA-13-0920 TCGA-13-0921 TCGA-13-0924 TCGA-13-2071 
       48.79        48.76        85.94        25.41 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.30               0.26 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            180.20             153.37 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            26.960             35.065 
[1] "0.3 - 180.2 (27.0)" "0.3 - 153.4 (35.1)"
[1] "hr=" "1.1"
D19V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  10P GAIN MUTATED         2   181                2
  10P GAIN WILD-TYPE       1   377                0
D19V3, multiclass
                  clus
vv                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  OMENTUM                         2                  1
  OVARY                         181                377
  PERITONEUM OVARY                2                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V4, binary
                    cls
clus                   0   1
  10P GAIN MUTATED   177   2
  10P GAIN WILD-TYPE 364   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED    177    2
  10P GAIN WILD-TYPE  364    3
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO               177                364
  YES                2                  3
[1] 2 2
[1] FALSE
D19V5, continuous
                    vv
clus                 R0 R1 R2 RX
  10P GAIN MUTATED    4 11  2  1
  10P GAIN WILD-TYPE 11 15  3  2
D19V6, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0                4                 11
  R1               11                 15
  R2                2                  3
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     2 110
  10P GAIN WILD-TYPE   8 217
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2  110
  10P GAIN WILD-TYPE    8  217
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO              110                217
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    43  63
  10Q GAIN WILD-TYPE 185 268
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               106                453 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                63                268 
$`10Q GAIN MUTATED`
TCGA-04-1332 TCGA-04-1349 TCGA-04-1350 TCGA-04-1353 TCGA-04-1356 TCGA-04-1362 
       41.00        21.57        63.98         0.53        49.28        44.32 
TCGA-04-1517 TCGA-04-1530 TCGA-04-1542 TCGA-04-1646 TCGA-04-1652 TCGA-04-1655 
       19.99       119.08        84.20        27.88        31.86        45.37 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 
        9.99        38.43        55.36        17.98         5.85         8.55 
TCGA-09-2055 TCGA-13-1477 TCGA-13-1481 TCGA-13-1484 TCGA-13-1495 TCGA-13-1504 
       26.93        54.64        87.06       124.44        90.38        34.82 
TCGA-13-2061 TCGA-20-0990 TCGA-20-1682 TCGA-20-1685 TCGA-23-1021 TCGA-23-1022 
       76.90        25.94        27.52        16.70        47.54        49.68 
TCGA-23-1110 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2077 TCGA-23-2643 
       54.51        39.09        33.47        58.13       115.89         4.70 
TCGA-24-0982 TCGA-24-1424 TCGA-24-1427 TCGA-24-1428 TCGA-24-1548 TCGA-24-1564 
       22.32         6.02         4.83        17.39        16.21        25.87 
TCGA-24-1616 TCGA-24-2019 TCGA-24-2020 TCGA-24-2261 TCGA-24-2293 TCGA-25-1312 
       38.24         4.87       152.02         0.79        16.64         1.02 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1321 TCGA-25-1623 TCGA-25-1626 TCGA-25-1631 
        2.01        34.98        33.96        18.58        17.03         0.30 
TCGA-25-1634 TCGA-25-1877 TCGA-25-2392 TCGA-29-1702 TCGA-29-1710 TCGA-29-1763 
       35.87        24.00         1.02        23.93        31.27        66.81 
TCGA-29-1775 TCGA-29-1777 TCGA-29-1783 TCGA-29-2425 TCGA-29-2428 TCGA-29-2432 
       12.36        12.30         7.23        65.00        45.11        21.47 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1853 TCGA-30-1861 TCGA-30-1866 TCGA-31-1950 
        9.76        35.77        36.26        34.78        36.62        18.77 
TCGA-36-1578 TCGA-36-1580 TCGA-36-2529 TCGA-36-2548 TCGA-36-2552 TCGA-57-1582 
       27.85        24.23        35.05        14.17        11.47        24.03 
TCGA-57-1583 TCGA-57-1994 TCGA-59-2352 TCGA-59-2372 TCGA-61-1722 TCGA-61-1730 
       11.38        25.02         9.40        44.81         8.09         4.34 
TCGA-61-1733 TCGA-61-1904 TCGA-61-1907 TCGA-61-1915 TCGA-61-2003 TCGA-61-2098 
       31.79         9.07        31.30        67.76         4.01        65.52 
TCGA-61-2101 TCGA-61-2111 TCGA-61-2612 TCGA-OY-A56Q TCGA-WR-A838 TCGA-09-0365 
       55.50       125.75         6.35        18.94         9.99         9.47 
TCGA-10-0930 TCGA-13-0727 TCGA-13-0730 TCGA-13-0757 TCGA-13-0802 TCGA-13-0884 
       34.19        15.19        17.82        11.18        51.02       107.18 
TCGA-13-0885 TCGA-13-0890 TCGA-13-0901 TCGA-13-0919 
      111.39       145.45        19.36        84.53 

$`10Q GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 
       13.81        20.52        11.87        43.92         1.81        49.15 
TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 
        2.01        46.62         1.08        18.51        11.87        65.52 
TCGA-04-1347 TCGA-04-1348 TCGA-04-1351 TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 
       63.09        48.76        65.46        32.52        33.67        76.57 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1519 TCGA-04-1525 
      103.40        82.39        56.55        41.59         0.79        38.37 
TCGA-04-1536 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 
       29.10        55.43        48.89        28.64        64.64        36.23 
TCGA-04-1654 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 
       47.70        89.33        74.93        41.62        57.60        61.87 
TCGA-09-1669 TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 
       30.51         3.02        97.55         6.18         6.12        35.15 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 
        4.54       112.41        71.11        63.09        39.75        20.94 
TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 
       12.46        77.10        81.17        28.54        83.31        55.23 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1482 TCGA-13-1483 
       57.27        81.01        17.46        32.35        61.71        29.42 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
       20.68        22.39        70.82        83.93        52.44       125.56 
TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 
       93.90         4.24       127.27        66.15       115.07        13.97 
TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 
       43.20        65.69        34.16        65.52        80.15        44.68 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2065 
       54.25        14.53        80.02        78.48        77.88        65.52 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 
       70.45         8.42        23.05        26.20        72.20        25.38 
TCGA-20-1684 TCGA-20-1686 TCGA-20-1687 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
       19.10         2.93         2.66        40.54        15.39        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       32.09        49.41         8.81        29.13        18.90         2.76 
TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 
       51.35         3.22        31.20        68.68        19.46        33.30 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1809 TCGA-23-2072 
       86.01       129.96         4.27         6.38         0.53        24.95 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2645 
       87.48        91.66        77.00        49.84         2.76         4.50 
TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 
        7.63        11.64        21.80        41.56         7.66        54.12 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 
       63.55        47.41         6.31         6.38         7.82         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 TCGA-24-1430 
        7.86         0.76         6.25         5.95         5.36        28.37 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 
       18.64        18.67        43.53         8.55        72.92        12.46 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 
       45.14       105.99         9.11         3.45         1.18        22.22 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 
       26.96        57.40        64.27        56.58        41.06        51.91 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 
       41.39        58.09        88.50        70.62        39.88        19.53 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       44.09        45.50        47.70        10.26        17.23        90.15 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 
       88.37        48.33         8.32         3.48         3.72         3.81 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 
        4.37        11.28         5.79         5.52         9.80        22.68 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2023 TCGA-24-2024 
       30.21        16.44        11.05        81.11        44.84        58.16 
TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 
       34.82       109.71        14.43        55.92        18.48        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 TCGA-24-2267 
       64.01        44.52        57.07        36.16         0.36        47.54 
TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 
       31.63        70.45        44.61         0.82        67.36        36.23 
TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 
       33.11        55.86        53.26        26.96        33.01        52.04 
TCGA-25-1316 TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 
       42.05        65.00        37.97         2.99        12.99        15.02 
TCGA-25-1625 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1632 TCGA-25-1633 
       27.62        12.95        20.61        38.20        59.15        62.17 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 
       52.04        14.96        24.99        85.05        13.02        49.05 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 
       38.04         3.02        12.00        45.01        19.99        42.02 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 
        2.96        29.03        31.00        26.99        78.90        47.61 
TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 
       48.33       101.79        39.02        40.41        33.93        31.20 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
       68.32        36.36        16.93        59.67        18.25        41.98 
TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 
       34.62        17.36        86.60        62.93        39.42        31.30 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 TCGA-29-1778 
       22.98        24.36        22.55        17.33        11.84        14.93 
TCGA-29-1781 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2429 
        8.38         5.36        36.30        86.17        62.47        13.84 
TCGA-29-2431 TCGA-29-2434 TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 
       42.25        11.47        38.07        51.91         2.47        15.68 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1867 TCGA-30-1880 
        0.26        48.10        44.91         6.12         1.22        57.57 
TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 
       24.26        30.05        48.79        45.57        30.18        22.49 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 
        6.71        42.51        44.12         2.20        28.77        29.10 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 
       21.53        22.85        22.55         8.55        30.08        25.74 
TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
       24.69        33.01        29.49        29.82        25.91        25.08 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 
       23.80        21.60         2.24        20.98        18.31        20.52 
TCGA-36-2549 TCGA-36-2551 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 
        6.05        16.18        47.57        23.74        28.93        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 
       10.42        40.77         1.48        21.14         1.74        22.32 
TCGA-57-1992 TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 
       29.00        25.08       180.20        80.12        22.32       116.12 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 
       34.39         2.14         5.42        11.11        20.94        31.43 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
       18.54        27.88        28.47        48.79        44.84        35.80 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
        2.43        33.67        43.69         1.45         8.42         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1906 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 
       11.41        13.02        34.13        37.05        42.51        48.92 
TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
       56.61        43.43        15.75        38.17         2.01         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 
       14.50        17.98        30.64        39.85        30.64         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 
       45.96        45.40         4.80         4.77        51.72        71.74 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       61.64        58.39        60.62         6.48        76.87        20.68 
TCGA-61-2110 TCGA-61-2113 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-VG-A8LO 
       44.52        22.22        31.07         8.61        39.68         0.79 
TCGA-09-0364 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-10-0925 TCGA-10-0926 
       29.16        57.76        17.98        35.57        54.31        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 
       81.86        18.51        32.88        14.66         6.71        35.44 
TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
       36.92        19.99        20.91         6.21        24.59        44.55 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0751 TCGA-13-0755 
       39.58         2.73        12.39        31.20        55.17         2.50 
TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 
       11.38        11.54        38.01       111.78        61.84        56.71 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 
       58.65        40.24       118.42       107.28        63.09        20.35 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 
       69.73        83.34        87.48        45.99        43.86        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 
       35.31        13.61        68.94       153.37        66.67        92.42 
TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       95.15       102.84        43.36        71.74        66.15       134.04 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
      127.79        50.37       123.16       118.98        60.59       116.65 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 
       44.55        37.64       109.32        58.68        48.79        48.76 
TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       83.74        85.94        25.41 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.30               0.26 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            152.02             180.20 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            27.225             33.930 
[1] "0.3 - 152.0 (27.2)" "0.3 - 180.2 (33.9)"
[1] "hr=" "1.1"
D20V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  10Q GAIN MUTATED         2   104                1
  10Q GAIN WILD-TYPE       1   454                1
D20V3, multiclass
                  clus
vv                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  OMENTUM                         2                  1
  OVARY                         104                454
  PERITONEUM OVARY                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V4, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED   103   0
  10Q GAIN WILD-TYPE 438   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED    103    0
  10Q GAIN WILD-TYPE  438    5
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO               103                438
  YES                0                  5
[1] 2 2
[1] FALSE
D20V5, continuous
                    vv
clus                 R0 R1 R2 RX
  10Q GAIN MUTATED    3  6  0  1
  10Q GAIN WILD-TYPE 12 20  5  2
D20V6, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0                3                 12
  R1                6                 20
  R2                0                  5
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     2  58
  10Q GAIN WILD-TYPE   8 269
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2   58
  10Q GAIN WILD-TYPE    8  269
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO               58                269
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    36  36
  11P GAIN WILD-TYPE 192 295
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                72                487 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                36                295 
$`11P GAIN MUTATED`
TCGA-04-1343 TCGA-04-1346 TCGA-04-1350 TCGA-04-1361 TCGA-04-1362 TCGA-09-2043 
       11.87        65.52        63.98        32.52        44.32         6.18 
TCGA-09-2051 TCGA-13-1407 TCGA-13-1410 TCGA-13-1497 TCGA-13-1499 TCGA-13-2057 
       63.09        83.31        81.01       127.27       115.07        80.02 
TCGA-23-1021 TCGA-23-1024 TCGA-23-1026 TCGA-23-1029 TCGA-23-1030 TCGA-23-1109 
       47.54        15.39        26.83         8.81        29.13        51.35 
TCGA-23-1111 TCGA-23-1116 TCGA-23-1119 TCGA-23-2072 TCGA-23-2084 TCGA-23-2645 
        3.22        19.46       129.96        24.95        49.84         4.50 
TCGA-24-1434 TCGA-24-1471 TCGA-24-1548 TCGA-24-1551 TCGA-24-1556 TCGA-24-1564 
       18.67         1.18        16.21        51.91        70.62        25.87 
TCGA-24-1604 TCGA-24-1842 TCGA-24-1844 TCGA-24-1850 TCGA-24-1928 TCGA-24-2030 
       88.37         8.32         3.72         5.52        11.05        55.92 
TCGA-25-1312 TCGA-25-1321 TCGA-25-1322 TCGA-25-1635 TCGA-25-1877 TCGA-25-2400 
        1.02        33.96         2.99        52.04        24.00        42.02 
TCGA-29-1691 TCGA-29-1701 TCGA-29-1774 TCGA-29-1775 TCGA-29-1783 TCGA-30-1718 
       48.33        16.93        17.33        12.36         7.23        51.91 
TCGA-30-1855 TCGA-30-1857 TCGA-30-1859 TCGA-36-1574 TCGA-36-1576 TCGA-36-1578 
        2.47         0.26        48.10        22.55        30.08        27.85 
TCGA-42-2587 TCGA-59-2348 TCGA-59-2351 TCGA-61-1740 TCGA-61-1907 TCGA-61-1915 
       23.74       180.20       116.12         2.43        31.30        67.76 
TCGA-61-2097 TCGA-OY-A56P TCGA-09-0369 TCGA-10-0931 TCGA-13-0724 TCGA-13-0727 
       60.62        39.68        35.57        32.88         2.73        15.19 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 
       20.35        69.73       111.39        66.67        92.42       145.45 

$`11P GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1347 
       49.15         2.01        46.62         1.08        18.51        63.09 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1364 
       48.76        21.57        65.46         0.53        49.28        33.67 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 
       76.57       103.40        82.39        56.55        41.59        19.99 
TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 
        0.79        38.37       119.08        29.10        84.20        55.43 
TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 
       48.89        27.88        28.64        64.64        36.23        31.86 
TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       47.70        45.37         9.99        38.43        89.33        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 
       41.62        57.60        61.87        55.36        30.51        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 
        5.85         3.02         8.55        97.55         6.12        35.15 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 
        4.54       112.41        71.11        39.75        20.94        26.93 
TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1409 
       12.46        77.10        81.17        28.54        55.23        57.27 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
       17.46        32.35        54.64        87.06        61.71        29.42 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
      124.44        20.68        22.39        70.82        83.93        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1500 
      125.56        93.90        90.38         4.24        66.15        13.97 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       43.20        34.82        65.69        34.16        65.52        80.15 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 
       44.68        54.25        14.53        78.48        77.88        76.90 
TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
       65.52        70.45         8.42        23.05        25.94        26.20 
TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 
       72.20        27.52        25.38        19.10        16.70         2.93 
TCGA-20-1687 TCGA-23-1022 TCGA-23-1023 TCGA-23-1027 TCGA-23-1028 TCGA-23-1031 
        2.66        49.68        40.54        32.09        49.41        18.90 
TCGA-23-1032 TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 TCGA-23-1117 TCGA-23-1118 
        2.76        54.51        31.20        68.68        33.30        86.01 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 
        4.27         6.38        39.09        33.47        58.13         0.53 
TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 
      115.89        87.48        91.66        77.00         2.76         4.70 
TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
        7.63        11.64        21.80        41.56         7.66        22.32 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 
       54.12        63.55        47.41         6.31         6.38         7.82 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 
        7.99         7.86         0.76         6.25         6.02         5.95 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 
        5.36         4.83        17.39        28.37        18.64        43.53 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 
        8.55        72.92        12.46        45.14       105.99         9.11 
TCGA-24-1470 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1549 
        3.45        22.22        26.96        57.40        64.27        56.58 
TCGA-24-1550 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1557 TCGA-24-1558 
       41.06        41.39        58.09        88.50        39.88        19.53 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       44.09        45.50        47.70        10.26        17.23        90.15 
TCGA-24-1614 TCGA-24-1616 TCGA-24-1843 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 
       48.33        38.24         3.48         3.81         4.37        11.28 
TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 
        5.79         9.80        22.68        30.21        16.44        81.11 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 
        4.87       152.02        44.84        58.16        34.82       109.71 
TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 
       14.43        18.48        28.18        64.01        44.52        57.07 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       36.16         0.79         0.36        47.54        31.63        70.45 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 
       44.61         0.82        67.36        36.23        16.64        33.11 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 
       55.86        53.26        26.96        33.01        52.04        42.05 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1323 TCGA-25-1329 
        2.01        34.98        65.00        37.97        12.99        15.02 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 
       18.58        27.62        17.03        12.95        20.61        38.20 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 
        0.30        59.15        62.17        35.87        14.96        24.99 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 
       85.05        13.02        49.05         1.02        38.04         3.02 
TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 
       12.00        45.01        19.99         2.96        29.03        31.00 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 
       26.99        78.90        47.61       101.79        39.02        40.41 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1702 TCGA-29-1703 
       33.93        31.20        68.32        36.36        23.93        59.67 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 
       18.25        41.98        31.27        34.62        17.36        86.60 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 
       66.81        62.93        39.42        31.30        22.98        24.36 
TCGA-29-1771 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1784 
       22.55        11.84        12.30        14.93         8.38         5.36 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 
       36.30        86.17        65.00        62.47        45.11        13.84 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 
       42.25        21.47        11.47         9.76        35.77        38.07 
TCGA-30-1853 TCGA-30-1856 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 
       36.26        15.68        44.91        34.78         6.12        36.62 
TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 
        1.22        57.57        24.26        30.05        48.79        45.57 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 
       30.18        18.77        22.49         6.71        42.51        44.12 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1575 
        2.20        28.77        29.10        21.53        22.85         8.55 
TCGA-36-1577 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 
       25.74        24.23        24.69        35.05        33.01        29.49 
TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 
       29.82        25.91        25.08        23.80        21.60         2.24 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 
       20.98        18.31        20.52        14.17         6.05        16.18 
TCGA-36-2552 TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
       11.47        47.57        28.93        42.02        10.42        40.77 
TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 
        1.48        24.03        11.38        21.14         1.74        22.32 
TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2349 TCGA-59-2350 TCGA-59-2352 
       29.00        25.08        25.02        80.12        22.32         9.40 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 
       34.39         2.14         5.42        44.81        11.11         8.09 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 
       20.94        31.43        18.54        27.88         4.34        31.79 
TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1741 TCGA-61-1743 
       28.47        48.79        44.84        35.80        33.67        43.69 
TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 
        1.45         8.42         5.79        11.41        13.02         9.07 
TCGA-61-1906 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 
       34.13        37.05        42.51        48.92        56.61        43.43 
TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       15.75        38.17         2.01         5.52        14.50        17.98 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 
        4.01        30.64        39.85        30.64         1.18        45.96 
TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       45.40         4.80         4.77        51.72        71.74        61.64 
TCGA-61-2096 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       58.39        65.52        55.50         6.48        76.87        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       44.52       125.75        22.22         6.35        31.07         8.61 
TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 
       18.94         0.79         9.99        29.16         9.47        57.76 
TCGA-09-0367 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       17.98        54.31        25.91        81.86        18.51        34.19 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 
       14.66         6.71        35.44        36.92        19.99        20.91 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 
        6.21        24.59        44.55        39.58        12.39        31.20 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 
       17.82        55.17         2.50        11.18        11.38        11.54 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 
       38.01       111.78        61.84        56.71        58.65        40.24 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
      118.42       107.28        63.09        83.34        87.48        45.99 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
       51.02        43.86        35.28        35.31        13.61        68.94 
TCGA-13-0884 TCGA-13-0886 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 
      107.18       153.37        95.15       102.84        43.36        71.74 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       66.15       134.04        19.36       127.79        50.37       123.16 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
      118.98        60.59       116.65        44.55        37.64       109.32 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       58.68        84.53        48.79        48.76        83.74        85.94 
TCGA-13-2071 
       25.41 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.26               0.30 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            180.20             153.37 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             31.91              33.01 
[1] "0.3 - 180.2 (31.9)" "0.3 - 153.4 (33.0)"
[1] "hr=" "1.4"
D21V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  11P GAIN MUTATED         0    73                0
  11P GAIN WILD-TYPE       3   485                2
D21V3, multiclass
                  clus
vv                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  OMENTUM                         0                  3
  OVARY                          73                485
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V4, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    71   0
  11P GAIN WILD-TYPE 470   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     71    0
  11P GAIN WILD-TYPE  470    5
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                71                470
  YES                0                  5
[1] 2 2
[1] FALSE
D21V5, continuous
                    vv
clus                 R0 R1 R2 RX
  11P GAIN MUTATED    0  1  1  0
  11P GAIN WILD-TYPE 15 25  4  3
D21V6, multiclass
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 47 
        TCGA-3P-A9WA         TCGA-5X-AA5U         TCGA-04-1516 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-04-1644         TCGA-13-A5FT         TCGA-13-A5FU 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-24-2033         TCGA-29-2414         TCGA-29-2425 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-29-2427         TCGA-29-2428         TCGA-29-2429 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-29-2431         TCGA-29-2432         TCGA-29-2434 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-29-2436         TCGA-36-2529         TCGA-36-2530 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-36-2532         TCGA-36-2534         TCGA-36-2537 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-36-2538         TCGA-36-2540         TCGA-36-2542 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-36-2543         TCGA-36-2544         TCGA-36-2545 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-36-2547         TCGA-36-2548         TCGA-36-2549 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-36-2551         TCGA-36-2552         TCGA-42-2582 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-42-2588         TCGA-42-2589         TCGA-42-2590 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-42-2593         TCGA-57-1993         TCGA-59-2363 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-59-2372         TCGA-61-2612         TCGA-61-2613 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-61-2614         TCGA-OY-A56Q         TCGA-VG-A8LO 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-13-0807         TCGA-13-0911 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1  45
  11P GAIN WILD-TYPE   9 282
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   45
  11P GAIN WILD-TYPE    9  282
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO               45                282
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    44  63
  11Q GAIN WILD-TYPE 184 268
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
               107                452 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                63                268 
$`11Q GAIN MUTATED`
TCGA-04-1343 TCGA-04-1346 TCGA-04-1350 TCGA-04-1361 TCGA-04-1646 TCGA-04-1652 
       11.87        65.52        63.98        32.52        27.88        31.86 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1667 TCGA-09-1668 TCGA-13-1407 TCGA-13-1410 
        9.99        38.43        61.87        55.36        83.31        81.01 
TCGA-13-1412 TCGA-13-1484 TCGA-13-1497 TCGA-13-1499 TCGA-13-1506 TCGA-13-2057 
       32.35       124.44       127.27       115.07        34.16        80.02 
TCGA-20-1685 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1024 TCGA-23-1029 
       16.70         2.66        47.54        49.68        15.39         8.81 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1111 TCGA-23-1119 
       29.13        18.90         2.76        51.35         3.22       129.96 
TCGA-23-2072 TCGA-23-2084 TCGA-23-2643 TCGA-23-2645 TCGA-24-1427 TCGA-24-1431 
       24.95        49.84         4.70         4.50         4.83        18.64 
TCGA-24-1434 TCGA-24-1436 TCGA-24-1471 TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 
       18.67         8.55         1.18        16.21        56.58        51.91 
TCGA-24-1556 TCGA-24-1558 TCGA-24-1563 TCGA-24-1564 TCGA-24-1604 TCGA-24-1616 
       70.62        19.53        47.70        25.87        88.37        38.24 
TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 TCGA-24-1850 TCGA-24-1928 TCGA-24-2026 
        8.32         3.72         3.81         5.52        11.05        34.82 
TCGA-24-2027 TCGA-24-2033 TCGA-25-1312 TCGA-25-1322 TCGA-25-1630 TCGA-25-1631 
      109.71        18.48         1.02         2.99        38.20         0.30 
TCGA-25-1635 TCGA-25-1877 TCGA-25-1878 TCGA-25-2400 TCGA-29-1691 TCGA-29-1701 
       52.04        24.00        85.05        42.02        48.33        16.93 
TCGA-29-1702 TCGA-29-1763 TCGA-29-1764 TCGA-29-1774 TCGA-29-1783 TCGA-29-2425 
       23.93        66.81        62.93        17.33         7.23        65.00 
TCGA-29-2429 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1862 
       13.84        51.91         2.47        15.68         0.26         6.12 
TCGA-36-1574 TCGA-36-1576 TCGA-36-1578 TCGA-36-2551 TCGA-42-2587 TCGA-57-1584 
       22.55        30.08        27.85        16.18        23.74        21.14 
TCGA-59-2351 TCGA-61-1722 TCGA-61-1740 TCGA-61-1906 TCGA-61-1907 TCGA-61-1915 
      116.12         8.09         2.43        34.13        31.30        67.76 
TCGA-61-1918 TCGA-61-2097 TCGA-61-2109 TCGA-61-2612 TCGA-OY-A56P TCGA-VG-A8LO 
       15.75        60.62        20.68         6.35        39.68         0.79 
TCGA-09-0369 TCGA-10-0931 TCGA-13-0726 TCGA-13-0764 TCGA-13-0797 TCGA-13-0885 
       35.57        32.88        31.20        61.84        69.73       111.39 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 
       66.67        92.42       145.45        43.36        71.74 

$`11Q GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1347 
       49.15         2.01        46.62         1.08        18.51        63.09 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1362 
       48.76        21.57        65.46         0.53        49.28        44.32 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 
       33.67        76.57       103.40        82.39        56.55        41.59 
TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 
       19.99         0.79        38.37       119.08        29.10        84.20 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 
       55.43        48.89        28.64        64.64        36.23        47.70 
TCGA-04-1655 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 
       45.37        89.33        74.93        41.62        57.60        30.51 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 
       17.98         5.85         3.02         8.55        97.55         6.18 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
        6.12        35.15         4.54       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 
       39.75        20.94        26.93        12.46        77.10        81.17 
TCGA-13-1405 TCGA-13-1408 TCGA-13-1409 TCGA-13-1411 TCGA-13-1477 TCGA-13-1481 
       28.54        55.23        57.27        17.46        54.64        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 
       61.71        29.42        20.68        22.39        70.82        83.93 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 
       52.44       125.56        93.90        90.38         4.24        66.15 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1507 TCGA-13-1509 
       13.97        43.20        34.82        65.69        65.52        80.15 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 
       44.68        54.25        14.53        78.48        77.88        76.90 
TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
       65.52        70.45         8.42        23.05        25.94        26.20 
TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1686 TCGA-23-1023 
       72.20        27.52        25.38        19.10         2.93        40.54 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 
       26.83        32.09        49.41        54.51        31.20        68.68 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 
       19.46        33.30        86.01         4.27         6.38        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 
       33.47        58.13         0.53       115.89        87.48        91.66 
TCGA-23-2081 TCGA-23-2641 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
       77.00         2.76         7.63        11.64        21.80        41.56 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 
        7.66        22.32        54.12        63.55        47.41         6.31 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 
        6.38         7.82         7.99         7.86         0.76         6.25 
TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 TCGA-24-1435 
        6.02         5.95         5.36        17.39        28.37        43.53 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 
       72.92        12.46        45.14       105.99         9.11         3.45 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1550 TCGA-24-1552 
       22.22        26.96        57.40        64.27        41.06        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1557 TCGA-24-1560 TCGA-24-1562 TCGA-24-1565 
       58.09        88.50        39.88        44.09        45.50        10.26 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1614 TCGA-24-1843 TCGA-24-1846 TCGA-24-1847 
       17.23        90.15        48.33         3.48         4.37        11.28 
TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 
        5.79         9.80        22.68        30.21        16.44        81.11 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2029 TCGA-24-2030 
        4.87       152.02        44.84        58.16        14.43        55.92 
TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 
       28.18        64.01        44.52        57.07        36.16         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
        0.36        47.54        31.63        70.45        44.61         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 
       67.36        36.23        16.64        33.11        55.86        53.26 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
       26.96        33.01        52.04        42.05         2.01        34.98 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
       65.00        37.97        33.96        12.99        15.02        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1632 TCGA-25-1633 
       27.62        17.03        12.95        20.61        59.15        62.17 
TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 
       35.87        14.96        24.99        13.02        49.05         1.02 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2401 
       38.04         3.02        12.00        45.01        19.99         2.96 
TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 
       29.03        31.00        26.99        78.90        47.61       101.79 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
       39.02        40.41        33.93        31.20        68.32        36.36 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 
       59.67        18.25        41.98        31.27        34.62        17.36 
TCGA-29-1762 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 
       86.60        39.42        31.30        22.98        24.36        22.55 
TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1784 
       12.36        11.84        12.30        14.93         8.38         5.36 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2428 TCGA-29-2431 TCGA-29-2432 
       36.30        86.17        62.47        45.11        42.25        21.47 
TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1853 TCGA-30-1859 
       11.47         9.76        35.77        38.07        36.26        48.10 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 
       44.91        34.78        36.62         1.22        57.57        24.26 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 
       30.05        48.79        45.57        30.18        18.77        22.49 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 
        6.71        42.51        44.12         2.20        28.77        29.10 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1575 TCGA-36-1577 TCGA-36-1580 TCGA-36-1581 
       21.53        22.85         8.55        25.74        24.23        24.69 
TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
       35.05        33.01        29.49        29.82        25.91        25.08 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 
       23.80        21.60         2.24        20.98        18.31        20.52 
TCGA-36-2548 TCGA-36-2549 TCGA-36-2552 TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 
       14.17         6.05        11.47        47.57        28.93        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1585 
       10.42        40.77         1.48        24.03        11.38         1.74 
TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 
       22.32        29.00        25.08        25.02       180.20        80.12 
TCGA-59-2350 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 
       22.32         9.40        34.39         2.14         5.42        44.81 
TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 
       11.11        20.94        31.43        18.54        27.88         4.34 
TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1741 
       31.79        28.47        48.79        44.84        35.80        33.67 
TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 
       43.69         1.45         8.42         5.79        11.41        13.02 
TCGA-61-1904 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 
        9.07        37.05        42.51        48.92        56.61        43.43 
TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 
       38.17         2.01         5.52        14.50        17.98         4.01 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
       30.64        39.85        30.64         1.18        45.96        45.40 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 
        4.80         4.77        51.72        71.74        61.64        58.39 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 
       65.52        55.50         6.48        76.87        44.52       125.75 
TCGA-61-2113 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56Q TCGA-WR-A838 TCGA-09-0364 
       22.22        31.07         8.61        18.94         9.99        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 
        9.47        57.76        17.98        54.31        25.91        81.86 
TCGA-10-0928 TCGA-10-0930 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 
       18.51        34.19        14.66         6.71        35.44        36.92 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 
       19.99        20.91         6.21        24.59        44.55        39.58 
TCGA-13-0724 TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 
        2.73        12.39        15.19        17.82        55.17         2.50 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0766 
       11.18        11.38        11.54        38.01       111.78        56.71 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 
       58.65        40.24       118.42       107.28        63.09        20.35 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 
       83.34        87.48        45.99        51.02        43.86        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 TCGA-13-0889 
       35.31        13.61        68.94       107.18       153.37        95.15 
TCGA-13-0891 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 
      102.84        66.15       134.04        19.36       127.79        50.37 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
      123.16       118.98        60.59       116.65        44.55        37.64 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 
      109.32        58.68        84.53        48.79        48.76        83.74 
TCGA-13-0924 TCGA-13-2071 
       85.94        25.41 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.26               0.36 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            145.45             180.20 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             31.20              33.57 
[1] "0.3 - 145.4 (31.2)" "0.4 - 180.2 (33.6)"
[1] "hr=" "1"  
D22V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  11Q GAIN MUTATED         0   109                0
  11Q GAIN WILD-TYPE       3   449                2
D22V3, multiclass
                  clus
vv                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  OMENTUM                         0                  3
  OVARY                         109                449
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V4, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED   106   0
  11Q GAIN WILD-TYPE 435   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED    106    0
  11Q GAIN WILD-TYPE  435    5
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO               106                435
  YES                0                  5
[1] 2 2
[1] FALSE
D22V5, continuous
                    vv
clus                 R0 R1 R2 RX
  11Q GAIN MUTATED    0  6  2  0
  11Q GAIN WILD-TYPE 15 20  3  3
D22V6, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0                0                 15
  R1                6                 20
  R2                2                  3
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     0  64
  11Q GAIN WILD-TYPE  10 263
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0   64
  11Q GAIN WILD-TYPE   10  263
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               64                263
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    97 148
  12P GAIN WILD-TYPE 131 183
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               245                314 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               148                183 
$`12P GAIN MUTATED`
TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1341 TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 
       11.87        41.00         1.08        18.51        65.52        63.09 
TCGA-04-1351 TCGA-04-1356 TCGA-04-1362 TCGA-04-1371 TCGA-04-1516 TCGA-04-1517 
       65.46        49.28        44.32        82.39        41.59        19.99 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1646 TCGA-04-1652 
       38.37       119.08        29.10        84.20        27.88        31.86 
TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 
       45.37         9.99        38.43        55.36        17.98         5.85 
TCGA-09-1674 TCGA-09-2043 TCGA-09-2049 TCGA-09-2051 TCGA-09-2053 TCGA-13-1407 
        8.55         6.18       112.41        63.09        39.75        83.31 
TCGA-13-1411 TCGA-13-1481 TCGA-13-1484 TCGA-13-1485 TCGA-13-1489 TCGA-13-1495 
       17.46        87.06       124.44        20.68        83.93        90.38 
TCGA-13-1496 TCGA-13-1499 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-2057 
        4.24       115.07        34.82        65.69        34.16        80.02 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FU TCGA-20-1682 
       78.48        77.88        76.90        65.52         8.42        27.52 
TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 TCGA-23-1024 TCGA-23-1030 TCGA-23-1032 
       16.70         2.93        47.54        15.39        29.13         2.76 
TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 TCGA-23-1118 TCGA-23-1124 TCGA-23-1809 
        3.22        68.68        19.46        86.01        58.13         0.53 
TCGA-23-2079 TCGA-23-2643 TCGA-23-2645 TCGA-24-0982 TCGA-24-1418 TCGA-24-1422 
       91.66         4.70         4.50        22.32         7.99         0.76 
TCGA-24-1424 TCGA-24-1427 TCGA-24-1430 TCGA-24-1434 TCGA-24-1436 TCGA-24-1464 
        6.02         4.83        28.37        18.67         8.55        12.46 
TCGA-24-1466 TCGA-24-1469 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 
       45.14         9.11        22.22        26.96        57.40        64.27 
TCGA-24-1548 TCGA-24-1553 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1563 
       16.21        58.09        39.88        19.53        44.09        47.70 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 
       25.87        10.26        17.23        88.37        48.33        38.24 
TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 
        8.32         3.72         3.81        11.28         5.52         9.80 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2033 TCGA-24-2038 
       11.05        81.11         4.87       152.02        18.48        44.52 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2293 
       36.16         0.79        44.61         0.82        67.36        16.64 
TCGA-24-2295 TCGA-25-1312 TCGA-25-1313 TCGA-25-1315 TCGA-25-1318 TCGA-25-1321 
       33.11         1.02        26.96        52.04        34.98        33.96 
TCGA-25-1323 TCGA-25-1626 TCGA-25-1627 TCGA-25-1630 TCGA-25-1634 TCGA-25-1635 
       12.99        17.03        12.95        38.20        35.87        52.04 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2392 
       14.96        24.99        24.00        85.05        13.02         1.02 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 TCGA-25-2400 TCGA-29-1690 TCGA-29-1695 
       38.04         3.02        45.01        42.02        47.61        40.41 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1702 TCGA-29-1710 TCGA-29-1761 TCGA-29-1763 
       68.32        36.36        23.93        31.27        17.36        66.81 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1774 TCGA-29-1775 TCGA-29-1777 
       39.42        31.30        22.98        17.33        12.36        12.30 
TCGA-29-1778 TCGA-29-1783 TCGA-29-1784 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 
       14.93         7.23         5.36        86.17        65.00        45.11 
TCGA-29-2431 TCGA-29-A5NZ TCGA-30-1856 TCGA-30-1859 TCGA-30-1866 TCGA-30-1867 
       42.25        35.77        15.68        48.10        36.62         1.22 
TCGA-30-1887 TCGA-30-1891 TCGA-31-1950 TCGA-31-1955 TCGA-31-1959 TCGA-36-1569 
       24.26        30.05        18.77        42.51         2.20        29.10 
TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1580 TCGA-36-2529 TCGA-36-2543 
       22.85         8.55        30.08        24.23        35.05         2.24 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-57-1582 TCGA-57-1583 
       20.52        14.17        16.18        11.47        24.03        11.38 
TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2351 TCGA-59-2352 
       22.32        25.08        25.02       180.20       116.12         9.40 
TCGA-59-2363 TCGA-59-2372 TCGA-61-1722 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 
        5.42        44.81         8.09        27.88         4.34        31.79 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1900 TCGA-61-1904 
        2.43        33.67        43.69         1.45         5.79         9.07 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1915 TCGA-61-1917 TCGA-61-2002 TCGA-61-2009 
       34.13        31.30        67.76        43.43        17.98        39.85 
TCGA-61-2012 TCGA-61-2097 TCGA-61-2111 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       30.64        60.62       125.75         6.35        31.07         8.61 
TCGA-OY-A56P TCGA-OY-A56Q TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 
       39.68        18.94         9.99        29.16         9.47        57.76 
TCGA-09-0367 TCGA-09-0369 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       17.98        35.57        25.91        81.86        18.51        34.19 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0938 TCGA-13-0717 TCGA-13-0723 TCGA-13-0727 
       32.88        14.66        20.91        24.59        39.58        15.19 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0760 TCGA-13-0762 TCGA-13-0764 
       17.82        55.17        11.18        11.54       111.78        61.84 
TCGA-13-0792 TCGA-13-0794 TCGA-13-0795 TCGA-13-0800 TCGA-13-0802 TCGA-13-0883 
      118.42        63.09        20.35        87.48        51.02        68.94 
TCGA-13-0884 TCGA-13-0888 TCGA-13-0890 TCGA-13-0899 TCGA-13-0901 TCGA-13-0904 
      107.18        92.42       145.45        66.15        19.36        50.37 
TCGA-13-0906 TCGA-13-0912 TCGA-13-0920 TCGA-13-0923 TCGA-13-2071 
      118.98        37.64        48.79        83.74        25.41 

$`12P GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 
       13.81        20.52        43.92         1.81        49.15         2.01 
TCGA-04-1338 TCGA-04-1343 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1353 
       46.62        11.87        48.76        21.57        63.98         0.53 
TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 TCGA-04-1519 
       32.52        33.67        76.57       103.40        56.55         0.79 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 
       55.43        48.89        28.64        64.64        36.23        47.70 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 
       89.33        74.93        41.62        57.60        61.87        30.51 
TCGA-09-1673 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 
        3.02        97.55         6.12        35.15         4.54        71.11 
TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
       20.94        26.93        12.46        77.10        81.17        28.54 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 
       55.23        57.27        81.01        32.35        54.64        61.71 
TCGA-13-1483 TCGA-13-1487 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       29.42        22.39        70.82        52.44       125.56        93.90 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1507 TCGA-13-1509 
      127.27        66.15        13.97        43.20        65.52        80.15 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 
       44.68        54.25        14.53        70.45        23.05        25.94 
TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 TCGA-20-1687 TCGA-23-1022 
       26.20        72.20        25.38        19.10         2.66        49.68 
TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1031 
       40.54        26.83        32.09        49.41         8.81        18.90 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 TCGA-23-1117 TCGA-23-1119 TCGA-23-1120 
       51.35        54.51        31.20        33.30       129.96         4.27 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 
        6.38        39.09        33.47        24.95       115.89        87.48 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 
       77.00        49.84         2.76         7.63        11.64        21.80 
TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 
       41.56         7.66        54.12        63.55        47.41         6.31 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 
        6.38         7.82         7.86         6.25         5.95         5.36 
TCGA-24-1428 TCGA-24-1431 TCGA-24-1435 TCGA-24-1463 TCGA-24-1467 TCGA-24-1470 
       17.39        18.64        43.53        72.92       105.99         3.45 
TCGA-24-1471 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 
        1.18        56.58        41.06        51.91        41.39        88.50 
TCGA-24-1556 TCGA-24-1562 TCGA-24-1603 TCGA-24-1843 TCGA-24-1846 TCGA-24-1849 
       70.62        45.50        90.15         3.48         4.37         5.79 
TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 
       22.68        30.21        16.44        44.84        58.16        34.82 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 TCGA-24-2254 
      109.71        14.43        55.92        28.18        64.01        57.07 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2290 TCGA-24-2297 
        0.36        47.54        31.63        70.45        36.23        55.86 
TCGA-24-2298 TCGA-25-1314 TCGA-25-1316 TCGA-25-1317 TCGA-25-1319 TCGA-25-1320 
       53.26        33.01        42.05         2.01        65.00        37.97 
TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1628 TCGA-25-1631 
        2.99        15.02        18.58        27.62        20.61         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-2391 TCGA-25-2397 TCGA-25-2399 TCGA-25-2401 
       59.15        62.17        49.05        12.00        19.99         2.96 
TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1691 TCGA-29-1693 
       29.03        31.00        26.99        78.90        48.33       101.79 
TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 
       39.02        33.93        31.20        16.93        59.67        18.25 
TCGA-29-1707 TCGA-29-1711 TCGA-29-1762 TCGA-29-1764 TCGA-29-1770 TCGA-29-1771 
       41.98        34.62        86.60        62.93        24.36        22.55 
TCGA-29-1776 TCGA-29-1781 TCGA-29-1785 TCGA-29-2427 TCGA-29-2429 TCGA-29-2432 
       11.84         8.38        36.30        62.47        13.84        21.47 
TCGA-29-2434 TCGA-29-2436 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 
       11.47         9.76        38.07        51.91        36.26         2.47 
TCGA-30-1857 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1880 TCGA-30-1892 
        0.26        44.91        34.78         6.12        57.57        48.79 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 TCGA-31-1956 TCGA-36-1568 
       45.57        30.18        22.49         6.71        44.12        28.77 
TCGA-36-1570 TCGA-36-1574 TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 TCGA-36-2530 
       21.53        22.55        25.74        27.85        24.69        33.01 
TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 
       29.49        29.82        25.91        25.08        23.80        21.60 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2549 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
       20.98        18.31         6.05        47.57        23.74        28.93 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1584 TCGA-57-1585 
       42.02        10.42        40.77         1.48        21.14         1.74 
TCGA-57-1992 TCGA-59-2349 TCGA-59-2350 TCGA-59-2354 TCGA-59-2355 TCGA-61-1721 
       29.00        80.12        22.32        34.39         2.14        11.11 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       20.94        31.43        18.54        28.47        48.79        44.84 
TCGA-61-1738 TCGA-61-1899 TCGA-61-1901 TCGA-61-1903 TCGA-61-1910 TCGA-61-1911 
       35.80         8.42        11.41        13.02        37.05        42.51 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
       48.92        56.61        15.75        38.17         2.01         5.52 
TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
       14.50         4.01        30.64         1.18        45.96        45.40 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 
        4.80         4.77        51.72        71.74        61.64        58.39 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       65.52        55.50         6.48        76.87        20.68        44.52 
TCGA-61-2113 TCGA-VG-A8LO TCGA-10-0925 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 
       22.22         0.79        54.31         6.71        35.44        36.92 
TCGA-10-0937 TCGA-13-0714 TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 
       19.99         6.21        44.55         2.73        12.39        31.20 
TCGA-13-0755 TCGA-13-0758 TCGA-13-0761 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 
        2.50        11.38        38.01        56.71        58.65        40.24 
TCGA-13-0793 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 
      107.28        69.73        83.34        45.99        43.86        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 
       35.31        13.61       111.39       153.37        66.67        95.15 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0903 TCGA-13-0905 
      102.84        43.36        71.74       134.04       127.79       123.16 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
       60.59       116.65        44.55       109.32        58.68        84.53 
TCGA-13-0921 TCGA-13-0924 
       48.76        85.94 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.53               0.26 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            180.20             153.37 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            29.160             34.985 
[1] "0.5 - 180.2 (29.2)" "0.3 - 153.4 (35.0)"
[1] "hr=" "1.1"
D23V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  12P GAIN MUTATED         2   245                2
  12P GAIN WILD-TYPE       1   313                0
D23V3, multiclass
                  clus
vv                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  OMENTUM                         2                  1
  OVARY                         245                313
  PERITONEUM OVARY                2                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V4, binary
                    cls
clus                   0   1
  12P GAIN MUTATED   238   3
  12P GAIN WILD-TYPE 303   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED    238    3
  12P GAIN WILD-TYPE  303    2
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO               238                303
  YES                3                  2
[1] 2 2
[1] FALSE
D23V5, continuous
                    vv
clus                 R0 R1 R2 RX
  12P GAIN MUTATED    8 11  2  1
  12P GAIN WILD-TYPE  7 15  3  2
D23V6, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0                8                  7
  R1               11                 15
  R2                2                  3
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     2 130
  12P GAIN WILD-TYPE   8 197
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2  130
  12P GAIN WILD-TYPE    8  197
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO              130                197
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    68 100
  12Q GAIN WILD-TYPE 160 231
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               168                391 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               100                231 
$`12Q GAIN MUTATED`
TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1337 TCGA-04-1341 TCGA-04-1342 TCGA-04-1346 
       11.87        41.00         2.01         1.08        18.51        65.52 
TCGA-04-1347 TCGA-04-1362 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1646 
       63.09        44.32        38.37       119.08        29.10        27.88 
TCGA-04-1652 TCGA-04-1655 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 TCGA-09-2048 
       31.86        45.37        55.36        17.98         5.85         4.54 
TCGA-09-2049 TCGA-09-2053 TCGA-13-1407 TCGA-13-1481 TCGA-13-1484 TCGA-13-1485 
      112.41        39.75        83.31        87.06       124.44        20.68 
TCGA-13-1496 TCGA-13-1499 TCGA-13-1505 TCGA-13-1506 TCGA-13-2057 TCGA-13-2060 
        4.24       115.07        65.69        34.16        80.02        77.88 
TCGA-13-2061 TCGA-13-2065 TCGA-20-1682 TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 
       76.90        65.52        27.52        16.70         2.93        47.54 
TCGA-23-1032 TCGA-23-1111 TCGA-23-1116 TCGA-23-1809 TCGA-23-2643 TCGA-23-2645 
        2.76         3.22        19.46         0.53         4.70         4.50 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1424 TCGA-24-1427 TCGA-24-1434 TCGA-24-1464 
        7.99         7.86         6.02         4.83        18.67        12.46 
TCGA-24-1466 TCGA-24-1469 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 
       45.14         9.11        22.22        26.96        57.40        16.21 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 
       39.88        19.53        44.09        47.70        25.87        10.26 
TCGA-24-1616 TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 TCGA-24-1850 TCGA-24-1928 
       38.24         3.72         3.81        11.28         5.52        11.05 
TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2033 TCGA-24-2038 TCGA-24-2260 
       81.11         4.87       152.02        18.48        44.52        36.16 
TCGA-24-2261 TCGA-24-2281 TCGA-24-2288 TCGA-24-2293 TCGA-24-2295 TCGA-25-1312 
        0.79        44.61         0.82        16.64        33.11         1.02 
TCGA-25-1313 TCGA-25-1315 TCGA-25-1318 TCGA-25-1321 TCGA-25-1323 TCGA-25-1627 
       26.96        52.04        34.98        33.96        12.99        12.95 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-2392 TCGA-25-2398 
       35.87        52.04        14.96        24.99         1.02        45.01 
TCGA-29-1690 TCGA-29-1695 TCGA-29-1698 TCGA-29-1699 TCGA-29-1710 TCGA-29-1761 
       47.61        40.41        68.32        36.36        31.27        17.36 
TCGA-29-1763 TCGA-29-1766 TCGA-29-1768 TCGA-29-1774 TCGA-29-1778 TCGA-29-1783 
       66.81        39.42        31.30        17.33        14.93         7.23 
TCGA-29-1784 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2431 TCGA-29-A5NZ 
        5.36        86.17        65.00        45.11        42.25        35.77 
TCGA-30-1856 TCGA-30-1859 TCGA-30-1866 TCGA-30-1867 TCGA-31-1950 TCGA-31-1955 
       15.68        48.10        36.62         1.22        18.77        42.51 
TCGA-31-1959 TCGA-36-1571 TCGA-36-1575 TCGA-36-2529 TCGA-36-2543 TCGA-36-2547 
        2.20        22.85         8.55        35.05         2.24        20.52 
TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-57-1583 TCGA-57-1586 TCGA-57-1993 
       14.17        16.18        11.47        11.38        22.32        25.08 
TCGA-57-1994 TCGA-59-2348 TCGA-59-2351 TCGA-59-2352 TCGA-59-2372 TCGA-61-1730 
       25.02       180.20       116.12         9.40        44.81         4.34 
TCGA-61-1733 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1906 TCGA-61-1907 
       31.79         2.43        33.67        43.69        34.13        31.30 
TCGA-61-2002 TCGA-61-2009 TCGA-61-2012 TCGA-61-2088 TCGA-61-2097 TCGA-61-2102 
       17.98        39.85        30.64         4.77        60.62         6.48 
TCGA-61-2111 TCGA-61-2613 TCGA-61-2614 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 
      125.75        31.07         8.61         9.47        57.76        17.98 
TCGA-09-0369 TCGA-10-0926 TCGA-10-0927 TCGA-10-0930 TCGA-10-0936 TCGA-13-0717 
       35.57        25.91        81.86        34.19        36.92        24.59 
TCGA-13-0723 TCGA-13-0727 TCGA-13-0762 TCGA-13-0795 TCGA-13-0800 TCGA-13-0804 
       39.58        15.19       111.78        20.35        87.48        35.28 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0888 TCGA-13-0890 TCGA-13-0912 TCGA-13-0920 
       68.94       107.18        92.42       145.45        37.64        48.79 

$`12Q GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 
       13.81        20.52        43.92         1.81        49.15        46.62 
TCGA-04-1343 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 
       11.87        48.76        21.57        63.98        65.46         0.53 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 
       49.28        32.52        33.67        76.57       103.40        82.39 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1542 TCGA-04-1638 
       56.55        41.59        19.99         0.79        84.20        55.43 
TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-09-1659 
       48.89        28.64        64.64        36.23        47.70         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 
       38.43        89.33        74.93        41.62        57.60        61.87 
TCGA-09-1669 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 
       30.51         3.02         8.55        97.55         6.18         6.12 
TCGA-09-2045 TCGA-09-2050 TCGA-09-2051 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 
       35.15        71.11        63.09        20.94        26.93        12.46 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
       77.10        81.17        28.54        55.23        57.27        81.01 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1487 
       17.46        32.35        54.64        61.71        29.42        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       70.82        83.93        52.44       125.56        93.90        90.38 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1507 
      127.27        66.15        13.97        43.20        34.82        65.52 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-A5FT 
       80.15        44.68        54.25        14.53        78.48        70.45 
TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 
        8.42        23.05        25.94        26.20        72.20        25.38 
TCGA-20-1684 TCGA-20-1687 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
       19.10         2.66        49.68        40.54        15.39        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1109 
       32.09        49.41         8.81        29.13        18.90        51.35 
TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 
       54.51        31.20        68.68        33.30        86.01       129.96 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 
        4.27         6.38        39.09        33.47        58.13        24.95 
TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
      115.89        87.48        91.66        77.00        49.84         2.76 
TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
        7.63        11.64        21.80        41.56         7.66        22.32 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 
       54.12        63.55        47.41         6.31         6.38         7.82 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 
        0.76         6.25         5.95         5.36        17.39        28.37 
TCGA-24-1431 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1467 TCGA-24-1470 
       18.64        43.53         8.55        72.92       105.99         3.45 
TCGA-24-1471 TCGA-24-1546 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
        1.18        64.27        56.58        41.06        51.91        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1562 TCGA-24-1567 TCGA-24-1603 
       58.09        88.50        70.62        45.50        17.23        90.15 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1842 TCGA-24-1843 TCGA-24-1846 TCGA-24-1849 
       88.37        48.33         8.32         3.48         4.37         5.79 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-2023 TCGA-24-2024 
        9.80        22.68        30.21        16.44        44.84        58.16 
TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 
       34.82       109.71        14.43        55.92        28.18        64.01 
TCGA-24-2254 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2289 
       57.07         0.36        47.54        31.63        70.45        67.36 
TCGA-24-2290 TCGA-24-2297 TCGA-24-2298 TCGA-25-1314 TCGA-25-1316 TCGA-25-1317 
       36.23        55.86        53.26        33.01        42.05         2.01 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       65.00        37.97         2.99        15.02        18.58        27.62 
TCGA-25-1626 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
       17.03        20.61        38.20         0.30        59.15        62.17 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 
       24.00        85.05        13.02        49.05        38.04         3.02 
TCGA-25-2397 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 
       12.00        19.99        42.02         2.96        29.03        31.00 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 
       26.99        78.90        48.33       101.79        39.02        33.93 
TCGA-29-1697 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
       31.20        16.93        23.93        59.67        18.25        41.98 
TCGA-29-1711 TCGA-29-1762 TCGA-29-1764 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 
       34.62        86.60        62.93        22.98        24.36        22.55 
TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1785 TCGA-29-2427 
       12.36        11.84        12.30         8.38        36.30        62.47 
TCGA-29-2429 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-30-1714 TCGA-30-1718 
       13.84        21.47        11.47         9.76        38.07        51.91 
TCGA-30-1853 TCGA-30-1855 TCGA-30-1857 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 
       36.26         2.47         0.26        44.91        34.78         6.12 
TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 
       57.57        24.26        30.05        48.79        45.57        30.18 
TCGA-31-1951 TCGA-31-1953 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
       22.49         6.71        44.12        28.77        29.10        21.53 
TCGA-36-1574 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 
       22.55        30.08        25.74        27.85        24.23        24.69 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       33.01        29.49        29.82        25.91        25.08        23.80 
TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 TCGA-36-2549 TCGA-42-2582 TCGA-42-2587 
       21.60        20.98        18.31         6.05        47.57        23.74 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 
       28.93        42.02        10.42        40.77         1.48        24.03 
TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 TCGA-59-2349 TCGA-59-2350 TCGA-59-2354 
       21.14         1.74        29.00        80.12        22.32        34.39 
TCGA-59-2355 TCGA-59-2363 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
        2.14         5.42        11.11         8.09        20.94        31.43 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
       18.54        27.88        28.47        48.79        44.84        35.80 
TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 
        1.45         8.42         5.79        11.41        13.02         9.07 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 
       37.05        42.51        48.92        56.61        67.76        43.43 
TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 
       15.75        38.17         2.01         5.52        14.50         4.01 
TCGA-61-2008 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 
       30.64         1.18        45.96        45.40         4.80        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 
       71.74        61.64        58.39        65.52        55.50        76.87 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2113 TCGA-61-2612 TCGA-OY-A56P TCGA-OY-A56Q 
       20.68        44.52        22.22         6.35        39.68        18.94 
TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 TCGA-10-0925 TCGA-10-0928 TCGA-10-0931 
        0.79         9.99        29.16        54.31        18.51        32.88 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
       14.66         6.71        35.44        19.99        20.91         6.21 
TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0730 TCGA-13-0751 
       44.55         2.73        12.39        31.20        17.82        55.17 
TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 
        2.50        11.18        11.38        11.54        38.01        61.84 
TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 
       56.71        58.65        40.24       118.42       107.28        63.09 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0805 
       69.73        83.34        45.99        51.02        43.86        35.31 
TCGA-13-0807 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0891 
       13.61       111.39       153.37        66.67        95.15       102.84 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       43.36        71.74        66.15       134.04        19.36       127.79 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       50.37       123.16       118.98        60.59       116.65        44.55 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
      109.32        58.68        84.53        48.76        83.74        85.94 
TCGA-13-2071 
       25.41 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.53               0.26 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            180.20             153.37 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            30.855             33.930 
[1] "0.5 - 180.2 (30.9)" "0.3 - 153.4 (33.9)"
[1] "hr=" "1.2"
D24V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  12Q GAIN MUTATED         2   167                2
  12Q GAIN WILD-TYPE       1   391                0
D24V3, multiclass
                  clus
vv                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  OMENTUM                         2                  1
  OVARY                         167                391
  PERITONEUM OVARY                2                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V4, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED   162   3
  12Q GAIN WILD-TYPE 379   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED    162    3
  12Q GAIN WILD-TYPE  379    2
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO               162                379
  YES                3                  2
[1] 2 2
[1] FALSE
D24V5, continuous
                    vv
clus                 R0 R1 R2 RX
  12Q GAIN MUTATED    6 10  0  0
  12Q GAIN WILD-TYPE  9 16  5  3
D24V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0                6                  9
  R1               10                 16
  R2                0                  5
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     1  84
  12Q GAIN WILD-TYPE   9 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1   84
  12Q GAIN WILD-TYPE    9  243
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO               84                243
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    21  38
  13Q GAIN WILD-TYPE 207 293
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                59                500 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                38                293 
$`13Q GAIN MUTATED`
TCGA-5X-AA5U TCGA-04-1337 TCGA-04-1351 TCGA-04-1371 TCGA-09-2049 TCGA-13-1407 
       11.87         2.01        65.46        82.39       112.41        83.31 
TCGA-13-1408 TCGA-13-1481 TCGA-13-1484 TCGA-13-1506 TCGA-23-1030 TCGA-23-1109 
       55.23        87.06       124.44        34.16        29.13        51.35 
TCGA-23-2072 TCGA-24-0970 TCGA-24-1418 TCGA-24-1422 TCGA-24-1434 TCGA-24-1467 
       24.95        11.64         7.99         0.76        18.67       105.99 
TCGA-24-1471 TCGA-24-1930 TCGA-25-1312 TCGA-25-1317 TCGA-25-1320 TCGA-25-1323 
        1.18        81.11         1.02         2.01        37.97        12.99 
TCGA-25-1626 TCGA-25-1870 TCGA-25-2398 TCGA-29-1695 TCGA-29-1710 TCGA-29-1761 
       17.03        14.96        45.01        40.41        31.27        17.36 
TCGA-29-1770 TCGA-29-1783 TCGA-29-2425 TCGA-29-2428 TCGA-30-1714 TCGA-30-1718 
       24.36         7.23        65.00        45.11        38.07        51.91 
TCGA-30-1853 TCGA-30-1880 TCGA-36-1576 TCGA-36-2552 TCGA-42-2591 TCGA-57-1993 
       36.26        57.57        30.08        11.47        40.77        25.08 
TCGA-59-2355 TCGA-61-1911 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2098 
        2.14        42.51         4.01        30.64        39.85        65.52 
TCGA-61-2102 TCGA-09-0364 TCGA-09-0365 TCGA-09-0369 TCGA-10-0933 TCGA-10-0935 
        6.48        29.16         9.47        35.57        14.66        35.44 
TCGA-13-0727 TCGA-13-0757 TCGA-13-0802 TCGA-13-0899 TCGA-13-0921 
       15.19        11.18        51.02        66.15        48.76 

$`13Q GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 
       13.81        20.52        43.92        41.00         1.81        49.15 
TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 
       46.62         1.08        18.51        11.87        65.52        63.09 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 
       48.76        21.57        63.98         0.53        49.28        32.52 
TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 TCGA-04-1516 
       44.32        33.67        76.57       103.40        56.55        41.59 
TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 
       19.99         0.79        38.37       119.08        29.10        84.20 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 
       55.43        48.89        27.88        28.64        64.64        36.23 
TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       31.86        47.70        45.37         9.99        38.43        89.33 
TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 
       74.93        41.62        57.60        61.87        55.36        30.51 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 
       17.98         5.85         3.02         8.55        97.55         6.18 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 
        6.12        35.15         4.54        71.11        63.09        39.75 
TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
       20.94        26.93        12.46        77.10        81.17        28.54 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 
       57.27        81.01        17.46        32.35        54.64        61.71 
TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
       29.42        20.68        22.39        70.82        83.93        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
      125.56        93.90        90.38         4.24       127.27        66.15 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1507 
      115.07        13.97        43.20        34.82        65.69        65.52 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 
       80.15        44.68        54.25        14.53        80.02        78.48 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
       77.88        76.90        65.52        70.45         8.42        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 
       25.94        26.20        72.20        27.52        25.38        19.10 
TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 
       16.70         2.93         2.66        47.54        49.68        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1031 
       15.39        26.83        32.09        49.41         8.81        18.90 
TCGA-23-1032 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 
        2.76        54.51         3.22        31.20        68.68        19.46 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 
       33.30        86.01       129.96         4.27         6.38        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 
       33.47        58.13         0.53       115.89        87.48        91.66 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 
       77.00        49.84         2.76         4.70         4.50         7.63 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 
       21.80        41.56         7.66        22.32        54.12        63.55 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 TCGA-24-1423 
       47.41         6.31         6.38         7.82         7.86         6.25 
TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 
        6.02         5.95         5.36         4.83        17.39        28.37 
TCGA-24-1431 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 
       18.64        43.53         8.55        72.92        12.46        45.14 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 
        9.11         3.45        22.22        26.96        57.40        64.27 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 
       16.21        56.58        41.06        51.91        41.39        58.09 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 
       88.50        70.62        39.88        19.53        44.09        45.50 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 
       47.70        25.87        10.26        17.23        90.15        88.37 
TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 
       48.33        38.24         8.32         3.48         3.72         3.81 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 
        4.37        11.28         5.79         5.52         9.80        22.68 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 
       30.21        16.44        11.05         4.87       152.02        44.84 
TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 
       58.16        34.82       109.71        14.43        55.92        18.48 
TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 
       28.18        64.01        44.52        57.07        36.16         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
        0.36        47.54        31.63        70.45        44.61         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 
       67.36        36.23        16.64        33.11        55.86        53.26 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1318 TCGA-25-1319 
       26.96        33.01        52.04        42.05        34.98        65.00 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1627 
       33.96         2.99        15.02        18.58        27.62        12.95 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
       20.61        38.20         0.30        59.15        62.17        35.87 
TCGA-25-1635 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 
       52.04        24.99        24.00        85.05        13.02        49.05 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 TCGA-25-2400 
        1.02        38.04         3.02        12.00        19.99        42.02 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 
        2.96        29.03        31.00        26.99        78.90        47.61 
TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 
       48.33       101.79        39.02        33.93        31.20        68.32 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
       36.36        16.93        23.93        59.67        18.25        41.98 
TCGA-29-1711 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 
       34.62        86.60        66.81        62.93        39.42        31.30 
TCGA-29-1769 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 
       22.98        22.55        17.33        12.36        11.84        12.30 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 
       14.93         8.38         5.36        36.30        86.17        62.47 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ 
       13.84        42.25        21.47        11.47         9.76        35.77 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 
        2.47        15.68         0.26        48.10        44.91        34.78 
TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 
        6.12        36.62         1.22        24.26        30.05        48.79 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 
       45.57        30.18        18.77        22.49         6.71        42.51 
TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 
       44.12         2.20        28.77        29.10        21.53        22.85 
TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 
       22.55         8.55        25.74        27.85        24.23        24.69 
TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
       35.05        33.01        29.49        29.82        25.91        25.08 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 
       23.80        21.60         2.24        20.98        18.31        20.52 
TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
       14.17         6.05        16.18        47.57        23.74        28.93 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 
       42.02        10.42         1.48        24.03        11.38        21.14 
TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 
        1.74        22.32        29.00        25.02       180.20        80.12 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 TCGA-59-2372 
       22.32       116.12         9.40        34.39         5.42        44.81 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 
       11.11         8.09        20.94        31.43        18.54        27.88 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
        4.34        31.79        28.47        48.79        44.84        35.80 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
        2.43        33.67        43.69         1.45         8.42         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 
       11.41        13.02         9.07        34.13        31.30        37.05 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 
       48.92        56.61        67.76        43.43        15.75        38.17 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2012 TCGA-61-2016 
        2.01         5.52        14.50        17.98        30.64         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 
       45.96        45.40         4.80         4.77        51.72        71.74 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2101 TCGA-61-2104 TCGA-61-2109 
       61.64        58.39        60.62        55.50        76.87        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       44.52       125.75        22.22         6.35        31.07         8.61 
TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0366 TCGA-09-0367 
       39.68        18.94         0.79         9.99        57.76        17.98 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       54.31        25.91        81.86        18.51        34.19        32.88 
TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
        6.71        36.92        19.99        20.91         6.21        24.59 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0730 
       44.55        39.58         2.73        12.39        31.20        17.82 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 
       55.17         2.50        11.38        11.54        38.01       111.78 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       61.84        56.71        58.65        40.24       118.42       107.28 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
       63.09        20.35        69.73        83.34        87.48        45.99 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
       43.86        35.28        35.31        13.61        68.94       107.18 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 
      111.39       153.37        66.67        92.42        95.15       145.45 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
      102.84        43.36        71.74       134.04        19.36       127.79 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       50.37       123.16       118.98        60.59       116.65        44.55 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 
       37.64       109.32        58.68        84.53        48.79        83.74 
TCGA-13-0924 TCGA-13-2071 
       85.94        25.41 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.76               0.26 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            124.44             180.20 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            31.270             32.945 
[1] "0.8 - 124.4 (31.3)" "0.3 - 180.2 (32.9)"
[1] "hr=" "1.2"
D25V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  13Q GAIN MUTATED         0    59                0
  13Q GAIN WILD-TYPE       3   499                2
D25V3, multiclass
                  clus
vv                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  OMENTUM                         0                  3
  OVARY                          59                499
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V4, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    58   0
  13Q GAIN WILD-TYPE 483   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     58    0
  13Q GAIN WILD-TYPE  483    5
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                58                483
  YES                0                  5
[1] 2 2
[1] FALSE
D25V5, continuous
                    vv
clus                 R0 R1 R2 RX
  13Q GAIN MUTATED    3  2  0  0
  13Q GAIN WILD-TYPE 12 24  5  3
D25V6, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0                3                 12
  R1                2                 24
  R2                0                  5
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     0  39
  13Q GAIN WILD-TYPE  10 288
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0   39
  13Q GAIN WILD-TYPE   10  288
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               39                288
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    21  35
  14Q GAIN WILD-TYPE 207 296
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                56                503 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                35                296 
$`14Q GAIN MUTATED`
TCGA-04-1514 TCGA-04-1517 TCGA-04-1646 TCGA-04-1652 TCGA-09-1668 TCGA-09-1669 
       56.55        19.99        27.88        31.86        55.36        30.51 
TCGA-13-1408 TCGA-13-1501 TCGA-13-1505 TCGA-13-2057 TCGA-13-2059 TCGA-20-0991 
       55.23        43.20        65.69        80.02        78.48        26.20 
TCGA-23-1116 TCGA-23-1809 TCGA-24-1103 TCGA-24-1417 TCGA-24-1422 TCGA-24-1545 
       19.46         0.53        54.12         7.82         0.76        57.40 
TCGA-24-1555 TCGA-24-1842 TCGA-24-1844 TCGA-24-1923 TCGA-24-2030 TCGA-24-2261 
       88.50         8.32         3.72        22.68        55.92         0.79 
TCGA-25-1314 TCGA-25-1317 TCGA-25-1628 TCGA-25-1878 TCGA-25-2401 TCGA-25-2408 
       33.01         2.01        20.61        85.05         2.96        31.00 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1784 TCGA-29-2428 TCGA-30-1714 TCGA-30-1853 
       16.93        23.93         5.36        45.11        38.07        36.26 
TCGA-30-1866 TCGA-31-1959 TCGA-36-1570 TCGA-36-2544 TCGA-36-2545 TCGA-36-2548 
       36.62         2.20        21.53        20.98        18.31        14.17 
TCGA-57-1583 TCGA-59-2352 TCGA-59-2355 TCGA-61-1730 TCGA-61-2012 TCGA-61-2097 
       11.38         9.40         2.14         4.34        30.64        60.62 
TCGA-61-2612 TCGA-WR-A838 TCGA-09-0364 TCGA-13-0762 TCGA-13-0768 TCGA-13-0795 
        6.35         9.99        29.16       111.78        58.65        20.35 
TCGA-13-0899 TCGA-13-0901 
       66.15        19.36 

$`14Q GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 
       49.15         2.01        46.62         1.08        18.51        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 
       65.52        63.09        48.76        21.57        63.98        65.46 
TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
        0.53        49.28        32.52        44.32        33.67        76.57 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1516 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 
      103.40        82.39        41.59         0.79        38.37       119.08 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 
       29.10        84.20        55.43        48.89        28.64        64.64 
TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       36.23        47.70        45.37         9.99        38.43        89.33 
TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1670 TCGA-09-1672 
       74.93        41.62        57.60        61.87        17.98         5.85 
TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 
        3.02         8.55        97.55         6.18         6.12        35.15 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 
        4.54       112.41        71.11        63.09        39.75        20.94 
TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 
       26.93        12.46        77.10        81.17        28.54        83.31 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
       57.27        81.01        17.46        32.35        54.64        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 
       61.71        29.42       124.44        20.68        22.39        70.82 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
       83.93        52.44       125.56        93.90        90.38         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 TCGA-13-1506 
      127.27        66.15       115.07        13.97        34.82        34.16 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2060 
       65.52        80.15        44.68        54.25        14.53        77.88 
TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
       76.90        65.52        70.45         8.42        23.05        25.94 
TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 
       72.20        27.52        25.38        19.10        16.70         2.93 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
        2.66        47.54        49.68        40.54        15.39        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       32.09        49.41         8.81        29.13        18.90         2.76 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1117 
       51.35        54.51         3.22        31.20        68.68        33.30 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 
       86.01       129.96         4.27         6.38        39.09        33.47 
TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
       58.13        24.95       115.89        87.48        91.66        77.00 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 
       49.84         2.76         4.70         4.50         7.63        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1104 TCGA-24-1105 
       21.80        41.56         7.66        22.32        63.55        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1418 TCGA-24-1419 TCGA-24-1423 TCGA-24-1424 
        6.31         6.38         7.99         7.86         6.25         6.02 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 
        5.95         5.36         4.83        17.39        28.37        18.64 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 
       18.67        43.53         8.55        72.92        12.46        45.14 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
      105.99         9.11         3.45         1.18        22.22        26.96 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
       64.27        16.21        56.58        41.06        51.91        41.39 
TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 
       58.09        70.62        39.88        19.53        44.09        45.50 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 
       47.70        25.87        10.26        17.23        90.15        88.37 
TCGA-24-1614 TCGA-24-1616 TCGA-24-1843 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 
       48.33        38.24         3.48         3.81         4.37        11.28 
TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 
        5.79         5.52         9.80        30.21        16.44        11.05 
TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 
       81.11         4.87       152.02        44.84        58.16        34.82 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
      109.71        14.43        18.48        28.18        64.01        44.52 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       57.07        36.16         0.36        47.54        31.63        70.45 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 
       44.61         0.82        67.36        36.23        16.64        33.11 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 
       55.86        53.26         1.02        26.96        52.04        42.05 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 
       34.98        65.00        37.97        33.96         2.99        12.99 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1630 
       15.02        18.58        27.62        17.03        12.95        38.20 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 
        0.30        59.15        62.17        35.87        52.04        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 
       24.99        24.00        13.02        49.05         1.02        38.04 
TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2404 
        3.02        12.00        45.01        19.99        42.02        29.03 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 
       26.99        78.90        47.61        48.33       101.79        39.02 
TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1703 
       40.41        33.93        31.20        68.32        36.36        59.67 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 
       18.25        41.98        31.27        34.62        17.36        86.60 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 
       66.81        62.93        39.42        31.30        22.98        24.36 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 
       22.55        17.33        12.36        11.84        12.30        14.93 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 
        8.38         7.23        36.30        86.17        65.00        62.47 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ 
       13.84        42.25        21.47        11.47         9.76        35.77 
TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 
       51.91         2.47        15.68         0.26        48.10        44.91 
TCGA-30-1861 TCGA-30-1862 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 
       34.78         6.12         1.22        57.57        24.26        30.05 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 
       48.79        45.57        30.18        18.77        22.49         6.71 
TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1571 TCGA-36-1574 
       42.51        44.12        28.77        29.10        22.85        22.55 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 
        8.55        30.08        25.74        27.85        24.23        24.69 
TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
       35.05        33.01        29.49        29.82        25.91        25.08 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2547 TCGA-36-2549 TCGA-36-2551 
       23.80        21.60         2.24        20.52         6.05        16.18 
TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
       11.47        47.57        23.74        28.93        42.02        10.42 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 
       40.77         1.48        24.03        21.14         1.74        22.32 
TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 
       29.00        25.08        25.02       180.20        80.12        22.32 
TCGA-59-2351 TCGA-59-2354 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 
      116.12        34.39         5.42        44.81        11.11         8.09 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 TCGA-61-1734 
       20.94        31.43        18.54        27.88        31.79        28.47 
TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 
       48.79        44.84        35.80         2.43        33.67        43.69 
TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 
        1.45         8.42         5.79        11.41        13.02         9.07 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 
       34.13        31.30        37.05        42.51        48.92        56.61 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
       67.76        43.43        15.75        38.17         2.01         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 
       14.50        17.98         4.01        30.64        39.85         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 
       45.96        45.40         4.80         4.77        51.72        71.74 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 
       61.64        58.39        65.52        55.50         6.48        76.87 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2613 TCGA-61-2614 
       20.68        44.52       125.75        22.22        31.07         8.61 
TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 
       39.68        18.94         0.79         9.47        57.76        17.98 
TCGA-09-0369 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       35.57        54.31        25.91        81.86        18.51        34.19 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 
       32.88        14.66         6.71        35.44        36.92        19.99 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 
       20.91         6.21        24.59        44.55        39.58         2.73 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 
       12.39        31.20        15.19        17.82        55.17         2.50 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 
       11.18        11.38        11.54        38.01        61.84        56.71 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 
       40.24       118.42       107.28        63.09        69.73        83.34 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 
       87.48        45.99        51.02        43.86        35.28        35.31 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
       13.61        68.94       107.18       111.39       153.37        66.67 
TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 
       92.42        95.15       145.45       102.84        43.36        71.74 
TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 
      134.04       127.79        50.37       123.16       118.98        60.59 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
      116.65        44.55        37.64       109.32        58.68        84.53 
TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       48.79        48.76        83.74        85.94        25.41 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.53               0.26 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            111.78             180.20 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            25.065             33.930 
[1] "0.5 - 111.8 (25.1)" "0.3 - 180.2 (33.9)"
[1] "hr=" "1.4"
D26V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  14Q GAIN MUTATED         0    57                0
  14Q GAIN WILD-TYPE       3   501                2
D26V3, multiclass
                  clus
vv                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  OMENTUM                         0                  3
  OVARY                          57                501
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V4, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    54   1
  14Q GAIN WILD-TYPE 487   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     54    1
  14Q GAIN WILD-TYPE  487    4
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                54                487
  YES                1                  4
[1] 2 2
[1] FALSE
D26V5, continuous
                    vv
clus                 R0 R1 R2 RX
  14Q GAIN MUTATED    1  4  0  0
  14Q GAIN WILD-TYPE 14 22  5  3
D26V6, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0                1                 14
  R1                4                 22
  R2                0                  5
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     0  30
  14Q GAIN WILD-TYPE  10 297
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0   30
  14Q GAIN WILD-TYPE   10  297
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               30                297
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    19  17
  15Q GAIN WILD-TYPE 209 314
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                36                523 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                17                314 
$`15Q GAIN MUTATED`
TCGA-04-1349 TCGA-04-1351 TCGA-04-1361 TCGA-04-1362 TCGA-09-1675 TCGA-09-2053 
       21.57        65.46        32.52        44.32        97.55        39.75 
TCGA-13-1412 TCGA-13-1499 TCGA-13-2059 TCGA-13-2065 TCGA-23-1021 TCGA-23-2072 
       32.35       115.07        78.48        65.52        47.54        24.95 
TCGA-23-2079 TCGA-24-1413 TCGA-24-1419 TCGA-24-1551 TCGA-24-1558 TCGA-25-1627 
       91.66         6.31         7.86        51.91        19.53        12.95 
TCGA-30-1853 TCGA-31-1959 TCGA-36-1571 TCGA-36-2542 TCGA-57-1582 TCGA-57-1994 
       36.26         2.20        22.85        21.60        24.03        25.02 
TCGA-61-1730 TCGA-61-1907 TCGA-61-1915 TCGA-61-2009 TCGA-WR-A838 TCGA-09-0369 
        4.34        31.30        67.76        39.85         9.99        35.57 
TCGA-10-0938 TCGA-13-0761 TCGA-13-0792 TCGA-13-0890 TCGA-13-0919 TCGA-13-2071 
       20.91        38.01       118.42       145.45        84.53        25.41 

$`15Q GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 
       49.15         2.01        46.62         1.08        18.51        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1350 TCGA-04-1353 TCGA-04-1356 
       65.52        63.09        48.76        63.98         0.53        49.28 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 
       33.67        76.57       103.40        82.39        56.55        41.59 
TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 
       19.99         0.79        38.37       119.08        29.10        84.20 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 
       55.43        48.89        27.88        28.64        64.64        36.23 
TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       31.86        47.70        45.37         9.99        38.43        89.33 
TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 
       74.93        41.62        57.60        61.87        55.36        30.51 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-2043 TCGA-09-2044 
       17.98         5.85         3.02         8.55         6.18         6.12 
TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2054 
       35.15         4.54       112.41        71.11        63.09        20.94 
TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 
       26.93        12.46        77.10        81.17        28.54        83.31 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1477 TCGA-13-1481 
       55.23        57.27        81.01        17.46        54.64        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 
       61.71        29.42       124.44        20.68        22.39        70.82 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
       83.93        52.44       125.56        93.90        90.38         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 
      127.27        66.15        13.97        43.20        34.82        65.69 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
       34.16        65.52        80.15        44.68        54.25        14.53 
TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
       80.02        77.88        76.90        70.45         8.42        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 
       25.94        26.20        72.20        27.52        25.38        19.10 
TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 
       16.70         2.93         2.66        49.68        40.54        15.39 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 
       26.83        32.09        49.41         8.81        29.13        18.90 
TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 
        2.76        51.35        54.51         3.22        31.20        68.68 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 
       19.46        33.30        86.01       129.96         4.27         6.38 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2078 
       39.09        33.47        58.13         0.53       115.89        87.48 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 
       77.00        49.84         2.76         4.70         4.50         7.63 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 
       11.64        21.80        41.56         7.66        22.32        54.12 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1422 
       63.55        47.41         6.38         7.82         7.99         0.76 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        6.25         6.02         5.95         5.36         4.83        17.39 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 
       28.37        18.64        18.67        43.53         8.55        72.92 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 
       12.46        45.14       105.99         9.11         3.45         1.18 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 
       22.22        26.96        57.40        64.27        16.21        56.58 
TCGA-24-1550 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       41.06        41.39        58.09        88.50        70.62        39.88 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 
       44.09        45.50        47.70        25.87        10.26        17.23 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 
       90.15        88.37        48.33        38.24         8.32         3.48 
TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 
        3.72         3.81         4.37        11.28         5.79         5.52 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 
        9.80        22.68        30.21        16.44        11.05        81.11 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 
        4.87       152.02        44.84        58.16        34.82       109.71 
TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
       14.43        55.92        18.48        28.18        64.01        44.52 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 
       57.07        36.16         0.79         0.36        47.54        31.63 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 
       70.45        44.61         0.82        67.36        36.23        16.64 
TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 
       33.11        55.86        53.26         1.02        26.96        33.01 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 
       52.04        42.05         2.01        34.98        65.00        37.97 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       33.96         2.99        12.99        15.02        18.58        27.62 
TCGA-25-1626 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
       17.03        20.61        38.20         0.30        59.15        62.17 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 
       35.87        52.04        14.96        24.99        24.00        85.05 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 
       13.02        49.05         1.02        38.04         3.02        12.00 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 
       45.01        19.99        42.02         2.96        29.03        31.00 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 
       26.99        78.90        47.61        48.33       101.79        39.02 
TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 
       40.41        33.93        31.20        68.32        36.36        16.93 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 
       23.93        59.67        18.25        41.98        31.27        34.62 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 
       17.36        86.60        66.81        62.93        39.42        31.30 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 
       22.98        24.36        22.55        17.33        12.36        11.84 
TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 
       12.30        14.93         8.38         7.23         5.36        36.30 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 
       86.17        65.00        62.47        45.11        13.84        42.25 
TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 
       21.47        11.47         9.76        35.77        38.07        51.91 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 
        2.47        15.68         0.26        48.10        44.91        34.78 
TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 
        6.12        36.62         1.22        57.57        24.26        30.05 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 
       48.79        45.57        30.18        18.77        22.49         6.71 
TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 
       42.51        44.12        28.77        29.10        21.53        22.55 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 
        8.55        30.08        25.74        27.85        24.23        24.69 
TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
       35.05        33.01        29.49        29.82        25.91        25.08 
TCGA-36-2540 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 
       23.80         2.24        20.98        18.31        20.52        14.17 
TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
        6.05        16.18        11.47        47.57        23.74        28.93 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 
       42.02        10.42        40.77         1.48        11.38        21.14 
TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 
        1.74        22.32        29.00        25.08       180.20        80.12 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       22.32       116.12         9.40        34.39         2.14         5.42 
TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
       44.81        11.11         8.09        20.94        31.43        18.54 
TCGA-61-1728 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
       27.88        31.79        28.47        48.79        44.84        35.80 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
        2.43        33.67        43.69         1.45         8.42         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1910 TCGA-61-1911 
       11.41        13.02         9.07        34.13        37.05        42.51 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 
       48.92        56.61        43.43        15.75        38.17         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 
        5.52        14.50        17.98         4.01        30.64        30.64 
TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 
        1.18        45.96        45.40         4.80         4.77        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 
       71.74        61.64        58.39        60.62        65.52        55.50 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
        6.48        76.87        20.68        44.52       125.75        22.22 
TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
        6.35        31.07         8.61        39.68        18.94         0.79 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-10-0925 TCGA-10-0926 
       29.16         9.47        57.76        17.98        54.31        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       81.86        18.51        34.19        32.88        14.66         6.71 
TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
       35.44        36.92        19.99         6.21        24.59        44.55 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 
       39.58         2.73        12.39        31.20        15.19        17.82 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0762 
       55.17         2.50        11.18        11.38        11.54       111.78 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0793 TCGA-13-0794 
       61.84        56.71        58.65        40.24       107.28        63.09 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 
       20.35        69.73        83.34        87.48        45.99        51.02 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
       43.86        35.28        35.31        13.61        68.94       107.18 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 
      111.39       153.37        66.67        92.42        95.15       102.84 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       43.36        71.74        66.15       134.04        19.36       127.79 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       50.37       123.16       118.98        60.59       116.65        44.55 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 
       37.64       109.32        58.68        48.79        48.76        83.74 
TCGA-13-0924 
       85.94 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              2.20               0.26 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            145.45             180.20 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            34.045             32.880 
[1] "2.2 - 145.4 (34.0)" "0.3 - 180.2 (32.9)"
[1] "hr=" "1.5"
D27V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  15Q GAIN MUTATED         0    37                0
  15Q GAIN WILD-TYPE       3   521                2
D27V3, multiclass
                  clus
vv                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  OMENTUM                         0                  3
  OVARY                          37                521
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V4, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    37   0
  15Q GAIN WILD-TYPE 504   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     37    0
  15Q GAIN WILD-TYPE  504    5
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                37                504
  YES                0                  5
[1] 2 2
[1] FALSE
D27V5, continuous
                    vv
clus                 R0 R1 R2 RX
  15Q GAIN MUTATED    0  1  0  0
  15Q GAIN WILD-TYPE 15 25  5  3
D27V6, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                 48 
        TCGA-3P-A9WA         TCGA-5X-AA5U         TCGA-04-1516 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-04-1644         TCGA-13-A5FT         TCGA-13-A5FU 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-24-2033         TCGA-29-2414         TCGA-29-2425 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-29-2427         TCGA-29-2428         TCGA-29-2429 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-29-2431         TCGA-29-2432         TCGA-29-2434 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-29-2436         TCGA-36-2529         TCGA-36-2530 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-36-2532         TCGA-36-2534         TCGA-36-2537 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-36-2538         TCGA-36-2540         TCGA-36-2543 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-36-2544         TCGA-36-2545         TCGA-36-2547 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-36-2548         TCGA-36-2549         TCGA-36-2551 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-36-2552         TCGA-42-2582         TCGA-42-2587 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-42-2588         TCGA-42-2589         TCGA-42-2590 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-42-2593         TCGA-57-1993         TCGA-59-2363 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-59-2372         TCGA-61-2612         TCGA-61-2613 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-61-2614         TCGA-OY-A56P         TCGA-OY-A56Q 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-VG-A8LO         TCGA-13-0807         TCGA-13-0911 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     0  23
  15Q GAIN WILD-TYPE  10 304
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0   23
  15Q GAIN WILD-TYPE   10  304
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               23                304
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    23  35
  16P GAIN WILD-TYPE 205 296
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                58                501 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                35                296 
$`16P GAIN MUTATED`
TCGA-04-1351 TCGA-04-1371 TCGA-04-1519 TCGA-04-1525 TCGA-04-1542 TCGA-04-1646 
       65.46        82.39         0.79        38.37        84.20        27.88 
TCGA-04-1648 TCGA-04-1655 TCGA-09-1672 TCGA-09-2051 TCGA-13-1487 TCGA-13-1510 
       28.64        45.37         5.85        63.09        22.39        44.68 
TCGA-13-2059 TCGA-20-1682 TCGA-23-1021 TCGA-23-1124 TCGA-23-1809 TCGA-23-2643 
       78.48        27.52        47.54        58.13         0.53         4.70 
TCGA-24-0966 TCGA-24-1434 TCGA-24-1464 TCGA-24-1565 TCGA-24-1604 TCGA-24-1614 
        7.63        18.67        12.46        10.26        88.37        48.33 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1845 TCGA-25-1321 TCGA-25-1633 TCGA-25-1871 
       38.24         8.32         3.81        33.96        62.17        24.99 
TCGA-25-1877 TCGA-25-1878 TCGA-29-1691 TCGA-29-1774 TCGA-29-1784 TCGA-29-2432 
       24.00        85.05        48.33        17.33         5.36        21.47 
TCGA-36-1581 TCGA-36-2547 TCGA-36-2552 TCGA-59-2372 TCGA-61-1733 TCGA-61-1738 
       24.69        20.52        11.47        44.81        31.79        35.80 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-2009 TCGA-61-2101 TCGA-61-2111 
       67.76        43.43        15.75        39.85        55.50       125.75 
TCGA-OY-A56Q TCGA-09-0364 TCGA-09-0365 TCGA-09-0369 TCGA-10-0936 TCGA-13-0724 
       18.94        29.16         9.47        35.57        36.92         2.73 
TCGA-13-0889 TCGA-13-0897 TCGA-13-0901 TCGA-13-0921 
       95.15        71.74        19.36        48.76 

$`16P GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 
       49.15         2.01        46.62         1.08        18.51        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1353 
       65.52        63.09        48.76        21.57        63.98         0.53 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       49.28        32.52        44.32        33.67        76.57       103.40 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1530 TCGA-04-1536 TCGA-04-1638 
       56.55        41.59        19.99       119.08        29.10        55.43 
TCGA-04-1644 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-09-1659 
       48.89        64.64        36.23        31.86        47.70         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 
       38.43        89.33        74.93        41.62        57.60        61.87 
TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 
       55.36        30.51        17.98         3.02         8.55        97.55 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 
        6.18         6.12        35.15         4.54       112.41        71.11 
TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 
       39.75        20.94        26.93        12.46        77.10        81.17 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
       28.54        83.31        55.23        57.27        81.01        17.46 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
       32.35        54.64        87.06        61.71        29.42       124.44 
TCGA-13-1485 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       20.68        70.82        83.93        52.44       125.56        93.90 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 
       90.38         4.24       127.27        66.15       115.07        13.97 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       43.20        34.82        65.69        34.16        65.52        80.15 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 
       54.25        14.53        80.02        77.88        76.90        65.52 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 
       70.45         8.42        23.05        25.94        26.20        72.20 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1022 
       25.38        19.10        16.70         2.93         2.66        49.68 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 
       40.54        15.39        26.83        32.09        49.41         8.81 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
       29.13        18.90         2.76        51.35        54.51         3.22 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 
       31.20        68.68        19.46        33.30        86.01       129.96 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-2072 TCGA-23-2077 
        4.27         6.38        39.09        33.47        24.95       115.89 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2645 
       87.48        91.66        77.00        49.84         2.76         4.50 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 
       11.64        21.80        41.56         7.66        22.32        54.12 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 
       63.55        47.41         6.31         6.38         7.82         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 
        7.86         0.76         6.25         6.02         5.95         5.36 
TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 TCGA-24-1436 
        4.83        17.39        28.37        18.64        43.53         8.55 
TCGA-24-1463 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 
       72.92        45.14       105.99         9.11         3.45         1.18 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 
       22.22        26.96        57.40        64.27        16.21        56.58 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 
       41.06        51.91        41.39        58.09        88.50        70.62 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
       39.88        19.53        44.09        45.50        47.70        25.87 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 
       17.23        90.15         3.48         3.72         4.37        11.28 
TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 
        5.79         5.52         9.80        22.68        30.21        16.44 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 
       11.05        81.11         4.87       152.02        44.84        58.16 
TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 
       34.82       109.71        14.43        55.92        18.48        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 
       64.01        44.52        57.07        36.16         0.79         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 
       47.54        31.63        70.45        44.61         0.82        67.36 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 
       36.23        16.64        33.11        55.86        53.26         1.02 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
       26.96        33.01        52.04        42.05         2.01        34.98 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
       65.00        37.97         2.99        12.99        15.02        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
       27.62        17.03        12.95        20.61        38.20         0.30 
TCGA-25-1632 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-2042 TCGA-25-2391 
       59.15        35.87        52.04        14.96        13.02        49.05 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 
        1.02        38.04         3.02        12.00        45.01        19.99 
TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 
       42.02         2.96        29.03        31.00        26.99        78.90 
TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 
       47.61       101.79        39.02        40.41        33.93        31.20 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 
       68.32        36.36        16.93        23.93        59.67        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
       41.98        31.27        34.62        17.36        86.60        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 
       62.93        39.42        31.30        22.98        24.36        22.55 
TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 
       12.36        11.84        12.30        14.93         8.38         7.23 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 
       36.30        86.17        65.00        62.47        45.11        13.84 
TCGA-29-2431 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 
       42.25        11.47         9.76        35.77        38.07        51.91 
TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 
       36.26         2.47        15.68         0.26        48.10        44.91 
TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 
       34.78         6.12        36.62         1.22        57.57        24.26 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 
       30.05        48.79        45.57        30.18        18.77        22.49 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 
        6.71        42.51        44.12         2.20        28.77        29.10 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 
       21.53        22.85        22.55         8.55        30.08        25.74 
TCGA-36-1578 TCGA-36-1580 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       27.85        24.23        35.05        33.01        29.49        29.82 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 
       25.91        25.08        23.80        21.60         2.24        20.98 
TCGA-36-2545 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-42-2582 TCGA-42-2587 
       18.31        14.17         6.05        16.18        47.57        23.74 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 
       28.93        42.02        10.42        40.77         1.48        24.03 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 
       11.38        21.14         1.74        22.32        29.00        25.08 
TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       25.02       180.20        80.12        22.32       116.12         9.40 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 
       34.39         2.14         5.42        11.11         8.09        20.94 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1734 TCGA-61-1736 
       31.43        18.54        27.88         4.34        28.47        48.79 
TCGA-61-1737 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 
       44.84         2.43        33.67        43.69         1.45         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        5.79        11.41        13.02         9.07        34.13        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1919 TCGA-61-1995 
       37.05        42.51        48.92        56.61        38.17         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 
        5.52        14.50        17.98         4.01        30.64        30.64 
TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 
        1.18        45.96        45.40         4.80         4.77        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2102 
       71.74        61.64        58.39        60.62        65.52         6.48 
TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 
       76.87        20.68        44.52        22.22         6.35        31.07 
TCGA-61-2614 TCGA-OY-A56P TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0366 TCGA-09-0367 
        8.61        39.68         0.79         9.99        57.76        17.98 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       54.31        25.91        81.86        18.51        34.19        32.88 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
       14.66         6.71        35.44        19.99        20.91         6.21 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 
       24.59        44.55        39.58        12.39        31.20        15.19 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 
       17.82        55.17         2.50        11.18        11.38        11.54 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 
       38.01       111.78        61.84        56.71        58.65        40.24 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 
      118.42       107.28        63.09        20.35        69.73        83.34 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 
       87.48        45.99        51.02        43.86        35.28        35.31 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
       13.61        68.94       107.18       111.39       153.37        66.67 
TCGA-13-0888 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 TCGA-13-0900 
       92.42       145.45       102.84        43.36        66.15       134.04 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
      127.79        50.37       123.16       118.98        60.59       116.65 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       44.55        37.64       109.32        58.68        84.53        48.79 
TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       83.74        85.94        25.41 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.53               0.26 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            125.75             180.20 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            32.875             32.880 
[1] "0.5 - 125.8 (32.9)" "0.3 - 180.2 (32.9)"
[1] "hr=" "1.1"
D28V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  16P GAIN MUTATED         0    59                0
  16P GAIN WILD-TYPE       3   499                2
D28V3, multiclass
                  clus
vv                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  OMENTUM                         0                  3
  OVARY                          59                499
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V4, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    57   0
  16P GAIN WILD-TYPE 484   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     57    0
  16P GAIN WILD-TYPE  484    5
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                57                484
  YES                0                  5
[1] 2 2
[1] FALSE
D28V5, continuous
                    vv
clus                 R0 R1 R2 RX
  16P GAIN MUTATED    3  1  0  1
  16P GAIN WILD-TYPE 12 25  5  2
D28V6, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0                3                 12
  R1                1                 25
  R2                0                  5
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     1  33
  16P GAIN WILD-TYPE   9 294
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   33
  16P GAIN WILD-TYPE    9  294
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO               33                294
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    11  20
  16Q GAIN WILD-TYPE 217 311
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                31                528 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                20                311 
$`16Q GAIN MUTATED`
TCGA-04-1519 TCGA-04-1542 TCGA-04-1646 TCGA-04-1648 TCGA-09-1672 TCGA-13-1510 
        0.79        84.20        27.88        28.64         5.85        44.68 
TCGA-13-2059 TCGA-23-1021 TCGA-24-1464 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 
       78.48        47.54        12.46        88.37        48.33        38.24 
TCGA-24-1845 TCGA-25-1321 TCGA-25-1633 TCGA-29-1774 TCGA-36-1581 TCGA-36-2538 
        3.81        33.96        62.17        17.33        24.69        25.08 
TCGA-36-2547 TCGA-59-2351 TCGA-59-2372 TCGA-61-1738 TCGA-61-1915 TCGA-61-1917 
       20.52       116.12        44.81        35.80        67.76        43.43 
TCGA-61-1918 TCGA-OY-A56Q TCGA-09-0364 TCGA-09-0365 TCGA-09-0369 TCGA-13-0897 
       15.75        18.94        29.16         9.47        35.57        71.74 
TCGA-13-0921 
       48.76 

$`16Q GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 
       49.15         2.01        46.62         1.08        18.51        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 
       65.52        63.09        48.76        21.57        63.98        65.46 
TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
        0.53        49.28        32.52        44.32        33.67        76.57 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 
      103.40        82.39        56.55        41.59        19.99        38.37 
TCGA-04-1530 TCGA-04-1536 TCGA-04-1638 TCGA-04-1644 TCGA-04-1649 TCGA-04-1651 
      119.08        29.10        55.43        48.89        64.64        36.23 
TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       31.86        47.70        45.37         9.99        38.43        89.33 
TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 
       74.93        41.62        57.60        61.87        55.36        30.51 
TCGA-09-1670 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 
       17.98         3.02         8.55        97.55         6.18         6.12 
TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 
       35.15         4.54       112.41        71.11        63.09        39.75 
TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
       20.94        26.93        12.46        77.10        81.17        28.54 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
       83.31        55.23        57.27        81.01        17.46        32.35 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 
       54.64        87.06        61.71        29.42       124.44        20.68 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       22.39        70.82        83.93        52.44       125.56        93.90 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 
       90.38         4.24       127.27        66.15       115.07        13.97 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       43.20        34.82        65.69        34.16        65.52        80.15 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 
       54.25        14.53        80.02        77.88        76.90        65.52 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 
       70.45         8.42        23.05        25.94        26.20        72.20 
TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 
       27.52        25.38        19.10        16.70         2.93         2.66 
TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       49.68        40.54        15.39        26.83        32.09        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 
        8.81        29.13        18.90         2.76        51.35        54.51 
TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
        3.22        31.20        68.68        19.46        33.30        86.01 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 
      129.96         4.27         6.38        39.09        33.47        58.13 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
        0.53        24.95       115.89        87.48        91.66        77.00 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 
       49.84         2.76         4.70         4.50         7.63        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 
       21.80        41.56         7.66        22.32        54.12        63.55 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       47.41         6.31         6.38         7.82         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        0.76         6.25         6.02         5.95         5.36         4.83 
TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
       17.39        28.37        18.64        18.67        43.53         8.55 
TCGA-24-1463 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 
       72.92        45.14       105.99         9.11         3.45         1.18 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 
       22.22        26.96        57.40        64.27        16.21        56.58 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 
       41.06        51.91        41.39        58.09        88.50        70.62 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
       39.88        19.53        44.09        45.50        47.70        25.87 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
       10.26        17.23        90.15         8.32         3.48         3.72 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 
        4.37        11.28         5.79         5.52         9.80        22.68 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 
       30.21        16.44        11.05        81.11         4.87       152.02 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 
       44.84        58.16        34.82       109.71        14.43        55.92 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 
       18.48        28.18        64.01        44.52        57.07        36.16 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 
        0.79         0.36        47.54        31.63        70.45        44.61 
TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 
        0.82        67.36        36.23        16.64        33.11        55.86 
TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 
       53.26         1.02        26.96        33.01        52.04        42.05 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 
        2.01        34.98        65.00        37.97         2.99        12.99 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 
       15.02        18.58        27.62        17.03        12.95        20.61 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 
       38.20         0.30        59.15        35.87        52.04        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 
       24.99        24.00        85.05        13.02        49.05         1.02 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 
       38.04         3.02        12.00        45.01        19.99        42.02 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 
        2.96        29.03        31.00        26.99        78.90        47.61 
TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 
       48.33       101.79        39.02        40.41        33.93        31.20 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 
       68.32        36.36        16.93        23.93        59.67        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
       41.98        31.27        34.62        17.36        86.60        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 
       62.93        39.42        31.30        22.98        24.36        22.55 
TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 
       12.36        11.84        12.30        14.93         8.38         7.23 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 
        5.36        36.30        86.17        65.00        62.47        45.11 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ 
       13.84        42.25        21.47        11.47         9.76        35.77 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 
       38.07        51.91        36.26         2.47        15.68         0.26 
TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 
       48.10        44.91        34.78         6.12        36.62         1.22 
TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 
       57.57        24.26        30.05        48.79        45.57        30.18 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 
       18.77        22.49         6.71        42.51        44.12         2.20 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 
       28.77        29.10        21.53        22.85        22.55         8.55 
TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-2529 TCGA-36-2530 
       30.08        25.74        27.85        24.23        35.05        33.01 
TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 
       29.49        29.82        25.91        23.80        21.60         2.24 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 
       20.98        18.31        14.17         6.05        16.18        11.47 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
       47.57        23.74        28.93        42.02        10.42        40.77 
TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 
        1.48        24.03        11.38        21.14         1.74        22.32 
TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 
       29.00        25.08        25.02       180.20        80.12        22.32 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-61-1721 TCGA-61-1722 
        9.40        34.39         2.14         5.42        11.11         8.09 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 
       20.94        31.43        18.54        27.88         4.34        31.79 
TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 
       28.47        48.79        44.84         2.43        33.67        43.69 
TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 
        1.45         8.42         5.79        11.41        13.02         9.07 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 
       34.13        31.30        37.05        42.51        48.92        56.61 
TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 
       38.17         2.01         5.52        14.50        17.98         4.01 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
       30.64        39.85        30.64         1.18        45.96        45.40 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 
        4.80         4.77        51.72        71.74        61.64        58.39 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       60.62        65.52        55.50         6.48        76.87        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       44.52       125.75        22.22         6.35        31.07         8.61 
TCGA-OY-A56P TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0366 TCGA-09-0367 TCGA-10-0925 
       39.68         0.79         9.99        57.76        17.98        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 
       25.91        81.86        18.51        34.19        32.88        14.66 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
        6.71        35.44        36.92        19.99        20.91         6.21 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 
       24.59        44.55        39.58         2.73        12.39        31.20 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 
       15.19        17.82        55.17         2.50        11.18        11.38 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 
       11.54        38.01       111.78        61.84        56.71        58.65 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 
       40.24       118.42       107.28        63.09        20.35        69.73 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 
       83.34        87.48        45.99        51.02        43.86        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 
       35.31        13.61        68.94       107.18       111.39       153.37 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
       66.67        92.42        95.15       145.45       102.84        43.36 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       66.15       134.04        19.36       127.79        50.37       123.16 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
      118.98        60.59       116.65        44.55        37.64       109.32 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       58.68        84.53        48.79        83.74        85.94        25.41 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.79               0.26 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            116.12             180.20 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            35.570             32.435 
[1] "0.8 - 116.1 (35.6)" "0.3 - 180.2 (32.4)"
[1] "hr=" "1.1"
D29V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  16Q GAIN MUTATED         0    32                0
  16Q GAIN WILD-TYPE       3   526                2
D29V3, multiclass
                  clus
vv                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  OMENTUM                         0                  3
  OVARY                          32                526
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V4, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    29   0
  16Q GAIN WILD-TYPE 512   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     29    0
  16Q GAIN WILD-TYPE  512    5
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                29                512
  YES                0                  5
[1] 2 2
[1] FALSE
D29V5, continuous
                    vv
clus                 R0 R1 R2 RX
  16Q GAIN MUTATED    2  1  0  1
  16Q GAIN WILD-TYPE 13 25  5  2
D29V6, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0                2                 13
  R1                1                 25
  R2                0                  5
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     0  17
  16Q GAIN WILD-TYPE  10 310
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0   17
  16Q GAIN WILD-TYPE   10  310
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               17                310
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    13   7
  17P GAIN WILD-TYPE 215 324
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                20                539 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 7                324 
$`17P GAIN MUTATED`
TCGA-09-2051 TCGA-13-1412 TCGA-13-2057 TCGA-13-2060 TCGA-20-1683 TCGA-23-1114 
       63.09        32.35        80.02        77.88        25.38        68.68 
TCGA-24-1845 TCGA-29-1763 TCGA-29-2429 TCGA-36-1569 TCGA-36-1578 TCGA-36-1580 
        3.81        66.81        13.84        29.10        27.85        24.23 
TCGA-36-1581 TCGA-36-2552 TCGA-61-1900 TCGA-61-1904 TCGA-09-0369 TCGA-13-0800 
       24.69        11.47         5.79         9.07        35.57        87.48 
TCGA-13-0897 TCGA-13-0920 
       71.74        48.79 

$`17P GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 
       49.15         2.01        46.62         1.08        18.51        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 
       65.52        63.09        48.76        21.57        63.98        65.46 
TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
        0.53        49.28        32.52        44.32        33.67        76.57 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 
      103.40        82.39        56.55        41.59        19.99         0.79 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 
       38.37       119.08        29.10        84.20        55.43        48.89 
TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 
       27.88        28.64        64.64        36.23        31.86        47.70 
TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       45.37         9.99        38.43        89.33        74.93        41.62 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 
       57.60        61.87        55.36        30.51        17.98         5.85 
TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 
        3.02         8.55        97.55         6.18         6.12        35.15 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 
        4.54       112.41        71.11        39.75        20.94        26.93 
TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 
       12.46        77.10        81.17        28.54        83.31        55.23 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 
       57.27        81.01        17.46        54.64        87.06        61.71 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 
       29.42       124.44        20.68        22.39        70.82        83.93 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 
       52.44       125.56        93.90        90.38         4.24       127.27 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 
       66.15       115.07        13.97        43.20        34.82        65.69 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
       34.16        65.52        80.15        44.68        54.25        14.53 
TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
       78.48        76.90        65.52        70.45         8.42        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 
       25.94        26.20        72.20        27.52        19.10        16.70 
TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 
        2.93         2.66        47.54        49.68        40.54        15.39 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 
       26.83        32.09        49.41         8.81        29.13        18.90 
TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 
        2.76        51.35        54.51         3.22        31.20        19.46 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 
       33.30        86.01       129.96         4.27         6.38        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 
       33.47        58.13         0.53        24.95       115.89        87.48 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 
       91.66        77.00        49.84         2.76         4.70         4.50 
TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
        7.63        11.64        21.80        41.56         7.66        22.32 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 
       54.12        63.55        47.41         6.31         6.38         7.82 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 
        7.99         7.86         0.76         6.25         6.02         5.95 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 
        5.36         4.83        17.39        28.37        18.64        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 
       43.53         8.55        72.92        12.46        45.14       105.99 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 
        9.11         3.45         1.18        22.22        26.96        57.40 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
       64.27        16.21        56.58        41.06        51.91        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 
       58.09        88.50        70.62        39.88        19.53        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       45.50        47.70        25.87        10.26        17.23        90.15 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
       88.37        48.33        38.24         8.32         3.48         3.72 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 
        4.37        11.28         5.79         5.52         9.80        22.68 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 
       30.21        16.44        11.05        81.11         4.87       152.02 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 
       44.84        58.16        34.82       109.71        14.43        55.92 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 
       18.48        28.18        64.01        44.52        57.07        36.16 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 
        0.79         0.36        47.54        31.63        70.45        44.61 
TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 
        0.82        67.36        36.23        16.64        33.11        55.86 
TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 
       53.26         1.02        26.96        33.01        52.04        42.05 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 
        2.01        34.98        65.00        37.97        33.96         2.99 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 
       12.99        15.02        18.58        27.62        17.03        12.95 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
       20.61        38.20         0.30        59.15        62.17        35.87 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 
       52.04        14.96        24.99        24.00        85.05        13.02 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 
       49.05         1.02        38.04         3.02        12.00        45.01 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       19.99        42.02         2.96        29.03        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 
       78.90        47.61        48.33       101.79        39.02        40.41 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 
       33.93        31.20        68.32        36.36        16.93        23.93 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 
       59.67        18.25        41.98        31.27        34.62        17.36 
TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 
       86.60        62.93        39.42        31.30        22.98        24.36 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 
       22.55        17.33        12.36        11.84        12.30        14.93 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 
        8.38         7.23         5.36        36.30        86.17        65.00 
TCGA-29-2427 TCGA-29-2428 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 
       62.47        45.11        42.25        21.47        11.47         9.76 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 
       35.77        38.07        51.91        36.26         2.47        15.68 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 
        0.26        48.10        44.91        34.78         6.12        36.62 
TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 
        1.22        57.57        24.26        30.05        48.79        45.57 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 
       30.18        18.77        22.49         6.71        42.51        44.12 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 
        2.20        28.77        21.53        22.85        22.55         8.55 
TCGA-36-1576 TCGA-36-1577 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       30.08        25.74        35.05        33.01        29.49        29.82 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 
       25.91        25.08        23.80        21.60         2.24        20.98 
TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-42-2582 
       18.31        20.52        14.17         6.05        16.18        47.57 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 
       23.74        28.93        42.02        10.42        40.77         1.48 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 
       24.03        11.38        21.14         1.74        22.32        29.00 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 
       25.08        25.02       180.20        80.12        22.32       116.12 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 
        9.40        34.39         2.14         5.42        44.81        11.11 
TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 
        8.09        20.94        31.43        18.54        27.88         4.34 
TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 
       31.79        28.47        48.79        44.84        35.80         2.43 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1901 TCGA-61-1903 
       33.67        43.69         1.45         8.42        11.41        13.02 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 
       34.13        31.30        37.05        42.51        48.92        56.61 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
       67.76        43.43        15.75        38.17         2.01         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 
       14.50        17.98         4.01        30.64        39.85        30.64 
TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 
        1.18        45.96        45.40         4.80         4.77        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 
       71.74        61.64        58.39        60.62        65.52        55.50 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
        6.48        76.87        20.68        44.52       125.75        22.22 
TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
        6.35        31.07         8.61        39.68        18.94         0.79 
TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-10-0925 
        9.99        29.16         9.47        57.76        17.98        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 
       25.91        81.86        18.51        34.19        32.88        14.66 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
        6.71        35.44        36.92        19.99        20.91         6.21 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 
       24.59        44.55        39.58         2.73        12.39        31.20 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 
       15.19        17.82        55.17         2.50        11.18        11.38 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 
       11.54        38.01       111.78        61.84        56.71        58.65 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 
       40.24       118.42       107.28        63.09        20.35        69.73 
TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 
       83.34        45.99        51.02        43.86        35.28        35.31 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
       13.61        68.94       107.18       111.39       153.37        66.67 
TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 
       92.42        95.15       145.45       102.84        43.36        66.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
      134.04        19.36       127.79        50.37       123.16       118.98 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       60.59       116.65        44.55        37.64       109.32        58.68 
TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       84.53        48.76        83.74        85.94        25.41 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              3.81               0.26 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             87.48             180.20 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            30.725             33.010 
[1] "3.8 - 87.5 (30.7)"  "0.3 - 180.2 (33.0)"
[1] "hr=" "1.8"
D30V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  17P GAIN MUTATED         0    20                0
  17P GAIN WILD-TYPE       3   538                2
D30V3, multiclass
                  clus
vv                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  OMENTUM                         0                  3
  OVARY                          20                538
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V4, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    19   0
  17P GAIN WILD-TYPE 522   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     19    0
  17P GAIN WILD-TYPE  522    5
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                19                522
  YES                0                  5
[1] 2 2
[1] FALSE
D30V5, continuous
                    vv
clus                 R0 R1 R2 RX
  17P GAIN MUTATED    1  1  0  0
  17P GAIN WILD-TYPE 14 25  5  3
D30V6, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                 47 
        TCGA-3P-A9WA         TCGA-5X-AA5U         TCGA-04-1516 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-04-1644         TCGA-13-A5FT         TCGA-13-A5FU 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-24-2033         TCGA-29-2414         TCGA-29-2425 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-29-2427         TCGA-29-2428         TCGA-29-2431 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-29-2432         TCGA-29-2434         TCGA-29-2436 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-36-2529         TCGA-36-2530         TCGA-36-2532 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-36-2534         TCGA-36-2537         TCGA-36-2538 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-36-2540         TCGA-36-2542         TCGA-36-2543 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-36-2544         TCGA-36-2545         TCGA-36-2547 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-36-2548         TCGA-36-2549         TCGA-36-2551 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-42-2582         TCGA-42-2587         TCGA-42-2588 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-42-2589         TCGA-42-2590         TCGA-42-2593 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-57-1993         TCGA-59-2363         TCGA-59-2372 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-61-2612         TCGA-61-2613         TCGA-61-2614 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-OY-A56P         TCGA-OY-A56Q         TCGA-VG-A8LO 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-13-0807         TCGA-13-0911 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0  11
  17P GAIN WILD-TYPE  10 316
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   11
  17P GAIN WILD-TYPE   10  316
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               11                316
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    15  26
  17Q GAIN WILD-TYPE 213 305
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                41                518 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                26                305 
$`17Q GAIN MUTATED`
TCGA-04-1337 TCGA-04-1530 TCGA-13-1408 TCGA-13-1412 TCGA-13-1477 TCGA-13-1483 
        2.01       119.08        55.23        32.35        54.64        29.42 
TCGA-13-1489 TCGA-13-2057 TCGA-23-1109 TCGA-23-1114 TCGA-24-1464 TCGA-24-1845 
       83.93        80.02        51.35        68.68        12.46         3.81 
TCGA-24-1850 TCGA-24-2020 TCGA-24-2298 TCGA-25-1319 TCGA-25-2392 TCGA-29-1699 
        5.52       152.02        53.26        65.00         1.02        36.36 
TCGA-30-1862 TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 TCGA-36-1578 TCGA-36-1580 
        6.12        29.10        21.53        22.55        27.85        24.23 
TCGA-36-1581 TCGA-36-2552 TCGA-42-2588 TCGA-42-2593 TCGA-61-1737 TCGA-61-1900 
       24.69        11.47        28.93         1.48        44.84         5.79 
TCGA-61-1913 TCGA-61-1914 TCGA-61-2098 TCGA-61-2612 TCGA-09-0369 TCGA-10-0936 
       48.92        56.61        65.52         6.35        35.57        36.92 
TCGA-13-0760 TCGA-13-0768 TCGA-13-0800 TCGA-13-0897 TCGA-13-0920 
       11.54        58.65        87.48        71.74        48.79 

$`17Q GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1336 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 
       49.15        46.62         1.08        18.51        11.87        65.52 
TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 
       63.09        48.76        21.57        63.98        65.46         0.53 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       49.28        32.52        44.32        33.67        76.57       103.40 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 
       82.39        56.55        41.59        19.99         0.79        38.37 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 
       29.10        84.20        55.43        48.89        27.88        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 
       64.64        36.23        31.86        47.70        45.37         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 
       38.43        89.33        74.93        41.62        57.60        61.87 
TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 
       55.36        30.51        17.98         5.85         3.02         8.55 
TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 
       97.55         6.18         6.12        35.15         4.54       112.41 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 
       71.11        63.09        39.75        20.94        26.93        12.46 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 
       77.10        81.17        28.54        83.31        57.27        81.01 
TCGA-13-1411 TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 
       17.46        87.06        61.71       124.44        20.68        22.39 
TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
       70.82        52.44       125.56        93.90        90.38         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 
      127.27        66.15       115.07        13.97        43.20        34.82 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
       65.69        34.16        65.52        80.15        44.68        54.25 
TCGA-13-1512 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT 
       14.53        78.48        77.88        76.90        65.52        70.45 
TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 
        8.42        23.05        25.94        26.20        72.20        27.52 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 
       25.38        19.10        16.70         2.93         2.66        47.54 
TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       49.68        40.54        15.39        26.83        32.09        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1111 
        8.81        29.13        18.90         2.76        54.51         3.22 
TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 
       31.20        19.46        33.30        86.01       129.96         4.27 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 
        6.38        39.09        33.47        58.13         0.53        24.95 
TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
      115.89        87.48        91.66        77.00        49.84         2.76 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        4.70         4.50         7.63        11.64        21.80        41.56 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 
        7.66        22.32        54.12        63.55        47.41         6.31 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 
        6.38         7.82         7.99         7.86         0.76         6.25 
TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 
        6.02         5.95         5.36         4.83        17.39        28.37 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 
       18.64        18.67        43.53         8.55        72.92        45.14 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
      105.99         9.11         3.45         1.18        22.22        26.96 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 
       57.40        64.27        16.21        56.58        41.06        51.91 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 
       41.39        58.09        88.50        70.62        39.88        19.53 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 
       44.09        45.50        47.70        25.87        10.26        17.23 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 
       90.15        88.37        48.33        38.24         8.32         3.48 
TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 
        3.72         4.37        11.28         5.79         9.80        22.68 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 
       30.21        16.44        11.05        81.11         4.87        44.84 
TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 
       58.16        34.82       109.71        14.43        55.92        18.48 
TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 
       28.18        64.01        44.52        57.07        36.16         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
        0.36        47.54        31.63        70.45        44.61         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 
       67.36        36.23        16.64        33.11        55.86         1.02 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
       26.96        33.01        52.04        42.05         2.01        34.98 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
       37.97        33.96         2.99        12.99        15.02        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
       27.62        17.03        12.95        20.61        38.20         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 
       59.15        62.17        35.87        52.04        14.96        24.99 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 
       24.00        85.05        13.02        49.05        38.04         3.02 
TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 
       12.00        45.01        19.99        42.02         2.96        29.03 
TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 
       31.00        26.99        78.90        47.61        48.33       101.79 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1701 
       39.02        40.41        33.93        31.20        68.32        16.93 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 
       23.93        59.67        18.25        41.98        31.27        34.62 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 
       17.36        86.60        66.81        62.93        39.42        31.30 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 
       22.98        24.36        22.55        17.33        12.36        11.84 
TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 
       12.30        14.93         8.38         7.23         5.36        36.30 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 
       86.17        65.00        62.47        45.11        13.84        42.25 
TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 
       21.47        11.47         9.76        35.77        38.07        51.91 
TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 
       36.26         2.47        15.68         0.26        48.10        44.91 
TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 
       34.78        36.62         1.22        57.57        24.26        30.05 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 
       48.79        45.57        30.18        18.77        22.49         6.71 
TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1571 TCGA-36-1575 
       42.51        44.12         2.20        28.77        22.85         8.55 
TCGA-36-1576 TCGA-36-1577 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       30.08        25.74        35.05        33.01        29.49        29.82 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 
       25.91        25.08        23.80        21.60         2.24        20.98 
TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-42-2582 
       18.31        20.52        14.17         6.05        16.18        47.57 
TCGA-42-2587 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 TCGA-57-1583 
       23.74        42.02        10.42        40.77        24.03        11.38 
TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 
       21.14         1.74        22.32        29.00        25.08        25.02 
TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 
      180.20        80.12        22.32       116.12         9.40        34.39 
TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 
        2.14         5.42        44.81        11.11         8.09        20.94 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 
       31.43        18.54        27.88         4.34        31.79        28.47 
TCGA-61-1736 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 
       48.79        35.80         2.43        33.67        43.69         1.45 
TCGA-61-1899 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        8.42        11.41        13.02         9.07        34.13        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 
       37.05        42.51        67.76        43.43        15.75        38.17 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 
        2.01         5.52        14.50        17.98         4.01        30.64 
TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
       39.85        30.64         1.18        45.96        45.40         4.80 
TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 
        4.77        51.72        71.74        61.64        58.39        60.62 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       55.50         6.48        76.87        20.68        44.52       125.75 
TCGA-61-2113 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
       22.22        31.07         8.61        39.68        18.94         0.79 
TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-10-0925 
        9.99        29.16         9.47        57.76        17.98        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 
       25.91        81.86        18.51        34.19        32.88        14.66 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
        6.71        35.44        19.99        20.91         6.21        24.59 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 
       44.55        39.58         2.73        12.39        31.20        15.19 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0761 
       17.82        55.17         2.50        11.18        11.38        38.01 
TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
      111.78        61.84        56.71        40.24       118.42       107.28 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 
       63.09        20.35        69.73        83.34        45.99        51.02 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
       43.86        35.28        35.31        13.61        68.94       107.18 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 
      111.39       153.37        66.67        92.42        95.15       145.45 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
      102.84        43.36        66.15       134.04        19.36       127.79 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       50.37       123.16       118.98        60.59       116.65        44.55 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 
       37.64       109.32        58.68        84.53        48.76        83.74 
TCGA-13-0924 TCGA-13-2071 
       85.94        25.41 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              1.02               0.26 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            152.02             180.20 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             35.57              32.70 
[1] "1.0 - 152.0 (35.6)" "0.3 - 180.2 (32.7)"
[1] "hr=" "1"  
D31V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  17Q GAIN MUTATED         0    41                0
  17Q GAIN WILD-TYPE       3   517                2
D31V3, multiclass
                  clus
vv                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  OMENTUM                         0                  3
  OVARY                          41                517
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V4, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    40   0
  17Q GAIN WILD-TYPE 501   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     40    0
  17Q GAIN WILD-TYPE  501    5
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                40                501
  YES                0                  5
[1] 2 2
[1] FALSE
D31V5, continuous
                    vv
clus                 R0 R1 R2 RX
  17Q GAIN MUTATED    1  1  2  0
  17Q GAIN WILD-TYPE 14 25  3  3
D31V6, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0                1                 14
  R1                1                 25
  R2                2                  3
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     0  25
  17Q GAIN WILD-TYPE  10 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0   25
  17Q GAIN WILD-TYPE   10  302
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               25                302
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    52  63
  18P GAIN WILD-TYPE 176 268
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               115                444 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                63                268 
$`18P GAIN MUTATED`
TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 TCGA-04-1361 
       11.87        41.00        65.52        63.09        21.57        32.52 
TCGA-04-1371 TCGA-04-1516 TCGA-04-1525 TCGA-04-1536 TCGA-04-1542 TCGA-04-1644 
       82.39        41.59        38.37        29.10        84.20        48.89 
TCGA-04-1646 TCGA-04-1652 TCGA-09-1665 TCGA-09-1668 TCGA-09-2054 TCGA-09-2055 
       27.88        31.86        41.62        55.36        20.94        26.93 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1481 TCGA-13-1489 TCGA-13-1497 
       83.31        55.23        81.01        87.06        83.93       127.27 
TCGA-13-1499 TCGA-13-1504 TCGA-13-1507 TCGA-13-1510 TCGA-13-2059 TCGA-13-2060 
      115.07        34.82        65.52        44.68        78.48        77.88 
TCGA-20-0987 TCGA-20-1686 TCGA-23-1022 TCGA-23-1024 TCGA-23-1032 TCGA-23-1110 
       23.05         2.93        49.68        15.39         2.76        54.51 
TCGA-23-1114 TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 
       68.68         6.38        33.47        58.13         0.53       115.89 
TCGA-24-1428 TCGA-24-1430 TCGA-24-1434 TCGA-24-1466 TCGA-24-1558 TCGA-24-1567 
       17.39        28.37        18.67        45.14        19.53        17.23 
TCGA-24-1616 TCGA-24-1844 TCGA-24-1845 TCGA-24-1850 TCGA-24-1924 TCGA-24-2020 
       38.24         3.72         3.81         5.52        30.21       152.02 
TCGA-24-2026 TCGA-24-2030 TCGA-24-2261 TCGA-24-2289 TCGA-25-1314 TCGA-25-1318 
       34.82        55.92         0.79        67.36        33.01        34.98 
TCGA-25-1319 TCGA-25-1321 TCGA-25-1623 TCGA-25-1628 TCGA-25-1635 TCGA-25-2400 
       65.00        33.96        18.58        20.61        52.04        42.02 
TCGA-29-1695 TCGA-29-1698 TCGA-29-1711 TCGA-29-1778 TCGA-29-1784 TCGA-29-2425 
       40.41        68.32        34.62        14.93         5.36        65.00 
TCGA-29-2432 TCGA-29-2434 TCGA-30-1853 TCGA-30-1866 TCGA-31-1959 TCGA-36-1581 
       21.47        11.47        36.26        36.62         2.20        24.69 
TCGA-36-2537 TCGA-36-2547 TCGA-42-2589 TCGA-57-1583 TCGA-57-1586 TCGA-57-1992 
       25.91        20.52        42.02        11.38        22.32        29.00 
TCGA-57-1994 TCGA-59-2352 TCGA-59-2355 TCGA-61-1722 TCGA-61-1728 TCGA-61-1730 
       25.02         9.40         2.14         8.09        27.88         4.34 
TCGA-61-1733 TCGA-61-1740 TCGA-61-1899 TCGA-61-1907 TCGA-61-1917 TCGA-61-2008 
       31.79         2.43         8.42        31.30        43.43        30.64 
TCGA-61-2018 TCGA-61-2096 TCGA-61-2111 TCGA-61-2614 TCGA-WR-A838 TCGA-09-0369 
       45.40        58.39       125.75         8.61         9.99        35.57 
TCGA-10-0930 TCGA-10-0937 TCGA-13-0762 TCGA-13-0768 TCGA-13-0795 TCGA-13-0802 
       34.19        19.99       111.78        58.65        20.35        51.02 
TCGA-13-0885 TCGA-13-0888 TCGA-13-0890 TCGA-13-0899 TCGA-13-0901 TCGA-13-0904 
      111.39        92.42       145.45        66.15        19.36        50.37 
TCGA-13-0919 
       84.53 

$`18P GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 
       13.81        20.52        43.92         1.81        49.15         2.01 
TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1348 TCGA-04-1350 
       46.62         1.08        18.51        11.87        48.76        63.98 
TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
       65.46         0.53        49.28        44.32        33.67        76.57 
TCGA-04-1367 TCGA-04-1514 TCGA-04-1517 TCGA-04-1519 TCGA-04-1530 TCGA-04-1638 
      103.40        56.55        19.99         0.79       119.08        55.43 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 
       28.64        64.64        36.23        47.70        45.37         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 
       38.43        89.33        74.93        57.60        61.87        30.51 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 
       17.98         5.85         3.02         8.55        97.55         6.18 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
        6.12        35.15         4.54       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1409 
       39.75        12.46        77.10        81.17        28.54        57.27 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
       17.46        32.35        54.64        61.71        29.42       124.44 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       20.68        22.39        70.82        52.44       125.56        93.90 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1505 
       90.38         4.24        66.15        13.97        43.20        65.69 
TCGA-13-1506 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2061 
       34.16        80.15        54.25        14.53        80.02        76.90 
TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 
       65.52        70.45         8.42        25.94        26.20        72.20 
TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1687 TCGA-23-1021 
       27.52        25.38        19.10        16.70         2.66        47.54 
TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
       40.54        26.83        32.09        49.41         8.81        29.13 
TCGA-23-1031 TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 
       18.90        51.35         3.22        31.20        19.46        33.30 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 TCGA-23-2072 TCGA-23-2078 
       86.01       129.96         4.27        39.09        24.95        87.48 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 
       91.66        77.00        49.84         2.76         4.70         4.50 
TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
        7.63        11.64        21.80        41.56         7.66        22.32 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 
       54.12        63.55        47.41         6.31         6.38         7.82 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 
        7.99         7.86         0.76         6.25         6.02         5.95 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1431 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 
        5.36         4.83        18.64        43.53         8.55        72.92 
TCGA-24-1464 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 
       12.46       105.99         9.11         3.45         1.18        22.22 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 
       26.96        57.40        64.27        16.21        56.58        41.06 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       51.91        41.39        58.09        88.50        70.62        39.88 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1603 
       44.09        45.50        47.70        25.87        10.26        90.15 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1842 TCGA-24-1843 TCGA-24-1846 TCGA-24-1847 
       88.37        48.33         8.32         3.48         4.37        11.28 
TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 
        5.79         9.80        22.68        16.44        11.05        81.11 
TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 
        4.87        44.84        58.16       109.71        14.43        18.48 
TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 
       28.18        64.01        44.52        57.07        36.16         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2290 
       47.54        31.63        70.45        44.61         0.82        36.23 
TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 
       16.64        33.11        55.86        53.26         1.02        26.96 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 
       52.04        42.05         2.01        37.97         2.99        12.99 
TCGA-25-1329 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 
       15.02        27.62        17.03        12.95        38.20         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
       59.15        62.17        35.87        14.96        24.99        24.00 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 
       85.05        13.02        49.05         1.02        38.04         3.02 
TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 
       12.00        45.01        19.99         2.96        29.03        31.00 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 
       26.99        78.90        47.61        48.33       101.79        39.02 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 
       33.93        31.20        36.36        16.93        23.93        59.67 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
       18.25        41.98        31.27        17.36        86.60        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 
       62.93        39.42        31.30        22.98        24.36        22.55 
TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 
       17.33        12.36        11.84        12.30         8.38         7.23 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 
       36.30        86.17        62.47        45.11        13.84        42.25 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 
        9.76        35.77        38.07        51.91         2.47        15.68 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1867 
        0.26        48.10        44.91        34.78         6.12         1.22 
TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 
       57.57        24.26        30.05        48.79        45.57        30.18 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 
       18.77        22.49         6.71        42.51        44.12        28.77 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 
       29.10        21.53        22.85        22.55         8.55        30.08 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 
       25.74        27.85        24.23        35.05        33.01        29.49 
TCGA-36-2534 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 
       29.82        25.08        23.80        21.60         2.24        20.98 
TCGA-36-2545 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 
       18.31        14.17         6.05        16.18        11.47        47.57 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 
       23.74        28.93        10.42        40.77         1.48        24.03 
TCGA-57-1584 TCGA-57-1585 TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 
       21.14         1.74        25.08       180.20        80.12        22.32 
TCGA-59-2351 TCGA-59-2354 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1724 
      116.12        34.39         5.42        44.81        11.11        20.94 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
       31.43        18.54        28.47        48.79        44.84        35.80 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 
       33.67        43.69         1.45         5.79        11.41        13.02 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 
        9.07        34.13        37.05        42.51        48.92        56.61 
TCGA-61-1915 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       67.76        15.75        38.17         2.01         5.52        14.50 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 
       17.98         4.01        39.85        30.64         1.18        45.96 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 
        4.80         4.77        51.72        71.74        61.64        60.62 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       65.52        55.50         6.48        76.87        20.68        44.52 
TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
       22.22         6.35        31.07        39.68        18.94         0.79 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-10-0925 TCGA-10-0926 
       29.16         9.47        57.76        17.98        54.31        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 
       81.86        18.51        32.88        14.66         6.71        35.44 
TCGA-10-0936 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 
       36.92        20.91         6.21        24.59        44.55        39.58 
TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
        2.73        12.39        31.20        15.19        17.82        55.17 
TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 
        2.50        11.18        11.38        11.54        38.01        61.84 
TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 
       56.71        40.24       118.42       107.28        63.09        69.73 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 
       83.34        87.48        45.99        43.86        35.28        35.31 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 
       13.61        68.94       107.18       153.37        66.67        95.15 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0903 TCGA-13-0905 
      102.84        43.36        71.74       134.04       127.79       123.16 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
      118.98        60.59       116.65        44.55        37.64       109.32 
TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       58.68        48.79        48.76        83.74        85.94        25.41 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.53               0.26 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            152.02             180.20 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            34.620             31.365 
[1] "0.5 - 152.0 (34.6)" "0.3 - 180.2 (31.4)"
[1] "hr=" "1.2"
D32V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  18P GAIN MUTATED         0   117                0
  18P GAIN WILD-TYPE       3   441                2
D32V3, multiclass
                  clus
vv                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  OMENTUM                         0                  3
  OVARY                         117                441
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V4, binary
                    cls
clus                   0   1
  18P GAIN MUTATED   114   0
  18P GAIN WILD-TYPE 427   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED    114    0
  18P GAIN WILD-TYPE  427    5
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO               114                427
  YES                0                  5
[1] 2 2
[1] FALSE
D32V5, continuous
                    vv
clus                 R0 R1 R2 RX
  18P GAIN MUTATED    5  5  0  0
  18P GAIN WILD-TYPE 10 21  5  3
D32V6, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0                5                 10
  R1                5                 21
  R2                0                  5
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     2  67
  18P GAIN WILD-TYPE   8 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2   67
  18P GAIN WILD-TYPE    8  260
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO               67                260
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    29  35
  18Q GAIN WILD-TYPE 199 296
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                64                495 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                35                296 
$`18Q GAIN MUTATED`
TCGA-04-1346 TCGA-04-1349 TCGA-04-1516 TCGA-04-1536 TCGA-04-1644 TCGA-04-1646 
       65.52        21.57        41.59        29.10        48.89        27.88 
TCGA-04-1652 TCGA-09-1661 TCGA-09-1665 TCGA-09-1668 TCGA-09-2055 TCGA-13-1410 
       31.86        38.43        41.62        55.36        26.93        81.01 
TCGA-13-1489 TCGA-13-1497 TCGA-13-1504 TCGA-13-1507 TCGA-13-1510 TCGA-13-2060 
       83.93       127.27        34.82        65.52        44.68        77.88 
TCGA-23-1024 TCGA-23-1114 TCGA-23-1123 TCGA-23-1809 TCGA-23-2077 TCGA-24-1430 
       15.39        68.68        33.47         0.53       115.89        28.37 
TCGA-24-1434 TCGA-24-1466 TCGA-24-1604 TCGA-24-1845 TCGA-24-1924 TCGA-24-2026 
       18.67        45.14        88.37         3.81        30.21        34.82 
TCGA-25-1314 TCGA-25-1318 TCGA-25-1319 TCGA-25-1635 TCGA-29-1695 TCGA-29-1698 
       33.01        34.98        65.00        52.04        40.41        68.32 
TCGA-29-1705 TCGA-29-1778 TCGA-29-1784 TCGA-29-2432 TCGA-30-1853 TCGA-36-1581 
       18.25        14.93         5.36        21.47        36.26        24.69 
TCGA-36-2537 TCGA-61-1722 TCGA-61-1728 TCGA-61-1733 TCGA-61-1899 TCGA-61-1907 
       25.91         8.09        27.88        31.79         8.42        31.30 
TCGA-61-1917 TCGA-61-1998 TCGA-61-2008 TCGA-61-2096 TCGA-61-2101 TCGA-61-2111 
       43.43         5.52        30.64        58.39        55.50       125.75 
TCGA-61-2614 TCGA-09-0369 TCGA-13-0717 TCGA-13-0762 TCGA-13-0795 TCGA-13-0802 
        8.61        35.57        24.59       111.78        20.35        51.02 
TCGA-13-0890 TCGA-13-0901 TCGA-13-0904 TCGA-13-0919 
      145.45        19.36        50.37        84.53 

$`18Q GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 
       49.15         2.01        46.62         1.08        18.51        11.87 
TCGA-04-1347 TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 
       63.09        48.76        63.98        65.46         0.53        49.28 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 
       32.52        44.32        33.67        76.57       103.40        82.39 
TCGA-04-1514 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 
       56.55        19.99         0.79        38.37       119.08        84.20 
TCGA-04-1638 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 
       55.43        28.64        64.64        36.23        47.70        45.37 
TCGA-09-1659 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 
        9.99        89.33        74.93        57.60        61.87        30.51 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 
       17.98         5.85         3.02         8.55        97.55         6.18 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
        6.12        35.15         4.54       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2054 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
       39.75        20.94        12.46        77.10        81.17        28.54 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 
       83.31        55.23        57.27        17.46        32.35        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 
       87.06        61.71        29.42       124.44        20.68        22.39 
TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
       70.82        52.44       125.56        93.90        90.38         4.24 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 
       66.15       115.07        13.97        43.20        65.69        34.16 
TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2061 
       80.15        54.25        14.53        80.02        78.48        76.90 
TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
       65.52        70.45         8.42        23.05        25.94        26.20 
TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 
       72.20        27.52        25.38        19.10        16.70         2.93 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 
        2.66        47.54        49.68        40.54        26.83        32.09 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 
       49.41         8.81        29.13        18.90         2.76        51.35 
TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
       54.51         3.22        31.20        19.46        33.30        86.01 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1124 TCGA-23-2072 
      129.96         4.27         6.38        39.09        58.13        24.95 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 
       87.48        91.66        77.00        49.84         2.76         4.70 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        4.50         7.63        11.64        21.80        41.56         7.66 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
       22.32        54.12        63.55        47.41         6.31         6.38 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
        7.82         7.99         7.86         0.76         6.25         6.02 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 TCGA-24-1435 
        5.95         5.36         4.83        17.39        18.64        43.53 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 
        8.55        72.92        12.46       105.99         9.11         3.45 
TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 
        1.18        22.22        26.96        57.40        64.27        16.21 
TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       56.58        41.06        51.91        41.39        58.09        88.50 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       70.62        39.88        19.53        44.09        45.50        47.70 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1614 TCGA-24-1616 
       25.87        10.26        17.23        90.15        48.33        38.24 
TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 
        8.32         3.48         3.72         4.37        11.28         5.79 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 
        5.52         9.80        22.68        16.44        11.05        81.11 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 
        4.87       152.02        44.84        58.16       109.71        14.43 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 
       55.92        18.48        28.18        64.01        44.52        57.07 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       36.16         0.79         0.36        47.54        31.63        70.45 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 
       44.61         0.82        67.36        36.23        16.64        33.11 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 
       55.86        53.26         1.02        26.96        52.04        42.05 
TCGA-25-1317 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 
        2.01        37.97        33.96         2.99        12.99        15.02 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 
       18.58        27.62        17.03        12.95        20.61        38.20 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 
        0.30        59.15        62.17        35.87        14.96        24.99 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 
       24.00        85.05        13.02        49.05         1.02        38.04 
TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 
        3.02        12.00        45.01        19.99        42.02         2.96 
TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 
       29.03        31.00        26.99        78.90        47.61        48.33 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 TCGA-29-1701 
      101.79        39.02        33.93        31.20        36.36        16.93 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 
       23.93        59.67        41.98        31.27        34.62        17.36 
TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 
       86.60        66.81        62.93        39.42        31.30        22.98 
TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 
       24.36        22.55        17.33        12.36        11.84        12.30 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 
        8.38         7.23        36.30        86.17        65.00        62.47 
TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ 
       45.11        13.84        42.25        11.47         9.76        35.77 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 
       38.07        51.91         2.47        15.68         0.26        48.10 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 
       44.91        34.78         6.12        36.62         1.22        57.57 
TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 
       24.26        30.05        48.79        45.57        30.18        18.77 
TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 
       22.49         6.71        42.51        44.12         2.20        28.77 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 
       29.10        21.53        22.85        22.55         8.55        30.08 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 
       25.74        27.85        24.23        35.05        33.01        29.49 
TCGA-36-2534 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 
       29.82        25.08        23.80        21.60         2.24        20.98 
TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 
       18.31        20.52        14.17         6.05        16.18        11.47 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
       47.57        23.74        28.93        42.02        10.42        40.77 
TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 
        1.48        24.03        11.38        21.14         1.74        22.32 
TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 
       29.00        25.08        25.02       180.20        80.12        22.32 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 
      116.12         9.40        34.39         2.14         5.42        44.81 
TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1730 TCGA-61-1734 
       11.11        20.94        31.43        18.54         4.34        28.47 
TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 
       48.79        44.84        35.80         2.43        33.67        43.69 
TCGA-61-1895 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 
        1.45         5.79        11.41        13.02         9.07        34.13 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 
       37.05        42.51        48.92        56.61        67.76        15.75 
TCGA-61-1919 TCGA-61-1995 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2009 
       38.17         2.01        14.50        17.98         4.01        39.85 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
       30.64         1.18        45.96        45.40         4.80         4.77 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 TCGA-61-2098 TCGA-61-2102 
       51.72        71.74        61.64        60.62        65.52         6.48 
TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 
       76.87        20.68        44.52        22.22         6.35        31.07 
TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 
       39.68        18.94         0.79         9.99        29.16         9.47 
TCGA-09-0366 TCGA-09-0367 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       57.76        17.98        54.31        25.91        81.86        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 
       34.19        32.88        14.66         6.71        35.44        36.92 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 
       19.99        20.91         6.21        44.55        39.58         2.73 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 
       12.39        31.20        15.19        17.82        55.17         2.50 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 
       11.18        11.38        11.54        38.01        61.84        56.71 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 
       58.65        40.24       118.42       107.28        63.09        69.73 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 
       83.34        87.48        45.99        43.86        35.28        35.31 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
       13.61        68.94       107.18       111.39       153.37        66.67 
TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 
       92.42        95.15       102.84        43.36        71.74        66.15 
TCGA-13-0900 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
      134.04       127.79       123.16       118.98        60.59       116.65 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 
       44.55        37.64       109.32        58.68        48.79        48.76 
TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       83.74        85.94        25.41 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.53               0.26 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            145.45             180.20 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             34.90              31.63 
[1] "0.5 - 145.4 (34.9)" "0.3 - 180.2 (31.6)"
[1] "hr=" "1.3"
D33V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  18Q GAIN MUTATED         0    66                0
  18Q GAIN WILD-TYPE       3   492                2
D33V3, multiclass
                  clus
vv                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  OMENTUM                         0                  3
  OVARY                          66                492
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V4, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    65   0
  18Q GAIN WILD-TYPE 476   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     65    0
  18Q GAIN WILD-TYPE  476    5
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                65                476
  YES                0                  5
[1] 2 2
[1] FALSE
D33V5, continuous
                    vv
clus                 R0 R1 R2 RX
  18Q GAIN MUTATED    1  4  0  0
  18Q GAIN WILD-TYPE 14 22  5  3
D33V6, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0                1                 14
  R1                4                 22
  R2                0                  5
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     0  39
  18Q GAIN WILD-TYPE  10 288
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0   39
  18Q GAIN WILD-TYPE   10  288
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               39                288
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    72  93
  19P GAIN WILD-TYPE 156 238
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               165                394 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                93                238 
$`19P GAIN MUTATED`
TCGA-5X-AA5U TCGA-04-1335 TCGA-04-1338 TCGA-04-1346 TCGA-04-1514 TCGA-04-1516 
       11.87         1.81        46.62        65.52        56.55        41.59 
TCGA-04-1519 TCGA-04-1525 TCGA-04-1542 TCGA-04-1648 TCGA-04-1649 TCGA-04-1652 
        0.79        38.37        84.20        28.64        64.64        31.86 
TCGA-09-1665 TCGA-09-1667 TCGA-09-1669 TCGA-09-1670 TCGA-09-1674 TCGA-09-1675 
       41.62        61.87        30.51        17.98         8.55        97.55 
TCGA-09-2043 TCGA-09-2054 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1481 
        6.18        20.94        83.31        55.23        81.01        87.06 
TCGA-13-1482 TCGA-13-1484 TCGA-13-1491 TCGA-13-1495 TCGA-13-1501 TCGA-13-1506 
       61.71       124.44        52.44        90.38        43.20        34.16 
TCGA-13-1510 TCGA-13-2057 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 
       44.68        80.02        23.05        25.94        26.20        27.52 
TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1024 TCGA-23-1026 
        2.93         2.66        47.54        49.68        15.39        26.83 
TCGA-23-1109 TCGA-23-1111 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1121 
       51.35         3.22        19.46        33.30        86.01         6.38 
TCGA-23-1809 TCGA-23-2645 TCGA-24-0982 TCGA-24-1105 TCGA-24-1417 TCGA-24-1426 
        0.53         4.50        22.32        47.41         7.82         5.36 
TCGA-24-1428 TCGA-24-1436 TCGA-24-1469 TCGA-24-1471 TCGA-24-1545 TCGA-24-1548 
       17.39         8.55         9.11         1.18        57.40        16.21 
TCGA-24-1551 TCGA-24-1557 TCGA-24-1558 TCGA-24-1614 TCGA-24-1616 TCGA-24-1843 
       51.91        39.88        19.53        48.33        38.24         3.48 
TCGA-24-1845 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1928 TCGA-24-2020 
        3.81         5.52         9.80        22.68        11.05       152.02 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2261 TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 
       55.92        18.48         0.79        47.54        70.45        44.61 
TCGA-24-2295 TCGA-25-1312 TCGA-25-1314 TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 
       33.11         1.02        33.01        34.98        37.97        33.96 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1628 TCGA-25-2398 TCGA-29-1695 
       12.99        15.02        18.58        20.61        45.01        40.41 
TCGA-29-1698 TCGA-29-1702 TCGA-29-1711 TCGA-29-1770 TCGA-29-1775 TCGA-29-1783 
       68.32        23.93        34.62        24.36        12.36         7.23 
TCGA-29-1785 TCGA-29-2429 TCGA-29-2432 TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1714 
       36.30        13.84        21.47        11.47        35.77        38.07 
TCGA-30-1855 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1867 
        2.47         0.26        48.10        44.91         6.12         1.22 
TCGA-30-1892 TCGA-31-1950 TCGA-36-1578 TCGA-36-2529 TCGA-36-2534 TCGA-36-2543 
       48.79        18.77        27.85        35.05        29.82         2.24 
TCGA-36-2544 TCGA-36-2547 TCGA-36-2552 TCGA-42-2582 TCGA-42-2589 TCGA-57-1582 
       20.98        20.52        11.47        47.57        42.02        24.03 
TCGA-57-1583 TCGA-57-1586 TCGA-59-2348 TCGA-59-2351 TCGA-59-2355 TCGA-61-1725 
       11.38        22.32       180.20       116.12         2.14        31.43 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1899 TCGA-61-1904 TCGA-61-1906 TCGA-61-1911 
       27.88         4.34         8.42         9.07        34.13        42.51 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1918 TCGA-61-2000 TCGA-61-2009 TCGA-61-2012 
       48.92        56.61        15.75        14.50        39.85        30.64 
TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2104 TCGA-61-2111 TCGA-61-2113 
       58.39        60.62        65.52        76.87       125.75        22.22 
TCGA-OY-A56Q TCGA-WR-A838 TCGA-09-0367 TCGA-09-0369 TCGA-10-0926 TCGA-10-0933 
       18.94         9.99        17.98        35.57        25.91        14.66 
TCGA-10-0938 TCGA-13-0727 TCGA-13-0751 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 
       20.91        15.19        55.17        11.38        11.54        38.01 
TCGA-13-0764 TCGA-13-0791 TCGA-13-0802 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
       61.84        40.24        51.02        13.61        68.94       107.18 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0905 
       66.67        92.42       123.16 

$`19P GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 
       13.81        20.52        43.92        41.00        49.15         2.01 
TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 
        1.08        18.51        11.87        63.09        48.76        21.57 
TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 
       63.98        65.46         0.53        49.28        32.52        44.32 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1517 TCGA-04-1530 
       33.67        76.57       103.40        82.39        19.99       119.08 
TCGA-04-1536 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1651 TCGA-04-1654 
       29.10        55.43        48.89        27.88        36.23        47.70 
TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 
       45.37         9.99        38.43        89.33        74.93        57.60 
TCGA-09-1668 TCGA-09-1672 TCGA-09-1673 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 
       55.36         5.85         3.02         6.12        35.15         4.54 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2055 TCGA-09-2056 
      112.41        71.11        63.09        39.75        26.93        12.46 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1409 TCGA-13-1411 TCGA-13-1412 
       77.10        81.17        28.54        57.27        17.46        32.35 
TCGA-13-1477 TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 
       54.64        29.42        20.68        22.39        70.82        83.93 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 
      125.56        93.90         4.24       127.27        66.15       115.07 
TCGA-13-1500 TCGA-13-1504 TCGA-13-1505 TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 
       13.97        34.82        65.69        65.52        80.15        54.25 
TCGA-13-1512 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT 
       14.53        78.48        77.88        76.90        65.52        70.45 
TCGA-13-A5FU TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-23-1023 
        8.42        72.20        25.38        19.10        16.70        40.54 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       32.09        49.41         8.81        29.13        18.90         2.76 
TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 
       54.51        31.20        68.68       129.96         4.27        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 
       33.47        58.13        24.95       115.89        87.48        91.66 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-24-0966 TCGA-24-0970 
       77.00        49.84         2.76         4.70         7.63        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 TCGA-24-1413 
       21.80        41.56         7.66        54.12        63.55         6.31 
TCGA-24-1416 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
        6.38         7.99         7.86         0.76         6.25         6.02 
TCGA-24-1425 TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 
        5.95         4.83        28.37        18.64        18.67        43.53 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1474 
       72.92        12.46        45.14       105.99         3.45        22.22 
TCGA-24-1544 TCGA-24-1546 TCGA-24-1549 TCGA-24-1550 TCGA-24-1552 TCGA-24-1553 
       26.96        64.27        56.58        41.06        41.39        58.09 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
       88.50        70.62        44.09        45.50        47.70        25.87 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1842 TCGA-24-1844 
       10.26        17.23        90.15        88.37         8.32         3.72 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 
        4.37        11.28         5.79        30.21        16.44        81.11 
TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 
        4.87        44.84        58.16        34.82       109.71        14.43 
TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 
       28.18        64.01        44.52        57.07        36.16         0.36 
TCGA-24-2271 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 
       31.63         0.82        67.36        36.23        16.64        55.86 
TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1319 
       53.26        26.96        52.04        42.05         2.01        65.00 
TCGA-25-1322 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 
        2.99        27.62        17.03        12.95        38.20         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 
       59.15        62.17        35.87        52.04        14.96        24.99 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 
       24.00        85.05        13.02        49.05         1.02        38.04 
TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 
        3.02        12.00        19.99        42.02         2.96        29.03 
TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 
       31.00        26.99        78.90        47.61        48.33       101.79 
TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 
       39.02        33.93        31.20        36.36        16.93        59.67 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
       18.25        41.98        31.27        17.36        86.60        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 TCGA-29-1774 
       62.93        39.42        31.30        22.98        22.55        17.33 
TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1784 TCGA-29-2414 
       11.84        12.30        14.93         8.38         5.36        86.17 
TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2431 TCGA-29-2436 TCGA-30-1718 
       65.00        62.47        45.11        42.25         9.76        51.91 
TCGA-30-1853 TCGA-30-1856 TCGA-30-1861 TCGA-30-1866 TCGA-30-1880 TCGA-30-1887 
       36.26        15.68        34.78        36.62        57.57        24.26 
TCGA-30-1891 TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 
       30.05        45.57        30.18        22.49         6.71        42.51 
TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 
       44.12         2.20        28.77        29.10        21.53        22.85 
TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1580 TCGA-36-1581 
       22.55         8.55        30.08        25.74        24.23        24.69 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 
       33.01        29.49        25.91        25.08        23.80        21.60 
TCGA-36-2545 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-42-2587 TCGA-42-2588 
       18.31        14.17         6.05        16.18        23.74        28.93 
TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 
       10.42        40.77         1.48        21.14         1.74        29.00 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2349 TCGA-59-2350 TCGA-59-2352 TCGA-59-2354 
       25.08        25.02        80.12        22.32         9.40        34.39 
TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1727 
        5.42        44.81        11.11         8.09        20.94        18.54 
TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 
       31.79        28.47        48.79        44.84        35.80         2.43 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 
       33.67        43.69         1.45         5.79        11.41        13.02 
TCGA-61-1907 TCGA-61-1910 TCGA-61-1915 TCGA-61-1917 TCGA-61-1919 TCGA-61-1995 
       31.30        37.05        67.76        43.43        38.17         2.01 
TCGA-61-1998 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2016 TCGA-61-2017 
        5.52        17.98         4.01        30.64         1.18        45.96 
TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       45.40         4.80         4.77        51.72        71.74        61.64 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2109 TCGA-61-2110 TCGA-61-2612 TCGA-61-2613 
       55.50         6.48        20.68        44.52         6.35        31.07 
TCGA-61-2614 TCGA-OY-A56P TCGA-VG-A8LO TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 
        8.61        39.68         0.79        29.16         9.47        57.76 
TCGA-10-0925 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 
       54.31        81.86        18.51        34.19        32.88         6.71 
TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
       35.44        36.92        19.99         6.21        24.59        44.55 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0730 TCGA-13-0755 
       39.58         2.73        12.39        31.20        17.82         2.50 
TCGA-13-0757 TCGA-13-0762 TCGA-13-0766 TCGA-13-0768 TCGA-13-0792 TCGA-13-0793 
       11.18       111.78        56.71        58.65       118.42       107.28 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
       63.09        20.35        69.73        83.34        87.48        45.99 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0885 TCGA-13-0886 TCGA-13-0889 
       43.86        35.28        35.31       111.39       153.37        95.15 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
      145.45       102.84        43.36        71.74        66.15       134.04 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
       19.36       127.79        50.37       118.98        60.59       116.65 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       44.55        37.64       109.32        58.68        84.53        48.79 
TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       48.76        83.74        85.94        25.41 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.26               0.30 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            180.20             153.37 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             30.51              33.67 
[1] "0.3 - 180.2 (30.5)" "0.3 - 153.4 (33.7)"
[1] "hr=" "1.1"
D34V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  19P GAIN MUTATED         1   164                1
  19P GAIN WILD-TYPE       2   394                1
D34V3, multiclass
                  clus
vv                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  OMENTUM                         1                  2
  OVARY                         164                394
  PERITONEUM OVARY                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V4, binary
                    cls
clus                   0   1
  19P GAIN MUTATED   157   3
  19P GAIN WILD-TYPE 384   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED    157    3
  19P GAIN WILD-TYPE  384    2
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO               157                384
  YES                3                  2
[1] 2 2
[1] FALSE
D34V5, continuous
                    vv
clus                 R0 R1 R2 RX
  19P GAIN MUTATED    7  8  0  1
  19P GAIN WILD-TYPE  8 18  5  2
D34V6, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0                7                  8
  R1                8                 18
  R2                0                  5
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     2  94
  19P GAIN WILD-TYPE   8 233
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      2   94
  19P GAIN WILD-TYPE    8  233
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO               94                233
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    60  98
  19Q GAIN WILD-TYPE 168 233
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               158                401 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                98                233 
$`19Q GAIN MUTATED`
TCGA-04-1332 TCGA-04-1338 TCGA-04-1343 TCGA-04-1346 TCGA-04-1516 TCGA-04-1517 
       41.00        46.62        11.87        65.52        41.59        19.99 
TCGA-04-1519 TCGA-04-1525 TCGA-04-1536 TCGA-04-1542 TCGA-04-1648 TCGA-04-1652 
        0.79        38.37        29.10        84.20        28.64        31.86 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1674 TCGA-09-2043 TCGA-13-1408 TCGA-13-1410 
       30.51        17.98         8.55         6.18        55.23        81.01 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 TCGA-13-1492 TCGA-13-1495 TCGA-13-1501 
       87.06        61.71       124.44       125.56        90.38        43.20 
TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
       34.82        34.16        65.52        23.05        25.94        26.20 
TCGA-20-1682 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1026 
       27.52         2.93         2.66        47.54        49.68        26.83 
TCGA-23-1111 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1121 TCGA-23-1809 
        3.22        19.46        33.30        86.01         6.38         0.53 
TCGA-23-2645 TCGA-24-0982 TCGA-24-1105 TCGA-24-1417 TCGA-24-1426 TCGA-24-1428 
        4.50        22.32        47.41         7.82         5.36        17.39 
TCGA-24-1436 TCGA-24-1469 TCGA-24-1471 TCGA-24-1545 TCGA-24-1548 TCGA-24-1550 
        8.55         9.11         1.18        57.40        16.21        41.06 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1557 TCGA-24-1614 TCGA-24-1616 
       51.91        41.39        58.09        39.88        48.33        38.24 
TCGA-24-1843 TCGA-24-1845 TCGA-24-1847 TCGA-24-1850 TCGA-24-1923 TCGA-24-2020 
        3.48         3.81        11.28         5.52        22.68       152.02 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2261 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
       55.92        18.48         0.79        70.45        44.61         0.82 
TCGA-24-2295 TCGA-25-1312 TCGA-25-1314 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 
       33.11         1.02        33.01         2.01        34.98        65.00 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1628 
       37.97        33.96        12.99        15.02        18.58        20.61 
TCGA-25-2398 TCGA-29-1691 TCGA-29-1695 TCGA-29-1698 TCGA-29-1701 TCGA-29-1766 
       45.01        48.33        40.41        68.32        16.93        39.42 
TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1785 TCGA-29-2429 TCGA-29-2432 
       24.36        17.33        12.36        36.30        13.84        21.47 
TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1857 
       11.47        35.77        38.07        51.91         2.47         0.26 
TCGA-30-1859 TCGA-30-1860 TCGA-30-1867 TCGA-30-1892 TCGA-31-1959 TCGA-36-1578 
       48.10        44.91         1.22        48.79         2.20        27.85 
TCGA-36-2529 TCGA-36-2534 TCGA-36-2543 TCGA-36-2544 TCGA-36-2552 TCGA-42-2582 
       35.05        29.82         2.24        20.98        11.47        47.57 
TCGA-42-2589 TCGA-57-1582 TCGA-57-1586 TCGA-59-2348 TCGA-59-2351 TCGA-59-2355 
       42.02        24.03        22.32       180.20       116.12         2.14 
TCGA-61-1722 TCGA-61-1728 TCGA-61-1730 TCGA-61-1741 TCGA-61-1904 TCGA-61-1906 
        8.09        27.88         4.34        33.67         9.07        34.13 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1918 TCGA-61-2009 TCGA-61-2012 
       42.51        48.92        56.61        15.75        39.85        30.64 
TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2113 TCGA-OY-A56Q TCGA-WR-A838 
       58.39        60.62        65.52        22.22        18.94         9.99 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0367 TCGA-09-0369 TCGA-10-0926 TCGA-10-0933 
       29.16         9.47        17.98        35.57        25.91        14.66 
TCGA-13-0717 TCGA-13-0727 TCGA-13-0751 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 
       24.59        15.19        55.17        11.38        11.54        38.01 
TCGA-13-0791 TCGA-13-0794 TCGA-13-0802 TCGA-13-0883 TCGA-13-0885 TCGA-13-0888 
       40.24        63.09        51.02        68.94       111.39        92.42 
TCGA-13-0905 TCGA-13-0920 
      123.16        48.79 

$`19Q GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 
       13.81        20.52        11.87        43.92         1.81        49.15 
TCGA-04-1337 TCGA-04-1341 TCGA-04-1342 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 
        2.01         1.08        18.51        63.09        48.76        21.57 
TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 
       63.98        65.46         0.53        49.28        32.52        44.32 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1530 
       33.67        76.57       103.40        82.39        56.55       119.08 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 
       55.43        48.89        27.88        64.64        36.23        47.70 
TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       45.37         9.99        38.43        89.33        74.93        41.62 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 
       57.60        61.87        55.36         5.85         3.02        97.55 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
        6.12        35.15         4.54       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 
       39.75        20.94        26.93        12.46        77.10        81.17 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1409 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 
       28.54        83.31        57.27        17.46        32.35        54.64 
TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
       29.42        20.68        22.39        70.82        83.93        52.44 
TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 
       93.90         4.24       127.27        66.15       115.07        13.97 
TCGA-13-1505 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 
       65.69        80.15        44.68        54.25        14.53        80.02 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU 
       78.48        77.88        76.90        65.52        70.45         8.42 
TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-23-1023 TCGA-23-1024 
       72.20        25.38        19.10        16.70        40.54        15.39 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       32.09        49.41         8.81        29.13        18.90         2.76 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 TCGA-23-1119 TCGA-23-1120 
       51.35        54.51        31.20        68.68       129.96         4.27 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 
       39.09        33.47        58.13        24.95       115.89        87.48 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-24-0966 
       91.66        77.00        49.84         2.76         4.70         7.63 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 
       11.64        21.80        41.56         7.66        54.12        63.55 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 
        6.31         6.38         7.99         7.86         0.76         6.25 
TCGA-24-1424 TCGA-24-1425 TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 
        6.02         5.95         4.83        28.37        18.64        18.67 
TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 
       43.53        72.92        12.46        45.14       105.99         3.45 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1546 TCGA-24-1549 TCGA-24-1555 TCGA-24-1556 
       22.22        26.96        64.27        56.58        88.50        70.62 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 
       19.53        44.09        45.50        47.70        25.87        10.26 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1842 TCGA-24-1844 TCGA-24-1846 
       17.23        90.15        88.37         8.32         3.72         4.37 
TCGA-24-1849 TCGA-24-1920 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 
        5.79         9.80        30.21        16.44        11.05        81.11 
TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 
        4.87        44.84        58.16        34.82       109.71        14.43 
TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 
       28.18        64.01        44.52        57.07        36.16         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 
       47.54        31.63        67.36        36.23        16.64        55.86 
TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1322 TCGA-25-1625 
       53.26        26.96        52.04        42.05         2.99        27.62 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
       17.03        12.95        38.20         0.30        59.15        62.17 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 
       35.87        52.04        14.96        24.99        24.00        85.05 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 
       13.02        49.05         1.02        38.04         3.02        12.00 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       19.99        42.02         2.96        29.03        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 
       78.90        47.61       101.79        39.02        33.93        31.20 
TCGA-29-1699 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 
       36.36        23.93        59.67        18.25        41.98        31.27 
TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1768 
       34.62        17.36        86.60        66.81        62.93        31.30 
TCGA-29-1769 TCGA-29-1771 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 
       22.98        22.55        11.84        12.30        14.93         8.38 
TCGA-29-1783 TCGA-29-1784 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 
        7.23         5.36        86.17        65.00        62.47        45.11 
TCGA-29-2431 TCGA-29-2436 TCGA-30-1853 TCGA-30-1856 TCGA-30-1861 TCGA-30-1862 
       42.25         9.76        36.26        15.68        34.78         6.12 
TCGA-30-1866 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-31-1944 TCGA-31-1946 
       36.62        57.57        24.26        30.05        45.57        30.18 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 
       18.77        22.49         6.71        42.51        44.12        28.77 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 
       29.10        21.53        22.85        22.55         8.55        30.08 
TCGA-36-1577 TCGA-36-1580 TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 TCGA-36-2537 
       25.74        24.23        24.69        33.01        29.49        25.91 
TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 
       25.08        23.80        21.60        18.31        20.52        14.17 
TCGA-36-2549 TCGA-36-2551 TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 TCGA-42-2591 
        6.05        16.18        23.74        28.93        10.42        40.77 
TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 TCGA-57-1993 
        1.48        11.38        21.14         1.74        29.00        25.08 
TCGA-57-1994 TCGA-59-2349 TCGA-59-2350 TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 
       25.02        80.12        22.32         9.40        34.39         5.42 
TCGA-59-2372 TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1733 
       44.81        11.11        20.94        31.43        18.54        31.79 
TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1743 
       28.47        48.79        44.84        35.80         2.43        43.69 
TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1907 
        1.45         8.42         5.79        11.41        13.02        31.30 
TCGA-61-1910 TCGA-61-1915 TCGA-61-1917 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
       37.05        67.76        43.43        38.17         2.01         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2016 TCGA-61-2017 
       14.50        17.98         4.01        30.64         1.18        45.96 
TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       45.40         4.80         4.77        51.72        71.74        61.64 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       55.50         6.48        76.87        20.68        44.52       125.75 
TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-VG-A8LO TCGA-09-0366 
        6.35        31.07         8.61        39.68         0.79        57.76 
TCGA-10-0925 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 
       54.31        81.86        18.51        34.19        32.88         6.71 
TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 
       35.44        36.92        19.99        20.91         6.21        44.55 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0730 TCGA-13-0755 
       39.58         2.73        12.39        31.20        17.82         2.50 
TCGA-13-0757 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0792 
       11.18       111.78        61.84        56.71        58.65       118.42 
TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
      107.28        20.35        69.73        83.34        87.48        45.99 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0884 TCGA-13-0886 
       43.86        35.28        35.31        13.61       107.18       153.37 
TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 
       66.67        95.15       145.45       102.84        43.36        71.74 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 
       66.15       134.04        19.36       127.79        50.37       118.98 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       60.59       116.65        44.55        37.64       109.32        58.68 
TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       84.53        48.76        83.74        85.94        25.41 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.26               0.30 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            180.20             153.37 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            30.575             33.470 
[1] "0.3 - 180.2 (30.6)" "0.3 - 153.4 (33.5)"
[1] "hr=" "1.3"
D35V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  19Q GAIN MUTATED         1   157                2
  19Q GAIN WILD-TYPE       2   401                0
D35V3, multiclass
                  clus
vv                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  OMENTUM                         1                  2
  OVARY                         157                401
  PERITONEUM OVARY                2                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V4, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED   150   3
  19Q GAIN WILD-TYPE 391   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED    150    3
  19Q GAIN WILD-TYPE  391    2
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO               150                391
  YES                3                  2
[1] 2 2
[1] FALSE
D35V5, continuous
                    vv
clus                 R0 R1 R2 RX
  19Q GAIN MUTATED    5  7  0  1
  19Q GAIN WILD-TYPE 10 19  5  2
D35V6, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0                5                 10
  R1                7                 19
  R2                0                  5
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     2  91
  19Q GAIN WILD-TYPE   8 236
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2   91
  19Q GAIN WILD-TYPE    8  236
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO               91                236
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   103 177
  20P GAIN WILD-TYPE 125 154
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               280                279 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               177                154 
$`20P GAIN MUTATED`
TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1337 TCGA-04-1338 
       20.52        11.87        43.92        41.00         2.01        46.62 
TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 
        1.08        18.51        11.87        65.52        63.09        21.57 
TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1364 TCGA-04-1514 TCGA-04-1517 
       63.98        65.46        49.28        33.67        56.55        19.99 
TCGA-04-1542 TCGA-04-1646 TCGA-04-1649 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 
       84.20        27.88        64.64        45.37         9.99        38.43 
TCGA-09-1665 TCGA-09-1668 TCGA-09-1670 TCGA-09-1674 TCGA-09-2043 TCGA-09-2051 
       41.62        55.36        17.98         8.55         6.18        63.09 
TCGA-09-2053 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1481 TCGA-13-1482 
       39.75        83.31        55.23        57.27        87.06        61.71 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1492 TCGA-13-1497 
      124.44        20.68        22.39        70.82       125.56       127.27 
TCGA-13-1499 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-2057 
      115.07        34.82        65.69        34.16        65.52        80.02 
TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-1685 
       76.90        65.52         8.42        25.94        26.20        16.70 
TCGA-20-1686 TCGA-23-1021 TCGA-23-1022 TCGA-23-1024 TCGA-23-1031 TCGA-23-1032 
        2.93        47.54        49.68        15.39        18.90         2.76 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 TCGA-23-1121 TCGA-23-1122 
       51.35        54.51         3.22        68.68         6.38        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2084 TCGA-23-2643 
       33.47        58.13         0.53       115.89        49.84         4.70 
TCGA-23-2645 TCGA-24-0975 TCGA-24-0982 TCGA-24-1105 TCGA-24-1413 TCGA-24-1422 
        4.50        21.80        22.32        47.41         6.31         0.76 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 
        6.25         6.02        28.37        18.64        18.67         8.55 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 
       12.46        45.14         9.11        22.22        26.96        57.40 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 TCGA-24-1564 
       64.27        16.21        58.09        70.62        39.88        25.87 
TCGA-24-1604 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 
       88.37         8.32         3.48         3.72         3.81        11.28 
TCGA-24-1850 TCGA-24-1923 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 
        5.52        22.68        11.05        81.11         4.87       152.02 
TCGA-24-2026 TCGA-24-2027 TCGA-24-2030 TCGA-24-2033 TCGA-24-2260 TCGA-24-2261 
       34.82       109.71        55.92        18.48        36.16         0.79 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 
       70.45        44.61         0.82        67.36        36.23        16.64 
TCGA-24-2295 TCGA-25-1312 TCGA-25-1313 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
       33.11         1.02        26.96        42.05         2.01        34.98 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 
       65.00        37.97        33.96         2.99        12.99        15.02 
TCGA-25-1623 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 
       18.58        17.03        12.95        20.61         0.30        59.15 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
       62.17        35.87        52.04        14.96        24.99        24.00 
TCGA-25-1878 TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 TCGA-25-2400 TCGA-25-2404 
       85.05        38.04         3.02        45.01        42.02        29.03 
TCGA-25-2408 TCGA-29-1688 TCGA-29-1691 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 
       31.00        78.90        48.33        40.41        31.20        68.32 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 TCGA-29-1707 TCGA-29-1710 TCGA-29-1761 
       36.36        16.93        59.67        41.98        31.27        17.36 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 TCGA-29-1775 
       66.81        62.93        39.42        22.98        24.36        12.36 
TCGA-29-1778 TCGA-29-1783 TCGA-29-1784 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 
       14.93         7.23         5.36        86.17        65.00        45.11 
TCGA-29-2429 TCGA-29-2431 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 
       13.84        42.25        35.77        38.07        51.91         2.47 
TCGA-30-1856 TCGA-30-1859 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 
       15.68        48.10        34.78         6.12        36.62         1.22 
TCGA-30-1892 TCGA-31-1950 TCGA-31-1951 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 
       48.79        18.77        22.49         2.20        28.77        29.10 
TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1580 TCGA-36-2534 TCGA-36-2547 
       22.85         8.55        30.08        24.23        29.82        20.52 
TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 TCGA-42-2590 TCGA-42-2593 
       14.17        16.18        11.47        23.74        10.42         1.48 
TCGA-57-1583 TCGA-57-1585 TCGA-57-1586 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 
       11.38         1.74        22.32       116.12         9.40         2.14 
TCGA-59-2363 TCGA-59-2372 TCGA-61-1722 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 
        5.42        44.81         8.09        18.54        27.88         4.34 
TCGA-61-1733 TCGA-61-1743 TCGA-61-1899 TCGA-61-1900 TCGA-61-1903 TCGA-61-1904 
       31.79        43.69         8.42         5.79        13.02         9.07 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1911 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 
       34.13        31.30        42.51        56.61        67.76        43.43 
TCGA-61-1918 TCGA-61-1919 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 
       15.75        38.17         4.01        30.64        39.85        30.64 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2113 
       60.62        65.52        55.50         6.48        76.87        22.22 
TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-09-0366 
        6.35         8.61        39.68        18.94         0.79        57.76 
TCGA-09-0367 TCGA-09-0369 TCGA-10-0933 TCGA-10-0935 TCGA-10-0936 TCGA-10-0938 
       17.98        35.57        14.66        35.44        36.92        20.91 
TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0727 TCGA-13-0751 
       24.59        39.58         2.73        12.39        15.19        55.17 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 
       11.18        11.38        11.54       111.78        61.84        56.71 
TCGA-13-0794 TCGA-13-0800 TCGA-13-0802 TCGA-13-0803 TCGA-13-0884 TCGA-13-0885 
       63.09        87.48        51.02        43.86       107.18       111.39 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 TCGA-13-0899 TCGA-13-0904 TCGA-13-0913 
       66.67        92.42       145.45        66.15        50.37       109.32 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 
       84.53        48.79        83.74        85.94 

$`20P GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-04-1335 TCGA-04-1336 TCGA-04-1348 TCGA-04-1353 TCGA-04-1361 
       13.81         1.81        49.15        48.76         0.53        32.52 
TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1516 TCGA-04-1519 
       44.32        76.57       103.40        82.39        41.59         0.79 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 
       38.37       119.08        29.10        55.43        48.89        28.64 
TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 
       36.23        31.86        47.70        89.33        74.93        57.60 
TCGA-09-1667 TCGA-09-1669 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 TCGA-09-2044 
       61.87        30.51         5.85         3.02        97.55         6.12 
TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2054 TCGA-09-2055 
       35.15         4.54       112.41        71.11        20.94        26.93 
TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1410 TCGA-13-1411 
       12.46        77.10        81.17        28.54        81.01        17.46 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1483 TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 
       32.35        54.64        29.42        83.93        52.44        93.90 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1509 
       90.38         4.24        66.15        13.97        43.20        80.15 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2060 TCGA-13-A5FT 
       44.68        54.25        14.53        78.48        77.88        70.45 
TCGA-20-0987 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1687 
       23.05        72.20        27.52        25.38        19.10         2.66 
TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
       40.54        26.83        32.09        49.41         8.81        29.13 
TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 
       31.20        19.46        33.30        86.01       129.96         4.27 
TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2641 TCGA-24-0966 
       24.95        87.48        91.66        77.00         2.76         7.63 
TCGA-24-0970 TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 TCGA-24-1416 
       11.64        41.56         7.66        54.12        63.55         6.38 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        7.82         7.99         7.86         5.95         5.36         4.83 
TCGA-24-1428 TCGA-24-1435 TCGA-24-1463 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 
       17.39        43.53        72.92       105.99         3.45         1.18 
TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 TCGA-24-1558 
       56.58        41.06        51.91        41.39        88.50        19.53 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       44.09        45.50        47.70        10.26        17.23        90.15 
TCGA-24-1614 TCGA-24-1616 TCGA-24-1846 TCGA-24-1849 TCGA-24-1920 TCGA-24-1924 
       48.33        38.24         4.37         5.79         9.80        30.21 
TCGA-24-1927 TCGA-24-2023 TCGA-24-2024 TCGA-24-2029 TCGA-24-2035 TCGA-24-2036 
       16.44        44.84        58.16        14.43        28.18        64.01 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2297 
       44.52        57.07         0.36        47.54        31.63        55.86 
TCGA-24-2298 TCGA-25-1314 TCGA-25-1315 TCGA-25-1625 TCGA-25-1630 TCGA-25-2042 
       53.26        33.01        52.04        27.62        38.20        13.02 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2397 TCGA-25-2399 TCGA-25-2401 TCGA-25-2409 
       49.05         1.02        12.00        19.99         2.96        26.99 
TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1702 TCGA-29-1705 
       47.61       101.79        39.02        33.93        23.93        18.25 
TCGA-29-1711 TCGA-29-1762 TCGA-29-1768 TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 
       34.62        86.60        31.30        22.55        17.33        11.84 
TCGA-29-1777 TCGA-29-1781 TCGA-29-1785 TCGA-29-2427 TCGA-29-2432 TCGA-29-2434 
       12.30         8.38        36.30        62.47        21.47        11.47 
TCGA-29-2436 TCGA-30-1853 TCGA-30-1857 TCGA-30-1860 TCGA-30-1880 TCGA-30-1887 
        9.76        36.26         0.26        44.91        57.57        24.26 
TCGA-30-1891 TCGA-31-1944 TCGA-31-1946 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 
       30.05        45.57        30.18         6.71        42.51        44.12 
TCGA-36-1570 TCGA-36-1574 TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 
       21.53        22.55        25.74        27.85        24.69        35.05 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 
       33.01        29.49        25.91        25.08        23.80        21.60 
TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2549 TCGA-42-2582 TCGA-42-2588 
        2.24        20.98        18.31         6.05        47.57        28.93 
TCGA-42-2589 TCGA-42-2591 TCGA-57-1582 TCGA-57-1584 TCGA-57-1992 TCGA-57-1993 
       42.02        40.77        24.03        21.14        29.00        25.08 
TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2354 TCGA-61-1721 
       25.02       180.20        80.12        22.32        34.39        11.11 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
       20.94        31.43        28.47        48.79        44.84        35.80 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 TCGA-61-1901 TCGA-61-1910 TCGA-61-1913 
        2.43        33.67         1.45        11.41        37.05        48.92 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2016 TCGA-61-2017 
        2.01         5.52        14.50        17.98         1.18        45.96 
TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       45.40         4.80         4.77        51.72        71.74        61.64 
TCGA-61-2096 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2613 TCGA-WR-A838 
       58.39        20.68        44.52       125.75        31.07         9.99 
TCGA-09-0364 TCGA-09-0365 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       29.16         9.47        54.31        25.91        81.86        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 TCGA-10-0937 TCGA-13-0714 TCGA-13-0720 
       34.19        32.88         6.71        19.99         6.21        44.55 
TCGA-13-0726 TCGA-13-0730 TCGA-13-0755 TCGA-13-0761 TCGA-13-0768 TCGA-13-0791 
       31.20        17.82         2.50        38.01        58.65        40.24 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 
      118.42       107.28        20.35        69.73        83.34        45.99 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0886 TCGA-13-0889 
       35.28        35.31        13.61        68.94       153.37        95.15 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
      102.84        43.36        71.74       134.04        19.36       127.79 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
      123.16       118.98        60.59       116.65        44.55        37.64 
TCGA-13-0916 TCGA-13-0921 TCGA-13-2071 
       58.68        48.76        25.41 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.30               0.26 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            152.02             180.20 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            31.285             33.010 
[1] "0.3 - 152.0 (31.3)" "0.3 - 180.2 (33.0)"
[1] "hr=" "1.2"
D36V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  20P GAIN MUTATED         3   278                1
  20P GAIN WILD-TYPE       0   280                1
D36V3, multiclass
                  clus
vv                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  OMENTUM                         3                  0
  OVARY                         278                280
  PERITONEUM OVARY                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V4, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   272   1
  20P GAIN WILD-TYPE 269   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    272    1
  20P GAIN WILD-TYPE  269    4
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO               272                269
  YES                1                  4
[1] 2 2
[1] FALSE
D36V5, continuous
                    vv
clus                 R0 R1 R2 RX
  20P GAIN MUTATED    6 12  4  1
  20P GAIN WILD-TYPE  9 14  1  2
D36V6, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0                6                  9
  R1               12                 14
  R2                4                  1
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     4 160
  20P GAIN WILD-TYPE   6 167
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      4  160
  20P GAIN WILD-TYPE    6  167
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  6
  NOT HISPANIC OR LATINO              160                167
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   127 190
  20Q GAIN WILD-TYPE 101 141
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               317                242 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               190                141 
$`20Q GAIN MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1337 
       13.81        20.52        11.87        43.92        41.00         2.01 
TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 
       46.62         1.08        18.51        11.87        65.52        63.09 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1364 
       21.57        63.98        65.46         0.53        49.28        33.67 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 TCGA-04-1525 TCGA-04-1542 TCGA-04-1646 
       82.39        56.55        19.99        38.37        84.20        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1652 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 
       28.64        64.64        31.86        45.37         9.99        38.43 
TCGA-09-1665 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1674 TCGA-09-2051 
       41.62        55.36        30.51        17.98         8.55        63.09 
TCGA-09-2053 TCGA-13-1403 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
       39.75        77.10        83.31        55.23        57.27        81.01 
TCGA-13-1412 TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 
       32.35        87.06        61.71       124.44        20.68        22.39 
TCGA-13-1492 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
      125.56       115.07        43.20        34.82        65.69        34.16 
TCGA-13-1507 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FU 
       65.52        80.02        77.88        76.90        65.52         8.42 
TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 
       25.94        26.20        27.52        16.70         2.93        47.54 
TCGA-23-1022 TCGA-23-1024 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 
       49.68        15.39        18.90         2.76        51.35        54.51 
TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1121 TCGA-23-1122 
        3.22        68.68        19.46        33.30         6.38        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2079 TCGA-23-2084 
       33.47        58.13         0.53       115.89        91.66        49.84 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0975 TCGA-24-0982 TCGA-24-1103 TCGA-24-1105 
        4.70         4.50        21.80        22.32        54.12        47.41 
TCGA-24-1413 TCGA-24-1417 TCGA-24-1418 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
        6.31         7.82         7.99         0.76         6.25         6.02 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1464 
        5.36         4.83        18.64        18.67         8.55        12.46 
TCGA-24-1466 TCGA-24-1469 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 
       45.14         9.11        22.22        26.96        57.40        64.27 
TCGA-24-1548 TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1604 
       16.21        58.09        70.62        39.88        19.53        88.37 
TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 TCGA-24-1849 
        8.32         3.48         3.72         3.81        11.28         5.79 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1928 TCGA-24-1930 
        5.52         9.80        22.68        30.21        11.05        81.11 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2026 TCGA-24-2027 TCGA-24-2033 TCGA-24-2260 
        4.87       152.02        34.82       109.71        18.48        36.16 
TCGA-24-2261 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 
        0.79        70.45        44.61         0.82        67.36        36.23 
TCGA-24-2293 TCGA-24-2295 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1316 
       16.64        33.11         1.02        26.96        33.01        42.05 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 
        2.01        34.98        65.00        37.97        33.96         2.99 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 
       12.99        15.02        18.58        17.03        12.95        20.61 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 
        0.30        59.15        62.17        35.87        52.04        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 
       24.99        24.00        85.05        38.04         3.02        45.01 
TCGA-25-2400 TCGA-25-2404 TCGA-25-2408 TCGA-29-1688 TCGA-29-1691 TCGA-29-1693 
       42.02        29.03        31.00        78.90        48.33       101.79 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 
       31.20        68.32        36.36        16.93        59.67        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1761 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 
       41.98        31.27        17.36        66.81        62.93        39.42 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1778 TCGA-29-1783 
       22.98        24.36        17.33        12.36        14.93         7.23 
TCGA-29-1784 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 
        5.36        86.17        65.00        45.11        13.84        42.25 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 
        9.76        35.77        38.07        51.91         2.47        15.68 
TCGA-30-1859 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1887 
       48.10        34.78         6.12        36.62         1.22        24.26 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1950 TCGA-31-1951 TCGA-31-1959 TCGA-36-1569 
       48.79        45.57        18.77        22.49         2.20        29.10 
TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1580 TCGA-36-1581 TCGA-36-2534 
       22.85         8.55        30.08        24.23        24.69        29.82 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 TCGA-42-2591 
       20.52        14.17        16.18        11.47        23.74        40.77 
TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 
        1.48        24.03        11.38         1.74        22.32        29.00 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2372 
       25.08        25.02       116.12         9.40         2.14        44.81 
TCGA-61-1722 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1737 
        8.09        18.54        27.88         4.34        31.79        44.84 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1899 TCGA-61-1900 TCGA-61-1903 TCGA-61-1904 
       33.67        43.69         8.42         5.79        13.02         9.07 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1911 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 
       34.13        31.30        42.51        56.61        67.76        43.43 
TCGA-61-1918 TCGA-61-1919 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 
       15.75        38.17         4.01        30.64        39.85        30.64 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2113 
       60.62        65.52        55.50         6.48        76.87        22.22 
TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-09-0364 
        6.35         8.61        39.68        18.94         0.79        29.16 
TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-10-0933 TCGA-10-0935 TCGA-10-0936 
       57.76        17.98        35.57        14.66        35.44        36.92 
TCGA-10-0938 TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0727 
       20.91        24.59        39.58         2.73        12.39        15.19 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0762 
       17.82        55.17        11.18        11.38        11.54       111.78 
TCGA-13-0766 TCGA-13-0794 TCGA-13-0795 TCGA-13-0800 TCGA-13-0802 TCGA-13-0803 
       56.71        63.09        20.35        87.48        51.02        43.86 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 
      107.18       111.39       153.37        66.67        92.42       145.45 
TCGA-13-0893 TCGA-13-0899 TCGA-13-0901 TCGA-13-0905 TCGA-13-0906 TCGA-13-0911 
       43.36        66.15        19.36       123.16       118.98        44.55 
TCGA-13-0913 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 
      109.32        84.53        48.79        83.74        85.94 

$`20Q GAIN WILD-TYPE`
TCGA-04-1335 TCGA-04-1336 TCGA-04-1348 TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 
        1.81        49.15        48.76        32.52        44.32        76.57 
TCGA-04-1367 TCGA-04-1516 TCGA-04-1519 TCGA-04-1530 TCGA-04-1536 TCGA-04-1638 
      103.40        41.59         0.79       119.08        29.10        55.43 
TCGA-04-1644 TCGA-04-1651 TCGA-04-1654 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 
       48.89        36.23        47.70        89.33        74.93        57.60 
TCGA-09-1667 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 
       61.87         5.85         3.02        97.55         6.18         6.12 
TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2054 TCGA-09-2055 
       35.15         4.54       112.41        71.11        20.94        26.93 
TCGA-09-2056 TCGA-13-1404 TCGA-13-1405 TCGA-13-1411 TCGA-13-1477 TCGA-13-1483 
       12.46        81.17        28.54        17.46        54.64        29.42 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
       70.82        83.93        52.44        93.90        90.38         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
      127.27        66.15        13.97        80.15        44.68        54.25 
TCGA-13-1512 TCGA-13-2059 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0996 TCGA-20-1683 
       14.53        78.48        70.45        23.05        72.20        25.38 
TCGA-20-1684 TCGA-20-1687 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       19.10         2.66        40.54        26.83        32.09        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1113 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 
        8.81        29.13        31.20        86.01       129.96         4.27 
TCGA-23-2072 TCGA-23-2078 TCGA-23-2081 TCGA-23-2641 TCGA-24-0966 TCGA-24-0970 
       24.95        87.48        77.00         2.76         7.63        11.64 
TCGA-24-0979 TCGA-24-0980 TCGA-24-1104 TCGA-24-1416 TCGA-24-1419 TCGA-24-1425 
       41.56         7.66        63.55         6.38         7.86         5.95 
TCGA-24-1428 TCGA-24-1430 TCGA-24-1435 TCGA-24-1463 TCGA-24-1467 TCGA-24-1470 
       17.39        28.37        43.53        72.92       105.99         3.45 
TCGA-24-1471 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 
        1.18        56.58        41.06        51.91        41.39        88.50 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 
       44.09        45.50        47.70        25.87        10.26        17.23 
TCGA-24-1603 TCGA-24-1614 TCGA-24-1616 TCGA-24-1846 TCGA-24-1927 TCGA-24-2023 
       90.15        48.33        38.24         4.37        16.44        44.84 
TCGA-24-2024 TCGA-24-2029 TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
       58.16        14.43        55.92        28.18        64.01        44.52 
TCGA-24-2254 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2297 TCGA-24-2298 
       57.07         0.36        47.54        31.63        55.86        53.26 
TCGA-25-1315 TCGA-25-1625 TCGA-25-1630 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 
       52.04        27.62        38.20        13.02        49.05         1.02 
TCGA-25-2397 TCGA-25-2399 TCGA-25-2401 TCGA-25-2409 TCGA-29-1690 TCGA-29-1694 
       12.00        19.99         2.96        26.99        47.61        39.02 
TCGA-29-1695 TCGA-29-1696 TCGA-29-1702 TCGA-29-1711 TCGA-29-1762 TCGA-29-1768 
       40.41        33.93        23.93        34.62        86.60        31.30 
TCGA-29-1771 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1785 TCGA-29-2427 
       22.55        11.84        12.30         8.38        36.30        62.47 
TCGA-29-2432 TCGA-29-2434 TCGA-30-1853 TCGA-30-1857 TCGA-30-1860 TCGA-30-1880 
       21.47        11.47        36.26         0.26        44.91        57.57 
TCGA-30-1891 TCGA-31-1946 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 
       30.05        30.18         6.71        42.51        44.12        28.77 
TCGA-36-1570 TCGA-36-1574 TCGA-36-1577 TCGA-36-1578 TCGA-36-2529 TCGA-36-2530 
       21.53        22.55        25.74        27.85        35.05        33.01 
TCGA-36-2532 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 
       29.49        25.91        25.08        23.80        21.60         2.24 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2549 TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 
       20.98        18.31         6.05        47.57        28.93        42.02 
TCGA-42-2590 TCGA-57-1584 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2354 
       10.42        21.14       180.20        80.12        22.32        34.39 
TCGA-59-2363 TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1734 TCGA-61-1736 
        5.42        11.11        20.94        31.43        28.47        48.79 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1895 TCGA-61-1901 TCGA-61-1910 TCGA-61-1913 
       35.80         2.43         1.45        11.41        37.05        48.92 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2016 TCGA-61-2017 
        2.01         5.52        14.50        17.98         1.18        45.96 
TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       45.40         4.80         4.77        51.72        71.74        61.64 
TCGA-61-2096 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2613 TCGA-WR-A838 
       58.39        20.68        44.52       125.75        31.07         9.99 
TCGA-09-0365 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
        9.47        54.31        25.91        81.86        18.51        34.19 
TCGA-10-0931 TCGA-10-0934 TCGA-10-0937 TCGA-13-0714 TCGA-13-0720 TCGA-13-0726 
       32.88         6.71        19.99         6.21        44.55        31.20 
TCGA-13-0755 TCGA-13-0761 TCGA-13-0764 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 
        2.50        38.01        61.84        58.65        40.24       118.42 
TCGA-13-0793 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0804 TCGA-13-0805 
      107.28        69.73        83.34        45.99        35.28        35.31 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0889 TCGA-13-0891 TCGA-13-0897 TCGA-13-0900 
       13.61        68.94        95.15       102.84        71.74       134.04 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 TCGA-13-0916 
      127.79        50.37        60.59       116.65        37.64        58.68 
TCGA-13-0921 TCGA-13-2071 
       48.76        25.41 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.30               0.26 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            153.37             180.20 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              31.0               35.1 
[1] "0.3 - 153.4 (31.0)" "0.3 - 180.2 (35.1)"
[1] "hr=" "1.1"
D37V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  20Q GAIN MUTATED         3   316                1
  20Q GAIN WILD-TYPE       0   242                1
D37V3, multiclass
                  clus
vv                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  OMENTUM                         3                  0
  OVARY                         316                242
  PERITONEUM OVARY                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V4, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   307   2
  20Q GAIN WILD-TYPE 234   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    307    2
  20Q GAIN WILD-TYPE  234    3
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO               307                234
  YES                2                  3
[1] 2 2
[1] FALSE
D37V5, continuous
                    vv
clus                 R0 R1 R2 RX
  20Q GAIN MUTATED    7 12  4  2
  20Q GAIN WILD-TYPE  8 14  1  1
D37V6, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0                7                  8
  R1               12                 14
  R2                4                  1
  RX                2                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     4 182
  20Q GAIN WILD-TYPE   6 145
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      4  182
  20Q GAIN WILD-TYPE    6  145
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  6
  NOT HISPANIC OR LATINO              182                145
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    42  60
  21Q GAIN WILD-TYPE 186 271
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               102                457 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                60                271 
$`21Q GAIN MUTATED`
TCGA-04-1332 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1349 TCGA-04-1361 
       41.00        18.51        11.87        65.52        21.57        32.52 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1536 TCGA-09-1670 
       82.39        56.55        41.59        19.99        29.10        17.98 
TCGA-09-2043 TCGA-13-1408 TCGA-13-1410 TCGA-13-1496 TCGA-13-1499 TCGA-13-1504 
        6.18        55.23        81.01         4.24       115.07        34.82 
TCGA-13-1505 TCGA-13-1506 TCGA-13-2059 TCGA-20-0990 TCGA-20-0991 TCGA-20-1683 
       65.69        34.16        78.48        25.94        26.20        25.38 
TCGA-23-1021 TCGA-23-1110 TCGA-23-1116 TCGA-23-1119 TCGA-23-1121 TCGA-23-2078 
       47.54        54.51        19.46       129.96         6.38        87.48 
TCGA-23-2643 TCGA-24-0979 TCGA-24-1104 TCGA-24-1424 TCGA-24-1427 TCGA-24-1436 
        4.70        41.56        63.55         6.02         4.83         8.55 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1474 TCGA-24-1552 TCGA-24-1558 TCGA-24-1842 
       12.46        45.14        22.22        41.39        19.53         8.32 
TCGA-24-1843 TCGA-24-1844 TCGA-24-1847 TCGA-24-1923 TCGA-24-1928 TCGA-24-2019 
        3.48         3.72        11.28        22.68        11.05         4.87 
TCGA-24-2020 TCGA-24-2260 TCGA-24-2295 TCGA-25-1312 TCGA-25-1319 TCGA-25-1323 
      152.02        36.16        33.11         1.02        65.00        12.99 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1628 TCGA-25-1877 TCGA-25-2393 
       15.02        18.58        17.03        20.61        24.00        38.04 
TCGA-25-2401 TCGA-29-1698 TCGA-29-1701 TCGA-29-1707 TCGA-29-1762 TCGA-29-1764 
        2.96        68.32        16.93        41.98        86.60        62.93 
TCGA-29-1766 TCGA-29-1778 TCGA-29-2428 TCGA-30-1861 TCGA-30-1862 TCGA-30-1867 
       39.42        14.93        45.11        34.78         6.12         1.22 
TCGA-31-1959 TCGA-36-1571 TCGA-36-1578 TCGA-36-2529 TCGA-36-2542 TCGA-57-1585 
        2.20        22.85        27.85        35.05        21.60         1.74 
TCGA-61-1722 TCGA-61-1743 TCGA-61-1906 TCGA-61-1907 TCGA-61-1914 TCGA-61-1915 
        8.09        43.69        34.13        31.30        56.61        67.76 
TCGA-61-2003 TCGA-61-2101 TCGA-61-2102 TCGA-61-2111 TCGA-61-2614 TCGA-09-0365 
        4.01        55.50         6.48       125.75         8.61         9.47 
TCGA-09-0366 TCGA-10-0928 TCGA-10-0936 TCGA-13-0724 TCGA-13-0726 TCGA-13-0762 
       57.76        18.51        36.92         2.73        31.20       111.78 
TCGA-13-0768 TCGA-13-0795 TCGA-13-0888 TCGA-13-0890 TCGA-13-0904 TCGA-13-0911 
       58.65        20.35        92.42       145.45        50.37        44.55 

$`21Q GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 
       13.81        20.52        11.87        43.92         1.81        49.15 
TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1347 TCGA-04-1348 TCGA-04-1350 
        2.01        46.62         1.08        63.09        48.76        63.98 
TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
       65.46         0.53        49.28        44.32        33.67        76.57 
TCGA-04-1367 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 
      103.40         0.79        38.37       119.08        84.20        55.43 
TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 
       48.89        27.88        28.64        64.64        36.23        31.86 
TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       47.70        45.37         9.99        38.43        89.33        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1672 
       41.62        57.60        61.87        55.36        30.51         5.85 
TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 
        3.02         8.55        97.55         6.12        35.15         4.54 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 
      112.41        71.11        63.09        39.75        20.94        26.93 
TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1409 
       12.46        77.10        81.17        28.54        83.31        57.27 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
       17.46        32.35        54.64        87.06        61.71        29.42 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
      124.44        20.68        22.39        70.82        83.93        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 
      125.56        93.90        90.38       127.27        66.15        13.97 
TCGA-13-1501 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
       43.20        65.52        80.15        44.68        54.25        14.53 
TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU 
       80.02        77.88        76.90        65.52        70.45         8.42 
TCGA-20-0987 TCGA-20-0996 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 
       23.05        72.20        27.52        19.10        16.70         2.93 
TCGA-20-1687 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
        2.66        49.68        40.54        15.39        26.83        32.09 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 
       49.41         8.81        29.13        18.90         2.76        51.35 
TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 
        3.22        31.20        68.68        33.30        86.01         4.27 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 
       39.09        33.47        58.13         0.53        24.95       115.89 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2645 TCGA-24-0966 
       91.66        77.00        49.84         2.76         4.50         7.63 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1105 
       11.64        21.80         7.66        22.32        54.12        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 
        6.31         6.38         7.82         7.99         7.86         0.76 
TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 
        6.25         5.95         5.36        17.39        28.37        18.64 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1463 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 
       18.67        43.53        72.92       105.99         9.11         3.45 
TCGA-24-1471 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 
        1.18        26.96        57.40        64.27        16.21        56.58 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       41.06        51.91        58.09        88.50        70.62        39.88 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 
       44.09        45.50        47.70        25.87        10.26        17.23 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1845 TCGA-24-1846 
       90.15        88.37        48.33        38.24         3.81         4.37 
TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 
        5.79         5.52         9.80        30.21        16.44        81.11 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 
       44.84        58.16        34.82       109.71        14.43        55.92 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2261 
       18.48        28.18        64.01        44.52        57.07         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
        0.36        47.54        31.63        70.45        44.61         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 
       67.36        36.23        16.64        55.86        53.26        26.96 
TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1320 
       33.01        52.04        42.05         2.01        34.98        37.97 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1625 TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 
       33.96         2.99        27.62        12.95        38.20         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 
       59.15        62.17        35.87        52.04        14.96        24.99 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2396 TCGA-25-2397 
       85.05        13.02        49.05         1.02         3.02        12.00 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       45.01        19.99        42.02        29.03        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 
       78.90        47.61        48.33       101.79        39.02        40.41 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 
       33.93        31.20        36.36        23.93        59.67        18.25 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1763 TCGA-29-1768 TCGA-29-1769 
       31.27        34.62        17.36        66.81        31.30        22.98 
TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 
       24.36        22.55        17.33        12.36        11.84        12.30 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 
        8.38         7.23         5.36        36.30        86.17        65.00 
TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 
       62.47        13.84        42.25        21.47        11.47         9.76 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 
       35.77        38.07        51.91        36.26         2.47        15.68 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1866 TCGA-30-1880 TCGA-30-1887 
        0.26        48.10        44.91        36.62        57.57        24.26 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 
       30.05        48.79        45.57        30.18        18.77        22.49 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
        6.71        42.51        44.12        28.77        29.10        21.53 
TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1580 TCGA-36-1581 
       22.55         8.55        30.08        25.74        24.23        24.69 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       33.01        29.49        29.82        25.91        25.08        23.80 
TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 
        2.24        20.98        18.31        20.52        14.17         6.05 
TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 
       16.18        11.47        47.57        23.74        28.93        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 
       10.42        40.77         1.48        24.03        11.38        21.14 
TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 
       22.32        29.00        25.08        25.02       180.20        80.12 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       22.32       116.12         9.40        34.39         2.14         5.42 
TCGA-59-2372 TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 
       44.81        11.11        20.94        31.43        18.54        27.88 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
        4.34        31.79        28.47        48.79        44.84        35.80 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 
        2.43        33.67         1.45         8.42         5.79        11.41 
TCGA-61-1903 TCGA-61-1904 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1917 
       13.02         9.07        37.05        42.51        48.92        43.43 
TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       15.75        38.17         2.01         5.52        14.50        17.98 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
       30.64        39.85        30.64         1.18        45.96        45.40 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 
        4.80         4.77        51.72        71.74        61.64        58.39 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2113 
       60.62        65.52        76.87        20.68        44.52        22.22 
TCGA-61-2612 TCGA-61-2613 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
        6.35        31.07        39.68        18.94         0.79         9.99 
TCGA-09-0364 TCGA-09-0367 TCGA-09-0369 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 
       29.16        17.98        35.57        54.31        25.91        81.86 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 
       34.19        32.88        14.66         6.71        35.44        19.99 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 
       20.91         6.21        24.59        44.55        39.58        12.39 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 
       15.19        17.82        55.17         2.50        11.18        11.38 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 
       11.54        38.01        61.84        56.71        40.24       118.42 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
      107.28        63.09        69.73        83.34        87.48        45.99 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
       51.02        43.86        35.28        35.31        13.61        68.94 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0891 
      107.18       111.39       153.37        66.67        95.15       102.84 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       43.36        71.74        66.15       134.04        19.36       127.79 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 
      123.16       118.98        60.59       116.65        37.64       109.32 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       58.68        84.53        48.79        48.76        83.74        85.94 
TCGA-13-2071 
       25.41 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              1.02               0.26 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            152.02             180.20 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            28.475             33.470 
[1] "1.0 - 152.0 (28.5)" "0.3 - 180.2 (33.5)"
[1] "hr=" "1.1"
D38V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  21Q GAIN MUTATED         0   102                2
  21Q GAIN WILD-TYPE       3   456                0
D38V3, multiclass
                  clus
vv                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  OMENTUM                         0                  3
  OVARY                         102                456
  PERITONEUM OVARY                2                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V4, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED   101   0
  21Q GAIN WILD-TYPE 440   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED    101    0
  21Q GAIN WILD-TYPE  440    5
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO               101                440
  YES                0                  5
[1] 2 2
[1] FALSE
D38V5, continuous
                    vv
clus                 R0 R1 R2 RX
  21Q GAIN MUTATED    1  5  0  0
  21Q GAIN WILD-TYPE 14 21  5  3
D38V6, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0                1                 14
  R1                5                 21
  R2                0                  5
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     2  55
  21Q GAIN WILD-TYPE   8 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      2   55
  21Q GAIN WILD-TYPE    8  272
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO               55                272
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    11  11
  22Q GAIN WILD-TYPE 217 320
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                22                537 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                11                320 
$`22Q GAIN MUTATED`
TCGA-13-1405 TCGA-13-1488 TCGA-23-1119 TCGA-23-2077 TCGA-24-1463 TCGA-24-1556 
       28.54        70.82       129.96       115.89        72.92        70.62 
TCGA-24-1928 TCGA-24-2290 TCGA-25-1627 TCGA-29-1699 TCGA-29-1764 TCGA-29-1770 
       11.05        36.23        12.95        36.36        62.93        24.36 
TCGA-29-1777 TCGA-29-2425 TCGA-29-2427 TCGA-30-1861 TCGA-31-1950 TCGA-36-2547 
       12.30        65.00        62.47        34.78        18.77        20.52 
TCGA-57-1585 TCGA-61-1904 TCGA-13-0760 TCGA-13-0762 
        1.74         9.07        11.54       111.78 

$`22Q GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 
       49.15         2.01        46.62         1.08        18.51        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 
       65.52        63.09        48.76        21.57        63.98        65.46 
TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
        0.53        49.28        32.52        44.32        33.67        76.57 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 
      103.40        82.39        56.55        41.59        19.99         0.79 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 
       38.37       119.08        29.10        84.20        55.43        48.89 
TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 
       27.88        28.64        64.64        36.23        31.86        47.70 
TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       45.37         9.99        38.43        89.33        74.93        41.62 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 
       57.60        61.87        55.36        30.51        17.98         5.85 
TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 
        3.02         8.55        97.55         6.18         6.12        35.15 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 
        4.54       112.41        71.11        63.09        39.75        20.94 
TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 
       26.93        12.46        77.10        81.17        83.31        55.23 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
       57.27        81.01        17.46        32.35        54.64        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1489 
       61.71        29.42       124.44        20.68        22.39        83.93 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 
       52.44       125.56        93.90        90.38         4.24       127.27 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 
       66.15       115.07        13.97        43.20        34.82        65.69 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
       34.16        65.52        80.15        44.68        54.25        14.53 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT 
       80.02        78.48        77.88        76.90        65.52        70.45 
TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 
        8.42        23.05        25.94        26.20        72.20        27.52 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 
       25.38        19.10        16.70         2.93         2.66        47.54 
TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       49.68        40.54        15.39        26.83        32.09        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 
        8.81        29.13        18.90         2.76        51.35        54.51 
TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
        3.22        31.20        68.68        19.46        33.30        86.01 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 
        4.27         6.38        39.09        33.47        58.13         0.53 
TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
       24.95        87.48        91.66        77.00        49.84         2.76 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        4.70         4.50         7.63        11.64        21.80        41.56 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 
        7.66        22.32        54.12        63.55        47.41         6.31 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 
        6.38         7.82         7.99         7.86         0.76         6.25 
TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 
        6.02         5.95         5.36         4.83        17.39        28.37 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 
       18.64        18.67        43.53         8.55        12.46        45.14 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
      105.99         9.11         3.45         1.18        22.22        26.96 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 
       57.40        64.27        16.21        56.58        41.06        51.91 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 
       41.39        58.09        88.50        39.88        19.53        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       45.50        47.70        25.87        10.26        17.23        90.15 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
       88.37        48.33        38.24         8.32         3.48         3.72 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 
        3.81         4.37        11.28         5.79         5.52         9.80 
TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 
       22.68        30.21        16.44        81.11         4.87       152.02 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 
       44.84        58.16        34.82       109.71        14.43        55.92 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 
       18.48        28.18        64.01        44.52        57.07        36.16 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 
        0.79         0.36        47.54        31.63        70.45        44.61 
TCGA-24-2288 TCGA-24-2289 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 
        0.82        67.36        16.64        33.11        55.86        53.26 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
        1.02        26.96        33.01        52.04        42.05         2.01 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 
       34.98        65.00        37.97        33.96         2.99        12.99 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1628 TCGA-25-1630 
       15.02        18.58        27.62        17.03        20.61        38.20 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 
        0.30        59.15        62.17        35.87        52.04        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 
       24.99        24.00        85.05        13.02        49.05         1.02 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 
       38.04         3.02        12.00        45.01        19.99        42.02 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 
        2.96        29.03        31.00        26.99        78.90        47.61 
TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 
       48.33       101.79        39.02        40.41        33.93        31.20 
TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
       68.32        16.93        23.93        59.67        18.25        41.98 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1766 
       31.27        34.62        17.36        86.60        66.81        39.42 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 
       31.30        22.98        22.55        17.33        12.36        11.84 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 
       14.93         8.38         7.23         5.36        36.30        86.17 
TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 
       45.11        13.84        42.25        21.47        11.47         9.76 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 
       35.77        38.07        51.91        36.26         2.47        15.68 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 
        0.26        48.10        44.91         6.12        36.62         1.22 
TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 
       57.57        24.26        30.05        48.79        45.57        30.18 
TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 
       22.49         6.71        42.51        44.12         2.20        28.77 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 
       29.10        21.53        22.85        22.55         8.55        30.08 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 
       25.74        27.85        24.23        24.69        35.05        33.01 
TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 
       29.49        29.82        25.91        25.08        23.80        21.60 
TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 
        2.24        20.98        18.31        14.17         6.05        16.18 
TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
       11.47        47.57        23.74        28.93        42.02        10.42 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 
       40.77         1.48        24.03        11.38        21.14        22.32 
TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 
       29.00        25.08        25.02       180.20        80.12        22.32 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 
      116.12         9.40        34.39         2.14         5.42        44.81 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 
       11.11         8.09        20.94        31.43        18.54        27.88 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
        4.34        31.79        28.47        48.79        44.84        35.80 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
        2.43        33.67        43.69         1.45         8.42         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 
       11.41        13.02        34.13        31.30        37.05        42.51 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 
       48.92        56.61        67.76        43.43        15.75        38.17 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 
        2.01         5.52        14.50        17.98         4.01        30.64 
TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
       39.85        30.64         1.18        45.96        45.40         4.80 
TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 
        4.77        51.72        71.74        61.64        58.39        60.62 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       65.52        55.50         6.48        76.87        20.68        44.52 
TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P 
      125.75        22.22         6.35        31.07         8.61        39.68 
TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 
       18.94         0.79         9.99        29.16         9.47        57.76 
TCGA-09-0367 TCGA-09-0369 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       17.98        35.57        54.31        25.91        81.86        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 
       34.19        32.88        14.66         6.71        35.44        36.92 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 
       19.99        20.91         6.21        24.59        44.55        39.58 
TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
        2.73        12.39        31.20        15.19        17.82        55.17 
TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 
        2.50        11.18        11.38        38.01        61.84        56.71 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 
       58.65        40.24       118.42       107.28        63.09        20.35 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 
       69.73        83.34        87.48        45.99        51.02        43.86 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 
       35.28        35.31        13.61        68.94       107.18       111.39 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 
      153.37        66.67        92.42        95.15       145.45       102.84 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       43.36        71.74        66.15       134.04        19.36       127.79 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       50.37       123.16       118.98        60.59       116.65        44.55 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 
       37.64       109.32        58.68        84.53        48.79        48.76 
TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       83.74        85.94        25.41 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              1.74               0.26 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            129.96             180.20 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            35.505             32.520 
[1] "1.7 - 130.0 (35.5)" "0.3 - 180.2 (32.5)"
[1] "hr=" "1.5"
D39V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  22Q GAIN MUTATED         1    22                0
  22Q GAIN WILD-TYPE       2   536                2
D39V3, multiclass
                  clus
vv                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  OMENTUM                         1                  2
  OVARY                          22                536
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V4, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    20   0
  22Q GAIN WILD-TYPE 521   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     20    0
  22Q GAIN WILD-TYPE  521    5
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                20                521
  YES                0                  5
[1] 2 2
[1] FALSE
D39V5, continuous
                    vv
clus                 R0 R1 R2 RX
  22Q GAIN MUTATED    1  2  0  0
  22Q GAIN WILD-TYPE 14 24  5  3
D39V6, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0                1                 14
  R1                2                 24
  R2                0                  5
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     0  12
  22Q GAIN WILD-TYPE  10 315
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0   12
  22Q GAIN WILD-TYPE   10  315
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               12                315
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    29  48
  XP GAIN WILD-TYPE 199 283
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               77               482 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               48               283 
$`XP GAIN MUTATED`
TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1351 
       11.87        41.00         1.08        18.51        11.87        65.46 
TCGA-09-1674 TCGA-09-2043 TCGA-09-2045 TCGA-09-2048 TCGA-13-1409 TCGA-13-1485 
        8.55         6.18        35.15         4.54        57.27        20.68 
TCGA-13-1488 TCGA-13-1497 TCGA-13-1507 TCGA-13-2057 TCGA-13-2060 TCGA-13-2065 
       70.82       127.27        65.52        80.02        77.88        65.52 
TCGA-23-1110 TCGA-23-1114 TCGA-23-1117 TCGA-23-1122 TCGA-23-1124 TCGA-23-1809 
       54.51        68.68        33.30        39.09        58.13         0.53 
TCGA-23-2084 TCGA-24-1425 TCGA-24-1466 TCGA-24-1470 TCGA-24-1474 TCGA-24-1556 
       49.84         5.95        45.14         3.45        22.22        70.62 
TCGA-24-1564 TCGA-24-1604 TCGA-24-1843 TCGA-24-1924 TCGA-24-1927 TCGA-24-2038 
       25.87        88.37         3.48        30.21        16.44        44.52 
TCGA-24-2261 TCGA-24-2281 TCGA-25-1319 TCGA-25-1329 TCGA-25-1633 TCGA-25-1877 
        0.79        44.61        65.00        15.02        62.17        24.00 
TCGA-25-2398 TCGA-29-1691 TCGA-29-1764 TCGA-29-1766 TCGA-29-1776 TCGA-30-1855 
       45.01        48.33        62.93        39.42        11.84         2.47 
TCGA-30-1862 TCGA-30-1867 TCGA-36-2529 TCGA-42-2589 TCGA-57-1993 TCGA-59-2348 
        6.12         1.22        35.05        42.02        25.08       180.20 
TCGA-59-2372 TCGA-61-1722 TCGA-61-1741 TCGA-61-1900 TCGA-61-1911 TCGA-61-2109 
       44.81         8.09        33.67         5.79        42.51        20.68 
TCGA-VG-A8LO TCGA-10-0933 TCGA-10-0936 TCGA-13-0723 TCGA-13-0726 TCGA-13-0727 
        0.79        14.66        36.92        39.58        31.20        15.19 
TCGA-13-0751 TCGA-13-0768 TCGA-13-0800 TCGA-13-0884 TCGA-13-0890 TCGA-13-0897 
       55.17        58.65        87.48       107.18       145.45        71.74 
TCGA-13-0901 TCGA-13-0916 TCGA-13-0921 TCGA-13-0923 TCGA-13-2071 
       19.36        58.68        48.76        83.74        25.41 

$`XP GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 
       13.81        20.52        43.92         1.81        49.15         2.01 
TCGA-04-1338 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 
       46.62        65.52        63.09        48.76        21.57        63.98 
TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
        0.53        49.28        32.52        44.32        33.67        76.57 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 
      103.40        82.39        56.55        41.59        19.99         0.79 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 
       38.37       119.08        29.10        84.20        55.43        48.89 
TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 
       27.88        28.64        64.64        36.23        31.86        47.70 
TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       45.37         9.99        38.43        89.33        74.93        41.62 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 
       57.60        61.87        55.36        30.51        17.98         5.85 
TCGA-09-1673 TCGA-09-1675 TCGA-09-2044 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
        3.02        97.55         6.12       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 
       39.75        20.94        26.93        12.46        77.10        81.17 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
       28.54        83.31        55.23        81.01        17.46        32.35 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 
       54.64        87.06        61.71        29.42       124.44        22.39 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
       83.93        52.44       125.56        93.90        90.38         4.24 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 
       66.15       115.07        13.97        43.20        34.82        65.69 
TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 
       34.16        80.15        44.68        54.25        14.53        78.48 
TCGA-13-2061 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
       76.90        70.45         8.42        23.05        25.94        26.20 
TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 
       72.20        27.52        25.38        19.10        16.70         2.93 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
        2.66        47.54        49.68        40.54        15.39        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       32.09        49.41         8.81        29.13        18.90         2.76 
TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1118 TCGA-23-1119 
       51.35         3.22        31.20        19.46        86.01       129.96 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1123 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 
        4.27         6.38        33.47        24.95       115.89        87.48 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 
       91.66        77.00         2.76         4.70         4.50         7.63 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 
       11.64        21.80        41.56         7.66        22.32        54.12 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 
       63.55        47.41         6.31         6.38         7.82         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1426 TCGA-24-1427 
        7.86         0.76         6.25         6.02         5.36         4.83 
TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
       17.39        28.37        18.64        18.67        43.53         8.55 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1467 TCGA-24-1469 TCGA-24-1471 TCGA-24-1544 
       72.92        12.46       105.99         9.11         1.18        26.96 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 
       57.40        64.27        16.21        56.58        41.06        51.91 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 
       41.39        58.09        88.50        39.88        19.53        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1614 
       45.50        47.70        10.26        17.23        90.15        48.33 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 
       38.24         8.32         3.72         3.81         4.37        11.28 
TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1928 TCGA-24-1930 
        5.79         5.52         9.80        22.68        11.05        81.11 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 
        4.87       152.02        44.84        58.16        34.82       109.71 
TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2254 
       14.43        55.92        18.48        28.18        64.01        57.07 
TCGA-24-2260 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2288 
       36.16         0.36        47.54        31.63        70.45         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 
       67.36        36.23        16.64        33.11        55.86        53.26 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
        1.02        26.96        33.01        52.04        42.05         2.01 
TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1623 
       34.98        37.97        33.96         2.99        12.99        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
       27.62        17.03        12.95        20.61        38.20         0.30 
TCGA-25-1632 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 
       59.15        35.87        52.04        14.96        24.99        85.05 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 
       13.02        49.05         1.02        38.04         3.02        12.00 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       19.99        42.02         2.96        29.03        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       78.90        47.61       101.79        39.02        40.41        33.93 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 
       31.20        68.32        36.36        16.93        23.93        59.67 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 
       18.25        41.98        31.27        34.62        17.36        86.60 
TCGA-29-1763 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
       66.81        31.30        22.98        24.36        22.55        17.33 
TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
       12.36        12.30        14.93         8.38         7.23         5.36 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 
       36.30        86.17        65.00        62.47        45.11        13.84 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 
       42.25        21.47        11.47         9.76        35.77        38.07 
TCGA-30-1718 TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 
       51.91        36.26        15.68         0.26        48.10        44.91 
TCGA-30-1861 TCGA-30-1866 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 
       34.78        36.62        57.57        24.26        30.05        48.79 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 
       45.57        30.18        18.77        22.49         6.71        42.51 
TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 
       44.12         2.20        28.77        29.10        21.53        22.85 
TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 
       22.55         8.55        30.08        25.74        27.85        24.23 
TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
       24.69        33.01        29.49        29.82        25.91        25.08 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 
       23.80        21.60         2.24        20.98        18.31        20.52 
TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 
       14.17         6.05        16.18        11.47        47.57        23.74 
TCGA-42-2588 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 
       28.93        10.42        40.77         1.48        24.03        11.38 
TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1994 TCGA-59-2349 
       21.14         1.74        22.32        29.00        25.02        80.12 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       22.32       116.12         9.40        34.39         2.14         5.42 
TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 
       11.11        20.94        31.43        18.54        27.88         4.34 
TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 
       31.79        28.47        48.79        44.84        35.80         2.43 
TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 
       43.69         1.45         8.42        11.41        13.02         9.07 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 
       34.13        31.30        37.05        48.92        56.61        67.76 
TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       43.43        15.75        38.17         2.01         5.52        14.50 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 
       17.98         4.01        30.64        39.85        30.64         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 
       45.96        45.40         4.80         4.77        51.72        71.74 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 
       61.64        58.39        60.62        65.52        55.50         6.48 
TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 
       76.87        44.52       125.75        22.22         6.35        31.07 
TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 
        8.61        39.68        18.94         9.99        29.16         9.47 
TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 
       57.76        17.98        35.57        54.31        25.91        81.86 
TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 
       18.51        34.19        32.88         6.71        35.44        19.99 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 
       20.91         6.21        24.59        44.55         2.73        12.39 
TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 
       17.82         2.50        11.18        11.38        11.54        38.01 
TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
      111.78        61.84        56.71        40.24       118.42       107.28 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 
       63.09        20.35        69.73        83.34        45.99        51.02 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0885 
       43.86        35.28        35.31        13.61        68.94       111.39 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 
      153.37        66.67        92.42        95.15       102.84        43.36 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
       66.15       134.04       127.79        50.37       123.16       118.98 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0919 
       60.59       116.65        44.55        37.64       109.32        84.53 
TCGA-13-0920 TCGA-13-0924 
       48.79        85.94 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.53              0.26 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           180.20            153.37 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            39.09             31.71 
[1] "0.5 - 180.2 (39.1)" "0.3 - 153.4 (31.7)"
[1] "hr=" "1"  
D40V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  XP GAIN MUTATED         0    76                2
  XP GAIN WILD-TYPE       3   482                0
D40V3, multiclass
                  clus
vv                 XP GAIN MUTATED XP GAIN WILD-TYPE
  OMENTUM                        0                 3
  OVARY                         76               482
  PERITONEUM OVARY               2                 0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V4, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    74   1
  XP GAIN WILD-TYPE 467   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     74    1
  XP GAIN WILD-TYPE  467    4
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               74               467
  YES               1                 4
[1] 2 2
[1] FALSE
D40V5, continuous
                   vv
clus                R0 R1 R2 RX
  XP GAIN MUTATED    4  1  1  0
  XP GAIN WILD-TYPE 11 25  4  3
D40V6, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  R0               4                11
  R1               1                25
  R2               1                 4
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     1  48
  XP GAIN WILD-TYPE   9 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      1   48
  XP GAIN WILD-TYPE    9  279
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              48               279
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    43  65
  XQ GAIN WILD-TYPE 185 266
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              108               451 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               65               266 
$`XQ GAIN MUTATED`
TCGA-5X-AA5U TCGA-04-1342 TCGA-04-1346 TCGA-04-1351 TCGA-04-1525 TCGA-04-1652 
       11.87        18.51        65.52        65.46        38.37        31.86 
TCGA-04-1655 TCGA-09-1674 TCGA-09-2043 TCGA-09-2045 TCGA-09-2048 TCGA-13-1404 
       45.37         8.55         6.18        35.15         4.54        81.17 
TCGA-13-1409 TCGA-13-1485 TCGA-13-1488 TCGA-13-1504 TCGA-13-1505 TCGA-13-2057 
       57.27        20.68        70.82        34.82        65.69        80.02 
TCGA-13-2060 TCGA-13-2065 TCGA-20-0987 TCGA-20-0991 TCGA-20-1683 TCGA-20-1685 
       77.88        65.52        23.05        26.20        25.38        16.70 
TCGA-20-1686 TCGA-20-1687 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 
        2.93         2.66        51.35        54.51         3.22        68.68 
TCGA-23-1809 TCGA-23-2077 TCGA-23-2079 TCGA-23-2084 TCGA-24-1104 TCGA-24-1474 
        0.53       115.89        91.66        49.84        63.55        22.22 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1563 TCGA-24-1564 TCGA-24-1843 TCGA-24-1846 
       88.50        70.62        47.70        25.87         3.48         4.37 
TCGA-24-1924 TCGA-24-2033 TCGA-24-2038 TCGA-24-2261 TCGA-24-2281 TCGA-25-1319 
       30.21        18.48        44.52         0.79        44.61        65.00 
TCGA-25-1320 TCGA-25-1329 TCGA-25-1871 TCGA-25-1877 TCGA-25-2397 TCGA-25-2398 
       37.97        15.02        24.99        24.00        12.00        45.01 
TCGA-25-2400 TCGA-29-1691 TCGA-29-1699 TCGA-29-1702 TCGA-29-1710 TCGA-29-1764 
       42.02        48.33        36.36        23.93        31.27        62.93 
TCGA-29-1766 TCGA-29-1776 TCGA-29-1778 TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1855 
       39.42        11.84        14.93        35.77        51.91         2.47 
TCGA-30-1862 TCGA-30-1867 TCGA-30-1887 TCGA-31-1951 TCGA-36-2529 TCGA-57-1584 
        6.12         1.22        24.26        22.49        35.05        21.14 
TCGA-57-1586 TCGA-59-2348 TCGA-59-2372 TCGA-61-1722 TCGA-61-1741 TCGA-61-1899 
       22.32       180.20        44.81         8.09        33.67         8.42 
TCGA-61-1900 TCGA-61-1911 TCGA-61-1915 TCGA-61-2003 TCGA-61-2087 TCGA-61-2109 
        5.79        42.51        67.76         4.01         4.80        20.68 
TCGA-61-2612 TCGA-61-2614 TCGA-VG-A8LO TCGA-10-0927 TCGA-10-0933 TCGA-10-0936 
        6.35         8.61         0.79        81.86        14.66        36.92 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0727 TCGA-13-0751 TCGA-13-0757 
       24.59        44.55        39.58        15.19        55.17        11.18 
TCGA-13-0761 TCGA-13-0768 TCGA-13-0795 TCGA-13-0797 TCGA-13-0800 TCGA-13-0804 
       38.01        58.65        20.35        69.73        87.48        35.28 
TCGA-13-0884 TCGA-13-0890 TCGA-13-0897 TCGA-13-0901 TCGA-13-0916 TCGA-13-0921 
      107.18       145.45        71.74        19.36        58.68        48.76 

$`XQ GAIN WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 
       13.81        20.52        43.92        41.00         1.81        49.15 
TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1343 TCGA-04-1347 TCGA-04-1348 
        2.01        46.62         1.08        11.87        63.09        48.76 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 
       21.57        63.98         0.53        49.28        32.52        44.32 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 
       33.67        76.57       103.40        82.39        56.55        41.59 
TCGA-04-1517 TCGA-04-1519 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 
       19.99         0.79       119.08        29.10        84.20        55.43 
TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 
       48.89        27.88        28.64        64.64        36.23        47.70 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 
        9.99        38.43        89.33        74.93        41.62        57.60 
TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       61.87        55.36        30.51        17.98         5.85         3.02 
TCGA-09-1675 TCGA-09-2044 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 
       97.55         6.12       112.41        71.11        63.09        39.75 
TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1405 TCGA-13-1407 
       20.94        26.93        12.46        77.10        28.54        83.31 
TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
       55.23        81.01        17.46        32.35        54.64        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 
       61.71        29.42       124.44        22.39        83.93        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
      125.56        93.90        90.38         4.24       127.27        66.15 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
      115.07        13.97        43.20        34.16        65.52        80.15 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2061 TCGA-13-A5FT 
       44.68        54.25        14.53        78.48        76.90        70.45 
TCGA-13-A5FU TCGA-20-0990 TCGA-20-0996 TCGA-20-1682 TCGA-20-1684 TCGA-23-1021 
        8.42        25.94        72.20        27.52        19.10        47.54 
TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       49.68        40.54        15.39        26.83        32.09        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1113 TCGA-23-1116 
        8.81        29.13        18.90         2.76        31.20        19.46 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 
       33.30        86.01       129.96         4.27         6.38        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2078 TCGA-23-2081 TCGA-23-2641 
       33.47        58.13        24.95        87.48        77.00         2.76 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        4.70         4.50         7.63        11.64        21.80        41.56 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
        7.66        22.32        54.12        47.41         6.31         6.38 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
        7.82         7.99         7.86         0.76         6.25         6.02 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 
        5.95         5.36         4.83        17.39        28.37        18.64 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 
       18.67        43.53         8.55        72.92        12.46        45.14 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1544 TCGA-24-1545 
      105.99         9.11         3.45         1.18        26.96        57.40 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
       64.27        16.21        56.58        41.06        51.91        41.39 
TCGA-24-1553 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1565 
       58.09        39.88        19.53        44.09        45.50        10.26 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 
       17.23        90.15        88.37        48.33        38.24         8.32 
TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 
        3.72         3.81        11.28         5.79         5.52         9.80 
TCGA-24-1923 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 
       22.68        16.44        11.05        81.11         4.87       152.02 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 
       44.84        58.16        34.82       109.71        14.43        55.92 
TCGA-24-2035 TCGA-24-2036 TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 TCGA-24-2267 
       28.18        64.01        57.07        36.16         0.36        47.54 
TCGA-24-2271 TCGA-24-2280 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 
       31.63        70.45         0.82        67.36        36.23        16.64 
TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 
       33.11        55.86        53.26         1.02        26.96        33.01 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1321 TCGA-25-1322 
       52.04        42.05         2.01        34.98        33.96         2.99 
TCGA-25-1323 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 
       12.99        18.58        27.62        17.03        12.95        20.61 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 
       38.20         0.30        59.15        62.17        35.87        52.04 
TCGA-25-1870 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 
       14.96        85.05        13.02        49.05         1.02        38.04 
TCGA-25-2396 TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
        3.02        19.99         2.96        29.03        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       78.90        47.61       101.79        39.02        40.41        33.93 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
       31.20        68.32        16.93        59.67        18.25        41.98 
TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1768 TCGA-29-1769 
       34.62        17.36        86.60        66.81        31.30        22.98 
TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1777 TCGA-29-1781 
       24.36        22.55        17.33        12.36        12.30         8.38 
TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 
        7.23         5.36        36.30        86.17        65.00        62.47 
TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 
       45.11        13.84        42.25        21.47        11.47         9.76 
TCGA-30-1714 TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 
       38.07        36.26        15.68         0.26        48.10        44.91 
TCGA-30-1861 TCGA-30-1866 TCGA-30-1880 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 
       34.78        36.62        57.57        30.05        48.79        45.57 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 
       30.18        18.77         6.71        42.51        44.12         2.20 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 
       28.77        29.10        21.53        22.85        22.55         8.55 
TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2530 
       30.08        25.74        27.85        24.23        24.69        33.01 
TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 
       29.49        29.82        25.91        25.08        23.80        21.60 
TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 
        2.24        20.98        18.31        20.52        14.17         6.05 
TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 
       16.18        11.47        47.57        23.74        28.93        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1585 
       10.42        40.77         1.48        24.03        11.38         1.74 
TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 
       29.00        25.08        25.02        80.12        22.32       116.12 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-61-1721 TCGA-61-1724 
        9.40        34.39         2.14         5.42        11.11        20.94 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 
       31.43        18.54        27.88         4.34        31.79        28.47 
TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1743 TCGA-61-1895 
       48.79        44.84        35.80         2.43        43.69         1.45 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 
       11.41        13.02         9.07        34.13        31.30        37.05 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 
       48.92        56.61        43.43        15.75        38.17         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 
        5.52        14.50        17.98        30.64        39.85        30.64 
TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 
        1.18        45.96        45.40         4.77        51.72        71.74 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 
       61.64        58.39        60.62        65.52        55.50         6.48 
TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2613 TCGA-OY-A56P 
       76.87        44.52       125.75        22.22        31.07        39.68 
TCGA-OY-A56Q TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 
       18.94         9.99        29.16         9.47        57.76        17.98 
TCGA-09-0369 TCGA-10-0925 TCGA-10-0926 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       35.57        54.31        25.91        18.51        34.19        32.88 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0724 
        6.71        35.44        19.99        20.91         6.21         2.73 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0730 TCGA-13-0755 TCGA-13-0758 TCGA-13-0760 
       12.39        31.20        17.82         2.50        11.38        11.54 
TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
      111.78        61.84        56.71        40.24       118.42       107.28 
TCGA-13-0794 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0805 
       63.09        83.34        45.99        51.02        43.86        35.31 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 
       13.61        68.94       111.39       153.37        66.67        92.42 
TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 
       95.15       102.84        43.36        66.15       134.04       127.79 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       50.37       123.16       118.98        60.59       116.65        44.55 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 
       37.64       109.32        84.53        48.79        83.74        85.94 
TCGA-13-2071 
       25.41 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.53              0.26 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           180.20            153.37 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           34.935            32.350 
[1] "0.5 - 180.2 (34.9)" "0.3 - 153.4 (32.4)"
[1] "hr=" "1"  
D41V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  XQ GAIN MUTATED         1   105                2
  XQ GAIN WILD-TYPE       2   453                0
D41V3, multiclass
                  clus
vv                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  OMENTUM                        1                 2
  OVARY                        105               453
  PERITONEUM OVARY               2                 0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V4, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED   105   0
  XQ GAIN WILD-TYPE 436   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED    105    0
  XQ GAIN WILD-TYPE  436    5
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO              105               436
  YES               0                 5
[1] 2 2
[1] FALSE
D41V5, continuous
                   vv
clus                R0 R1 R2 RX
  XQ GAIN MUTATED    2  4  1  0
  XQ GAIN WILD-TYPE 13 22  4  3
D41V6, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0               2                13
  R1               4                22
  R2               1                 4
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     2  69
  XQ GAIN WILD-TYPE   8 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      2   69
  XQ GAIN WILD-TYPE    8  258
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 8
  NOT HISPANIC OR LATINO              69               258
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    24  35
  1P LOSS WILD-TYPE 204 296
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               59               500 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               35               296 
$`1P LOSS MUTATED`
TCGA-59-A5PD TCGA-04-1341 TCGA-04-1351 TCGA-04-1362 TCGA-04-1514 TCGA-04-1519 
       20.52         1.08        65.46        44.32        56.55         0.79 
TCGA-04-1542 TCGA-04-1638 TCGA-09-1669 TCGA-09-1672 TCGA-09-2056 TCGA-13-1409 
       84.20        55.43        30.51         5.85        12.46        57.27 
TCGA-13-1477 TCGA-13-1484 TCGA-13-1489 TCGA-13-1497 TCGA-13-2065 TCGA-20-1682 
       54.64       124.44        83.93       127.27        65.52        27.52 
TCGA-20-1686 TCGA-20-1687 TCGA-23-1022 TCGA-23-2643 TCGA-23-2645 TCGA-24-1103 
        2.93         2.66        49.68         4.70         4.50        54.12 
TCGA-24-1105 TCGA-24-1423 TCGA-24-1424 TCGA-24-1428 TCGA-24-1850 TCGA-24-2020 
       47.41         6.25         6.02        17.39         5.52       152.02 
TCGA-25-1316 TCGA-25-2396 TCGA-25-2408 TCGA-29-1690 TCGA-29-1705 TCGA-29-1768 
       42.05         3.02        31.00        47.61        18.25        31.30 
TCGA-29-2429 TCGA-30-1853 TCGA-30-1859 TCGA-30-1860 TCGA-36-1576 TCGA-36-1580 
       13.84        36.26        48.10        44.91        30.08        24.23 
TCGA-36-2540 TCGA-36-2543 TCGA-36-2552 TCGA-57-1585 TCGA-59-2352 TCGA-61-1727 
       23.80         2.24        11.47         1.74         9.40        18.54 
TCGA-61-1918 TCGA-61-2012 TCGA-61-2101 TCGA-61-2612 TCGA-WR-A838 TCGA-10-0928 
       15.75        30.64        55.50         6.35         9.99        18.51 
TCGA-10-0935 TCGA-13-0761 TCGA-13-0762 TCGA-13-0794 TCGA-13-0905 
       35.44        38.01       111.78        63.09       123.16 

$`1P LOSS WILD-TYPE`
TCGA-3P-A9WA TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 
       13.81        11.87        43.92        41.00         1.81        49.15 
TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 
        2.01        46.62        18.51        11.87        65.52        63.09 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 
       48.76        21.57        63.98         0.53        49.28        32.52 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1516 TCGA-04-1517 
       33.67        76.57       103.40        82.39        41.59        19.99 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 
       38.37       119.08        29.10        48.89        27.88        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 
       64.64        36.23        31.86        47.70        45.37         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 
       38.43        89.33        74.93        41.62        57.60        61.87 
TCGA-09-1668 TCGA-09-1670 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 
       55.36        17.98         3.02         8.55        97.55         6.18 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
        6.12        35.15         4.54       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
       39.75        20.94        26.93        77.10        81.17        28.54 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 
       83.31        55.23        81.01        17.46        32.35        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1491 
       61.71        29.42        20.68        22.39        70.82        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 
      125.56        93.90        90.38         4.24        66.15       115.07 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
       13.97        43.20        34.82        65.69        34.16        65.52 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 
       80.15        44.68        54.25        14.53        80.02        78.48 
TCGA-13-2060 TCGA-13-2061 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
       77.88        76.90        70.45         8.42        23.05        25.94 
TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-23-1021 
       26.20        72.20        25.38        19.10        16.70        47.54 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 
       40.54        15.39        26.83        32.09        49.41         8.81 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
       29.13        18.90         2.76        51.35        54.51         3.22 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 
       31.20        68.68        19.46        33.30        86.01       129.96 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 
        4.27         6.38        39.09        33.47        58.13         0.53 
TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 
       24.95       115.89        87.48        91.66        77.00        49.84 
TCGA-23-2641 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        2.76         7.63        11.64        21.80        41.56         7.66 
TCGA-24-0982 TCGA-24-1104 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 
       22.32        63.55         6.31         6.38         7.82         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1430 
        7.86         0.76         5.95         5.36         4.83        28.37 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 
       18.64        18.67        43.53         8.55        72.92        12.46 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 
       45.14       105.99         9.11         3.45         1.18        22.22 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 
       26.96        57.40        64.27        16.21        56.58        41.06 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       51.91        41.39        58.09        88.50        70.62        39.88 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 
       19.53        44.09        45.50        47.70        25.87        10.26 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 
       17.23        90.15        88.37        48.33        38.24         8.32 
TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 
        3.48         3.72         3.81         4.37        11.28         5.79 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 
        9.80        22.68        30.21        16.44        11.05        81.11 
TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 
        4.87        44.84        58.16        34.82       109.71        14.43 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 
       55.92        18.48        28.18        64.01        44.52        57.07 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       36.16         0.79         0.36        47.54        31.63        70.45 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 
       44.61         0.82        67.36        36.23        16.64        33.11 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 
       55.86        53.26         1.02        26.96        33.01        52.04 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 
        2.01        34.98        65.00        37.97        33.96         2.99 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 
       12.99        15.02        18.58        27.62        17.03        12.95 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
       20.61        38.20         0.30        59.15        62.17        35.87 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 
       52.04        14.96        24.99        24.00        85.05        13.02 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 
       49.05         1.02        38.04        12.00        45.01        19.99 
TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2409 TCGA-29-1688 TCGA-29-1691 
       42.02         2.96        29.03        26.99        78.90        48.33 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 
      101.79        39.02        40.41        33.93        31.20        68.32 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 TCGA-29-1710 
       36.36        16.93        23.93        59.67        41.98        31.27 
TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 
       34.62        17.36        86.60        66.81        62.93        39.42 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 
       22.98        24.36        22.55        17.33        12.36        11.84 
TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 
       12.30        14.93         8.38         7.23         5.36        36.30 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2431 TCGA-29-2432 
       86.17        65.00        62.47        45.11        42.25        21.47 
TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 
       11.47         9.76        35.77        38.07        51.91         2.47 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 
       15.68         0.26        34.78         6.12        36.62         1.22 
TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 
       57.57        24.26        30.05        48.79        45.57        30.18 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 
       18.77        22.49         6.71        42.51        44.12         2.20 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 
       28.77        29.10        21.53        22.85        22.55         8.55 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 
       25.74        27.85        24.69        35.05        33.01        29.49 
TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 
       29.82        25.91        25.08        21.60        20.98        18.31 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-42-2582 TCGA-42-2587 
       20.52        14.17         6.05        16.18        47.57        23.74 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 
       28.93        42.02        10.42        40.77         1.48        24.03 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 
       11.38        21.14        22.32        29.00        25.08        25.02 
TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2354 TCGA-59-2355 
      180.20        80.12        22.32       116.12        34.39         2.14 
TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
        5.42        44.81        11.11         8.09        20.94        31.43 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       27.88         4.34        31.79        28.47        48.79        44.84 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 
       35.80         2.43        33.67        43.69         1.45         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        5.79        11.41        13.02         9.07        34.13        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 
       37.05        42.51        48.92        56.61        67.76        43.43 
TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 
       38.17         2.01         5.52        14.50        17.98         4.01 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
       30.64        39.85         1.18        45.96        45.40         4.80 
TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 
        4.77        51.72        71.74        61.64        58.39        60.62 
TCGA-61-2098 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       65.52         6.48        76.87        20.68        44.52       125.75 
TCGA-61-2113 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
       22.22        31.07         8.61        39.68        18.94         0.79 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-10-0925 
       29.16         9.47        57.76        17.98        35.57        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       25.91        81.86        34.19        32.88        14.66         6.71 
TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
       36.92        19.99        20.91         6.21        24.59        44.55 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 
       39.58         2.73        12.39        31.20        15.19        17.82 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0764 
       55.17         2.50        11.18        11.38        11.54        61.84 
TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 
       56.71        58.65        40.24       118.42       107.28        20.35 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 
       69.73        83.34        87.48        45.99        51.02        43.86 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 
       35.28        35.31        13.61        68.94       107.18       111.39 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 
      153.37        66.67        92.42        95.15       145.45       102.84 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       43.36        71.74        66.15       134.04        19.36       127.79 
TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       50.37       118.98        60.59       116.65        44.55        37.64 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 
      109.32        58.68        84.53        48.79        48.76        83.74 
TCGA-13-0924 TCGA-13-2071 
       85.94        25.41 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.79              0.26 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           152.02            180.20 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           30.510            33.205 
[1] "0.8 - 152.0 (30.5)" "0.3 - 180.2 (33.2)"
[1] "hr=" "1"  
D42V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  1P LOSS MUTATED         0    60                0
  1P LOSS WILD-TYPE       3   498                2
D42V3, multiclass
                  clus
vv                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  OMENTUM                        0                 3
  OVARY                         60               498
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V4, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    55   1
  1P LOSS WILD-TYPE 486   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     55    1
  1P LOSS WILD-TYPE  486    4
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               55               486
  YES               1                 4
[1] 2 2
[1] FALSE
D42V5, continuous
                   vv
clus                R0 R1 R2 RX
  1P LOSS MUTATED    1  4  0  0
  1P LOSS WILD-TYPE 14 22  5  3
D42V6, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0               1                14
  R1               4                22
  R2               0                 5
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     2  35
  1P LOSS WILD-TYPE   8 292
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2   35
  1P LOSS WILD-TYPE    8  292
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 8
  NOT HISPANIC OR LATINO              35               292
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    14  24
  1Q LOSS WILD-TYPE 214 307
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               38               521 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               24               307 
$`1Q LOSS MUTATED`
TCGA-59-A5PD TCGA-04-1341 TCGA-04-1351 TCGA-04-1362 TCGA-04-1519 TCGA-13-1407 
       20.52         1.08        65.46        44.32         0.79        83.31 
TCGA-13-1477 TCGA-13-1489 TCGA-13-1497 TCGA-13-2065 TCGA-20-1682 TCGA-23-1022 
       54.64        83.93       127.27        65.52        27.52        49.68 
TCGA-23-1109 TCGA-23-2643 TCGA-23-2645 TCGA-24-1103 TCGA-24-1105 TCGA-24-1424 
       51.35         4.70         4.50        54.12        47.41         6.02 
TCGA-24-1428 TCGA-25-2408 TCGA-29-1705 TCGA-29-1768 TCGA-29-2429 TCGA-30-1853 
       17.39        31.00        18.25        31.30        13.84        36.26 
TCGA-30-1859 TCGA-30-1860 TCGA-36-1580 TCGA-36-2543 TCGA-57-1585 TCGA-59-2352 
       48.10        44.91        24.23         2.24         1.74         9.40 
TCGA-61-1727 TCGA-61-2012 TCGA-61-2612 TCGA-WR-A838 TCGA-10-0928 TCGA-13-0761 
       18.54        30.64         6.35         9.99        18.51        38.01 
TCGA-13-0794 TCGA-13-0905 
       63.09       123.16 

$`1Q LOSS WILD-TYPE`
TCGA-3P-A9WA TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 
       13.81        11.87        43.92        41.00         1.81        49.15 
TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 
        2.01        46.62        18.51        11.87        65.52        63.09 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 
       48.76        21.57        63.98         0.53        49.28        32.52 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 
       33.67        76.57       103.40        82.39        56.55        41.59 
TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 
       19.99        38.37       119.08        29.10        84.20        55.43 
TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 
       48.89        27.88        28.64        64.64        36.23        31.86 
TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       47.70        45.37         9.99        38.43        89.33        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 
       41.62        57.60        61.87        55.36        30.51        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 
        5.85         3.02         8.55        97.55         6.18         6.12 
TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 
       35.15         4.54       112.41        71.11        63.09        39.75 
TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
       20.94        26.93        12.46        77.10        81.17        28.54 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 
       55.23        57.27        81.01        17.46        32.35        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 
       61.71        29.42       124.44        20.68        22.39        70.82 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 
       52.44       125.56        93.90        90.38         4.24        66.15 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
      115.07        13.97        43.20        34.82        65.69        34.16 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 
       65.52        80.15        44.68        54.25        14.53        80.02 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
       78.48        77.88        76.90        70.45         8.42        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 
       25.94        26.20        72.20        25.38        19.10        16.70 
TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
        2.93         2.66        47.54        40.54        15.39        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       32.09        49.41         8.81        29.13        18.90         2.76 
TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 
       54.51         3.22        31.20        68.68        19.46        33.30 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 
       86.01       129.96         4.27         6.38        39.09        33.47 
TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 
       58.13         0.53        24.95       115.89        87.48        91.66 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 
       77.00        49.84         2.76         7.63        11.64        21.80 
TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1104 TCGA-24-1413 TCGA-24-1416 
       41.56         7.66        22.32        63.55         6.31         6.38 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 
        7.82         7.99         7.86         0.76         6.25         5.95 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 
        5.36         4.83        28.37        18.64        18.67        43.53 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 
        8.55        72.92        12.46        45.14       105.99         9.11 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 
        3.45         1.18        22.22        26.96        57.40        64.27 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 
       16.21        56.58        41.06        51.91        41.39        58.09 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 
       88.50        70.62        39.88        19.53        44.09        45.50 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 
       47.70        25.87        10.26        17.23        90.15        88.37 
TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 
       48.33        38.24         8.32         3.48         3.72         3.81 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 
        4.37        11.28         5.79         5.52         9.80        22.68 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 
       30.21        16.44        11.05        81.11         4.87       152.02 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 
       44.84        58.16        34.82       109.71        14.43        55.92 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 
       18.48        28.18        64.01        44.52        57.07        36.16 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 
        0.79         0.36        47.54        31.63        70.45        44.61 
TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 
        0.82        67.36        36.23        16.64        33.11        55.86 
TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 
       53.26         1.02        26.96        33.01        52.04        42.05 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 
        2.01        34.98        65.00        37.97        33.96         2.99 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 
       12.99        15.02        18.58        27.62        17.03        12.95 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
       20.61        38.20         0.30        59.15        62.17        35.87 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 
       52.04        14.96        24.99        24.00        85.05        13.02 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 
       49.05         1.02        38.04         3.02        12.00        45.01 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2409 TCGA-29-1688 
       19.99        42.02         2.96        29.03        26.99        78.90 
TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       47.61        48.33       101.79        39.02        40.41        33.93 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 
       31.20        68.32        36.36        16.93        23.93        59.67 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
       41.98        31.27        34.62        17.36        86.60        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
       62.93        39.42        22.98        24.36        22.55        17.33 
TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 
       12.36        11.84        12.30        14.93         8.38         7.23 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 
        5.36        36.30        86.17        65.00        62.47        45.11 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 
       42.25        21.47        11.47         9.76        35.77        38.07 
TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1861 TCGA-30-1862 
       51.91         2.47        15.68         0.26        34.78         6.12 
TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 
       36.62         1.22        57.57        24.26        30.05        48.79 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 
       45.57        30.18        18.77        22.49         6.71        42.51 
TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 
       44.12         2.20        28.77        29.10        21.53        22.85 
TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 
       22.55         8.55        30.08        25.74        27.85        24.69 
TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
       35.05        33.01        29.49        29.82        25.91        25.08 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 
       23.80        21.60        20.98        18.31        20.52        14.17 
TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
        6.05        16.18        11.47        47.57        23.74        28.93 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 
       42.02        10.42        40.77         1.48        24.03        11.38 
TCGA-57-1584 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 
       21.14        22.32        29.00        25.08        25.02       180.20 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       80.12        22.32       116.12        34.39         2.14         5.42 
TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1728 
       44.81        11.11         8.09        20.94        31.43        27.88 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
        4.34        31.79        28.47        48.79        44.84        35.80 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
        2.43        33.67        43.69         1.45         8.42         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 
       11.41        13.02         9.07        34.13        31.30        37.05 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 
       42.51        48.92        56.61        67.76        43.43        15.75 
TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 
       38.17         2.01         5.52        14.50        17.98         4.01 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
       30.64        39.85         1.18        45.96        45.40         4.80 
TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 
        4.77        51.72        71.74        61.64        58.39        60.62 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       65.52        55.50         6.48        76.87        20.68        44.52 
TCGA-61-2111 TCGA-61-2113 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
      125.75        22.22        31.07         8.61        39.68        18.94 
TCGA-VG-A8LO TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 
        0.79        29.16         9.47        57.76        17.98        35.57 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 
       54.31        25.91        81.86        34.19        32.88        14.66 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
        6.71        35.44        36.92        19.99        20.91         6.21 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 
       24.59        44.55        39.58         2.73        12.39        31.20 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 
       15.19        17.82        55.17         2.50        11.18        11.38 
TCGA-13-0760 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 
       11.54       111.78        61.84        56.71        58.65        40.24 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 
      118.42       107.28        20.35        69.73        83.34        87.48 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
       45.99        51.02        43.86        35.28        35.31        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 
       68.94       107.18       111.39       153.37        66.67        92.42 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 
       95.15       145.45       102.84        43.36        71.74        66.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 
      134.04        19.36       127.79        50.37       118.98        60.59 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
      116.65        44.55        37.64       109.32        58.68        84.53 
TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       48.79        48.76        83.74        85.94        25.41 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.79              0.26 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           127.27            180.20 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            30.82             33.01 
[1] "0.8 - 127.3 (30.8)" "0.3 - 180.2 (33.0)"
[1] "hr=" "1.2"
D43V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  1Q LOSS MUTATED         0    39                0
  1Q LOSS WILD-TYPE       3   519                2
D43V3, multiclass
                  clus
vv                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  OMENTUM                        0                 3
  OVARY                         39               519
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V4, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    34   1
  1Q LOSS WILD-TYPE 507   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     34    1
  1Q LOSS WILD-TYPE  507    4
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO               34               507
  YES               1                 4
[1] 2 2
[1] FALSE
D43V5, continuous
                   vv
clus                R0 R1 R2 RX
  1Q LOSS MUTATED    0  3  0  0
  1Q LOSS WILD-TYPE 15 23  5  3
D43V6, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0               0                15
  R1               3                23
  R2               0                 5
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     1  23
  1Q LOSS WILD-TYPE   9 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1   23
  1Q LOSS WILD-TYPE    9  304
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              23               304
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    14  37
  2P LOSS WILD-TYPE 214 294
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               51               508 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               37               294 
$`2P LOSS MUTATED`
TCGA-04-1343 TCGA-04-1349 TCGA-04-1362 TCGA-04-1514 TCGA-04-1517 TCGA-04-1536 
       11.87        21.57        44.32        56.55        19.99        29.10 
TCGA-09-1673 TCGA-13-1411 TCGA-13-1484 TCGA-13-1494 TCGA-13-1507 TCGA-20-0991 
        3.02        17.46       124.44        93.90        65.52        26.20 
TCGA-20-1682 TCGA-23-1116 TCGA-24-1413 TCGA-24-1464 TCGA-24-1563 TCGA-24-1614 
       27.52        19.46         6.31        12.46        47.70        48.33 
TCGA-24-1847 TCGA-24-1923 TCGA-24-1930 TCGA-24-2020 TCGA-24-2260 TCGA-24-2280 
       11.28        22.68        81.11       152.02        36.16        70.45 
TCGA-25-1313 TCGA-25-1318 TCGA-25-1321 TCGA-25-1627 TCGA-25-1878 TCGA-25-2392 
       26.96        34.98        33.96        12.95        85.05         1.02 
TCGA-29-1688 TCGA-29-1693 TCGA-29-1699 TCGA-29-1761 TCGA-29-1770 TCGA-30-1853 
       78.90       101.79        36.36        17.36        24.36        36.26 
TCGA-30-1860 TCGA-36-2545 TCGA-61-1743 TCGA-61-2016 TCGA-61-2087 TCGA-61-2109 
       44.91        18.31        43.69         1.18         4.80        20.68 
TCGA-13-0723 TCGA-13-0751 TCGA-13-0762 TCGA-13-0883 TCGA-13-0890 TCGA-13-0891 
       39.58        55.17       111.78        68.94       145.45       102.84 
TCGA-13-0904 TCGA-13-0916 TCGA-13-0924 
       50.37        58.68        85.94 

$`2P LOSS WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1346 
       49.15         2.01        46.62         1.08        18.51        65.52 
TCGA-04-1347 TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 
       63.09        48.76        63.98        65.46         0.53        49.28 
TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1516 
       32.52        33.67        76.57       103.40        82.39        41.59 
TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 
        0.79        38.37       119.08        84.20        55.43        48.89 
TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 
       27.88        28.64        64.64        36.23        31.86        47.70 
TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       45.37         9.99        38.43        89.33        74.93        41.62 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 
       57.60        61.87        55.36        30.51        17.98         5.85 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 
        8.55        97.55         6.18         6.12        35.15         4.54 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 
      112.41        71.11        63.09        39.75        20.94        26.93 
TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 
       12.46        77.10        81.17        28.54        83.31        55.23 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 
       57.27        81.01        32.35        54.64        87.06        61.71 
TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
       29.42        20.68        22.39        70.82        83.93        52.44 
TCGA-13-1492 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 
      125.56        90.38         4.24       127.27        66.15       115.07 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 
       13.97        43.20        34.82        65.69        34.16        80.15 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
       44.68        54.25        14.53        80.02        78.48        77.88 
TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
       76.90        65.52        70.45         8.42        23.05        25.94 
TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 
       72.20        25.38        19.10        16.70         2.93         2.66 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
       47.54        49.68        40.54        15.39        26.83        32.09 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 
       49.41         8.81        29.13        18.90         2.76        51.35 
TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1117 TCGA-23-1118 
       54.51         3.22        31.20        68.68        33.30        86.01 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 
      129.96         4.27         6.38        39.09        33.47        58.13 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
        0.53        24.95       115.89        87.48        91.66        77.00 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 
       49.84         2.76         4.70         4.50         7.63        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 
       21.80        41.56         7.66        22.32        54.12        63.55 
TCGA-24-1105 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 
       47.41         6.38         7.82         7.99         7.86         0.76 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        6.25         6.02         5.95         5.36         4.83        17.39 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 
       28.37        18.64        18.67        43.53         8.55        72.92 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 
       45.14       105.99         9.11         3.45         1.18        22.22 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 
       26.96        57.40        64.27        16.21        56.58        41.06 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       51.91        41.39        58.09        88.50        70.62        39.88 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 
       19.53        44.09        45.50        25.87        10.26        17.23 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
       90.15        88.37        38.24         8.32         3.48         3.72 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 
        3.81         4.37         5.79         5.52         9.80        30.21 
TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 
       16.44        11.05         4.87        44.84        58.16        34.82 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 
      109.71        14.43        55.92        18.48        28.18        64.01 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 
       44.52        57.07         0.79         0.36        47.54        31.63 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 
       44.61         0.82        67.36        36.23        16.64        33.11 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 
       55.86        53.26         1.02        33.01        52.04        42.05 
TCGA-25-1317 TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 
        2.01        65.00        37.97         2.99        12.99        15.02 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
       18.58        27.62        17.03        20.61        38.20         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 
       59.15        62.17        35.87        52.04        14.96        24.99 
TCGA-25-1877 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 
       24.00        13.02        49.05        38.04         3.02        12.00 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 
       45.01        19.99        42.02         2.96        29.03        31.00 
TCGA-25-2409 TCGA-29-1690 TCGA-29-1691 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       26.99        47.61        48.33        39.02        40.41        33.93 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 
       31.20        68.32        16.93        23.93        59.67        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 
       41.98        31.27        34.62        86.60        66.81        62.93 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 
       39.42        31.30        22.98        22.55        17.33        12.36 
TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
       11.84        12.30        14.93         8.38         7.23         5.36 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 
       36.30        86.17        65.00        62.47        45.11        13.84 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 
       42.25        21.47        11.47         9.76        35.77        38.07 
TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1861 
       51.91         2.47        15.68         0.26        48.10        34.78 
TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 
        6.12        36.62         1.22        57.57        24.26        30.05 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 
       48.79        45.57        30.18        18.77        22.49         6.71 
TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
       42.51        44.12         2.20        28.77        29.10        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 
       22.85        22.55         8.55        30.08        25.74        27.85 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       24.23        24.69        35.05        33.01        29.49        29.82 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 
       25.91        25.08        23.80        21.60         2.24        20.98 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 
       20.52        14.17         6.05        16.18        11.47        47.57 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 
       23.74        28.93        42.02        10.42        40.77         1.48 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 
       24.03        11.38        21.14         1.74        22.32        29.00 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 
       25.08        25.02       180.20        80.12        22.32       116.12 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 
        9.40        34.39         2.14         5.42        44.81        11.11 
TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 
        8.09        20.94        31.43        18.54        27.88         4.34 
TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 
       31.79        28.47        48.79        44.84        35.80         2.43 
TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 
       33.67         1.45         8.42         5.79        11.41        13.02 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 
        9.07        34.13        31.30        37.05        42.51        48.92 
TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 
       56.61        67.76        43.43        15.75        38.17         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 
        5.52        14.50        17.98         4.01        30.64        39.85 
TCGA-61-2012 TCGA-61-2017 TCGA-61-2018 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 
       30.64        45.96        45.40         4.77        51.72        71.74 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 
       61.64        58.39        60.62        65.52        55.50         6.48 
TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 
       76.87        44.52       125.75        22.22         6.35        31.07 
TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 
        8.61        39.68        18.94         0.79         9.99        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-10-0925 TCGA-10-0926 
        9.47        57.76        17.98        35.57        54.31        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       81.86        18.51        34.19        32.88        14.66         6.71 
TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
       35.44        36.92        19.99        20.91         6.21        24.59 
TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 
       44.55         2.73        12.39        31.20        15.19        17.82 
TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 
        2.50        11.18        11.38        11.54        38.01        61.84 
TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 
       56.71        58.65        40.24       118.42       107.28        63.09 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 
       20.35        69.73        83.34        87.48        45.99        51.02 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0884 TCGA-13-0885 
       43.86        35.28        35.31        13.61       107.18       111.39 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0893 TCGA-13-0897 
      153.37        66.67        92.42        95.15        43.36        71.74 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 
       66.15       134.04        19.36       127.79       123.16       118.98 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0919 
       60.59       116.65        44.55        37.64       109.32        84.53 
TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-2071 
       48.79        48.76        83.74        25.41 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             1.02              0.26 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           152.02            180.20 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           36.260            31.975 
[1] "1.0 - 152.0 (36.3)" "0.3 - 180.2 (32.0)"
[1] "hr=" "1"  
D44V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  2P LOSS MUTATED         0    52                0
  2P LOSS WILD-TYPE       3   506                2
D44V3, multiclass
                  clus
vv                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  OMENTUM                        0                 3
  OVARY                         52               506
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V4, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    50   0
  2P LOSS WILD-TYPE 491   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     50    0
  2P LOSS WILD-TYPE  491    5
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               50               491
  YES               0                 5
[1] 2 2
[1] FALSE
D44V5, continuous
                   vv
clus                R0 R1 R2 RX
  2P LOSS MUTATED    1  0  0  0
  2P LOSS WILD-TYPE 14 26  5  3
D44V6, multiclass
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                48 
       TCGA-3P-A9WA        TCGA-5X-AA5U        TCGA-04-1516        TCGA-04-1644 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-13-A5FT        TCGA-13-A5FU        TCGA-24-2033        TCGA-29-2414 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-29-2425        TCGA-29-2427        TCGA-29-2428        TCGA-29-2429 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-29-2431        TCGA-29-2432        TCGA-29-2434        TCGA-29-2436 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-36-2529        TCGA-36-2530        TCGA-36-2532        TCGA-36-2534 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-36-2537        TCGA-36-2538        TCGA-36-2540        TCGA-36-2542 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-36-2543        TCGA-36-2544        TCGA-36-2547        TCGA-36-2548 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-36-2549        TCGA-36-2551        TCGA-36-2552        TCGA-42-2582 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-42-2587        TCGA-42-2588        TCGA-42-2589        TCGA-42-2590 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-42-2593        TCGA-57-1993        TCGA-59-2363        TCGA-59-2372 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-61-2612        TCGA-61-2613        TCGA-61-2614        TCGA-OY-A56P 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-OY-A56Q        TCGA-VG-A8LO        TCGA-13-0807        TCGA-13-0911 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D44V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     1  31
  2P LOSS WILD-TYPE   9 296
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      1   31
  2P LOSS WILD-TYPE    9  296
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              31               296
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    20  40
  2Q LOSS WILD-TYPE 208 291
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               60               499 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               40               291 
$`2Q LOSS MUTATED`
TCGA-04-1336 TCGA-04-1342 TCGA-04-1349 TCGA-04-1514 TCGA-04-1517 TCGA-09-1673 
       49.15        18.51        21.57        56.55        19.99         3.02 
TCGA-09-2054 TCGA-13-1411 TCGA-13-1484 TCGA-13-1494 TCGA-13-1507 TCGA-13-A5FU 
       20.94        17.46       124.44        93.90        65.52         8.42 
TCGA-20-0991 TCGA-20-1682 TCGA-20-1686 TCGA-23-1116 TCGA-24-1413 TCGA-24-1464 
       26.20        27.52         2.93        19.46         6.31        12.46 
TCGA-24-1563 TCGA-24-1614 TCGA-24-1847 TCGA-24-1923 TCGA-24-1930 TCGA-24-2020 
       47.70        48.33        11.28        22.68        81.11       152.02 
TCGA-24-2029 TCGA-24-2260 TCGA-24-2280 TCGA-25-1313 TCGA-25-1318 TCGA-25-1627 
       14.43        36.16        70.45        26.96        34.98        12.95 
TCGA-25-1635 TCGA-25-2392 TCGA-25-2409 TCGA-29-1688 TCGA-29-1693 TCGA-29-1699 
       52.04         1.02        26.99        78.90       101.79        36.36 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1761 TCGA-29-1770 TCGA-29-1774 TCGA-30-1853 
       16.93        23.93        17.36        24.36        17.33        36.26 
TCGA-30-1860 TCGA-30-1887 TCGA-36-1575 TCGA-36-2529 TCGA-36-2543 TCGA-36-2545 
       44.91        24.26         8.55        35.05         2.24        18.31 
TCGA-61-2016 TCGA-61-2087 TCGA-61-2092 TCGA-61-2109 TCGA-13-0723 TCGA-13-0751 
        1.18         4.80        51.72        20.68        39.58        55.17 
TCGA-13-0762 TCGA-13-0890 TCGA-13-0891 TCGA-13-0904 TCGA-13-0916 TCGA-13-0924 
      111.78       145.45       102.84        50.37        58.68        85.94 

$`2Q LOSS WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 
        2.01        46.62         1.08        11.87        65.52        63.09 
TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 
       48.76        63.98        65.46         0.53        49.28        32.52 
TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1516 
       44.32        33.67        76.57       103.40        82.39        41.59 
TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 
        0.79        38.37       119.08        29.10        84.20        55.43 
TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 
       48.89        27.88        28.64        64.64        36.23        31.86 
TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       47.70        45.37         9.99        38.43        89.33        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 
       41.62        57.60        61.87        55.36        30.51        17.98 
TCGA-09-1672 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 
        5.85         8.55        97.55         6.18         6.12        35.15 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2055 
        4.54       112.41        71.11        63.09        39.75        26.93 
TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 
       12.46        77.10        81.17        28.54        83.31        55.23 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 
       57.27        81.01        32.35        54.64        87.06        61.71 
TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
       29.42        20.68        22.39        70.82        83.93        52.44 
TCGA-13-1492 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 
      125.56        90.38         4.24       127.27        66.15       115.07 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 
       13.97        43.20        34.82        65.69        34.16        80.15 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
       44.68        54.25        14.53        80.02        78.48        77.88 
TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 TCGA-20-0996 
       76.90        65.52        70.45        23.05        25.94        72.20 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 
       25.38        19.10        16.70         2.66        47.54        49.68 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 
       40.54        15.39        26.83        32.09        49.41         8.81 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
       29.13        18.90         2.76        51.35        54.51         3.22 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 
       31.20        68.68        33.30        86.01       129.96         4.27 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 
        6.38        39.09        33.47        58.13         0.53        24.95 
TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
      115.89        87.48        91.66        77.00        49.84         2.76 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        4.70         4.50         7.63        11.64        21.80        41.56 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1416 
        7.66        22.32        54.12        63.55        47.41         6.38 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
        7.82         7.99         7.86         0.76         6.25         6.02 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 
        5.95         5.36         4.83        17.39        28.37        18.64 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 TCGA-24-1467 
       18.67        43.53         8.55        72.92        45.14       105.99 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 
        9.11         3.45         1.18        22.22        26.96        57.40 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
       64.27        16.21        56.58        41.06        51.91        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 
       58.09        88.50        70.62        39.88        19.53        44.09 
TCGA-24-1562 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 
       45.50        25.87        10.26        17.23        90.15        88.37 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 
       38.24         8.32         3.48         3.72         3.81         4.37 
TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 
        5.79         5.52         9.80        30.21        16.44        11.05 
TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2030 
        4.87        44.84        58.16        34.82       109.71        55.92 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2261 
       18.48        28.18        64.01        44.52        57.07         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 
        0.36        47.54        31.63        44.61         0.82        67.36 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 
       36.23        16.64        33.11        55.86        53.26         1.02 
TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1319 TCGA-25-1320 
       33.01        52.04        42.05         2.01        65.00        37.97 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       33.96         2.99        12.99        15.02        18.58        27.62 
TCGA-25-1626 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
       17.03        20.61        38.20         0.30        59.15        62.17 
TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 
       35.87        14.96        24.99        24.00        85.05        13.02 
TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 
       49.05        38.04         3.02        12.00        45.01        19.99 
TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-29-1690 TCGA-29-1691 
       42.02         2.96        29.03        31.00        47.61        48.33 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1703 
       39.02        40.41        33.93        31.20        68.32        59.67 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1762 TCGA-29-1763 
       18.25        41.98        31.27        34.62        86.60        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 TCGA-29-1775 
       62.93        39.42        31.30        22.98        22.55        12.36 
TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
       11.84        12.30        14.93         8.38         7.23         5.36 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 
       36.30        86.17        65.00        62.47        45.11        13.84 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 
       42.25        21.47        11.47         9.76        35.77        38.07 
TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1861 
       51.91         2.47        15.68         0.26        48.10        34.78 
TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1891 TCGA-30-1892 
        6.12        36.62         1.22        57.57        30.05        48.79 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 
       45.57        30.18        18.77        22.49         6.71        42.51 
TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 
       44.12         2.20        28.77        29.10        21.53        22.85 
TCGA-36-1574 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 
       22.55        30.08        25.74        27.85        24.23        24.69 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       33.01        29.49        29.82        25.91        25.08        23.80 
TCGA-36-2542 TCGA-36-2544 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 
       21.60        20.98        20.52        14.17         6.05        16.18 
TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
       11.47        47.57        23.74        28.93        42.02        10.42 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 
       40.77         1.48        24.03        11.38        21.14         1.74 
TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 
       22.32        29.00        25.08        25.02       180.20        80.12 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       22.32       116.12         9.40        34.39         2.14         5.42 
TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
       44.81        11.11         8.09        20.94        31.43        18.54 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       27.88         4.34        31.79        28.47        48.79        44.84 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 
       35.80         2.43        33.67        43.69         1.45         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        5.79        11.41        13.02         9.07        34.13        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 
       37.05        42.51        48.92        56.61        67.76        43.43 
TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       15.75        38.17         2.01         5.52        14.50        17.98 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2017 TCGA-61-2018 
        4.01        30.64        39.85        30.64        45.96        45.40 
TCGA-61-2088 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 
        4.77        71.74        61.64        58.39        60.62        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
       55.50         6.48        76.87        44.52       125.75        22.22 
TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
        6.35        31.07         8.61        39.68        18.94         0.79 
TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 
        9.99        29.16         9.47        57.76        17.98        35.57 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       54.31        25.91        81.86        18.51        34.19        32.88 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 
       14.66         6.71        35.44        36.92        19.99        20.91 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 
        6.21        24.59        44.55         2.73        12.39        31.20 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 
       15.19        17.82         2.50        11.18        11.38        11.54 
TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 
       38.01        61.84        56.71        58.65        40.24       118.42 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 
      107.28        63.09        20.35        69.73        83.34        87.48 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
       45.99        51.02        43.86        35.28        35.31        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 
       68.94       107.18       111.39       153.37        66.67        92.42 
TCGA-13-0889 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
       95.15        43.36        71.74        66.15       134.04        19.36 
TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
      127.79       123.16       118.98        60.59       116.65        44.55 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 
       37.64       109.32        84.53        48.79        48.76        83.74 
TCGA-13-2071 
       25.41 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             1.02              0.26 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           152.02            180.20 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           26.975            33.010 
[1] "1.0 - 152.0 (27.0)" "0.3 - 180.2 (33.0)"
[1] "hr=" "1.1"
D45V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  2Q LOSS MUTATED         0    60                1
  2Q LOSS WILD-TYPE       3   498                1
D45V3, multiclass
                  clus
vv                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  OMENTUM                        0                 3
  OVARY                         60               498
  PERITONEUM OVARY               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V4, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    59   0
  2Q LOSS WILD-TYPE 482   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     59    0
  2Q LOSS WILD-TYPE  482    5
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               59               482
  YES               0                 5
[1] 2 2
[1] FALSE
D45V5, continuous
                   vv
clus                R0 R1 R2 RX
  2Q LOSS MUTATED    1  2  1  0
  2Q LOSS WILD-TYPE 14 24  4  3
D45V6, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0               1                14
  R1               2                24
  R2               1                 4
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     1  32
  2Q LOSS WILD-TYPE   9 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      1   32
  2Q LOSS WILD-TYPE    9  295
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              32               295
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    40  54
  3P LOSS WILD-TYPE 188 277
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               94               465 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               54               277 
$`3P LOSS MUTATED`
TCGA-04-1346 TCGA-04-1347 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1365 
       65.52        63.09        65.46         0.53        49.28        76.57 
TCGA-04-1514 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-09-1667 TCGA-09-2050 
       56.55        38.37       119.08        84.20        61.87        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1411 
       63.09        39.75        83.31        55.23        57.27        17.46 
TCGA-13-1487 TCGA-13-1492 TCGA-13-1499 TCGA-13-1512 TCGA-13-2057 TCGA-13-2060 
       22.39       125.56       115.07        14.53        80.02        77.88 
TCGA-20-0990 TCGA-23-1024 TCGA-23-1031 TCGA-23-1032 TCGA-23-1114 TCGA-24-0970 
       25.94        15.39        18.90         2.76        68.68        11.64 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1464 TCGA-24-1469 TCGA-24-1545 TCGA-24-1548 
        7.82         7.99        12.46         9.11        57.40        16.21 
TCGA-24-1550 TCGA-24-1846 TCGA-24-1930 TCGA-24-2026 TCGA-24-2027 TCGA-24-2262 
       41.06         4.37        81.11        34.82       109.71         0.36 
TCGA-24-2288 TCGA-24-2293 TCGA-25-1312 TCGA-25-1317 TCGA-25-1320 TCGA-25-1323 
        0.82        16.64         1.02         2.01        37.97        12.99 
TCGA-25-1627 TCGA-25-1633 TCGA-25-1870 TCGA-25-2392 TCGA-25-2397 TCGA-29-1691 
       12.95        62.17        14.96         1.02        12.00        48.33 
TCGA-29-1693 TCGA-29-1699 TCGA-29-1763 TCGA-29-1764 TCGA-29-1777 TCGA-30-1853 
      101.79        36.36        66.81        62.93        12.30        36.26 
TCGA-30-1855 TCGA-30-1887 TCGA-31-1959 TCGA-36-1575 TCGA-36-1576 TCGA-36-1580 
        2.47        24.26         2.20         8.55        30.08        24.23 
TCGA-36-2530 TCGA-36-2552 TCGA-42-2589 TCGA-42-2593 TCGA-57-1992 TCGA-59-2363 
       33.01        11.47        42.02         1.48        29.00         5.42 
TCGA-61-1722 TCGA-61-1730 TCGA-61-1733 TCGA-61-1741 TCGA-61-1743 TCGA-61-1914 
        8.09         4.34        31.79        33.67        43.69        56.61 
TCGA-61-1917 TCGA-61-1919 TCGA-61-2012 TCGA-61-2016 TCGA-61-2104 TCGA-61-2113 
       43.43        38.17        30.64         1.18        76.87        22.22 
TCGA-09-0369 TCGA-10-0938 TCGA-13-0730 TCGA-13-0757 TCGA-13-0792 TCGA-13-0794 
       35.57        20.91        17.82        11.18       118.42        63.09 
TCGA-13-0888 TCGA-13-0890 TCGA-13-0905 TCGA-13-0920 
       92.42       145.45       123.16        48.79 

$`3P LOSS WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 
       49.15         2.01        46.62         1.08        18.51        11.87 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 
       48.76        21.57        63.98        32.52        44.32        33.67 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1536 
      103.40        82.39        41.59        19.99         0.79        29.10 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 
       55.43        48.89        27.88        28.64        64.64        36.23 
TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       31.86        47.70        45.37         9.99        38.43        89.33 
TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 
       74.93        41.62        57.60        55.36        30.51        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 
        5.85         3.02         8.55        97.55         6.18         6.12 
TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 
       35.15         4.54       112.41        20.94        26.93        12.46 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1410 TCGA-13-1412 TCGA-13-1477 
       77.10        81.17        28.54        81.01        32.35        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1488 
       87.06        61.71        29.42       124.44        20.68        70.82 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 
       83.93        52.44        93.90        90.38         4.24       127.27 
TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       66.15        13.97        43.20        34.82        65.69        34.16 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-2059 TCGA-13-2061 
       65.52        80.15        44.68        54.25        78.48        76.90 
TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0991 TCGA-20-0996 
       65.52        70.45         8.42        23.05        26.20        72.20 
TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 
       27.52        25.38        19.10        16.70         2.93         2.66 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       47.54        49.68        40.54        26.83        32.09        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 
        8.81        29.13        51.35        54.51         3.22        31.20 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 
       19.46        33.30        86.01       129.96         4.27         6.38 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 
       39.09        33.47        58.13         0.53        24.95       115.89 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 
       87.48        91.66        77.00        49.84         2.76         4.70 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
        4.50         7.63        21.80        41.56         7.66        22.32 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1419 
       54.12        63.55        47.41         6.31         6.38         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        0.76         6.25         6.02         5.95         5.36         4.83 
TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
       17.39        28.37        18.64        18.67        43.53         8.55 
TCGA-24-1463 TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 
       72.92        45.14       105.99         3.45         1.18        22.22 
TCGA-24-1544 TCGA-24-1546 TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 
       26.96        64.27        56.58        51.91        41.39        58.09 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 
       88.50        70.62        39.88        19.53        44.09        45.50 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 
       47.70        25.87        10.26        17.23        90.15        88.37 
TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 
       48.33        38.24         8.32         3.48         3.72         3.81 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 
       11.28         5.79         5.52         9.80        22.68        30.21 
TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 
       16.44        11.05         4.87       152.02        44.84        58.16 
TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
       14.43        55.92        18.48        28.18        64.01        44.52 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       57.07        36.16         0.79        47.54        31.63        70.45 
TCGA-24-2281 TCGA-24-2289 TCGA-24-2290 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 
       44.61        67.36        36.23        33.11        55.86        53.26 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1318 TCGA-25-1319 
       26.96        33.01        52.04        42.05        34.98        65.00 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 
       33.96         2.99        15.02        18.58        27.62        17.03 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1634 TCGA-25-1635 
       20.61        38.20         0.30        59.15        35.87        52.04 
TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 
       24.99        24.00        85.05        13.02        49.05        38.04 
TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 
        3.02        45.01        19.99        42.02         2.96        29.03 
TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1694 TCGA-29-1695 
       31.00        26.99        78.90        47.61        39.02        40.41 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 
       33.93        31.20        68.32        16.93        23.93        59.67 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 
       18.25        41.98        31.27        34.62        17.36        86.60 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
       39.42        31.30        22.98        24.36        22.55        17.33 
TCGA-29-1775 TCGA-29-1776 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
       12.36        11.84        14.93         8.38         7.23         5.36 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 
       36.30        86.17        65.00        62.47        45.11        13.84 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 
       42.25        21.47        11.47         9.76        35.77        38.07 
TCGA-30-1718 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 
       51.91        15.68         0.26        48.10        44.91        34.78 
TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1891 TCGA-30-1892 
        6.12        36.62         1.22        57.57        30.05        48.79 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 
       45.57        30.18        18.77        22.49         6.71        42.51 
TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
       44.12        28.77        29.10        21.53        22.85        22.55 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 TCGA-36-2532 TCGA-36-2534 
       25.74        27.85        24.69        35.05        29.49        29.82 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 
       25.91        25.08        23.80        21.60         2.24        20.98 
TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-42-2582 
       18.31        20.52        14.17         6.05        16.18        47.57 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 TCGA-57-1583 
       23.74        28.93        10.42        40.77        24.03        11.38 
TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 
       21.14         1.74        22.32        25.08        25.02       180.20 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 
       80.12        22.32       116.12         9.40        34.39         2.14 
TCGA-59-2372 TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 
       44.81        11.11        20.94        31.43        18.54        27.88 
TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1895 
       28.47        48.79        44.84        35.80         2.43         1.45 
TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 
        8.42         5.79        11.41        13.02         9.07        34.13 
TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1915 TCGA-61-1918 
       31.30        37.05        42.51        48.92        67.76        15.75 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 
        2.01         5.52        14.50        17.98         4.01        30.64 
TCGA-61-2009 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 
       39.85        45.96        45.40         4.80         4.77        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 
       71.74        61.64        58.39        60.62        65.52        55.50 
TCGA-61-2102 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2612 TCGA-61-2613 
        6.48        20.68        44.52       125.75         6.35        31.07 
TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 
        8.61        39.68        18.94         0.79         9.99        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 
        9.47        57.76        17.98        54.31        25.91        81.86 
TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 
       18.51        34.19        32.88        14.66         6.71        35.44 
TCGA-10-0936 TCGA-10-0937 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 
       36.92        19.99         6.21        24.59        44.55        39.58 
TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0751 TCGA-13-0755 
        2.73        12.39        31.20        15.19        55.17         2.50 
TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 
       11.38        11.54        38.01       111.78        61.84        56.71 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 
       58.65        40.24       107.28        20.35        69.73        83.34 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 
       87.48        45.99        51.02        43.86        35.28        35.31 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
       13.61        68.94       107.18       111.39       153.37        66.67 
TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       95.15       102.84        43.36        71.74        66.15       134.04 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
       19.36       127.79        50.37       118.98        60.59       116.65 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 
       44.55        37.64       109.32        58.68        84.53        48.76 
TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       83.74        85.94        25.41 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.36              0.26 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           145.45            180.20 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           34.245            32.350 
[1] "0.4 - 145.4 (34.2)" "0.3 - 180.2 (32.4)"
[1] "hr=" "1.1"
D46V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  3P LOSS MUTATED         1    95                0
  3P LOSS WILD-TYPE       2   463                2
D46V3, multiclass
                  clus
vv                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  OMENTUM                        1                 2
  OVARY                         95               463
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V4, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    92   1
  3P LOSS WILD-TYPE 449   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     92    1
  3P LOSS WILD-TYPE  449    4
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               92               449
  YES               1                 4
[1] 2 2
[1] FALSE
D46V5, continuous
                   vv
clus                R0 R1 R2 RX
  3P LOSS MUTATED    3  1  1  0
  3P LOSS WILD-TYPE 12 25  4  3
D46V6, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0               3                12
  R1               1                25
  R2               1                 4
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     1  59
  3P LOSS WILD-TYPE   9 268
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1   59
  3P LOSS WILD-TYPE    9  268
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              59               268
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    18  23
  3Q LOSS WILD-TYPE 210 308
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               41               518 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               23               308 
$`3Q LOSS MUTATED`
TCGA-04-1351 TCGA-04-1356 TCGA-04-1514 TCGA-09-2050 TCGA-13-1407 TCGA-13-1408 
       65.46        49.28        56.55        71.11        83.31        55.23 
TCGA-13-1492 TCGA-13-1499 TCGA-13-1512 TCGA-23-1024 TCGA-23-1032 TCGA-24-1418 
      125.56       115.07        14.53        15.39         2.76         7.99 
TCGA-24-1469 TCGA-24-1545 TCGA-24-1550 TCGA-24-2262 TCGA-24-2288 TCGA-24-2293 
        9.11        57.40        41.06         0.36         0.82        16.64 
TCGA-25-1320 TCGA-25-2392 TCGA-25-2397 TCGA-29-1691 TCGA-29-1699 TCGA-29-1763 
       37.97         1.02        12.00        48.33        36.36        66.81 
TCGA-29-1777 TCGA-30-1855 TCGA-31-1959 TCGA-36-1575 TCGA-36-1580 TCGA-42-2589 
       12.30         2.47         2.20         8.55        24.23        42.02 
TCGA-57-1992 TCGA-61-1730 TCGA-61-1741 TCGA-61-1743 TCGA-61-2012 TCGA-10-0938 
       29.00         4.34        33.67        43.69        30.64        20.91 
TCGA-13-0730 TCGA-13-0762 TCGA-13-0794 TCGA-13-0890 TCGA-13-0905 
       17.82       111.78        63.09       145.45       123.16 

$`3Q LOSS WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 
       49.15         2.01        46.62         1.08        18.51        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1353 
       65.52        63.09        48.76        21.57        63.98         0.53 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 
       32.52        44.32        33.67        76.57       103.40        82.39 
TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 
       41.59        19.99         0.79        38.37       119.08        29.10 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 
       84.20        55.43        48.89        27.88        28.64        64.64 
TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 
       36.23        31.86        47.70        45.37         9.99        38.43 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 
       89.33        74.93        41.62        57.60        61.87        55.36 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 
       30.51        17.98         5.85         3.02         8.55        97.55 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2051 
        6.18         6.12        35.15         4.54       112.41        63.09 
TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 
       39.75        20.94        26.93        12.46        77.10        81.17 
TCGA-13-1405 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 
       28.54        57.27        81.01        17.46        32.35        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 
       87.06        61.71        29.42       124.44        20.68        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
       70.82        83.93        52.44        93.90        90.38         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 
      127.27        66.15        13.97        43.20        34.82        65.69 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-2057 
       34.16        65.52        80.15        44.68        54.25        80.02 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU 
       78.48        77.88        76.90        65.52        70.45         8.42 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 
       23.05        25.94        26.20        72.20        27.52        25.38 
TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 
       19.10        16.70         2.93         2.66        47.54        49.68 
TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
       40.54        26.83        32.09        49.41         8.81        29.13 
TCGA-23-1031 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 
       18.90        51.35        54.51         3.22        31.20        68.68 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 
       19.46        33.30        86.01       129.96         4.27         6.38 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 
       39.09        33.47        58.13         0.53        24.95       115.89 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 
       87.48        91.66        77.00        49.84         2.76         4.70 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        4.50         7.63        11.64        21.80        41.56         7.66 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
       22.32        54.12        63.55        47.41         6.31         6.38 
TCGA-24-1417 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 
        7.82         7.86         0.76         6.25         6.02         5.95 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 
        5.36         4.83        17.39        28.37        18.64        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 
       43.53         8.55        72.92        12.46        45.14       105.99 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1546 TCGA-24-1548 
        3.45         1.18        22.22        26.96        64.27        16.21 
TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 
       56.58        51.91        41.39        58.09        88.50        70.62 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
       39.88        19.53        44.09        45.50        47.70        25.87 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 
       10.26        17.23        90.15        88.37        48.33        38.24 
TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 
        8.32         3.48         3.72         3.81         4.37        11.28 
TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 
        5.79         5.52         9.80        22.68        30.21        16.44 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 
       11.05        81.11         4.87       152.02        44.84        58.16 
TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 
       34.82       109.71        14.43        55.92        18.48        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 
       64.01        44.52        57.07        36.16         0.79        47.54 
TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2289 TCGA-24-2290 TCGA-24-2295 
       31.63        70.45        44.61        67.36        36.23        33.11 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 
       55.86        53.26         1.02        26.96        33.01        52.04 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 TCGA-25-1322 
       42.05         2.01        34.98        65.00        33.96         2.99 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 
       12.99        15.02        18.58        27.62        17.03        12.95 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
       20.61        38.20         0.30        59.15        62.17        35.87 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 
       52.04        14.96        24.99        24.00        85.05        13.02 
TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 
       49.05        38.04         3.02        45.01        19.99        42.02 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 
        2.96        29.03        31.00        26.99        78.90        47.61 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 
      101.79        39.02        40.41        33.93        31.20        68.32 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 
       16.93        23.93        59.67        18.25        41.98        31.27 
TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 
       34.62        17.36        86.60        62.93        39.42        31.30 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 
       22.98        24.36        22.55        17.33        12.36        11.84 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 
       14.93         8.38         7.23         5.36        36.30        86.17 
TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 
       65.00        62.47        45.11        13.84        42.25        21.47 
TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 
       11.47         9.76        35.77        38.07        51.91        36.26 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 
       15.68         0.26        48.10        44.91        34.78         6.12 
TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 
       36.62         1.22        57.57        24.26        30.05        48.79 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 
       45.57        30.18        18.77        22.49         6.71        42.51 
TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
       44.12        28.77        29.10        21.53        22.85        22.55 
TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 
       30.08        25.74        27.85        24.69        35.05        33.01 
TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 
       29.49        29.82        25.91        25.08        23.80        21.60 
TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 
        2.24        20.98        18.31        20.52        14.17         6.05 
TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 
       16.18        11.47        47.57        23.74        28.93        10.42 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 
       40.77         1.48        24.03        11.38        21.14         1.74 
TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 
       22.32        25.08        25.02       180.20        80.12        22.32 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 
      116.12         9.40        34.39         2.14         5.42        44.81 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 
       11.11         8.09        20.94        31.43        18.54        27.88 
TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 
       31.79        28.47        48.79        44.84        35.80         2.43 
TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 
        1.45         8.42         5.79        11.41        13.02         9.07 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 
       34.13        31.30        37.05        42.51        48.92        56.61 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
       67.76        43.43        15.75        38.17         2.01         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 
       14.50        17.98         4.01        30.64        39.85         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 
       45.96        45.40         4.80         4.77        51.72        71.74 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 
       61.64        58.39        60.62        65.52        55.50         6.48 
TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 
       76.87        20.68        44.52       125.75        22.22         6.35 
TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       31.07         8.61        39.68        18.94         0.79         9.99 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-10-0925 
       29.16         9.47        57.76        17.98        35.57        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 
       25.91        81.86        18.51        34.19        32.88        14.66 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-13-0714 TCGA-13-0717 
        6.71        35.44        36.92        19.99         6.21        24.59 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 
       44.55        39.58         2.73        12.39        31.20        15.19 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 
       55.17         2.50        11.18        11.38        11.54        38.01 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       61.84        56.71        58.65        40.24       118.42       107.28 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 
       20.35        69.73        83.34        87.48        45.99        51.02 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
       43.86        35.28        35.31        13.61        68.94       107.18 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 
      111.39       153.37        66.67        92.42        95.15       102.84 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       43.36        71.74        66.15       134.04        19.36       127.79 
TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       50.37       118.98        60.59       116.65        44.55        37.64 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 
      109.32        58.68        84.53        48.79        48.76        83.74 
TCGA-13-0924 TCGA-13-2071 
       85.94        25.41 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.36              0.26 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           145.45            180.20 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            33.67             32.70 
[1] "0.4 - 145.4 (33.7)" "0.3 - 180.2 (32.7)"
[1] "hr=" "1.2"
D47V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  3Q LOSS MUTATED         1    41                0
  3Q LOSS WILD-TYPE       2   517                2
D47V3, multiclass
                  clus
vv                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  OMENTUM                        1                 2
  OVARY                         41               517
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V4, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    39   1
  3Q LOSS WILD-TYPE 502   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     39    1
  3Q LOSS WILD-TYPE  502    4
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               39               502
  YES               1                 4
[1] 2 2
[1] FALSE
D47V5, continuous
                   vv
clus                R0 R1 R2 RX
  3Q LOSS MUTATED    1  0  0  0
  3Q LOSS WILD-TYPE 14 26  5  3
D47V6, multiclass
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                1                48 
       TCGA-3P-A9WA        TCGA-5X-AA5U        TCGA-04-1516        TCGA-04-1644 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-13-A5FT        TCGA-13-A5FU        TCGA-24-2033        TCGA-29-2414 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-29-2425        TCGA-29-2427        TCGA-29-2428        TCGA-29-2429 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-29-2431        TCGA-29-2432        TCGA-29-2434        TCGA-29-2436 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-36-2529        TCGA-36-2530        TCGA-36-2532        TCGA-36-2534 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-36-2537        TCGA-36-2538        TCGA-36-2540        TCGA-36-2542 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-36-2543        TCGA-36-2544        TCGA-36-2545        TCGA-36-2547 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-36-2548        TCGA-36-2549        TCGA-36-2551        TCGA-36-2552 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-42-2582        TCGA-42-2587        TCGA-42-2588        TCGA-42-2590 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-42-2593        TCGA-57-1993        TCGA-59-2363        TCGA-59-2372 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-61-2612        TCGA-61-2613        TCGA-61-2614        TCGA-OY-A56P 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-OY-A56Q        TCGA-VG-A8LO        TCGA-13-0807        TCGA-13-0911 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
D47V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     1  25
  3Q LOSS WILD-TYPE   9 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1   25
  3Q LOSS WILD-TYPE    9  302
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              25               302
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED   119 180
  4P LOSS WILD-TYPE 109 151
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              299               260 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              180               151 
$`4P LOSS MUTATED`
TCGA-59-A5PD TCGA-04-1331 TCGA-04-1332 TCGA-04-1338 TCGA-04-1341 TCGA-04-1343 
       20.52        43.92        41.00        46.62         1.08        11.87 
TCGA-04-1348 TCGA-04-1350 TCGA-04-1353 TCGA-04-1361 TCGA-04-1362 TCGA-04-1371 
       48.76        63.98         0.53        32.52        44.32        82.39 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 
       56.55        41.59        19.99        29.10        84.20        55.43 
TCGA-04-1644 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 
       48.89        64.64        36.23        31.86        47.70        45.37 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1667 TCGA-09-1669 TCGA-09-1670 
        9.99        38.43        89.33        61.87        30.51        17.98 
TCGA-09-1673 TCGA-09-2043 TCGA-09-2044 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
        3.02         6.18         6.12       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2054 TCGA-13-1403 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
       39.75        20.94        77.10        83.31        55.23        57.27 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 
       81.01        17.46        87.06        29.42       124.44        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1495 TCGA-13-1497 
       70.82        83.93        52.44       125.56        90.38       127.27 
TCGA-13-1498 TCGA-13-1500 TCGA-13-1504 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 
       66.15        13.97        34.82        80.15        54.25        14.53 
TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-20-0990 TCGA-20-0991 
       78.48        76.90        65.52        70.45        25.94        26.20 
TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 
       27.52        25.38        19.10         2.93         2.66        47.54 
TCGA-23-1022 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       49.68        49.41         8.81        29.13        18.90         2.76 
TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 
        3.22        31.20        19.46        33.30        86.01       129.96 
TCGA-23-1122 TCGA-23-1123 TCGA-23-2072 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 
       39.09        33.47        24.95        49.84         2.76         4.70 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0982 TCGA-24-1103 TCGA-24-1105 
       11.64        21.80        41.56        22.32        54.12        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1422 TCGA-24-1425 
        6.31         6.38         7.82         7.99         0.76         5.95 
TCGA-24-1426 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 TCGA-24-1469 
        5.36        18.64        18.67         8.55        72.92         9.11 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1548 TCGA-24-1551 TCGA-24-1552 
        3.45         1.18        22.22        16.21        51.91        41.39 
TCGA-24-1555 TCGA-24-1560 TCGA-24-1562 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 
       88.50        44.09        45.50        17.23        90.15        88.37 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 
       38.24         8.32         3.72         3.81         4.37        11.28 
TCGA-24-1850 TCGA-24-1923 TCGA-24-1924 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 
        5.52        22.68        30.21        81.11         4.87       152.02 
TCGA-24-2023 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2254 TCGA-24-2261 
       44.84       109.71        14.43        55.92        57.07         0.79 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2288 TCGA-24-2290 TCGA-24-2293 
       47.54        31.63        70.45         0.82        36.23        16.64 
TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1314 TCGA-25-1316 TCGA-25-1317 
       33.11        55.86        53.26        33.01        42.05         2.01 
TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1623 
       34.98        37.97        33.96         2.99        12.99        18.58 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 
       17.03        12.95        20.61         0.30        62.17        35.87 
TCGA-25-1870 TCGA-25-1871 TCGA-25-2400 TCGA-25-2404 TCGA-29-1688 TCGA-29-1694 
       14.96        24.99        42.02        29.03        78.90        39.02 
TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1762 
       40.41        31.20        68.32        36.36        16.93        86.60 
TCGA-29-1764 TCGA-29-1768 TCGA-29-1771 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 
       62.93        31.30        22.55        12.30        14.93         8.38 
TCGA-29-1783 TCGA-29-1784 TCGA-29-2425 TCGA-29-2428 TCGA-29-2431 TCGA-29-2434 
        7.23         5.36        65.00        45.11        42.25        11.47 
TCGA-30-1714 TCGA-30-1853 TCGA-30-1856 TCGA-30-1859 TCGA-30-1861 TCGA-30-1866 
       38.07        36.26        15.68        48.10        34.78        36.62 
TCGA-30-1880 TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 
       57.57        30.05        18.77         6.71        42.51         2.20 
TCGA-36-1568 TCGA-36-1576 TCGA-36-1577 TCGA-36-1580 TCGA-36-1581 TCGA-36-2532 
       28.77        30.08        25.74        24.23        24.69        29.49 
TCGA-36-2538 TCGA-36-2542 TCGA-36-2543 TCGA-36-2545 TCGA-36-2548 TCGA-36-2551 
       25.08        21.60         2.24        18.31        14.17        16.18 
TCGA-36-2552 TCGA-42-2587 TCGA-42-2588 TCGA-42-2591 TCGA-57-1582 TCGA-57-1584 
       11.47        23.74        28.93        40.77        24.03        21.14 
TCGA-57-1585 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2350 TCGA-59-2352 
        1.74        29.00        25.08        25.02        22.32         9.40 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1730 TCGA-61-1734 
       34.39         2.14         5.42        44.81         4.34        28.47 
TCGA-61-1736 TCGA-61-1737 TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
       48.79        44.84        33.67         1.45         8.42         5.79 
TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 
       13.02         9.07        34.13        48.92        56.61        43.43 
TCGA-61-1919 TCGA-61-1995 TCGA-61-2003 TCGA-61-2016 TCGA-61-2018 TCGA-61-2087 
       38.17         2.01         4.01         1.18        45.40         4.80 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2101 TCGA-61-2102 TCGA-61-2109 TCGA-61-2110 
       51.72        71.74        55.50         6.48        20.68        44.52 
TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-OY-A56P TCGA-OY-A56Q 
      125.75        22.22         6.35        31.07        39.68        18.94 
TCGA-09-0365 TCGA-09-0367 TCGA-09-0369 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
        9.47        17.98        35.57        81.86        18.51        34.19 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0935 TCGA-13-0717 TCGA-13-0725 TCGA-13-0727 
       32.88        14.66        35.44        24.59        12.39        15.19 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0760 TCGA-13-0762 
       17.82        55.17         2.50        11.18        11.54       111.78 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0793 TCGA-13-0795 TCGA-13-0801 TCGA-13-0803 
       61.84        56.71       107.28        20.35        45.99        43.86 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0884 TCGA-13-0885 TCGA-13-0888 TCGA-13-0889 
       35.28        35.31       107.18       111.39        92.42        95.15 
TCGA-13-0890 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0910 
      145.45        66.15       134.04       127.79        50.37       116.65 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0919 TCGA-13-0921 TCGA-13-0924 
       44.55        37.64        84.53        48.76        85.94 

$`4P LOSS WILD-TYPE`
TCGA-3P-A9WA TCGA-5X-AA5U TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 
       13.81        11.87         1.81        49.15         2.01        18.51 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 TCGA-04-1351 TCGA-04-1356 TCGA-04-1364 
       65.52        63.09        21.57        65.46        49.28        33.67 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1646 
       76.57       103.40         0.79        38.37       119.08        27.88 
TCGA-04-1648 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1668 TCGA-09-1672 
       28.64        74.93        41.62        57.60        55.36         5.85 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2045 TCGA-09-2048 TCGA-09-2055 TCGA-09-2056 
        8.55        97.55        35.15         4.54        26.93        12.46 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1485 
       81.17        28.54        32.35        54.64        61.71        20.68 
TCGA-13-1494 TCGA-13-1496 TCGA-13-1499 TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 
       93.90         4.24       115.07        43.20        65.69        34.16 
TCGA-13-1507 TCGA-13-1510 TCGA-13-2057 TCGA-13-2060 TCGA-13-A5FU TCGA-20-0987 
       65.52        44.68        80.02        77.88         8.42        23.05 
TCGA-20-0996 TCGA-20-1685 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
       72.20        16.70        40.54        15.39        26.83        32.09 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1114 TCGA-23-1120 TCGA-23-1121 TCGA-23-1124 
       51.35        54.51        68.68         4.27         6.38        58.13 
TCGA-23-1809 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2645 
        0.53       115.89        87.48        91.66        77.00         4.50 
TCGA-24-0966 TCGA-24-0980 TCGA-24-1104 TCGA-24-1419 TCGA-24-1423 TCGA-24-1424 
        7.63         7.66        63.55         7.86         6.25         6.02 
TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1435 TCGA-24-1464 TCGA-24-1466 
        4.83        17.39        28.37        43.53        12.46        45.14 
TCGA-24-1467 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1549 TCGA-24-1550 
      105.99        26.96        57.40        64.27        56.58        41.06 
TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1563 TCGA-24-1564 
       58.09        70.62        39.88        19.53        47.70        25.87 
TCGA-24-1565 TCGA-24-1614 TCGA-24-1843 TCGA-24-1849 TCGA-24-1920 TCGA-24-1927 
       10.26        48.33         3.48         5.79         9.80        16.44 
TCGA-24-1928 TCGA-24-2024 TCGA-24-2026 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 
       11.05        58.16        34.82        18.48        28.18        64.01 
TCGA-24-2038 TCGA-24-2260 TCGA-24-2262 TCGA-24-2281 TCGA-24-2289 TCGA-25-1312 
       44.52        36.16         0.36        44.61        67.36         1.02 
TCGA-25-1313 TCGA-25-1315 TCGA-25-1319 TCGA-25-1329 TCGA-25-1625 TCGA-25-1630 
       26.96        52.04        65.00        15.02        27.62        38.20 
TCGA-25-1632 TCGA-25-1635 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 
       59.15        52.04        24.00        85.05        13.02        49.05 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 
        1.02        38.04         3.02        12.00        45.01        19.99 
TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 
        2.96        31.00        26.99        47.61        48.33       101.79 
TCGA-29-1696 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 
       33.93        23.93        59.67        18.25        41.98        31.27 
TCGA-29-1711 TCGA-29-1761 TCGA-29-1763 TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 
       34.62        17.36        66.81        39.42        22.98        24.36 
TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 
       17.33        12.36        11.84        36.30        86.17        62.47 
TCGA-29-2429 TCGA-29-2432 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1855 
       13.84        21.47         9.76        35.77        51.91         2.47 
TCGA-30-1857 TCGA-30-1860 TCGA-30-1862 TCGA-30-1867 TCGA-30-1887 TCGA-30-1892 
        0.26        44.91         6.12         1.22        24.26        48.79 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1956 TCGA-36-1569 TCGA-36-1570 
       45.57        30.18        22.49        44.12        29.10        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1578 TCGA-36-2529 TCGA-36-2530 
       22.85        22.55         8.55        27.85        35.05        33.01 
TCGA-36-2534 TCGA-36-2537 TCGA-36-2540 TCGA-36-2544 TCGA-36-2547 TCGA-36-2549 
       29.82        25.91        23.80        20.98        20.52         6.05 
TCGA-42-2582 TCGA-42-2589 TCGA-42-2590 TCGA-42-2593 TCGA-57-1583 TCGA-57-1586 
       47.57        42.02        10.42         1.48        11.38        22.32 
TCGA-59-2348 TCGA-59-2349 TCGA-59-2351 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 
      180.20        80.12       116.12        11.11         8.09        20.94 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 TCGA-61-1738 TCGA-61-1740 
       31.43        18.54        27.88        31.79        35.80         2.43 
TCGA-61-1743 TCGA-61-1901 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1915 
       43.69        11.41        31.30        37.05        42.51        67.76 
TCGA-61-1918 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2008 TCGA-61-2009 
       15.75         5.52        14.50        17.98        30.64        39.85 
TCGA-61-2012 TCGA-61-2017 TCGA-61-2088 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 
       30.64        45.96         4.77        61.64        58.39        60.62 
TCGA-61-2098 TCGA-61-2104 TCGA-61-2614 TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 
       65.52        76.87         8.61         0.79         9.99        29.16 
TCGA-09-0366 TCGA-10-0925 TCGA-10-0926 TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 
       57.76        54.31        25.91         6.71        36.92        19.99 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 
       20.91         6.21        44.55        39.58         2.73        31.20 
TCGA-13-0758 TCGA-13-0761 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0794 
       11.38        38.01        58.65        40.24       118.42        63.09 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0802 TCGA-13-0807 TCGA-13-0883 
       69.73        83.34        87.48        51.02        13.61        68.94 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0901 
      153.37        66.67       102.84        43.36        71.74        19.36 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 
      123.16       118.98        60.59       109.32        58.68        48.79 
TCGA-13-0923 TCGA-13-2071 
       83.74        25.41 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.30              0.26 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           152.02            180.20 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            32.52             33.34 
[1] "0.3 - 152.0 (32.5)" "0.3 - 180.2 (33.3)"
[1] "hr=" "1.1"
D48V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  4P LOSS MUTATED         2   301                0
  4P LOSS WILD-TYPE       1   257                2
D48V3, multiclass
                  clus
vv                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  OMENTUM                        2                 1
  OVARY                        301               257
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V4, binary
                   cls
clus                  0   1
  4P LOSS MUTATED   291   3
  4P LOSS WILD-TYPE 250   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    291    3
  4P LOSS WILD-TYPE  250    2
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO              291               250
  YES               3                 2
[1] 2 2
[1] FALSE
D48V5, continuous
                   vv
clus                R0 R1 R2 RX
  4P LOSS MUTATED    9 12  2  2
  4P LOSS WILD-TYPE  6 14  3  1
D48V6, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0               9                 6
  R1              12                14
  R2               2                 3
  RX               2                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     5 175
  4P LOSS WILD-TYPE   5 152
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      5  175
  4P LOSS WILD-TYPE    5  152
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 5
  NOT HISPANIC OR LATINO             175               152
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED   147 200
  4Q LOSS WILD-TYPE  81 131
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              347               212 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              200               131 
$`4Q LOSS MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 
       13.81        20.52        11.87        43.92        41.00        49.15 
TCGA-04-1338 TCGA-04-1341 TCGA-04-1343 TCGA-04-1348 TCGA-04-1350 TCGA-04-1361 
       46.62         1.08        11.87        48.76        63.98        32.52 
TCGA-04-1362 TCGA-04-1364 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 
       44.32        33.67       103.40        82.39        56.55        41.59 
TCGA-04-1517 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
       19.99        29.10        84.20        55.43        48.89        27.88 
TCGA-04-1649 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 
       64.64        31.86        47.70        45.37         9.99        38.43 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 TCGA-09-1670 
       89.33        74.93        57.60        61.87        30.51        17.98 
TCGA-09-1673 TCGA-09-1674 TCGA-09-2043 TCGA-09-2044 TCGA-09-2049 TCGA-09-2050 
        3.02         8.55         6.18         6.12       112.41        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 
       63.09        39.75        20.94        26.93        12.46        77.10 
TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1481 
       81.17        83.31        55.23        57.27        81.01        87.06 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
       29.42       124.44        22.39        70.82        83.93        52.44 
TCGA-13-1492 TCGA-13-1495 TCGA-13-1497 TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 
      125.56        90.38       127.27       115.07        13.97        34.82 
TCGA-13-1505 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2061 
       65.69        80.15        54.25        14.53        78.48        76.90 
TCGA-13-2065 TCGA-13-A5FT TCGA-20-0990 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 
       65.52        70.45        25.94        27.52        25.38        19.10 
TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1028 TCGA-23-1029 
        2.93         2.66        47.54        49.68        49.41         8.81 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 
       29.13        18.90         2.76        54.51         3.22        31.20 
TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1122 
       68.68        19.46        33.30        86.01       129.96        39.09 
TCGA-23-1123 TCGA-23-2072 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-24-0970 
       33.47        24.95        49.84         2.76         4.70        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0982 TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 
       21.80        41.56        22.32        54.12        47.41         6.31 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 
        6.38         7.82         7.99         7.86         0.76         6.25 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 
        5.95         5.36        17.39        18.64        18.67         8.55 
TCGA-24-1463 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
       72.92         9.11         3.45         1.18        22.22        26.96 
TCGA-24-1545 TCGA-24-1548 TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 TCGA-24-1560 
       57.40        16.21        51.91        41.39        88.50        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 
       45.50        47.70        17.23        90.15        88.37        38.24 
TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 
        8.32         3.72         3.81         4.37        11.28         5.79 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 
        5.52         9.80        22.68        11.05        81.11         4.87 
TCGA-24-2020 TCGA-24-2023 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2254 
      152.02        44.84       109.71        14.43        55.92        57.07 
TCGA-24-2261 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
        0.79        47.54        31.63        70.45        44.61         0.82 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 
       36.23        16.64        33.11        55.86        53.26         1.02 
TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1320 
       33.01        52.04        42.05         2.01        34.98        37.97 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       33.96         2.99        12.99        15.02        18.58        27.62 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1633 
       17.03        12.95        20.61        38.20         0.30        62.17 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-2042 TCGA-25-2391 
       35.87        52.04        14.96        24.99        13.02        49.05 
TCGA-25-2392 TCGA-25-2398 TCGA-25-2400 TCGA-25-2404 TCGA-25-2408 TCGA-29-1688 
        1.02        45.01        42.02        29.03        31.00        78.90 
TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1705 TCGA-29-1762 
       40.41        31.20        68.32        36.36        18.25        86.60 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1769 TCGA-29-1771 TCGA-29-1776 TCGA-29-1777 
       66.81        62.93        22.98        22.55        11.84        12.30 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-2425 TCGA-29-2428 TCGA-29-2431 
        8.38         7.23         5.36        65.00        45.11        42.25 
TCGA-29-2434 TCGA-30-1714 TCGA-30-1853 TCGA-30-1856 TCGA-30-1859 TCGA-30-1861 
       11.47        38.07        36.26        15.68        48.10        34.78 
TCGA-30-1866 TCGA-30-1880 TCGA-30-1891 TCGA-31-1946 TCGA-31-1950 TCGA-31-1953 
       36.62        57.57        30.05        30.18        18.77         6.71 
TCGA-31-1955 TCGA-31-1959 TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 TCGA-36-1576 
       42.51         2.20        28.77        21.53        22.85        30.08 
TCGA-36-1577 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 
       25.74        24.23        24.69        35.05        33.01        29.49 
TCGA-36-2538 TCGA-36-2542 TCGA-36-2543 TCGA-36-2545 TCGA-36-2548 TCGA-36-2551 
       25.08        21.60         2.24        18.31        14.17        16.18 
TCGA-36-2552 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
       11.47        23.74        28.93        42.02        10.42        40.77 
TCGA-42-2593 TCGA-57-1582 TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 TCGA-57-1993 
        1.48        24.03        21.14         1.74        29.00        25.08 
TCGA-57-1994 TCGA-59-2350 TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 
       25.02        22.32         9.40         2.14         5.42        44.81 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1741 
        4.34        31.79        28.47        48.79        44.84        33.67 
TCGA-61-1899 TCGA-61-1900 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        8.42         5.79        13.02         9.07        34.13        31.30 
TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-2003 
       56.61        43.43        15.75        38.17         2.01         4.01 
TCGA-61-2009 TCGA-61-2016 TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 TCGA-61-2094 
       39.85         1.18        45.40         4.80        51.72        71.74 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       60.62        65.52        55.50         6.48        76.87        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       44.52       125.75        22.22         6.35        31.07         8.61 
TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-09-0367 TCGA-09-0369 TCGA-10-0926 
       39.68        18.94         0.79        17.98        35.57        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0935 
       81.86        18.51        34.19        32.88        14.66        35.44 
TCGA-10-0937 TCGA-13-0717 TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 TCGA-13-0727 
       19.99        24.59        44.55         2.73        12.39        15.19 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0760 TCGA-13-0762 TCGA-13-0766 
       17.82        55.17        11.18        11.54       111.78        56.71 
TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 
      107.28        20.35        69.73        45.99        43.86        35.28 
TCGA-13-0805 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 
       35.31       107.18       111.39        66.67        92.42        95.15 
TCGA-13-0890 TCGA-13-0899 TCGA-13-0903 TCGA-13-0904 TCGA-13-0910 TCGA-13-0911 
      145.45        66.15       127.79        50.37       116.65        44.55 
TCGA-13-0912 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0924 
       37.64        58.68        84.53        48.76        85.94 

$`4Q LOSS WILD-TYPE`
TCGA-04-1335 TCGA-04-1337 TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 
        1.81         2.01        18.51        65.52        63.09        21.57 
TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1365 TCGA-04-1519 TCGA-04-1525 
       65.46         0.53        49.28        76.57         0.79        38.37 
TCGA-04-1530 TCGA-04-1648 TCGA-04-1651 TCGA-09-1665 TCGA-09-1668 TCGA-09-1672 
      119.08        28.64        36.23        41.62        55.36         5.85 
TCGA-09-1675 TCGA-09-2045 TCGA-09-2048 TCGA-13-1405 TCGA-13-1411 TCGA-13-1412 
       97.55        35.15         4.54        28.54        17.46        32.35 
TCGA-13-1477 TCGA-13-1482 TCGA-13-1485 TCGA-13-1494 TCGA-13-1496 TCGA-13-1498 
       54.64        61.71        20.68        93.90         4.24        66.15 
TCGA-13-1501 TCGA-13-1506 TCGA-13-1507 TCGA-13-1510 TCGA-13-2057 TCGA-13-2060 
       43.20        34.16        65.52        44.68        80.02        77.88 
TCGA-13-A5FU TCGA-20-0987 TCGA-20-0991 TCGA-20-0996 TCGA-20-1685 TCGA-23-1023 
        8.42        23.05        26.20        72.20        16.70        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1109 TCGA-23-1120 TCGA-23-1121 
       15.39        26.83        32.09        51.35         4.27         6.38 
TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
       58.13         0.53       115.89        87.48        91.66        77.00 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0980 TCGA-24-1104 TCGA-24-1424 TCGA-24-1427 
        4.50         7.63         7.66        63.55         6.02         4.83 
TCGA-24-1430 TCGA-24-1435 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1546 
       28.37        43.53        12.46        45.14       105.99        64.27 
TCGA-24-1549 TCGA-24-1550 TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 
       56.58        41.06        58.09        70.62        39.88        19.53 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1614 TCGA-24-1843 TCGA-24-1924 TCGA-24-1927 
       25.87        10.26        48.33         3.48        30.21        16.44 
TCGA-24-2024 TCGA-24-2026 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
       58.16        34.82        18.48        28.18        64.01        44.52 
TCGA-24-2260 TCGA-24-2262 TCGA-24-2289 TCGA-25-1313 TCGA-25-1319 TCGA-25-1632 
       36.16         0.36        67.36        26.96        65.00        59.15 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 
       24.00        85.05        38.04         3.02        12.00        19.99 
TCGA-25-2401 TCGA-25-2409 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 
        2.96        26.99        47.61        48.33       101.79        39.02 
TCGA-29-1696 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 TCGA-29-1710 
       33.93        16.93        23.93        59.67        41.98        31.27 
TCGA-29-1711 TCGA-29-1761 TCGA-29-1766 TCGA-29-1768 TCGA-29-1770 TCGA-29-1774 
       34.62        17.36        39.42        31.30        24.36        17.33 
TCGA-29-1775 TCGA-29-1778 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2429 
       12.36        14.93        36.30        86.17        62.47        13.84 
TCGA-29-2432 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1855 TCGA-30-1857 
       21.47         9.76        35.77        51.91         2.47         0.26 
TCGA-30-1860 TCGA-30-1862 TCGA-30-1867 TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 
       44.91         6.12         1.22        24.26        48.79        45.57 
TCGA-31-1951 TCGA-31-1956 TCGA-36-1569 TCGA-36-1574 TCGA-36-1575 TCGA-36-1578 
       22.49        44.12        29.10        22.55         8.55        27.85 
TCGA-36-2534 TCGA-36-2537 TCGA-36-2540 TCGA-36-2544 TCGA-36-2547 TCGA-36-2549 
       29.82        25.91        23.80        20.98        20.52         6.05 
TCGA-42-2582 TCGA-57-1583 TCGA-57-1586 TCGA-59-2348 TCGA-59-2349 TCGA-59-2351 
       47.57        11.38        22.32       180.20        80.12       116.12 
TCGA-59-2354 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
       34.39        11.11         8.09        20.94        31.43        18.54 
TCGA-61-1728 TCGA-61-1738 TCGA-61-1740 TCGA-61-1743 TCGA-61-1895 TCGA-61-1901 
       27.88        35.80         2.43        43.69         1.45        11.41 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1915 TCGA-61-1998 TCGA-61-2000 
       37.05        42.51        48.92        67.76         5.52        14.50 
TCGA-61-2002 TCGA-61-2008 TCGA-61-2012 TCGA-61-2017 TCGA-61-2088 TCGA-61-2095 
       17.98        30.64        30.64        45.96         4.77        61.64 
TCGA-61-2096 TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-10-0925 
       58.39         9.99        29.16         9.47        57.76        54.31 
TCGA-10-0934 TCGA-10-0936 TCGA-10-0938 TCGA-13-0714 TCGA-13-0723 TCGA-13-0726 
        6.71        36.92        20.91         6.21        39.58        31.20 
TCGA-13-0755 TCGA-13-0758 TCGA-13-0761 TCGA-13-0764 TCGA-13-0768 TCGA-13-0791 
        2.50        11.38        38.01        61.84        58.65        40.24 
TCGA-13-0792 TCGA-13-0794 TCGA-13-0799 TCGA-13-0800 TCGA-13-0802 TCGA-13-0807 
      118.42        63.09        83.34        87.48        51.02        13.61 
TCGA-13-0883 TCGA-13-0886 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 
       68.94       153.37       102.84        43.36        71.74       134.04 
TCGA-13-0901 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0913 TCGA-13-0920 
       19.36       123.16       118.98        60.59       109.32        48.79 
TCGA-13-0923 TCGA-13-2071 
       83.74        25.41 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.30              0.26 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           152.02            180.20 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           31.860            34.275 
[1] "0.3 - 152.0 (31.9)" "0.3 - 180.2 (34.3)"
[1] "hr=" "1"  
D49V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  4Q LOSS MUTATED         2   348                1
  4Q LOSS WILD-TYPE       1   210                1
D49V3, multiclass
                  clus
vv                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  OMENTUM                        2                 1
  OVARY                        348               210
  PERITONEUM OVARY               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V4, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   339   4
  4Q LOSS WILD-TYPE 202   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    339    4
  4Q LOSS WILD-TYPE  202    1
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO              339               202
  YES               4                 1
[1] 2 2
[1] FALSE
D49V5, continuous
                   vv
clus                R0 R1 R2 RX
  4Q LOSS MUTATED   11 16  4  3
  4Q LOSS WILD-TYPE  4 10  1  0
D49V6, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0              11                 4
  R1              16                10
  R2               4                 1
  RX               3                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     8 197
  4Q LOSS WILD-TYPE   2 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      8  197
  4Q LOSS WILD-TYPE    2  130
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   8                 2
  NOT HISPANIC OR LATINO             197               130
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    53  77
  5P LOSS WILD-TYPE 175 254
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              130               429 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               77               254 
$`5P LOSS MUTATED`
TCGA-3P-A9WA TCGA-04-1332 TCGA-04-1336 TCGA-04-1338 TCGA-04-1351 TCGA-04-1356 
       13.81        41.00        49.15        46.62        65.46        49.28 
TCGA-04-1361 TCGA-04-1371 TCGA-04-1517 TCGA-04-1519 TCGA-04-1648 TCGA-09-1669 
       32.52        82.39        19.99         0.79        28.64        30.51 
TCGA-09-2044 TCGA-09-2049 TCGA-13-1405 TCGA-13-1412 TCGA-13-1491 TCGA-13-1496 
        6.12       112.41        28.54        32.35        52.44         4.24 
TCGA-13-1497 TCGA-13-1509 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-20-0991 
      127.27        80.15        80.02        78.48        77.88        26.20 
TCGA-20-1682 TCGA-20-1683 TCGA-23-1021 TCGA-23-1022 TCGA-23-1028 TCGA-23-1109 
       27.52        25.38        47.54        49.68        49.41        51.35 
TCGA-23-1114 TCGA-23-1118 TCGA-23-1122 TCGA-23-1123 TCGA-23-2072 TCGA-24-0970 
       68.68        86.01        39.09        33.47        24.95        11.64 
TCGA-24-1419 TCGA-24-1424 TCGA-24-1430 TCGA-24-1431 TCGA-24-1464 TCGA-24-1466 
        7.86         6.02        28.37        18.64        12.46        45.14 
TCGA-24-1548 TCGA-24-1558 TCGA-24-1567 TCGA-24-1614 TCGA-24-1842 TCGA-24-1843 
       16.21        19.53        17.23        48.33         8.32         3.48 
TCGA-24-1920 TCGA-24-2019 TCGA-24-2035 TCGA-24-2254 TCGA-24-2261 TCGA-24-2271 
        9.80         4.87        28.18        57.07         0.79        31.63 
TCGA-24-2280 TCGA-24-2293 TCGA-25-1312 TCGA-25-1313 TCGA-25-1317 TCGA-25-1320 
       70.45        16.64         1.02        26.96         2.01        37.97 
TCGA-25-1323 TCGA-25-1630 TCGA-25-1633 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 
       12.99        38.20        62.17        52.04        14.96        24.99 
TCGA-25-2398 TCGA-25-2400 TCGA-29-1697 TCGA-29-1702 TCGA-29-1711 TCGA-29-1762 
       45.01        42.02        31.20        23.93        34.62        86.60 
TCGA-29-1778 TCGA-29-1783 TCGA-29-1784 TCGA-29-2414 TCGA-29-2428 TCGA-30-1855 
       14.93         7.23         5.36        86.17        45.11         2.47 
TCGA-30-1859 TCGA-30-1861 TCGA-30-1867 TCGA-30-1887 TCGA-30-1891 TCGA-31-1953 
       48.10        34.78         1.22        24.26        30.05         6.71 
TCGA-31-1959 TCGA-36-1575 TCGA-36-2538 TCGA-36-2547 TCGA-36-2552 TCGA-57-1583 
        2.20         8.55        25.08        20.52        11.47        11.38 
TCGA-59-2348 TCGA-59-2351 TCGA-59-2352 TCGA-59-2363 TCGA-61-1724 TCGA-61-1728 
      180.20       116.12         9.40         5.42        20.94        27.88 
TCGA-61-1730 TCGA-61-1741 TCGA-61-1743 TCGA-61-1906 TCGA-61-1907 TCGA-61-1917 
        4.34        33.67        43.69        34.13        31.30        43.43 
TCGA-61-1998 TCGA-61-2094 TCGA-61-2097 TCGA-61-2102 TCGA-61-2104 TCGA-OY-A56Q 
        5.52        71.74        60.62         6.48        76.87        18.94 
TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-10-0938 TCGA-13-0714 TCGA-13-0724 
        9.99        29.16         9.47        20.91         6.21         2.73 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0791 TCGA-13-0795 TCGA-13-0800 TCGA-13-0803 
       38.01       111.78        40.24        20.35        87.48        43.86 
TCGA-13-0805 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 
       35.31       107.18       111.39        66.67        92.42       145.45 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0919 TCGA-13-0920 
      102.84        43.36        84.53        48.79 

$`5P LOSS WILD-TYPE`
TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1335 TCGA-04-1337 TCGA-04-1341 
       20.52        11.87        43.92         1.81         2.01         1.08 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 
       18.51        11.87        65.52        63.09        48.76        21.57 
TCGA-04-1350 TCGA-04-1353 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       63.98         0.53        44.32        33.67        76.57       103.40 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 
       56.55        41.59        38.37       119.08        29.10        84.20 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 
       55.43        48.89        27.88        64.64        36.23        31.86 
TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       47.70        45.37         9.99        38.43        89.33        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 
       41.62        57.60        61.87        55.36        17.98         5.85 
TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2045 TCGA-09-2048 
        3.02         8.55        97.55         6.18        35.15         4.54 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 
       71.11        63.09        39.75        20.94        26.93        12.46 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
       77.10        81.17        83.31        55.23        57.27        81.01 
TCGA-13-1411 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
       17.46        54.64        87.06        61.71        29.42       124.44 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1492 TCGA-13-1494 
       20.68        22.39        70.82        83.93       125.56        93.90 
TCGA-13-1495 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 
       90.38        66.15       115.07        13.97        43.20        34.82 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
       65.69        34.16        65.52        44.68        54.25        14.53 
TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
       76.90        65.52        70.45         8.42        23.05        25.94 
TCGA-20-0996 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1023 
       72.20        19.10        16.70         2.93         2.66        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 
       15.39        26.83        32.09         8.81        29.13        18.90 
TCGA-23-1032 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 
        2.76        54.51         3.22        31.20        19.46        33.30 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 
      129.96         4.27         6.38        58.13         0.53       115.89 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 
       87.48        91.66        77.00        49.84         2.76         4.70 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
        4.50         7.63        21.80        41.56         7.66        22.32 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 
       54.12        63.55        47.41         6.31         6.38         7.82 
TCGA-24-1418 TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        7.99         0.76         6.25         5.95         5.36         4.83 
TCGA-24-1428 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1467 
       17.39        18.67        43.53         8.55        72.92       105.99 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 
        9.11         3.45         1.18        22.22        26.96        57.40 
TCGA-24-1546 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 
       64.27        56.58        41.06        51.91        41.39        58.09 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       88.50        70.62        39.88        44.09        45.50        47.70 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-1844 
       25.87        10.26        90.15        88.37        38.24         3.72 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1923 
        3.81         4.37        11.28         5.79         5.52        22.68 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2020 TCGA-24-2023 
       30.21        16.44        11.05        81.11       152.02        44.84 
TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 
       58.16        34.82       109.71        14.43        55.92        18.48 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2260 TCGA-24-2262 TCGA-24-2267 TCGA-24-2281 
       64.01        44.52        36.16         0.36        47.54        44.61 
TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 
        0.82        67.36        36.23        33.11        55.86        53.26 
TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 
       33.01        52.04        42.05        34.98        65.00        33.96 
TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 
        2.99        15.02        18.58        27.62        17.03        12.95 
TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1634 TCGA-25-1877 TCGA-25-1878 
       20.61         0.30        59.15        35.87        24.00        85.05 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 
       13.02        49.05         1.02        38.04         3.02        12.00 
TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 
       19.99         2.96        29.03        31.00        26.99        78.90 
TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       47.61        48.33       101.79        39.02        40.41        33.93 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
       68.32        36.36        16.93        59.67        18.25        41.98 
TCGA-29-1710 TCGA-29-1761 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 
       31.27        17.36        66.81        62.93        39.42        31.30 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 
       22.98        24.36        22.55        17.33        12.36        11.84 
TCGA-29-1777 TCGA-29-1781 TCGA-29-1785 TCGA-29-2425 TCGA-29-2427 TCGA-29-2429 
       12.30         8.38        36.30        65.00        62.47        13.84 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 
       42.25        21.47        11.47         9.76        35.77        38.07 
TCGA-30-1718 TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 TCGA-30-1860 TCGA-30-1862 
       51.91        36.26        15.68         0.26        44.91         6.12 
TCGA-30-1866 TCGA-30-1880 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 
       36.62        57.57        48.79        45.57        30.18        18.77 
TCGA-31-1951 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
       22.49        42.51        44.12        28.77        29.10        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 
       22.85        22.55        30.08        25.74        27.85        24.23 
TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       24.69        35.05        33.01        29.49        29.82        25.91 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2548 
       23.80        21.60         2.24        20.98        18.31        14.17 
TCGA-36-2549 TCGA-36-2551 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 
        6.05        16.18        47.57        23.74        28.93        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1584 TCGA-57-1585 
       10.42        40.77         1.48        24.03        21.14         1.74 
TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2349 TCGA-59-2350 
       22.32        29.00        25.08        25.02        80.12        22.32 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1725 
       34.39         2.14        44.81        11.11         8.09        31.43 
TCGA-61-1727 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
       18.54        31.79        28.47        48.79        44.84        35.80 
TCGA-61-1740 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 
        2.43         1.45         8.42         5.79        11.41        13.02 
TCGA-61-1904 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 
        9.07        37.05        42.51        48.92        56.61        67.76 
TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 
       15.75        38.17         2.01        14.50        17.98         4.01 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
       30.64        39.85        30.64         1.18        45.96        45.40 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 
        4.80         4.77        51.72        61.64        58.39        65.52 
TCGA-61-2101 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 
       55.50        20.68        44.52       125.75        22.22         6.35 
TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-VG-A8LO TCGA-09-0366 TCGA-09-0367 
       31.07         8.61        39.68         0.79        57.76        17.98 
TCGA-09-0369 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       35.57        54.31        25.91        81.86        18.51        34.19 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 
       32.88        14.66         6.71        35.44        36.92        19.99 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 
       24.59        44.55        39.58        12.39        31.20        15.19 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 
       17.82        55.17         2.50        11.18        11.38        11.54 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 
       61.84        56.71        58.65       118.42       107.28        63.09 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 
       69.73        83.34        45.99        51.02        35.28        13.61 
TCGA-13-0883 TCGA-13-0886 TCGA-13-0889 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       68.94       153.37        95.15        71.74        66.15       134.04 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 
       19.36       127.79        50.37       123.16       118.98        60.59 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0921 
      116.65        44.55        37.64       109.32        58.68        48.76 
TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       83.74        85.94        25.41 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.79              0.26 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           180.20            153.37 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            31.25             33.30 
[1] "0.8 - 180.2 (31.2)" "0.3 - 153.4 (33.3)"
[1] "hr=" "1"  
D50V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  5P LOSS MUTATED         1   130                0
  5P LOSS WILD-TYPE       2   428                2
D50V3, multiclass
                  clus
vv                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  OMENTUM                        1                 2
  OVARY                        130               428
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V4, binary
                   cls
clus                  0   1
  5P LOSS MUTATED   124   0
  5P LOSS WILD-TYPE 417   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED    124    0
  5P LOSS WILD-TYPE  417    5
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO              124               417
  YES               0                 5
[1] 2 2
[1] FALSE
D50V5, continuous
                   vv
clus                R0 R1 R2 RX
  5P LOSS MUTATED    3  3  0  2
  5P LOSS WILD-TYPE 12 23  5  1
D50V6, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0               3                12
  R1               3                23
  R2               0                 5
  RX               2                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     3  77
  5P LOSS WILD-TYPE   7 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      3   77
  5P LOSS WILD-TYPE    7  250
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 7
  NOT HISPANIC OR LATINO              77               250
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    94 126
  5Q LOSS WILD-TYPE 134 205
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              220               339 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              126               205 
$`5Q LOSS MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1338 
       13.81        20.52        43.92        41.00        49.15        46.62 
TCGA-04-1341 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1371 
        1.08        63.98        65.46        49.28        32.52        82.39 
TCGA-04-1517 TCGA-04-1519 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 
       19.99         0.79        48.89        27.88        28.64        64.64 
TCGA-09-1669 TCGA-09-1674 TCGA-09-2043 TCGA-09-2044 TCGA-09-2049 TCGA-09-2054 
       30.51         8.55         6.18         6.12       112.41        20.94 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1411 TCGA-13-1412 TCGA-13-1484 TCGA-13-1491 
       28.54        83.31        17.46        32.35       124.44        52.44 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1499 TCGA-13-1505 TCGA-13-1509 TCGA-13-2057 
        4.24       127.27       115.07        65.69        80.15        80.02 
TCGA-13-2059 TCGA-13-2060 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1684 
       78.48        77.88        25.94        26.20        27.52        19.10 
TCGA-20-1686 TCGA-23-1021 TCGA-23-1022 TCGA-23-1026 TCGA-23-1028 TCGA-23-1030 
        2.93        47.54        49.68        26.83        49.41        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 
       18.90         2.76        51.35        54.51        31.20        68.68 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 
       86.01       129.96        39.09        33.47        58.13        24.95 
TCGA-23-2077 TCGA-23-2643 TCGA-24-0970 TCGA-24-1419 TCGA-24-1424 TCGA-24-1430 
      115.89         4.70        11.64         7.86         6.02        28.37 
TCGA-24-1431 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1548 
       18.64        12.46        45.14       105.99         9.11        16.21 
TCGA-24-1549 TCGA-24-1558 TCGA-24-1564 TCGA-24-1567 TCGA-24-1614 TCGA-24-1616 
       56.58        19.53        25.87        17.23        48.33        38.24 
TCGA-24-1842 TCGA-24-1843 TCGA-24-1920 TCGA-24-1924 TCGA-24-1928 TCGA-24-2019 
        8.32         3.48         9.80        30.21        11.05         4.87 
TCGA-24-2020 TCGA-24-2026 TCGA-24-2030 TCGA-24-2035 TCGA-24-2254 TCGA-24-2260 
      152.02        34.82        55.92        28.18        57.07        36.16 
TCGA-24-2261 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2293 TCGA-24-2295 
        0.79        31.63        70.45        44.61        16.64        33.11 
TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1315 TCGA-25-1317 TCGA-25-1318 
       53.26         1.02        26.96        52.04         2.01        34.98 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1626 TCGA-25-1630 
       37.97        33.96         2.99        12.99        17.03        38.20 
TCGA-25-1633 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-2396 
       62.17        52.04        14.96        24.99        24.00         3.02 
TCGA-25-2398 TCGA-25-2400 TCGA-25-2404 TCGA-29-1691 TCGA-29-1695 TCGA-29-1697 
       45.01        42.02        29.03        48.33        40.41        31.20 
TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 TCGA-29-1711 TCGA-29-1762 TCGA-29-1764 
       68.32        16.93        23.93        34.62        86.60        62.93 
TCGA-29-1766 TCGA-29-1775 TCGA-29-1778 TCGA-29-1783 TCGA-29-1784 TCGA-29-2425 
       39.42        12.36        14.93         7.23         5.36        65.00 
TCGA-29-2428 TCGA-30-1718 TCGA-30-1855 TCGA-30-1859 TCGA-30-1861 TCGA-30-1866 
       45.11        51.91         2.47        48.10        34.78        36.62 
TCGA-30-1867 TCGA-30-1887 TCGA-30-1891 TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 
        1.22        24.26        30.05         6.71        42.51         2.20 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1581 TCGA-36-2537 TCGA-36-2538 TCGA-36-2547 
        8.55        30.08        24.69        25.91        25.08        20.52 
TCGA-36-2552 TCGA-57-1582 TCGA-57-1583 TCGA-57-1992 TCGA-57-1994 TCGA-59-2348 
       11.47        24.03        11.38        29.00        25.02       180.20 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2363 TCGA-61-1722 TCGA-61-1724 TCGA-61-1728 
      116.12         9.40         5.42         8.09        20.94        27.88 
TCGA-61-1730 TCGA-61-1734 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1903 
        4.34        28.47        43.69         1.45         8.42        13.02 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1917 TCGA-61-1919 TCGA-61-1998 TCGA-61-2003 
       34.13        31.30        43.43        38.17         5.52         4.01 
TCGA-61-2008 TCGA-61-2012 TCGA-61-2088 TCGA-61-2094 TCGA-61-2097 TCGA-61-2102 
       30.64        30.64         4.77        71.74        60.62         6.48 
TCGA-61-2104 TCGA-61-2111 TCGA-OY-A56Q TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 
       76.87       125.75        18.94         9.99        29.16         9.47 
TCGA-09-0366 TCGA-10-0927 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0723 
       57.76        81.86        20.91         6.21        24.59        39.58 
TCGA-13-0724 TCGA-13-0730 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 
        2.73        17.82        11.54        38.01       111.78        61.84 
TCGA-13-0766 TCGA-13-0791 TCGA-13-0793 TCGA-13-0794 TCGA-13-0800 TCGA-13-0801 
       56.71        40.24       107.28        63.09        87.48        45.99 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 
       51.02        43.86       107.18       111.39        66.67        92.42 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 TCGA-13-0901 TCGA-13-0904 
      145.45       102.84        43.36        66.15        19.36        50.37 
TCGA-13-0906 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
      118.98        58.68        84.53        48.79 

$`5Q LOSS WILD-TYPE`
TCGA-5X-AA5U TCGA-04-1335 TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 
       11.87         1.81         2.01        18.51        11.87        65.52 
TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1353 TCGA-04-1362 TCGA-04-1364 
       63.09        48.76        21.57         0.53        44.32        33.67 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 TCGA-04-1516 TCGA-04-1525 TCGA-04-1530 
       76.57       103.40        56.55        41.59        38.37       119.08 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 
       29.10        84.20        55.43        36.23        31.86        47.70 
TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       45.37         9.99        38.43        89.33        74.93        41.62 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       57.60        61.87        55.36        17.98         5.85         3.02 
TCGA-09-1675 TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 
       97.55        35.15         4.54        71.11        63.09        39.75 
TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1408 TCGA-13-1409 
       26.93        12.46        77.10        81.17        55.23        57.27 
TCGA-13-1410 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 
       81.01        54.64        87.06        61.71        29.42        20.68 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       22.39        70.82        83.93       125.56        93.90        90.38 
TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 
       66.15        13.97        43.20        34.82        34.16        65.52 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT 
       44.68        54.25        14.53        76.90        65.52        70.45 
TCGA-13-A5FU TCGA-20-0987 TCGA-20-0996 TCGA-20-1683 TCGA-20-1685 TCGA-20-1687 
        8.42        23.05        72.20        25.38        16.70         2.66 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1027 TCGA-23-1029 TCGA-23-1111 TCGA-23-1116 
       40.54        15.39        32.09         8.81         3.22        19.46 
TCGA-23-1117 TCGA-23-1120 TCGA-23-1121 TCGA-23-1809 TCGA-23-2078 TCGA-23-2079 
       33.30         4.27         6.38         0.53        87.48        91.66 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2645 TCGA-24-0966 TCGA-24-0975 
       77.00        49.84         2.76         4.50         7.63        21.80 
TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 
       41.56         7.66        22.32        54.12        63.55        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1422 TCGA-24-1423 
        6.31         6.38         7.82         7.99         0.76         6.25 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1434 TCGA-24-1435 
        5.95         5.36         4.83        17.39        18.67        43.53 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
        8.55        72.92         3.45         1.18        22.22        26.96 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 
       57.40        64.27        41.06        51.91        41.39        58.09 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       88.50        70.62        39.88        44.09        45.50        47.70 
TCGA-24-1565 TCGA-24-1603 TCGA-24-1604 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 
       10.26        90.15        88.37         3.72         3.81         4.37 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1923 TCGA-24-1927 TCGA-24-1930 
       11.28         5.79         5.52        22.68        16.44        81.11 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 TCGA-24-2036 
       44.84        58.16       109.71        14.43        18.48        64.01 
TCGA-24-2038 TCGA-24-2262 TCGA-24-2267 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 
       44.52         0.36        47.54         0.82        67.36        36.23 
TCGA-24-2297 TCGA-25-1314 TCGA-25-1316 TCGA-25-1319 TCGA-25-1329 TCGA-25-1623 
       55.86        33.01        42.05        65.00        15.02        18.58 
TCGA-25-1625 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1634 
       27.62        12.95        20.61         0.30        59.15        35.87 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2397 
       85.05        13.02        49.05         1.02        38.04        12.00 
TCGA-25-2399 TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 
       19.99         2.96        31.00        26.99        78.90        47.61 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1699 TCGA-29-1703 TCGA-29-1705 
      101.79        39.02        33.93        36.36        59.67        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1761 TCGA-29-1763 TCGA-29-1768 TCGA-29-1769 
       41.98        31.27        17.36        66.81        31.30        22.98 
TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 
       24.36        22.55        17.33        11.84        12.30         8.38 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 
       36.30        86.17        62.47        13.84        42.25        21.47 
TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1853 TCGA-30-1856 
       11.47         9.76        35.77        38.07        36.26        15.68 
TCGA-30-1857 TCGA-30-1860 TCGA-30-1862 TCGA-30-1880 TCGA-30-1892 TCGA-31-1944 
        0.26        44.91         6.12        57.57        48.79        45.57 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 
       30.18        18.77        22.49        44.12        28.77        29.10 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 
       21.53        22.85        22.55        25.74        27.85        24.23 
TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2540 TCGA-36-2542 
       35.05        33.01        29.49        29.82        23.80        21.60 
TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 
        2.24        20.98        18.31        14.17         6.05        16.18 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
       47.57        23.74        28.93        42.02        10.42        40.77 
TCGA-42-2593 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1993 TCGA-59-2349 
        1.48        21.14         1.74        22.32        25.08        80.12 
TCGA-59-2350 TCGA-59-2354 TCGA-59-2355 TCGA-59-2372 TCGA-61-1721 TCGA-61-1725 
       22.32        34.39         2.14        44.81        11.11        31.43 
TCGA-61-1727 TCGA-61-1733 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 
       18.54        31.79        48.79        44.84        35.80         2.43 
TCGA-61-1741 TCGA-61-1900 TCGA-61-1901 TCGA-61-1904 TCGA-61-1910 TCGA-61-1911 
       33.67         5.79        11.41         9.07        37.05        42.51 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 TCGA-61-1995 TCGA-61-2000 
       48.92        56.61        67.76        15.75         2.01        14.50 
TCGA-61-2002 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
       17.98        39.85         1.18        45.96        45.40         4.80 
TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 TCGA-61-2101 TCGA-61-2109 
       51.72        61.64        58.39        65.52        55.50        20.68 
TCGA-61-2110 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P 
       44.52        22.22         6.35        31.07         8.61        39.68 
TCGA-VG-A8LO TCGA-09-0367 TCGA-09-0369 TCGA-10-0925 TCGA-10-0926 TCGA-10-0928 
        0.79        17.98        35.57        54.31        25.91        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 
       34.19        32.88        14.66         6.71        35.44        36.92 
TCGA-10-0937 TCGA-13-0720 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0751 
       19.99        44.55        12.39        31.20        15.19        55.17 
TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0768 TCGA-13-0792 TCGA-13-0795 
        2.50        11.18        11.38        58.65       118.42        20.35 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
       69.73        83.34        35.28        35.31        13.61        68.94 
TCGA-13-0886 TCGA-13-0889 TCGA-13-0897 TCGA-13-0900 TCGA-13-0903 TCGA-13-0905 
      153.37        95.15        71.74       134.04       127.79       123.16 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0921 
       60.59       116.65        44.55        37.64       109.32        48.76 
TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       83.74        85.94        25.41 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.79              0.26 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           180.20            153.37 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           31.465            33.300 
[1] "0.8 - 180.2 (31.5)" "0.3 - 153.4 (33.3)"
[1] "hr=" "1.1"
D51V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  5Q LOSS MUTATED         1   219                1
  5Q LOSS WILD-TYPE       2   339                1
D51V3, multiclass
                  clus
vv                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  OMENTUM                        1                 2
  OVARY                        219               339
  PERITONEUM OVARY               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V4, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED   211   2
  5Q LOSS WILD-TYPE 330   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED    211    2
  5Q LOSS WILD-TYPE  330    3
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO              211               330
  YES               2                 3
[1] 2 2
[1] FALSE
D51V5, continuous
                   vv
clus                R0 R1 R2 RX
  5Q LOSS MUTATED    3  5  0  2
  5Q LOSS WILD-TYPE 12 21  5  1
D51V6, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0               3                12
  R1               5                21
  R2               0                 5
  RX               2                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     5 131
  5Q LOSS WILD-TYPE   5 196
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      5  131
  5Q LOSS WILD-TYPE    5  196
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 5
  NOT HISPANIC OR LATINO             131               196
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    63  92
  6P LOSS WILD-TYPE 165 239
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              155               404 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               92               239 
$`6P LOSS MUTATED`
TCGA-59-A5PD TCGA-04-1331 TCGA-04-1348 TCGA-04-1351 TCGA-04-1367 TCGA-04-1519 
       20.52        43.92        48.76        65.46       103.40         0.79 
TCGA-04-1646 TCGA-04-1649 TCGA-04-1651 TCGA-04-1655 TCGA-09-1659 TCGA-09-1670 
       27.88        64.64        36.23        45.37         9.99        17.98 
TCGA-09-1672 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2053 TCGA-09-2056 
        5.85        97.55         6.18         6.12        39.75        12.46 
TCGA-13-1405 TCGA-13-1410 TCGA-13-1483 TCGA-13-1484 TCGA-13-1491 TCGA-13-1495 
       28.54        81.01        29.42       124.44        52.44        90.38 
TCGA-13-1497 TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 TCGA-13-1512 TCGA-13-2059 
      127.27        43.20        65.69        34.16        14.53        78.48 
TCGA-13-A5FU TCGA-20-1683 TCGA-23-1021 TCGA-23-1030 TCGA-23-1113 TCGA-23-1117 
        8.42        25.38        47.54        29.13        31.20        33.30 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1122 TCGA-23-1123 TCGA-23-2072 TCGA-23-2078 
       86.01       129.96        39.09        33.47        24.95        87.48 
TCGA-23-2641 TCGA-23-2643 TCGA-24-0966 TCGA-24-0970 TCGA-24-1416 TCGA-24-1426 
        2.76         4.70         7.63        11.64         6.38         5.36 
TCGA-24-1427 TCGA-24-1428 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1467 
        4.83        17.39        18.67        43.53         8.55       105.99 
TCGA-24-1471 TCGA-24-1546 TCGA-24-1552 TCGA-24-1553 TCGA-24-1560 TCGA-24-1842 
        1.18        64.27        41.39        58.09        44.09         8.32 
TCGA-24-1845 TCGA-24-1849 TCGA-24-1923 TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 
        3.81         5.79        22.68        16.44        11.05         4.87 
TCGA-24-2023 TCGA-24-2027 TCGA-24-2029 TCGA-24-2271 TCGA-24-2280 TCGA-24-2293 
       44.84       109.71        14.43        31.63        70.45        16.64 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1320 
       55.86        53.26        26.96        52.04        42.05        37.97 
TCGA-25-1322 TCGA-25-1329 TCGA-25-1627 TCGA-25-1628 TCGA-25-1635 TCGA-25-2396 
        2.99        15.02        12.95        20.61        52.04         3.02 
TCGA-25-2399 TCGA-29-1688 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 
       19.99        78.90       101.79        39.02        33.93        31.20 
TCGA-29-1707 TCGA-29-1763 TCGA-29-1769 TCGA-29-1781 TCGA-29-1784 TCGA-29-2428 
       41.98        66.81        22.98         8.38         5.36        45.11 
TCGA-30-1714 TCGA-30-1853 TCGA-30-1855 TCGA-30-1857 TCGA-30-1859 TCGA-30-1866 
       38.07        36.26         2.47         0.26        48.10        36.62 
TCGA-30-1880 TCGA-31-1951 TCGA-36-1569 TCGA-36-2543 TCGA-36-2548 TCGA-42-2588 
       57.57        22.49        29.10         2.24        14.17        28.93 
TCGA-42-2591 TCGA-59-2350 TCGA-59-2351 TCGA-59-2355 TCGA-59-2372 TCGA-61-1724 
       40.77        22.32       116.12         2.14        44.81        20.94 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1738 
       18.54        27.88        31.79        28.47        48.79        35.80 
TCGA-61-1740 TCGA-61-1904 TCGA-61-1906 TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 
        2.43         9.07        34.13        37.05        48.92        56.61 
TCGA-61-1995 TCGA-61-2008 TCGA-61-2096 TCGA-61-2110 TCGA-61-2613 TCGA-09-0365 
        2.01        30.64        58.39        44.52        31.07         9.47 
TCGA-10-0926 TCGA-13-0720 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0758 
       25.91        44.55        17.82        55.17        11.18        11.38 
TCGA-13-0762 TCGA-13-0766 TCGA-13-0801 TCGA-13-0803 TCGA-13-0884 TCGA-13-0887 
      111.78        56.71        45.99        43.86       107.18        66.67 
TCGA-13-0888 TCGA-13-0890 TCGA-13-0891 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       92.42       145.45       102.84        71.74        66.15       134.04 
TCGA-13-0905 TCGA-13-0910 TCGA-13-0911 TCGA-13-0919 TCGA-13-0921 
      123.16       116.65        44.55        84.53        48.76 

$`6P LOSS WILD-TYPE`
TCGA-3P-A9WA TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 
       13.81        11.87        41.00         1.81        49.15         2.01 
TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 
       46.62         1.08        18.51        11.87        65.52        63.09 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 
       21.57        63.98         0.53        49.28        32.52        44.32 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 
       33.67        76.57        82.39        56.55        41.59        19.99 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 
       38.37       119.08        29.10        84.20        55.43        48.89 
TCGA-04-1648 TCGA-04-1652 TCGA-04-1654 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       28.64        31.86        47.70        38.43        89.33        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1673 
       41.62        57.60        61.87        55.36        30.51         3.02 
TCGA-09-1674 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
        8.55        35.15         4.54       112.41        71.11        63.09 
TCGA-09-2054 TCGA-09-2055 TCGA-13-1403 TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 
       20.94        26.93        77.10        81.17        83.31        55.23 
TCGA-13-1409 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 
       57.27        17.46        32.35        54.64        87.06        61.71 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1492 TCGA-13-1494 
       20.68        22.39        70.82        83.93       125.56        93.90 
TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 TCGA-13-1507 
        4.24        66.15       115.07        13.97        34.82        65.52 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 
       80.15        44.68        54.25        80.02        77.88        76.90 
TCGA-13-2065 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 
       65.52        70.45        23.05        25.94        26.20        72.20 
TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1022 
       27.52        19.10        16.70         2.93         2.66        49.68 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 
       40.54        15.39        26.83        32.09        49.41         8.81 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 
       18.90         2.76        51.35        54.51         3.22        68.68 
TCGA-23-1116 TCGA-23-1120 TCGA-23-1121 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 
       19.46         4.27         6.38        58.13         0.53       115.89 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2645 TCGA-24-0975 TCGA-24-0979 
       91.66        77.00        49.84         4.50        21.80        41.56 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 
        7.66        22.32        54.12        63.55        47.41         6.31 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
        7.82         7.99         7.86         0.76         6.25         6.02 
TCGA-24-1425 TCGA-24-1430 TCGA-24-1431 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 
        5.95        28.37        18.64        72.92        12.46        45.14 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 
        9.11         3.45        22.22        26.96        57.40        16.21 
TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       56.58        41.06        51.91        88.50        70.62        39.88 
TCGA-24-1558 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 
       19.53        45.50        47.70        25.87        10.26        17.23 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1843 TCGA-24-1844 
       90.15        88.37        48.33        38.24         3.48         3.72 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-1930 
        4.37        11.28         5.52         9.80        30.21        81.11 
TCGA-24-2020 TCGA-24-2024 TCGA-24-2026 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 
      152.02        58.16        34.82        55.92        18.48        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 
       64.01        44.52        57.07        36.16         0.79         0.36 
TCGA-24-2267 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2295 
       47.54        44.61         0.82        67.36        36.23        33.11 
TCGA-25-1312 TCGA-25-1314 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 
        1.02        33.01         2.01        34.98        65.00        33.96 
TCGA-25-1323 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1630 TCGA-25-1631 
       12.99        18.58        27.62        17.03        38.20         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
       59.15        62.17        35.87        14.96        24.99        24.00 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2397 
       85.05        13.02        49.05         1.02        38.04        12.00 
TCGA-25-2398 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       45.01        42.02         2.96        29.03        31.00        26.99 
TCGA-29-1690 TCGA-29-1691 TCGA-29-1695 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 
       47.61        48.33        40.41        68.32        36.36        16.93 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 
       23.93        59.67        18.25        31.27        34.62        17.36 
TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1770 TCGA-29-1771 
       86.60        62.93        39.42        31.30        24.36        22.55 
TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1783 
       17.33        12.36        11.84        12.30        14.93         7.23 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 
       36.30        86.17        65.00        62.47        13.84        42.25 
TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1856 
       21.47        11.47         9.76        35.77        51.91        15.68 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1867 TCGA-30-1887 TCGA-30-1891 
       44.91        34.78         6.12         1.22        24.26        30.05 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1953 TCGA-31-1955 
       48.79        45.57        30.18        18.77         6.71        42.51 
TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
       44.12         2.20        28.77        21.53        22.85        22.55 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 
        8.55        30.08        25.74        27.85        24.23        24.69 
TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
       35.05        33.01        29.49        29.82        25.91        25.08 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 
       23.80        21.60        20.98        18.31        20.52         6.05 
TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2589 TCGA-42-2590 
       16.18        11.47        47.57        23.74        42.02        10.42 
TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 
        1.48        24.03        11.38        21.14         1.74        22.32 
TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2352 
       29.00        25.08        25.02       180.20        80.12         9.40 
TCGA-59-2354 TCGA-59-2363 TCGA-61-1721 TCGA-61-1722 TCGA-61-1725 TCGA-61-1730 
       34.39         5.42        11.11         8.09        31.43         4.34 
TCGA-61-1737 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
       44.84        33.67        43.69         1.45         8.42         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1907 TCGA-61-1911 TCGA-61-1915 TCGA-61-1917 
       11.41        13.02        31.30        42.51        67.76        43.43 
TCGA-61-1918 TCGA-61-1919 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 
       15.75        38.17         5.52        14.50        17.98         4.01 
TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
       39.85        30.64         1.18        45.96        45.40         4.80 
TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 TCGA-61-2098 
        4.77        51.72        71.74        61.64        60.62        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2111 TCGA-61-2113 
       55.50         6.48        76.87        20.68       125.75        22.22 
TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
        6.35         8.61        39.68        18.94         0.79         9.99 
TCGA-09-0364 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-10-0925 TCGA-10-0927 
       29.16        57.76        17.98        35.57        54.31        81.86 
TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 
       18.51        34.19        32.88        14.66         6.71        35.44 
TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0723 
       36.92        19.99        20.91         6.21        24.59        39.58 
TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0755 TCGA-13-0760 
        2.73        12.39        31.20        15.19         2.50        11.54 
TCGA-13-0761 TCGA-13-0764 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       38.01        61.84        58.65        40.24       118.42       107.28 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0802 
       63.09        20.35        69.73        83.34        87.48        51.02 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0885 TCGA-13-0886 
       35.28        35.31        13.61        68.94       111.39       153.37 
TCGA-13-0889 TCGA-13-0893 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 
       95.15        43.36        19.36       127.79        50.37       118.98 
TCGA-13-0908 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0923 
       60.59        37.64       109.32        58.68        48.79        83.74 
TCGA-13-0924 TCGA-13-2071 
       85.94        25.41 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.26              0.30 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           145.45            180.20 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           34.160            31.645 
[1] "0.3 - 145.4 (34.2)" "0.3 - 180.2 (31.6)"
[1] "hr=" "1.1"
D52V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  6P LOSS MUTATED         1   155                0
  6P LOSS WILD-TYPE       2   403                2
D52V3, multiclass
                  clus
vv                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  OMENTUM                        1                 2
  OVARY                        155               403
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V4, binary
                   cls
clus                  0   1
  6P LOSS MUTATED   146   2
  6P LOSS WILD-TYPE 395   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED    146    2
  6P LOSS WILD-TYPE  395    3
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO              146               395
  YES               2                 3
[1] 2 2
[1] FALSE
D52V5, continuous
                   vv
clus                R0 R1 R2 RX
  6P LOSS MUTATED    1  5  2  0
  6P LOSS WILD-TYPE 14 21  3  3
D52V6, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0               1                14
  R1               5                21
  R2               2                 3
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     2  95
  6P LOSS WILD-TYPE   8 232
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      2   95
  6P LOSS WILD-TYPE    8  232
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 8
  NOT HISPANIC OR LATINO              95               232
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    89 142
  6Q LOSS WILD-TYPE 139 189
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              231               328 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              142               189 
$`6Q LOSS MUTATED`
TCGA-59-A5PD TCGA-04-1331 TCGA-04-1337 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 
       20.52        43.92         2.01        48.76        21.57        63.98 
TCGA-04-1351 TCGA-04-1367 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1646 
       65.46       103.40        19.99         0.79        38.37        27.88 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       64.64        36.23        45.37         9.99        38.43        89.33 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 
       17.98         5.85        97.55         6.18         6.12        35.15 
TCGA-09-2053 TCGA-09-2055 TCGA-09-2056 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 
       39.75        26.93        12.46        81.17        28.54        83.31 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
       81.01        17.46        87.06        61.71        29.42       124.44 
TCGA-13-1491 TCGA-13-1495 TCGA-13-1497 TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 
       52.44        90.38       127.27        43.20        65.69        34.16 
TCGA-13-1512 TCGA-13-2059 TCGA-13-A5FU TCGA-20-1683 TCGA-20-1686 TCGA-23-1021 
       14.53        78.48         8.42        25.38         2.93        47.54 
TCGA-23-1027 TCGA-23-1029 TCGA-23-1030 TCGA-23-1109 TCGA-23-1113 TCGA-23-1117 
       32.09         8.81        29.13        51.35        31.20        33.30 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1122 TCGA-23-1123 TCGA-23-2072 TCGA-23-2078 
       86.01       129.96        39.09        33.47        24.95        87.48 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-24-0966 TCGA-24-0970 TCGA-24-0980 
       49.84         2.76         4.70         7.63        11.64         7.66 
TCGA-24-0982 TCGA-24-1105 TCGA-24-1416 TCGA-24-1417 TCGA-24-1426 TCGA-24-1427 
       22.32        47.41         6.38         7.82         5.36         4.83 
TCGA-24-1428 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1467 TCGA-24-1471 
       17.39        18.67        43.53         8.55       105.99         1.18 
TCGA-24-1546 TCGA-24-1552 TCGA-24-1553 TCGA-24-1560 TCGA-24-1562 TCGA-24-1564 
       64.27        41.39        58.09        44.09        45.50        25.87 
TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 TCGA-24-1849 TCGA-24-1923 TCGA-24-1927 
        8.32         3.72         3.81         5.79        22.68        16.44 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2029 TCGA-24-2261 TCGA-24-2262 
        4.87       152.02        44.84        14.43         0.79         0.36 
TCGA-24-2271 TCGA-24-2280 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 
       31.63        70.45        36.23        16.64        33.11        55.86 
TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
       53.26        26.96        52.04        42.05         2.01        34.98 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1627 
       37.97        33.96         2.99        12.99        15.02        12.95 
TCGA-25-1628 TCGA-25-1634 TCGA-25-1878 TCGA-25-2042 TCGA-25-2396 TCGA-25-2397 
       20.61        35.87        85.05        13.02         3.02        12.00 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2409 TCGA-29-1688 TCGA-29-1693 TCGA-29-1694 
       45.01        19.99        26.99        78.90       101.79        39.02 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1707 TCGA-29-1762 TCGA-29-1763 TCGA-29-1768 
       33.93        31.20        41.98        86.60        66.81        31.30 
TCGA-29-1769 TCGA-29-1771 TCGA-29-1781 TCGA-29-1784 TCGA-29-2428 TCGA-29-2432 
       22.98        22.55         8.38         5.36        45.11        21.47 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1857 TCGA-30-1859 
       38.07        51.91        36.26         2.47         0.26        48.10 
TCGA-30-1866 TCGA-30-1880 TCGA-31-1951 TCGA-31-1956 TCGA-31-1959 TCGA-36-1569 
       36.62        57.57        22.49        44.12         2.20        29.10 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1580 TCGA-36-2542 TCGA-36-2543 TCGA-36-2545 
       22.85        22.55        24.23        21.60         2.24        18.31 
TCGA-36-2547 TCGA-36-2548 TCGA-42-2588 TCGA-42-2589 TCGA-42-2591 TCGA-57-1583 
       20.52        14.17        28.93        42.02        40.77        11.38 
TCGA-57-1584 TCGA-59-2350 TCGA-59-2351 TCGA-59-2355 TCGA-59-2372 TCGA-61-1724 
       21.14        22.32       116.12         2.14        44.81        20.94 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 
       18.54        27.88         4.34        31.79        28.47        48.79 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1899 TCGA-61-1903 TCGA-61-1904 
       44.84        35.80         2.43         8.42        13.02         9.07 
TCGA-61-1906 TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 TCGA-61-1918 TCGA-61-1995 
       34.13        37.05        48.92        56.61        15.75         2.01 
TCGA-61-1998 TCGA-61-2002 TCGA-61-2008 TCGA-61-2096 TCGA-61-2097 TCGA-61-2101 
        5.52        17.98        30.64        58.39        60.62        55.50 
TCGA-61-2104 TCGA-61-2110 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-09-0365 
       76.87        44.52        31.07         8.61        39.68         9.47 
TCGA-09-0367 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0935 TCGA-10-0938 
       17.98        54.31        25.91        81.86        35.44        20.91 
TCGA-13-0717 TCGA-13-0726 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 
       24.59        31.20        55.17         2.50        11.18        11.38 
TCGA-13-0762 TCGA-13-0766 TCGA-13-0793 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 
      111.78        56.71       107.28        83.34        45.99        51.02 
TCGA-13-0803 TCGA-13-0883 TCGA-13-0884 TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 
       43.86        68.94       107.18        66.67        92.42       145.45 
TCGA-13-0891 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0905 TCGA-13-0910 
      102.84        71.74        66.15       134.04       123.16       116.65 
TCGA-13-0911 TCGA-13-0919 TCGA-13-0921 
       44.55        84.53        48.76 

$`6Q LOSS WILD-TYPE`
TCGA-3P-A9WA TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 
       13.81        11.87        41.00         1.81        49.15        46.62 
TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1353 
        1.08        18.51        11.87        65.52        63.09         0.53 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1371 
       49.28        32.52        44.32        33.67        76.57        82.39 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 
       56.55        41.59       119.08        29.10        84.20        55.43 
TCGA-04-1644 TCGA-04-1648 TCGA-04-1652 TCGA-04-1654 TCGA-09-1664 TCGA-09-1665 
       48.89        28.64        31.86        47.70        74.93        41.62 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1673 TCGA-09-1674 
       57.60        61.87        55.36        30.51         3.02         8.55 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2054 TCGA-13-1403 
        4.54       112.41        71.11        63.09        20.94        77.10 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1412 TCGA-13-1477 TCGA-13-1485 TCGA-13-1487 
       55.23        57.27        32.35        54.64        20.68        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1492 TCGA-13-1494 TCGA-13-1496 TCGA-13-1498 
       70.82        83.93       125.56        93.90         4.24        66.15 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 
      115.07        13.97        34.82        65.52        80.15        44.68 
TCGA-13-1511 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT 
       54.25        80.02        77.88        76.90        65.52        70.45 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1684 
       23.05        25.94        26.20        72.20        27.52        19.10 
TCGA-20-1685 TCGA-20-1687 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
       16.70         2.66        49.68        40.54        15.39        26.83 
TCGA-23-1028 TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 
       49.41        18.90         2.76        54.51         3.22        68.68 
TCGA-23-1116 TCGA-23-1120 TCGA-23-1121 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 
       19.46         4.27         6.38        58.13         0.53       115.89 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2645 TCGA-24-0975 TCGA-24-0979 TCGA-24-1103 
       91.66        77.00         4.50        21.80        41.56        54.12 
TCGA-24-1104 TCGA-24-1413 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 
       63.55         6.31         7.99         7.86         0.76         6.25 
TCGA-24-1424 TCGA-24-1425 TCGA-24-1430 TCGA-24-1431 TCGA-24-1463 TCGA-24-1464 
        6.02         5.95        28.37        18.64        72.92        12.46 
TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 
       45.14         9.11         3.45        22.22        26.96        57.40 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1555 TCGA-24-1556 
       16.21        56.58        41.06        51.91        88.50        70.62 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1563 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       39.88        19.53        47.70        10.26        17.23        90.15 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1843 TCGA-24-1846 TCGA-24-1847 
       88.37        48.33        38.24         3.48         4.37        11.28 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-1928 TCGA-24-1930 TCGA-24-2024 
        5.52         9.80        30.21        11.05        81.11        58.16 
TCGA-24-2026 TCGA-24-2027 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 
       34.82       109.71        55.92        18.48        28.18        64.01 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2267 TCGA-24-2281 TCGA-24-2288 
       44.52        57.07        36.16        47.54        44.61         0.82 
TCGA-24-2289 TCGA-25-1312 TCGA-25-1314 TCGA-25-1319 TCGA-25-1623 TCGA-25-1625 
       67.36         1.02        33.01        65.00        18.58        27.62 
TCGA-25-1626 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 
       17.03        38.20         0.30        59.15        62.17        52.04 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 
       14.96        24.99        24.00        49.05         1.02        38.04 
TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-29-1690 TCGA-29-1691 
       42.02         2.96        29.03        31.00        47.61        48.33 
TCGA-29-1695 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 
       40.41        68.32        36.36        16.93        23.93        59.67 
TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1764 TCGA-29-1766 
       18.25        31.27        34.62        17.36        62.93        39.42 
TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 
       24.36        17.33        12.36        11.84        12.30        14.93 
TCGA-29-1783 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2429 
        7.23        36.30        86.17        65.00        62.47        13.84 
TCGA-29-2431 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1856 TCGA-30-1860 
       42.25        11.47         9.76        35.77        15.68        44.91 
TCGA-30-1861 TCGA-30-1862 TCGA-30-1867 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 
       34.78         6.12         1.22        24.26        30.05        48.79 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1953 TCGA-31-1955 TCGA-36-1568 
       45.57        30.18        18.77         6.71        42.51        28.77 
TCGA-36-1570 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 
       21.53         8.55        30.08        25.74        27.85        24.69 
TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
       35.05        33.01        29.49        29.82        25.91        25.08 
TCGA-36-2540 TCGA-36-2544 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 
       23.80        20.98         6.05        16.18        11.47        47.57 
TCGA-42-2587 TCGA-42-2590 TCGA-42-2593 TCGA-57-1582 TCGA-57-1585 TCGA-57-1586 
       23.74        10.42         1.48        24.03         1.74        22.32 
TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2352 
       29.00        25.08        25.02       180.20        80.12         9.40 
TCGA-59-2354 TCGA-59-2363 TCGA-61-1721 TCGA-61-1722 TCGA-61-1725 TCGA-61-1741 
       34.39         5.42        11.11         8.09        31.43        33.67 
TCGA-61-1743 TCGA-61-1895 TCGA-61-1900 TCGA-61-1901 TCGA-61-1907 TCGA-61-1911 
       43.69         1.45         5.79        11.41        31.30        42.51 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1919 TCGA-61-2000 TCGA-61-2003 TCGA-61-2009 
       67.76        43.43        38.17        14.50         4.01        39.85 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
       30.64         1.18        45.96        45.40         4.80         4.77 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2098 TCGA-61-2102 TCGA-61-2109 
       51.72        71.74        61.64        65.52         6.48        20.68 
TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
      125.75        22.22         6.35        18.94         0.79         9.99 
TCGA-09-0364 TCGA-09-0366 TCGA-09-0369 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       29.16        57.76        35.57        18.51        34.19        32.88 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 TCGA-13-0714 TCGA-13-0720 
       14.66         6.71        36.92        19.99         6.21        44.55 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 TCGA-13-0760 
       39.58         2.73        12.39        15.19        17.82        11.54 
TCGA-13-0761 TCGA-13-0764 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0794 
       38.01        61.84        58.65        40.24       118.42        63.09 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0800 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
       20.35        69.73        87.48        35.28        35.31        13.61 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0889 TCGA-13-0893 TCGA-13-0901 TCGA-13-0903 
      111.39       153.37        95.15        43.36        19.36       127.79 
TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       50.37       118.98        60.59        37.64       109.32        58.68 
TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       48.79        83.74        85.94        25.41 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.26              0.30 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           152.02            180.20 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            33.11             32.70 
[1] "0.3 - 152.0 (33.1)" "0.3 - 180.2 (32.7)"
[1] "hr=" "1"  
D53V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  6Q LOSS MUTATED         2   230                0
  6Q LOSS WILD-TYPE       1   328                2
D53V3, multiclass
                  clus
vv                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  OMENTUM                        2                 1
  OVARY                        230               328
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V4, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED   223   2
  6Q LOSS WILD-TYPE 318   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED    223    2
  6Q LOSS WILD-TYPE  318    3
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO              223               318
  YES               2                 3
[1] 2 2
[1] FALSE
D53V5, continuous
                   vv
clus                R0 R1 R2 RX
  6Q LOSS MUTATED    4  8  3  0
  6Q LOSS WILD-TYPE 11 18  2  3
D53V6, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0               4                11
  R1               8                18
  R2               3                 2
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     3 141
  6Q LOSS WILD-TYPE   7 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      3  141
  6Q LOSS WILD-TYPE    7  186
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 7
  NOT HISPANIC OR LATINO             141               186
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    52  67
  7P LOSS WILD-TYPE 176 264
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
              119               440 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               67               264 
$`7P LOSS MUTATED`
TCGA-04-1338 TCGA-04-1341 TCGA-04-1347 TCGA-04-1349 TCGA-04-1362 TCGA-04-1536 
       46.62         1.08        63.09        21.57        44.32        29.10 
TCGA-04-1638 TCGA-09-1659 TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 TCGA-13-1409 
       55.43         9.99        57.60        55.36        30.51        57.27 
TCGA-13-1487 TCGA-13-1497 TCGA-13-1499 TCGA-13-1505 TCGA-13-1510 TCGA-13-2061 
       22.39       127.27       115.07        65.69        44.68        76.90 
TCGA-20-1685 TCGA-23-1029 TCGA-23-1109 TCGA-23-1114 TCGA-23-1118 TCGA-23-1119 
       16.70         8.81        51.35        68.68        86.01       129.96 
TCGA-23-1122 TCGA-23-2078 TCGA-23-2084 TCGA-23-2641 TCGA-24-0982 TCGA-24-1104 
       39.09        87.48        49.84         2.76        22.32        63.55 
TCGA-24-1105 TCGA-24-1417 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1434 
       47.41         7.82         5.95         5.36         4.83        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1469 TCGA-24-1546 
       43.53         8.55        72.92        12.46         9.11        64.27 
TCGA-24-1548 TCGA-24-1562 TCGA-24-1567 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
       16.21        45.50        17.23         8.32         3.48         3.72 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1850 TCGA-24-1930 TCGA-24-2254 TCGA-24-2260 
        4.37        11.28         5.52        81.11        57.07        36.16 
TCGA-24-2262 TCGA-24-2298 TCGA-25-1317 TCGA-25-1321 TCGA-25-1630 TCGA-25-1632 
        0.36        53.26         2.01        33.96        38.20        59.15 
TCGA-25-1633 TCGA-25-1635 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2396 
       62.17        52.04        13.02        49.05         1.02         3.02 
TCGA-25-2399 TCGA-29-1691 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1711 
       19.99        48.33        16.93        23.93        59.67        34.62 
TCGA-29-1761 TCGA-29-1766 TCGA-29-1776 TCGA-29-1781 TCGA-29-2414 TCGA-29-2425 
       17.36        39.42        11.84         8.38        86.17        65.00 
TCGA-29-2431 TCGA-30-1718 TCGA-30-1855 TCGA-30-1887 TCGA-36-1569 TCGA-36-1570 
       42.25        51.91         2.47        24.26        29.10        21.53 
TCGA-36-1574 TCGA-36-1578 TCGA-36-2552 TCGA-42-2589 TCGA-57-1992 TCGA-57-1994 
       22.55        27.85        11.47        42.02        29.00        25.02 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 TCGA-61-1722 TCGA-61-1724 TCGA-61-1740 
        9.40        34.39         5.42         8.09        20.94         2.43 
TCGA-61-1906 TCGA-61-1913 TCGA-61-1995 TCGA-61-2009 TCGA-61-2096 TCGA-61-2612 
       34.13        48.92         2.01        39.85        58.39         6.35 
TCGA-OY-A56P TCGA-WR-A838 TCGA-09-0369 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       39.68         9.99        35.57        18.51        34.19        32.88 
TCGA-10-0935 TCGA-10-0938 TCGA-13-0724 TCGA-13-0751 TCGA-13-0792 TCGA-13-0800 
       35.44        20.91         2.73        55.17       118.42        87.48 
TCGA-13-0885 TCGA-13-0887 TCGA-13-0890 TCGA-13-0897 TCGA-13-0919 
      111.39        66.67       145.45        71.74        84.53 

$`7P LOSS WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 
       49.15         2.01        18.51        11.87        65.52        48.76 
TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1364 
       63.98        65.46         0.53        49.28        32.52        33.67 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 
       76.57       103.40        82.39        56.55        41.59        19.99 
TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1644 TCGA-04-1646 
        0.79        38.37       119.08        84.20        48.89        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 
       28.64        64.64        36.23        31.86        47.70        45.37 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1667 TCGA-09-1670 
       38.43        89.33        74.93        41.62        61.87        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 
        5.85         3.02         8.55        97.55         6.18         6.12 
TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 
       35.15         4.54       112.41        71.11        63.09        39.75 
TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
       20.94        26.93        12.46        77.10        81.17        28.54 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 
       83.31        55.23        81.01        17.46        32.35        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1488 
       87.06        61.71        29.42       124.44        20.68        70.82 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
       83.93        52.44       125.56        93.90        90.38         4.24 
TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 
       66.15        13.97        43.20        34.82        34.16        65.52 
TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
       80.15        54.25        14.53        80.02        78.48        77.88 
TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
       65.52        70.45         8.42        23.05        25.94        26.20 
TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1686 TCGA-20-1687 
       72.20        27.52        25.38        19.10         2.93         2.66 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
       47.54        49.68        40.54        15.39        26.83        32.09 
TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1111 
       49.41        29.13        18.90         2.76        54.51         3.22 
TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1120 TCGA-23-1121 TCGA-23-1123 
       31.20        19.46        33.30         4.27         6.38        33.47 
TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 
       58.13         0.53        24.95       115.89        91.66        77.00 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        4.70         4.50         7.63        11.64        21.80        41.56 
TCGA-24-0980 TCGA-24-1103 TCGA-24-1413 TCGA-24-1416 TCGA-24-1418 TCGA-24-1419 
        7.66        54.12         6.31         6.38         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 
        0.76         6.25         6.02        17.39        28.37        18.64 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
       45.14       105.99         3.45         1.18        22.22        26.96 
TCGA-24-1545 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 
       57.40        56.58        41.06        51.91        41.39        58.09 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1563 
       88.50        70.62        39.88        19.53        44.09        47.70 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 
       25.87        10.26        90.15        88.37        48.33        38.24 
TCGA-24-1845 TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 
        3.81         5.79         9.80        22.68        30.21        16.44 
TCGA-24-1928 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 
       11.05         4.87       152.02        44.84        58.16        34.82 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 
      109.71        14.43        55.92        18.48        28.18        64.01 
TCGA-24-2038 TCGA-24-2261 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 
       44.52         0.79        47.54        31.63        70.45        44.61 
TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 
        0.82        67.36        36.23        16.64        33.11        55.86 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1318 
        1.02        26.96        33.01        52.04        42.05        34.98 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
       65.00        37.97         2.99        12.99        15.02        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1634 
       27.62        17.03        12.95        20.61         0.30        35.87 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2393 TCGA-25-2397 
       14.96        24.99        24.00        85.05        38.04        12.00 
TCGA-25-2398 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       45.01        42.02         2.96        29.03        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       78.90        47.61       101.79        39.02        40.41        33.93 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 
       31.20        68.32        36.36        18.25        41.98        31.27 
TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 
       86.60        66.81        62.93        31.30        22.98        24.36 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 TCGA-29-1783 
       22.55        17.33        12.36        12.30        14.93         7.23 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2432 
        5.36        36.30        62.47        45.11        13.84        21.47 
TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1853 TCGA-30-1856 
       11.47         9.76        35.77        38.07        36.26        15.68 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 
        0.26        48.10        44.91        34.78         6.12        36.62 
TCGA-30-1867 TCGA-30-1880 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 
        1.22        57.57        30.05        48.79        45.57        30.18 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 
       18.77        22.49         6.71        42.51        44.12         2.20 
TCGA-36-1568 TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1580 
       28.77        22.85         8.55        30.08        25.74        24.23 
TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       24.69        35.05        33.01        29.49        29.82        25.91 
TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 
       25.08        23.80        21.60         2.24        20.98        18.31 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-42-2582 TCGA-42-2587 
       20.52        14.17         6.05        16.18        47.57        23.74 
TCGA-42-2588 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 
       28.93        10.42        40.77         1.48        24.03        11.38 
TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 
       21.14         1.74        22.32        25.08       180.20        80.12 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2355 TCGA-59-2372 TCGA-61-1721 TCGA-61-1725 
       22.32       116.12         2.14        44.81        11.11        31.43 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 
       18.54        27.88         4.34        31.79        28.47        48.79 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 
       44.84        35.80        33.67        43.69         1.45         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1907 TCGA-61-1910 
        5.79        11.41        13.02         9.07        31.30        37.05 
TCGA-61-1911 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 
       42.51        56.61        67.76        43.43        15.75        38.17 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 
        5.52        14.50        17.98         4.01        30.64        30.64 
TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 
        1.18        45.96        45.40         4.80         4.77        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 
       71.74        61.64        60.62        65.52        55.50         6.48 
TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2613 
       76.87        20.68        44.52       125.75        22.22        31.07 
TCGA-61-2614 TCGA-OY-A56Q TCGA-VG-A8LO TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 
        8.61        18.94         0.79        29.16         9.47        57.76 
TCGA-09-0367 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0933 TCGA-10-0934 
       17.98        54.31        25.91        81.86        14.66         6.71 
TCGA-10-0936 TCGA-10-0937 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 
       36.92        19.99         6.21        24.59        44.55        39.58 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 
       12.39        31.20        15.19        17.82         2.50        11.18 
TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 
       11.38        11.54        38.01       111.78        61.84        56.71 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 
       58.65        40.24       107.28        63.09        20.35        69.73 
TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 
       83.34        45.99        51.02        43.86        35.28        35.31 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 TCGA-13-0888 TCGA-13-0889 
       13.61        68.94       107.18       153.37        92.42        95.15 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
      102.84        43.36        66.15       134.04        19.36       127.79 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       50.37       123.16       118.98        60.59       116.65        44.55 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 
       37.64       109.32        58.68        48.79        48.76        83.74 
TCGA-13-0924 TCGA-13-2071 
       85.94        25.41 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.36              0.26 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           145.45            180.20 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            34.13             32.22 
[1] "0.4 - 145.4 (34.1)" "0.3 - 180.2 (32.2)"
[1] "hr=" "1.1"
D54V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  7P LOSS MUTATED         0   118                1
  7P LOSS WILD-TYPE       3   440                1
D54V3, multiclass
                  clus
vv                 7P LOSS MUTATED 7P LOSS WILD-TYPE
  OMENTUM                        0                 3
  OVARY                        118               440
  PERITONEUM OVARY               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V4, binary
                   cls
clus                  0   1
  7P LOSS MUTATED   116   0
  7P LOSS WILD-TYPE 425   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED    116    0
  7P LOSS WILD-TYPE  425    5
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO              116               425
  YES               0                 5
[1] 2 2
[1] FALSE
D54V5, continuous
                   vv
clus                R0 R1 R2 RX
  7P LOSS MUTATED    4  3  1  0
  7P LOSS WILD-TYPE 11 23  4  3
D54V6, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  R0               4                11
  R1               3                23
  R2               1                 4
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     1  63
  7P LOSS WILD-TYPE   9 264
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1   63
  7P LOSS WILD-TYPE    9  264
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              63               264
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED    35  44
  7Q LOSS WILD-TYPE 193 287
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               79               480 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               44               287 
$`7Q LOSS MUTATED`
TCGA-04-1638 TCGA-09-1659 TCGA-09-1668 TCGA-13-1487 TCGA-13-1499 TCGA-13-1505 
       55.43         9.99        55.36        22.39       115.07        65.69 
TCGA-13-1510 TCGA-13-2061 TCGA-20-1683 TCGA-20-1685 TCGA-23-1029 TCGA-23-1114 
       44.68        76.90        25.38        16.70         8.81        68.68 
TCGA-23-2078 TCGA-23-2084 TCGA-24-0982 TCGA-24-1417 TCGA-24-1425 TCGA-24-1426 
       87.48        49.84        22.32         7.82         5.95         5.36 
TCGA-24-1427 TCGA-24-1434 TCGA-24-1435 TCGA-24-1463 TCGA-24-1469 TCGA-24-1564 
        4.83        18.67        43.53        72.92         9.11        25.87 
TCGA-24-1567 TCGA-24-1842 TCGA-24-1846 TCGA-24-1847 TCGA-24-1930 TCGA-24-2260 
       17.23         8.32         4.37        11.28        81.11        36.16 
TCGA-24-2298 TCGA-25-1317 TCGA-25-1321 TCGA-25-1630 TCGA-25-1632 TCGA-25-1633 
       53.26         2.01        33.96        38.20        59.15        62.17 
TCGA-25-1877 TCGA-25-2391 TCGA-25-2392 TCGA-25-2396 TCGA-29-1691 TCGA-29-1701 
       24.00        49.05         1.02         3.02        48.33        16.93 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1761 TCGA-29-1763 TCGA-29-1766 TCGA-29-1776 
       23.93        59.67        17.36        66.81        39.42        11.84 
TCGA-29-1781 TCGA-29-2425 TCGA-29-2431 TCGA-30-1718 TCGA-30-1855 TCGA-30-1887 
        8.38        65.00        42.25        51.91         2.47        24.26 
TCGA-31-1959 TCGA-36-1569 TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 TCGA-36-2552 
        2.20        29.10        25.74        27.85        24.69        11.47 
TCGA-57-1994 TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 TCGA-61-1724 TCGA-61-1995 
       25.02         9.40        34.39         5.42        20.94         2.01 
TCGA-61-2096 TCGA-61-2612 TCGA-09-0369 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       58.39         6.35        35.57        18.51        34.19        32.88 
TCGA-13-0751 TCGA-13-0792 TCGA-13-0800 TCGA-13-0887 TCGA-13-0890 TCGA-13-0897 
       55.17       118.42        87.48        66.67       145.45        71.74 
TCGA-13-0919 
       84.53 

$`7Q LOSS WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 
       49.15         2.01        46.62         1.08        18.51        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 
       65.52        63.09        48.76        21.57        63.98        65.46 
TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
        0.53        49.28        32.52        44.32        33.67        76.57 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 
      103.40        82.39        56.55        41.59        19.99         0.79 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1644 TCGA-04-1646 
       38.37       119.08        29.10        84.20        48.89        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 
       28.64        64.64        36.23        31.86        47.70        45.37 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 
       38.43        89.33        74.93        41.62        57.60        61.87 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 
       30.51        17.98         5.85         3.02         8.55        97.55 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 
        6.18         6.12        35.15         4.54       112.41        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 
       63.09        39.75        20.94        26.93        12.46        77.10 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
       81.17        28.54        83.31        55.23        57.27        81.01 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
       17.46        32.35        54.64        87.06        61.71        29.42 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
      124.44        20.68        70.82        83.93        52.44       125.56 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 
       93.90        90.38         4.24       127.27        66.15        13.97 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 
       43.20        34.82        34.16        65.52        80.15        54.25 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2065 TCGA-13-A5FT 
       14.53        80.02        78.48        77.88        65.52        70.45 
TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 
        8.42        23.05        25.94        26.20        72.20        27.52 
TCGA-20-1684 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 
       19.10         2.93         2.66        47.54        49.68        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 
       15.39        26.83        32.09        49.41        29.13        18.90 
TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 
        2.76        51.35        54.51         3.22        31.20        19.46 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 
       33.30        86.01       129.96         4.27         6.38        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2079 
       33.47        58.13         0.53        24.95       115.89        91.66 
TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 
       77.00         2.76         4.70         4.50         7.63        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 
       21.80        41.56         7.66        54.12        63.55        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 
        6.31         6.38         7.99         7.86         0.76         6.25 
TCGA-24-1424 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1436 TCGA-24-1464 
        6.02        17.39        28.37        18.64         8.55        12.46 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
       45.14       105.99         3.45         1.18        22.22        26.96 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 
       57.40        64.27        16.21        56.58        41.06        51.91 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 
       41.39        58.09        88.50        70.62        39.88        19.53 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1565 TCGA-24-1603 TCGA-24-1604 
       44.09        45.50        47.70        10.26        90.15        88.37 
TCGA-24-1614 TCGA-24-1616 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1849 
       48.33        38.24         3.48         3.72         3.81         5.79 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 
        5.52         9.80        22.68        30.21        16.44        11.05 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 
        4.87       152.02        44.84        58.16        34.82       109.71 
TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
       14.43        55.92        18.48        28.18        64.01        44.52 
TCGA-24-2254 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       57.07         0.79         0.36        47.54        31.63        70.45 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 
       44.61         0.82        67.36        36.23        16.64        33.11 
TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 
       55.86         1.02        26.96        33.01        52.04        42.05 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 
       34.98        65.00        37.97         2.99        12.99        15.02 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 
       18.58        27.62        17.03        12.95        20.61         0.30 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 TCGA-25-2042 
       35.87        52.04        14.96        24.99        85.05        13.02 
TCGA-25-2393 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 
       38.04        12.00        45.01        19.99        42.02         2.96 
TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 
       29.03        31.00        26.99        78.90        47.61       101.79 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
       39.02        40.41        33.93        31.20        68.32        36.36 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1762 TCGA-29-1764 
       18.25        41.98        31.27        34.62        86.60        62.93 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 
       31.30        22.98        24.36        22.55        17.33        12.36 
TCGA-29-1777 TCGA-29-1778 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 
       12.30        14.93         7.23         5.36        36.30        86.17 
TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 
       62.47        45.11        13.84        21.47        11.47         9.76 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 
       35.77        38.07        36.26        15.68         0.26        48.10 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 
       44.91        34.78         6.12        36.62         1.22        57.57 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 
       30.05        48.79        45.57        30.18        18.77        22.49 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 
        6.71        42.51        44.12        28.77        21.53        22.85 
TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1580 TCGA-36-2529 TCGA-36-2530 
       22.55         8.55        30.08        24.23        35.05        33.01 
TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 
       29.49        29.82        25.91        25.08        23.80        21.60 
TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 
        2.24        20.98        18.31        20.52        14.17         6.05 
TCGA-36-2551 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
       16.18        47.57        23.74        28.93        42.02        10.42 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 
       40.77         1.48        24.03        11.38        21.14         1.74 
TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 
       22.32        29.00        25.08       180.20        80.12        22.32 
TCGA-59-2351 TCGA-59-2355 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1725 
      116.12         2.14        44.81        11.11         8.09        31.43 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 
       18.54        27.88         4.34        31.79        28.47        48.79 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 
       44.84        35.80         2.43        33.67        43.69         1.45 
TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 
        8.42         5.79        11.41        13.02         9.07        34.13 
TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 
       31.30        37.05        42.51        48.92        56.61        67.76 
TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       43.43        15.75        38.17         5.52        14.50        17.98 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 
        4.01        30.64        39.85        30.64         1.18        45.96 
TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       45.40         4.80         4.77        51.72        71.74        61.64 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       60.62        65.52        55.50         6.48        76.87        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P 
       44.52       125.75        22.22        31.07         8.61        39.68 
TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 
       18.94         0.79         9.99        29.16         9.47        57.76 
TCGA-09-0367 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0933 TCGA-10-0934 
       17.98        54.31        25.91        81.86        14.66         6.71 
TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
       35.44        36.92        19.99        20.91         6.21        24.59 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 
       44.55        39.58         2.73        12.39        31.20        15.19 
TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 
       17.82         2.50        11.18        11.38        11.54        38.01 
TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0793 
      111.78        61.84        56.71        58.65        40.24       107.28 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 
       63.09        20.35        69.73        83.34        45.99        51.02 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
       43.86        35.28        35.31        13.61        68.94       107.18 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 
      111.39       153.37        92.42        95.15       102.84        43.36 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       66.15       134.04        19.36       127.79        50.37       123.16 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
      118.98        60.59       116.65        44.55        37.64       109.32 
TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       58.68        48.79        48.76        83.74        85.94        25.41 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             1.02              0.26 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           145.45            180.20 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            27.85             33.06 
[1] "1.0 - 145.4 (27.9)" "0.3 - 180.2 (33.1)"
[1] "hr=" "1"  
D55V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  7Q LOSS MUTATED         0    78                1
  7Q LOSS WILD-TYPE       3   480                1
D55V3, multiclass
                  clus
vv                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  OMENTUM                        0                 3
  OVARY                         78               480
  PERITONEUM OVARY               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V4, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    76   1
  7Q LOSS WILD-TYPE 465   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     76    1
  7Q LOSS WILD-TYPE  465    4
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO               76               465
  YES               1                 4
[1] 2 2
[1] FALSE
D55V5, continuous
                   vv
clus                R0 R1 R2 RX
  7Q LOSS MUTATED    3  2  0  0
  7Q LOSS WILD-TYPE 12 24  5  3
D55V6, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0               3                12
  R1               2                24
  R2               0                 5
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0  41
  7Q LOSS WILD-TYPE  10 286
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0   41
  7Q LOSS WILD-TYPE   10  286
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              41               286
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED   104 157
  8P LOSS WILD-TYPE 124 174
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              261               298 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              157               174 
$`8P LOSS MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1332 TCGA-04-1338 TCGA-04-1346 TCGA-04-1348 
       13.81        20.52        41.00        46.62        65.52        48.76 
TCGA-04-1361 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 
       32.52        76.57       103.40        82.39        56.55        19.99 
TCGA-04-1530 TCGA-04-1536 TCGA-04-1638 TCGA-04-1646 TCGA-04-1652 TCGA-04-1655 
      119.08        29.10        55.43        27.88        31.86        45.37 
TCGA-09-1661 TCGA-09-1664 TCGA-09-1668 TCGA-09-1670 TCGA-09-1674 TCGA-09-2050 
       38.43        74.93        55.36        17.98         8.55        71.11 
TCGA-09-2051 TCGA-09-2054 TCGA-09-2056 TCGA-13-1403 TCGA-13-1407 TCGA-13-1410 
       63.09        20.94        12.46        77.10        83.31        81.01 
TCGA-13-1411 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 
       17.46        87.06        61.71        29.42       124.44        22.39 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 
       93.90        90.38         4.24       115.07        13.97        43.20 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-2059 
       34.82        65.69        65.52        80.15        44.68        78.48 
TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 
       76.90        65.52        70.45         8.42        25.94        26.20 
TCGA-20-1684 TCGA-20-1686 TCGA-23-1021 TCGA-23-1024 TCGA-23-1031 TCGA-23-1114 
       19.10         2.93        47.54        15.39        18.90        68.68 
TCGA-23-1116 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 
       19.46         4.27         6.38        39.09        33.47        58.13 
TCGA-23-2072 TCGA-23-2077 TCGA-23-2643 TCGA-23-2645 TCGA-24-0975 TCGA-24-0980 
       24.95       115.89         4.70         4.50        21.80         7.66 
TCGA-24-0982 TCGA-24-1104 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 
       22.32        63.55         6.31         6.38         7.82         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 
        0.76         6.25         6.02         4.83        17.39        18.64 
TCGA-24-1434 TCGA-24-1436 TCGA-24-1464 TCGA-24-1467 TCGA-24-1470 TCGA-24-1544 
       18.67         8.55        12.46       105.99         3.45        26.96 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1552 TCGA-24-1558 
       64.27        16.21        56.58        41.06        41.39        19.53 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1842 TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 
       88.37        48.33         8.32         3.72         4.37        11.28 
TCGA-24-1850 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2024 
        5.52        30.21        16.44        11.05        81.11        58.16 
TCGA-24-2030 TCGA-24-2035 TCGA-24-2254 TCGA-24-2261 TCGA-24-2267 TCGA-24-2280 
       55.92        28.18        57.07         0.79        47.54        70.45 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 
       44.61         0.82        36.23        16.64        33.11        55.86 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 TCGA-25-1323 
       26.96        33.01        34.98        65.00        33.96        12.99 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 TCGA-25-1633 TCGA-25-1635 
       17.03        12.95        38.20         0.30        62.17        52.04 
TCGA-25-1871 TCGA-25-1878 TCGA-25-2393 TCGA-25-2396 TCGA-25-2399 TCGA-25-2400 
       24.99        85.05        38.04         3.02        19.99        42.02 
TCGA-25-2404 TCGA-29-1694 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
       29.03        39.02        40.41        31.20        68.32        36.36 
TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 TCGA-29-1710 TCGA-29-1761 TCGA-29-1762 
       16.93        59.67        18.25        31.27        17.36        86.60 
TCGA-29-1768 TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1783 TCGA-29-1784 
       31.30        24.36        17.33        12.36         7.23         5.36 
TCGA-29-2428 TCGA-29-2429 TCGA-29-2432 TCGA-29-2434 TCGA-30-1855 TCGA-30-1856 
       45.11        13.84        21.47        11.47         2.47        15.68 
TCGA-30-1857 TCGA-30-1862 TCGA-30-1866 TCGA-30-1887 TCGA-31-1944 TCGA-31-1950 
        0.26         6.12        36.62        24.26        45.57        18.77 
TCGA-31-1951 TCGA-31-1955 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
       22.49        42.51        29.10        21.53        22.85        22.55 
TCGA-36-1575 TCGA-36-1577 TCGA-36-1580 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
        8.55        25.74        24.23        29.82        25.91        25.08 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2547 TCGA-36-2552 TCGA-42-2587 TCGA-42-2588 
       21.60         2.24        20.52        11.47        23.74        28.93 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2593 TCGA-57-1583 TCGA-57-1585 TCGA-57-1586 
       42.02        10.42         1.48        11.38         1.74        22.32 
TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 
       29.00        25.08        25.02       180.20        22.32       116.12 
TCGA-59-2352 TCGA-59-2355 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 
        9.40         2.14        18.54        27.88         4.34        31.79 
TCGA-61-1737 TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 TCGA-61-1904 TCGA-61-1914 
       44.84         2.43        33.67         1.45         9.07        56.61 
TCGA-61-1915 TCGA-61-1919 TCGA-61-1998 TCGA-61-2000 TCGA-61-2008 TCGA-61-2016 
       67.76        38.17         5.52        14.50        30.64         1.18 
TCGA-61-2018 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 
       45.40        60.62        65.52        55.50         6.48        76.87 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2113 TCGA-61-2613 TCGA-61-2614 TCGA-VG-A8LO 
       20.68        44.52        22.22        31.07         8.61         0.79 
TCGA-WR-A838 TCGA-09-0366 TCGA-09-0367 TCGA-10-0925 TCGA-10-0927 TCGA-10-0928 
        9.99        57.76        17.98        54.31        81.86        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0936 TCGA-13-0725 TCGA-13-0730 TCGA-13-0757 
       34.19        32.88        36.92        12.39        17.82        11.18 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0802 
       38.01       111.78       118.42       107.28        20.35        51.02 
TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 
       43.86        35.31        13.61       111.39        66.67        92.42 
TCGA-13-0890 TCGA-13-0899 TCGA-13-0901 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
      145.45        66.15        19.36        37.64       109.32        58.68 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0924 
       84.53        48.79        85.94 

$`8P LOSS WILD-TYPE`
TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1341 
       11.87        43.92         1.81        49.15         2.01         1.08 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 
       18.51        11.87        63.09        21.57        63.98        65.46 
TCGA-04-1353 TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 TCGA-04-1516 TCGA-04-1519 
        0.53        49.28        44.32        33.67        41.59         0.79 
TCGA-04-1525 TCGA-04-1542 TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 
       38.37        84.20        48.89        28.64        64.64        36.23 
TCGA-04-1654 TCGA-09-1659 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 
       47.70         9.99        89.33        41.62        57.60        61.87 
TCGA-09-1669 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 
       30.51         5.85         3.02        97.55         6.18         6.12 
TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2053 TCGA-09-2055 TCGA-13-1404 
       35.15         4.54       112.41        39.75        26.93        81.17 
TCGA-13-1405 TCGA-13-1408 TCGA-13-1409 TCGA-13-1412 TCGA-13-1477 TCGA-13-1485 
       28.54        55.23        57.27        32.35        54.64        20.68 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1497 TCGA-13-1498 
       70.82        83.93        52.44       125.56       127.27        66.15 
TCGA-13-1506 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2060 TCGA-20-0987 
       34.16        54.25        14.53        80.02        77.88        23.05 
TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1685 TCGA-20-1687 TCGA-23-1022 
       72.20        27.52        25.38        16.70         2.66        49.68 
TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
       40.54        26.83        32.09        49.41         8.81        29.13 
TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1117 
        2.76        51.35        54.51         3.22        31.20        33.30 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1809 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
       86.01       129.96         0.53        87.48        91.66        77.00 
TCGA-23-2084 TCGA-23-2641 TCGA-24-0966 TCGA-24-0970 TCGA-24-0979 TCGA-24-1103 
       49.84         2.76         7.63        11.64        41.56        54.12 
TCGA-24-1105 TCGA-24-1418 TCGA-24-1425 TCGA-24-1426 TCGA-24-1430 TCGA-24-1435 
       47.41         7.99         5.95         5.36        28.37        43.53 
TCGA-24-1463 TCGA-24-1466 TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 TCGA-24-1545 
       72.92        45.14         9.11         1.18        22.22        57.40 
TCGA-24-1551 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1560 
       51.91        58.09        88.50        70.62        39.88        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       45.50        47.70        25.87        10.26        17.23        90.15 
TCGA-24-1616 TCGA-24-1843 TCGA-24-1845 TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 
       38.24         3.48         3.81         5.79         9.80        22.68 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 
        4.87       152.02        44.84        34.82       109.71        14.43 
TCGA-24-2033 TCGA-24-2036 TCGA-24-2038 TCGA-24-2260 TCGA-24-2262 TCGA-24-2271 
       18.48        64.01        44.52        36.16         0.36        31.63 
TCGA-24-2289 TCGA-24-2298 TCGA-25-1312 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
       67.36        53.26         1.02        52.04        42.05         2.01 
TCGA-25-1320 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1628 
       37.97         2.99        15.02        18.58        27.62        20.61 
TCGA-25-1632 TCGA-25-1634 TCGA-25-1870 TCGA-25-1877 TCGA-25-2042 TCGA-25-2391 
       59.15        35.87        14.96        24.00        13.02        49.05 
TCGA-25-2392 TCGA-25-2397 TCGA-25-2398 TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 
        1.02        12.00        45.01         2.96        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1696 TCGA-29-1702 
       78.90        47.61        48.33       101.79        33.93        23.93 
TCGA-29-1707 TCGA-29-1711 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1769 
       41.98        34.62        66.81        62.93        39.42        22.98 
TCGA-29-1771 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1785 
       22.55        11.84        12.30        14.93         8.38        36.30 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2431 TCGA-29-2436 TCGA-29-A5NZ 
       86.17        65.00        62.47        42.25         9.76        35.77 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 
       38.07        51.91        36.26        48.10        44.91        34.78 
TCGA-30-1867 TCGA-30-1880 TCGA-30-1891 TCGA-30-1892 TCGA-31-1946 TCGA-31-1953 
        1.22        57.57        30.05        48.79        30.18         6.71 
TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1576 TCGA-36-1578 TCGA-36-1581 
       44.12         2.20        28.77        30.08        27.85        24.69 
TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2540 TCGA-36-2544 TCGA-36-2545 
       35.05        33.01        29.49        23.80        20.98        18.31 
TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-42-2582 TCGA-42-2591 TCGA-57-1582 
       14.17         6.05        16.18        47.57        40.77        24.03 
TCGA-57-1584 TCGA-59-2349 TCGA-59-2354 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 
       21.14        80.12        34.39         5.42        44.81        11.11 
TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1734 TCGA-61-1736 TCGA-61-1738 
        8.09        20.94        31.43        28.47        48.79        35.80 
TCGA-61-1743 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1906 
       43.69         8.42         5.79        11.41        13.02        34.13 
TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1917 TCGA-61-1918 
       31.30        37.05        42.51        48.92        43.43        15.75 
TCGA-61-1995 TCGA-61-2002 TCGA-61-2003 TCGA-61-2009 TCGA-61-2012 TCGA-61-2017 
        2.01        17.98         4.01        39.85        30.64        45.96 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 
        4.80         4.77        51.72        71.74        61.64        58.39 
TCGA-61-2111 TCGA-61-2612 TCGA-OY-A56P TCGA-OY-A56Q TCGA-09-0364 TCGA-09-0365 
      125.75         6.35        39.68        18.94        29.16         9.47 
TCGA-09-0369 TCGA-10-0926 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 
       35.57        25.91        14.66         6.71        35.44        19.99 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 
       20.91         6.21        24.59        44.55        39.58         2.73 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0751 TCGA-13-0755 TCGA-13-0758 TCGA-13-0760 
       31.20        15.19        55.17         2.50        11.38        11.54 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0794 TCGA-13-0797 
       61.84        56.71        58.65        40.24        63.09        69.73 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0804 TCGA-13-0883 TCGA-13-0884 
       83.34        87.48        45.99        35.28        68.94       107.18 
TCGA-13-0886 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 
      153.37        95.15       102.84        43.36        71.74       134.04 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
      127.79        50.37       123.16       118.98        60.59       116.65 
TCGA-13-0911 TCGA-13-0921 TCGA-13-0923 TCGA-13-2071 
       44.55        48.76        83.74        25.41 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.26              0.36 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           180.20            153.37 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           29.030            35.505 
[1] "0.3 - 180.2 (29.0)" "0.4 - 153.4 (35.5)"
[1] "hr=" "1.1"
D56V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  8P LOSS MUTATED         2   261                0
  8P LOSS WILD-TYPE       1   297                2
D56V3, multiclass
                  clus
vv                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  OMENTUM                        2                 1
  OVARY                        261               297
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V4, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   250   2
  8P LOSS WILD-TYPE 291   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    250    2
  8P LOSS WILD-TYPE  291    3
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO              250               291
  YES               2                 3
[1] 2 2
[1] FALSE
D56V5, continuous
                   vv
clus                R0 R1 R2 RX
  8P LOSS MUTATED    5 13  4  2
  8P LOSS WILD-TYPE 10 13  1  1
D56V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0               5                10
  R1              13                13
  R2               4                 1
  RX               2                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     5 143
  8P LOSS WILD-TYPE   5 184
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      5  143
  8P LOSS WILD-TYPE    5  184
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 5
  NOT HISPANIC OR LATINO             143               184
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    36  51
  8Q LOSS WILD-TYPE 192 280
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               87               472 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               51               280 
$`8Q LOSS MUTATED`
TCGA-04-1332 TCGA-04-1346 TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 TCGA-04-1655 
       41.00        65.52        82.39        56.55        19.99        45.37 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2054 TCGA-13-1407 TCGA-13-1483 TCGA-13-1510 
       71.11        63.09        20.94        83.31        29.42        44.68 
TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-20-1684 TCGA-23-1021 TCGA-23-1032 
       76.90        65.52        70.45        19.10        47.54         2.76 
TCGA-23-1114 TCGA-23-1122 TCGA-24-0980 TCGA-24-0982 TCGA-24-1416 TCGA-24-1424 
       68.68        39.09         7.66        22.32         6.38         6.02 
TCGA-24-1427 TCGA-24-1431 TCGA-24-1544 TCGA-24-1548 TCGA-24-1842 TCGA-24-1850 
        4.83        18.64        26.96        16.21         8.32         5.52 
TCGA-24-1928 TCGA-24-2030 TCGA-24-2254 TCGA-24-2261 TCGA-24-2267 TCGA-24-2280 
       11.05        55.92        57.07         0.79        47.54        70.45 
TCGA-24-2288 TCGA-24-2297 TCGA-25-1318 TCGA-25-1319 TCGA-25-1626 TCGA-25-1630 
        0.82        55.86        34.98        65.00        17.03        38.20 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1871 TCGA-25-2393 TCGA-25-2400 TCGA-29-1701 
       35.87        52.04        24.99        38.04        42.02        16.93 
TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-2428 TCGA-30-1855 TCGA-31-1955 
       24.36        17.33        12.36        45.11         2.47        42.51 
TCGA-36-1571 TCGA-36-1575 TCGA-36-2537 TCGA-36-2547 TCGA-36-2552 TCGA-42-2587 
       22.85         8.55        25.91        20.52        11.47        23.74 
TCGA-42-2589 TCGA-57-1994 TCGA-59-2352 TCGA-59-2355 TCGA-61-1727 TCGA-61-1730 
       42.02        25.02         9.40         2.14        18.54         4.34 
TCGA-61-1733 TCGA-61-1904 TCGA-61-1915 TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 
       31.79         9.07        67.76        60.62        55.50         6.48 
TCGA-61-2110 TCGA-61-2113 TCGA-WR-A838 TCGA-09-0366 TCGA-13-0725 TCGA-13-0730 
       44.52        22.22         9.99        57.76        12.39        17.82 
TCGA-13-0757 TCGA-13-0762 TCGA-13-0803 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 
       11.18       111.78        43.86       111.39        66.67        92.42 
TCGA-13-0901 TCGA-13-0913 TCGA-13-0920 
       19.36       109.32        48.79 

$`8Q LOSS WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 
       13.81        20.52        11.87        43.92         1.81        49.15 
TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1347 
        2.01        46.62         1.08        18.51        11.87        63.09 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 
       48.76        21.57        63.98        65.46         0.53        49.28 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1516 
       32.52        44.32        33.67        76.57       103.40        41.59 
TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 
        0.79        38.37       119.08        29.10        84.20        55.43 
TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 
       48.89        27.88        28.64        64.64        36.23        31.86 
TCGA-04-1654 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       47.70         9.99        38.43        89.33        74.93        41.62 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 
       57.60        61.87        55.36        30.51        17.98         5.85 
TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 
        3.02         8.55        97.55         6.18         6.12        35.15 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2053 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 
        4.54       112.41        39.75        26.93        12.46        77.10 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
       81.17        28.54        55.23        57.27        81.01        17.46 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 TCGA-13-1485 
       32.35        54.64        87.06        61.71       124.44        20.68 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       22.39        70.82        83.93        52.44       125.56        93.90 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 
       90.38         4.24       127.27        66.15       115.07        13.97 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       43.20        34.82        65.69        34.16        65.52        80.15 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-A5FU 
       54.25        14.53        80.02        78.48        77.88         8.42 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 
       23.05        25.94        26.20        72.20        27.52        25.38 
TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 
       16.70         2.93         2.66        49.68        40.54        15.39 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 
       26.83        32.09        49.41         8.81        29.13        18.90 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 
       51.35        54.51         3.22        31.20        19.46        33.30 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 
       86.01       129.96         4.27         6.38        33.47        58.13 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
        0.53        24.95       115.89        87.48        91.66        77.00 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 
       49.84         2.76         4.70         4.50         7.63        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 
       21.80        41.56        54.12        63.55        47.41         6.31 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 
        7.82         7.99         7.86         0.76         6.25         5.95 
TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
        5.36        17.39        28.37        18.67        43.53         8.55 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 
       72.92        12.46        45.14       105.99         9.11         3.45 
TCGA-24-1471 TCGA-24-1474 TCGA-24-1545 TCGA-24-1546 TCGA-24-1549 TCGA-24-1550 
        1.18        22.22        57.40        64.27        56.58        41.06 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       51.91        41.39        58.09        88.50        70.62        39.88 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 
       19.53        44.09        45.50        47.70        25.87        10.26 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1843 
       17.23        90.15        88.37        48.33        38.24         3.48 
TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1920 
        3.72         3.81         4.37        11.28         5.79         9.80 
TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 
       22.68        30.21        16.44        81.11         4.87       152.02 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 
       44.84        58.16        34.82       109.71        14.43        18.48 
TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2260 TCGA-24-2262 TCGA-24-2271 
       28.18        64.01        44.52        36.16         0.36        31.63 
TCGA-24-2281 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2298 
       44.61        67.36        36.23        16.64        33.11        53.26 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
        1.02        26.96        33.01        52.04        42.05         2.01 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
       37.97        33.96         2.99        12.99        15.02        18.58 
TCGA-25-1625 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
       27.62        12.95        20.61         0.30        59.15        62.17 
TCGA-25-1870 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 
       14.96        24.00        85.05        13.02        49.05         1.02 
TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 
        3.02        12.00        45.01        19.99         2.96        29.03 
TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 
       31.00        26.99        78.90        47.61        48.33       101.79 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
       39.02        40.41        33.93        31.20        68.32        36.36 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 
       23.93        59.67        18.25        41.98        31.27        34.62 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 
       17.36        86.60        66.81        62.93        39.42        31.30 
TCGA-29-1769 TCGA-29-1771 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 
       22.98        22.55        11.84        12.30        14.93         8.38 
TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 
        7.23         5.36        36.30        86.17        65.00        62.47 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ 
       13.84        42.25        21.47        11.47         9.76        35.77 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 
       38.07        51.91        36.26        15.68         0.26        48.10 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 
       44.91        34.78         6.12        36.62         1.22        57.57 
TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 
       24.26        30.05        48.79        45.57        30.18        18.77 
TCGA-31-1951 TCGA-31-1953 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 
       22.49         6.71        44.12         2.20        28.77        29.10 
TCGA-36-1570 TCGA-36-1574 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 
       21.53        22.55        30.08        25.74        27.85        24.23 
TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2538 
       24.69        35.05        33.01        29.49        29.82        25.08 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2548 
       23.80        21.60         2.24        20.98        18.31        14.17 
TCGA-36-2549 TCGA-36-2551 TCGA-42-2582 TCGA-42-2588 TCGA-42-2590 TCGA-42-2591 
        6.05        16.18        47.57        28.93        10.42        40.77 
TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 
        1.48        24.03        11.38        21.14         1.74        22.32 
TCGA-57-1992 TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 
       29.00        25.08       180.20        80.12        22.32       116.12 
TCGA-59-2354 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 
       34.39         5.42        44.81        11.11         8.09        20.94 
TCGA-61-1725 TCGA-61-1728 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
       31.43        27.88        28.47        48.79        44.84        35.80 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
        2.43        33.67        43.69         1.45         8.42         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 
       11.41        13.02        34.13        31.30        37.05        42.51 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 
       48.92        56.61        43.43        15.75        38.17         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 
        5.52        14.50        17.98         4.01        30.64        39.85 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
       30.64         1.18        45.96        45.40         4.80         4.77 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 TCGA-61-2104 
       51.72        71.74        61.64        58.39        65.52        76.87 
TCGA-61-2109 TCGA-61-2111 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P 
       20.68       125.75         6.35        31.07         8.61        39.68 
TCGA-OY-A56Q TCGA-VG-A8LO TCGA-09-0364 TCGA-09-0365 TCGA-09-0367 TCGA-09-0369 
       18.94         0.79        29.16         9.47        17.98        35.57 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       54.31        25.91        81.86        18.51        34.19        32.88 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 
       14.66         6.71        35.44        36.92        19.99        20.91 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 
        6.21        24.59        44.55        39.58         2.73        31.20 
TCGA-13-0727 TCGA-13-0751 TCGA-13-0755 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 
       15.19        55.17         2.50        11.38        11.54        38.01 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       61.84        56.71        58.65        40.24       118.42       107.28 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
       63.09        20.35        69.73        83.34        87.48        45.99 
TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
       51.02        35.28        35.31        13.61        68.94       107.18 
TCGA-13-0886 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 
      153.37        95.15       145.45       102.84        43.36        71.74 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
       66.15       134.04       127.79        50.37       123.16       118.98 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 TCGA-13-0919 
       60.59       116.65        44.55        37.64        58.68        84.53 
TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       48.76        83.74        85.94        25.41 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.79              0.26 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           111.78            180.20 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            29.42             33.01 
[1] "0.8 - 111.8 (29.4)" "0.3 - 180.2 (33.0)"
[1] "hr=" "1.1"
D57V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  8Q LOSS MUTATED         0    87                0
  8Q LOSS WILD-TYPE       3   471                2
D57V3, multiclass
                  clus
vv                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  OMENTUM                        0                 3
  OVARY                         87               471
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V4, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    83   1
  8Q LOSS WILD-TYPE 458   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     83    1
  8Q LOSS WILD-TYPE  458    4
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               83               458
  YES               1                 4
[1] 2 2
[1] FALSE
D57V5, continuous
                   vv
clus                R0 R1 R2 RX
  8Q LOSS MUTATED    3  3  0  1
  8Q LOSS WILD-TYPE 12 23  5  2
D57V6, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0               3                12
  R1               3                23
  R2               0                 5
  RX               1                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     1  47
  8Q LOSS WILD-TYPE   9 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1   47
  8Q LOSS WILD-TYPE    9  280
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              47               280
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED   101 155
  9P LOSS WILD-TYPE 127 176
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              256               303 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              155               176 
$`9P LOSS MUTATED`
TCGA-59-A5PD TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 
       20.52        41.00        49.15         2.01        46.62         1.08 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 
       11.87        65.52        63.09        21.57        63.98        65.46 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1364 TCGA-04-1371 TCGA-04-1517 TCGA-04-1519 
       49.28        32.52        33.67        82.39        19.99         0.79 
TCGA-04-1525 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1646 TCGA-04-1649 
       38.37        29.10        84.20        55.43        27.88        64.64 
TCGA-04-1652 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 
       31.86        45.37         9.99        38.43        89.33        41.62 
TCGA-09-1667 TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 TCGA-09-1675 TCGA-09-2044 
       61.87        30.51        17.98         3.02        97.55         6.12 
TCGA-09-2049 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 
      112.41        39.75        20.94        26.93        12.46        77.10 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
       83.31        55.23        57.27        81.01        17.46        32.35 
TCGA-13-1481 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1489 
       87.06        29.42       124.44        20.68        22.39        83.93 
TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1500 TCGA-13-1509 TCGA-13-2057 
       52.44        93.90        90.38        13.97        80.15        80.02 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-1682 
       77.88        76.90        65.52        70.45         8.42        27.52 
TCGA-20-1684 TCGA-20-1685 TCGA-23-1021 TCGA-23-1022 TCGA-23-1027 TCGA-23-1028 
       19.10        16.70        47.54        49.68        32.09        49.41 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1114 TCGA-23-1116 TCGA-23-1118 TCGA-23-1119 
       29.13        18.90        68.68        19.46        86.01       129.96 
TCGA-23-2072 TCGA-23-2081 TCGA-23-2643 TCGA-23-2645 TCGA-24-0982 TCGA-24-1105 
       24.95        77.00         4.70         4.50        22.32        47.41 
TCGA-24-1413 TCGA-24-1419 TCGA-24-1422 TCGA-24-1426 TCGA-24-1427 TCGA-24-1430 
        6.31         7.86         0.76         5.36         4.83        28.37 
TCGA-24-1431 TCGA-24-1463 TCGA-24-1464 TCGA-24-1545 TCGA-24-1546 TCGA-24-1549 
       18.64        72.92        12.46        57.40        64.27        56.58 
TCGA-24-1550 TCGA-24-1560 TCGA-24-1563 TCGA-24-1564 TCGA-24-1603 TCGA-24-1604 
       41.06        44.09        47.70        25.87        90.15        88.37 
TCGA-24-1843 TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2029 
        3.48        81.11         4.87        44.84        58.16        14.43 
TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 
       55.92        28.18        64.01        36.16         0.79        47.54 
TCGA-24-2293 TCGA-24-2295 TCGA-25-1312 TCGA-25-1314 TCGA-25-1316 TCGA-25-1317 
       16.64        33.11         1.02        33.01        42.05         2.01 
TCGA-25-1318 TCGA-25-1321 TCGA-25-1323 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 
       34.98        33.96        12.99        27.62        17.03        12.95 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-2392 
       62.17        35.87        14.96        24.99        24.00         1.02 
TCGA-25-2393 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-29-1688 TCGA-29-1693 
       38.04        19.99        42.02         2.96        78.90       101.79 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1698 TCGA-29-1699 TCGA-29-1702 TCGA-29-1705 
       39.02        40.41        68.32        36.36        23.93        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1766 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
       41.98        31.27        39.42        24.36        22.55        17.33 
TCGA-29-1775 TCGA-29-1783 TCGA-29-2425 TCGA-29-2434 TCGA-29-2436 TCGA-30-1714 
       12.36         7.23        65.00        11.47         9.76        38.07 
TCGA-30-1718 TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 TCGA-30-1861 TCGA-30-1866 
       51.91        36.26        15.68         0.26        34.78        36.62 
TCGA-30-1880 TCGA-30-1891 TCGA-31-1944 TCGA-31-1955 TCGA-31-1959 TCGA-36-1569 
       57.57        30.05        45.57        42.51         2.20        29.10 
TCGA-36-1571 TCGA-36-1576 TCGA-36-1580 TCGA-36-2529 TCGA-36-2537 TCGA-36-2540 
       22.85        30.08        24.23        35.05        25.91        23.80 
TCGA-36-2542 TCGA-36-2544 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2552 
       21.60        20.98        20.52        14.17         6.05        11.47 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1585 
       42.02        10.42         1.48        24.03        11.38         1.74 
TCGA-57-1992 TCGA-57-1994 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 
       29.00        25.02       116.12         9.40         2.14         5.42 
TCGA-59-2372 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 TCGA-61-1899 
       44.81        27.88         4.34        31.79        48.79         8.42 
TCGA-61-1900 TCGA-61-1907 TCGA-61-1910 TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 
        5.79        31.30        37.05        56.61        67.76        15.75 
TCGA-61-1919 TCGA-61-1995 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 
       38.17         2.01        14.50        17.98         4.01        30.64 
TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 
       39.85        30.64         1.18        61.64        58.39        60.62 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2113 
       65.52        55.50         6.48        76.87        20.68        22.22 
TCGA-61-2612 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 
        6.35        39.68        18.94         0.79         9.99        29.16 
TCGA-09-0365 TCGA-09-0367 TCGA-09-0369 TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 
        9.47        17.98        35.57        81.86        34.19        32.88 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0724 TCGA-13-0760 TCGA-13-0762 
       20.91         6.21        24.59         2.73        11.54       111.78 
TCGA-13-0764 TCGA-13-0795 TCGA-13-0800 TCGA-13-0804 TCGA-13-0805 TCGA-13-0883 
       61.84        20.35        87.48        35.28        35.31        68.94 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0900 
      111.39       153.37        92.42        95.15       145.45       134.04 
TCGA-13-0904 TCGA-13-0908 TCGA-13-0921 TCGA-13-0924 
       50.37        60.59        48.76        85.94 

$`9P LOSS WILD-TYPE`
TCGA-3P-A9WA TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1335 TCGA-04-1342 TCGA-04-1348 
       13.81        11.87        43.92         1.81        18.51        48.76 
TCGA-04-1353 TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 TCGA-04-1516 
        0.53        44.32        76.57       103.40        56.55        41.59 
TCGA-04-1530 TCGA-04-1644 TCGA-04-1648 TCGA-04-1651 TCGA-04-1654 TCGA-09-1664 
      119.08        48.89        28.64        36.23        47.70        74.93 
TCGA-09-1666 TCGA-09-1668 TCGA-09-1672 TCGA-09-1674 TCGA-09-2043 TCGA-09-2045 
       57.60        55.36         5.85         8.55         6.18        35.15 
TCGA-09-2048 TCGA-09-2050 TCGA-09-2051 TCGA-13-1404 TCGA-13-1405 TCGA-13-1477 
        4.54        71.11        63.09        81.17        28.54        54.64 
TCGA-13-1482 TCGA-13-1488 TCGA-13-1492 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
       61.71        70.82       125.56         4.24       127.27        66.15 
TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
      115.07        43.20        34.82        65.69        34.16        65.52 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-20-0987 TCGA-20-0990 
       44.68        54.25        14.53        78.48        23.05        25.94 
TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 TCGA-20-1686 TCGA-20-1687 TCGA-23-1023 
       26.20        72.20        25.38         2.93         2.66        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1029 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 
       15.39        26.83         8.81         2.76        51.35        54.51 
TCGA-23-1111 TCGA-23-1113 TCGA-23-1117 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 
        3.22        31.20        33.30         4.27         6.38        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 
       33.47        58.13         0.53       115.89        87.48        91.66 
TCGA-23-2084 TCGA-23-2641 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
       49.84         2.76         7.63        11.64        21.80        41.56 
TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 
        7.66        54.12        63.55         6.38         7.82         7.99 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1428 TCGA-24-1434 TCGA-24-1435 
        6.25         6.02         5.95        17.39        18.67        43.53 
TCGA-24-1436 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 
        8.55        45.14       105.99         9.11         3.45         1.18 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1548 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 
       22.22        26.96        16.21        51.91        41.39        58.09 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1562 TCGA-24-1565 
       88.50        70.62        39.88        19.53        45.50        10.26 
TCGA-24-1567 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 
       17.23        48.33        38.24         8.32         3.72         3.81 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 
        4.37        11.28         5.79         5.52         9.80        22.68 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-2020 TCGA-24-2026 TCGA-24-2027 
       30.21        16.44        11.05       152.02        34.82       109.71 
TCGA-24-2033 TCGA-24-2038 TCGA-24-2254 TCGA-24-2262 TCGA-24-2271 TCGA-24-2280 
       18.48        44.52        57.07         0.36        31.63        70.45 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2297 TCGA-24-2298 
       44.61         0.82        67.36        36.23        55.86        53.26 
TCGA-25-1313 TCGA-25-1315 TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 TCGA-25-1329 
       26.96        52.04        65.00        37.97         2.99        15.02 
TCGA-25-1623 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1635 
       18.58        20.61        38.20         0.30        59.15        52.04 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 
       85.05        13.02        49.05         3.02        12.00        45.01 
TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1690 TCGA-29-1691 TCGA-29-1696 
       29.03        31.00        26.99        47.61        48.33        33.93 
TCGA-29-1697 TCGA-29-1701 TCGA-29-1703 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 
       31.20        16.93        59.67        34.62        17.36        86.60 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 TCGA-29-1776 TCGA-29-1777 
       66.81        62.93        31.30        22.98        11.84        12.30 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 
       14.93         8.38         5.36        36.30        86.17        62.47 
TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-A5NZ TCGA-30-1855 
       45.11        13.84        42.25        21.47        35.77         2.47 
TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1867 TCGA-30-1887 TCGA-30-1892 
       48.10        44.91         6.12         1.22        24.26        48.79 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1956 TCGA-36-1568 
       30.18        18.77        22.49         6.71        44.12        28.77 
TCGA-36-1570 TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 
       21.53        22.55         8.55        25.74        27.85        24.69 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2538 TCGA-36-2543 TCGA-36-2545 
       33.01        29.49        29.82        25.08         2.24        18.31 
TCGA-36-2551 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2591 TCGA-57-1584 
       16.18        47.57        23.74        28.93        40.77        21.14 
TCGA-57-1586 TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2354 
       22.32        25.08       180.20        80.12        22.32        34.39 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1734 
       11.11         8.09        20.94        31.43        18.54        28.47 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 
       44.84        35.80         2.43        33.67        43.69         1.45 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1911 TCGA-61-1913 
       11.41        13.02         9.07        34.13        42.51        48.92 
TCGA-61-1917 TCGA-61-1998 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
       43.43         5.52        45.96        45.40         4.80         4.77 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2110 TCGA-61-2111 TCGA-61-2613 TCGA-61-2614 
       51.72        71.74        44.52       125.75        31.07         8.61 
TCGA-09-0366 TCGA-10-0925 TCGA-10-0926 TCGA-10-0928 TCGA-10-0933 TCGA-10-0934 
       57.76        54.31        25.91        18.51        14.66         6.71 
TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 
       35.44        36.92        19.99        44.55        39.58        12.39 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 
       31.20        15.19        17.82        55.17         2.50        11.18 
TCGA-13-0758 TCGA-13-0761 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 
       11.38        38.01        56.71        58.65        40.24       118.42 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 
      107.28        63.09        69.73        83.34        45.99        51.02 
TCGA-13-0803 TCGA-13-0807 TCGA-13-0884 TCGA-13-0887 TCGA-13-0891 TCGA-13-0893 
       43.86        13.61       107.18        66.67       102.84        43.36 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0901 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 
       71.74        66.15        19.36       127.79       123.16       118.98 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
      116.65        44.55        37.64       109.32        58.68        84.53 
TCGA-13-0920 TCGA-13-0923 TCGA-13-2071 
       48.79        83.74        25.41 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.26              0.30 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           153.37            180.20 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            32.22             33.47 
[1] "0.3 - 153.4 (32.2)" "0.3 - 180.2 (33.5)"
[1] "hr=" "1"  
D58V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  9P LOSS MUTATED         1   255                2
  9P LOSS WILD-TYPE       2   303                0
D58V3, multiclass
                  clus
vv                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  OMENTUM                        1                 2
  OVARY                        255               303
  PERITONEUM OVARY               2                 0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V4, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   249   2
  9P LOSS WILD-TYPE 292   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    249    2
  9P LOSS WILD-TYPE  292    3
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO              249               292
  YES               2                 3
[1] 2 2
[1] FALSE
D58V5, continuous
                   vv
clus                R0 R1 R2 RX
  9P LOSS MUTATED    8  9  4  2
  9P LOSS WILD-TYPE  7 17  1  1
D58V6, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0               8                 7
  R1               9                17
  R2               4                 1
  RX               2                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     6 153
  9P LOSS WILD-TYPE   4 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      6  153
  9P LOSS WILD-TYPE    4  174
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                 4
  NOT HISPANIC OR LATINO             153               174
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED   109 167
  9Q LOSS WILD-TYPE 119 164
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              276               283 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              167               164 
$`9Q LOSS MUTATED`
TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       20.52        11.87        41.00        49.15         2.01        46.62 
TCGA-04-1341 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 
        1.08        11.87        65.52        63.09        21.57        63.98 
TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1364 TCGA-04-1371 TCGA-04-1517 
       65.46        49.28        32.52        33.67        82.39        19.99 
TCGA-04-1519 TCGA-04-1525 TCGA-04-1542 TCGA-04-1638 TCGA-04-1646 TCGA-04-1649 
        0.79        38.37        84.20        55.43        27.88        64.64 
TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1667 TCGA-09-1669 TCGA-09-1670 
       45.37         9.99        38.43        61.87        30.51        17.98 
TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2049 TCGA-09-2053 
        3.02         8.55        97.55         6.12       112.41        39.75 
TCGA-09-2054 TCGA-09-2055 TCGA-13-1403 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
       20.94        26.93        77.10        83.31        55.23        57.27 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1489 
       81.01        17.46        29.42       124.44        22.39        83.93 
TCGA-13-1491 TCGA-13-1495 TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 TCGA-13-1507 
       52.44        90.38       115.07        13.97        34.82        65.52 
TCGA-13-1509 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT 
       80.15        80.02        77.88        76.90        65.52        70.45 
TCGA-13-A5FU TCGA-20-0990 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 
        8.42        25.94        27.52        19.10        16.70         2.93 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 TCGA-23-1111 
       47.54        49.68        49.41        29.13        18.90         3.22 
TCGA-23-1114 TCGA-23-1116 TCGA-23-1118 TCGA-23-1119 TCGA-23-1123 TCGA-23-2072 
       68.68        19.46        86.01       129.96        33.47        24.95 
TCGA-23-2077 TCGA-23-2643 TCGA-23-2645 TCGA-24-0975 TCGA-24-0979 TCGA-24-0982 
      115.89         4.70         4.50        21.80        41.56        22.32 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1417 TCGA-24-1422 TCGA-24-1424 TCGA-24-1426 
       47.41         6.31         7.82         0.76         6.02         5.36 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1464 TCGA-24-1469 TCGA-24-1471 TCGA-24-1544 
       28.37        18.64        12.46         9.11         1.18        26.96 
TCGA-24-1545 TCGA-24-1549 TCGA-24-1550 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 
       57.40        56.58        41.06        19.53        44.09        45.50 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-1843 
       47.70        25.87        90.15        88.37        38.24         3.48 
TCGA-24-1845 TCGA-24-1924 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 
        3.81        30.21        11.05        81.11         4.87        44.84 
TCGA-24-2024 TCGA-24-2026 TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2260 
       58.16        34.82        14.43        18.48        28.18        36.16 
TCGA-24-2261 TCGA-24-2267 TCGA-24-2288 TCGA-24-2293 TCGA-24-2295 TCGA-25-1312 
        0.79        47.54         0.82        16.64        33.11         1.02 
TCGA-25-1314 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 
       33.01        42.05         2.01        34.98        37.97        33.96 
TCGA-25-1323 TCGA-25-1626 TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 TCGA-25-1633 
       12.99        17.03        12.95        38.20         0.30        62.17 
TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-2392 TCGA-25-2393 
       35.87        14.96        24.99        24.00         1.02        38.04 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-29-1688 TCGA-29-1693 TCGA-29-1694 
       45.01        19.99        42.02        78.90       101.79        39.02 
TCGA-29-1695 TCGA-29-1698 TCGA-29-1699 TCGA-29-1702 TCGA-29-1705 TCGA-29-1710 
       40.41        68.32        36.36        23.93        18.25        31.27 
TCGA-29-1761 TCGA-29-1763 TCGA-29-1766 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
       17.36        66.81        39.42        24.36        22.55        17.33 
TCGA-29-1775 TCGA-29-1777 TCGA-29-1783 TCGA-29-2425 TCGA-29-2434 TCGA-30-1714 
       12.36        12.30         7.23        65.00        11.47        38.07 
TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 
       36.26        15.68         0.26        34.78        36.62         1.22 
TCGA-30-1880 TCGA-31-1944 TCGA-31-1950 TCGA-31-1955 TCGA-36-1569 TCGA-36-1571 
       57.57        45.57        18.77        42.51        29.10        22.85 
TCGA-36-1576 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2537 TCGA-36-2543 
       30.08        24.23        24.69        35.05        25.91         2.24 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2552 
       20.98        18.31        20.52        14.17         6.05        11.47 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1585 
       42.02        10.42         1.48        24.03        11.38         1.74 
TCGA-57-1992 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 
       29.00       116.12         9.40         2.14         5.42        44.81 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 TCGA-61-1741 TCGA-61-1743 TCGA-61-1899 
        4.34        31.79        48.79        33.67        43.69         8.42 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 TCGA-61-1919 
        9.07        34.13        56.61        67.76        15.75        38.17 
TCGA-61-1995 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2009 TCGA-61-2012 
        2.01        14.50        17.98         4.01        39.85        30.64 
TCGA-61-2016 TCGA-61-2094 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 
        1.18        71.74        58.39        60.62        65.52        55.50 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 
        6.48        76.87        44.52       125.75        22.22         6.35 
TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-WR-A838 TCGA-09-0364 
       31.07         8.61        39.68        18.94         9.99        29.16 
TCGA-09-0365 TCGA-09-0367 TCGA-09-0369 TCGA-10-0927 TCGA-10-0936 TCGA-10-0938 
        9.47        17.98        35.57        81.86        36.92        20.91 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0724 TCGA-13-0751 TCGA-13-0757 TCGA-13-0760 
        6.21        24.59         2.73        55.17        11.18        11.54 
TCGA-13-0762 TCGA-13-0764 TCGA-13-0768 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 
      111.78        61.84        58.65       107.28        20.35        87.48 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
       43.86        35.28        35.31        13.61        68.94       107.18 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0888 TCGA-13-0889 TCGA-13-0899 TCGA-13-0900 
      111.39       153.37        92.42        95.15        66.15       134.04 
TCGA-13-0904 TCGA-13-0908 TCGA-13-0913 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       50.37        60.59       109.32        48.76        83.74        85.94 

$`9Q LOSS WILD-TYPE`
TCGA-3P-A9WA TCGA-04-1331 TCGA-04-1335 TCGA-04-1342 TCGA-04-1348 TCGA-04-1353 
       13.81        43.92         1.81        18.51        48.76         0.53 
TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 TCGA-04-1516 TCGA-04-1530 
       44.32        76.57       103.40        56.55        41.59       119.08 
TCGA-04-1536 TCGA-04-1644 TCGA-04-1648 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 
       29.10        48.89        28.64        36.23        31.86        47.70 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1668 TCGA-09-1672 
       89.33        74.93        41.62        57.60        55.36         5.85 
TCGA-09-2043 TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 TCGA-09-2051 TCGA-09-2056 
        6.18        35.15         4.54        71.11        63.09        12.46 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 
       81.17        28.54        32.35        54.64        87.06        61.71 
TCGA-13-1485 TCGA-13-1488 TCGA-13-1492 TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 
       20.68        70.82       125.56        93.90         4.24       127.27 
TCGA-13-1498 TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 TCGA-13-1510 TCGA-13-1511 
       66.15        43.20        65.69        34.16        44.68        54.25 
TCGA-13-1512 TCGA-13-2059 TCGA-20-0987 TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 
       14.53        78.48        23.05        26.20        72.20        25.38 
TCGA-20-1687 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1029 
        2.66        40.54        15.39        26.83        32.09         8.81 
TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 TCGA-23-1117 TCGA-23-1120 
        2.76        51.35        54.51        31.20        33.30         4.27 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1124 TCGA-23-1809 TCGA-23-2078 TCGA-23-2079 
        6.38        39.09        58.13         0.53        87.48        91.66 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-24-0966 TCGA-24-0970 TCGA-24-0980 
       77.00        49.84         2.76         7.63        11.64         7.66 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1416 TCGA-24-1418 TCGA-24-1419 TCGA-24-1423 
       54.12        63.55         6.38         7.99         7.86         6.25 
TCGA-24-1425 TCGA-24-1427 TCGA-24-1428 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
        5.95         4.83        17.39        18.67        43.53         8.55 
TCGA-24-1463 TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1474 TCGA-24-1546 
       72.92        45.14       105.99         3.45        22.22        64.27 
TCGA-24-1548 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 
       16.21        51.91        41.39        58.09        88.50        70.62 
TCGA-24-1557 TCGA-24-1565 TCGA-24-1567 TCGA-24-1614 TCGA-24-1842 TCGA-24-1844 
       39.88        10.26        17.23        48.33         8.32         3.72 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 
        4.37        11.28         5.79         5.52         9.80        22.68 
TCGA-24-1927 TCGA-24-2020 TCGA-24-2027 TCGA-24-2030 TCGA-24-2036 TCGA-24-2038 
       16.44       152.02       109.71        55.92        64.01        44.52 
TCGA-24-2254 TCGA-24-2262 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2289 
       57.07         0.36        31.63        70.45        44.61        67.36 
TCGA-24-2290 TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1319 
       36.23        55.86        53.26        26.96        52.04        65.00 
TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1628 TCGA-25-1632 
        2.99        15.02        18.58        27.62        20.61        59.15 
TCGA-25-1635 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2396 TCGA-25-2397 
       52.04        85.05        13.02        49.05         3.02        12.00 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1690 TCGA-29-1691 
        2.96        29.03        31.00        26.99        47.61        48.33 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1701 TCGA-29-1703 TCGA-29-1707 TCGA-29-1711 
       33.93        31.20        16.93        59.67        41.98        34.62 
TCGA-29-1762 TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 TCGA-29-1776 TCGA-29-1778 
       86.60        62.93        31.30        22.98        11.84        14.93 
TCGA-29-1781 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2428 
        8.38         5.36        36.30        86.17        62.47        45.11 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1718 
       13.84        42.25        21.47         9.76        35.77        51.91 
TCGA-30-1855 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1887 TCGA-30-1891 
        2.47        48.10        44.91         6.12        24.26        30.05 
TCGA-30-1892 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 TCGA-31-1956 TCGA-31-1959 
       48.79        30.18        22.49         6.71        44.12         2.20 
TCGA-36-1568 TCGA-36-1570 TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 TCGA-36-1578 
       28.77        21.53        22.55         8.55        25.74        27.85 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 
       33.01        29.49        29.82        25.08        23.80        21.60 
TCGA-36-2551 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2591 TCGA-57-1584 
       16.18        47.57        23.74        28.93        40.77        21.14 
TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 
       22.32        25.08        25.02       180.20        80.12        22.32 
TCGA-59-2354 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
       34.39        11.11         8.09        20.94        31.43        18.54 
TCGA-61-1728 TCGA-61-1734 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1895 
       27.88        28.47        44.84        35.80         2.43         1.45 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 
        5.79        11.41        13.02        31.30        37.05        42.51 
TCGA-61-1913 TCGA-61-1917 TCGA-61-1998 TCGA-61-2008 TCGA-61-2017 TCGA-61-2018 
       48.92        43.43         5.52        30.64        45.96        45.40 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2095 TCGA-61-2109 TCGA-VG-A8LO 
        4.80         4.77        51.72        61.64        20.68         0.79 
TCGA-09-0366 TCGA-10-0925 TCGA-10-0926 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       57.76        54.31        25.91        18.51        34.19        32.88 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-13-0720 TCGA-13-0723 
       14.66         6.71        35.44        19.99        44.55        39.58 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 TCGA-13-0758 
       12.39        31.20        15.19        17.82         2.50        11.38 
TCGA-13-0761 TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 TCGA-13-0794 TCGA-13-0797 
       38.01        56.71        40.24       118.42        63.09        69.73 
TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0887 TCGA-13-0890 TCGA-13-0891 
       83.34        45.99        51.02        66.67       145.45       102.84 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0901 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 
       43.36        71.74        19.36       127.79       123.16       118.98 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
      116.65        44.55        37.64        58.68        84.53        48.79 
TCGA-13-2071 
       25.41 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.26              0.36 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           153.37            180.20 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           32.765            32.880 
[1] "0.3 - 153.4 (32.8)" "0.4 - 180.2 (32.9)"
[1] "hr=" "1.1"
D59V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  9Q LOSS MUTATED         1   277                2
  9Q LOSS WILD-TYPE       2   281                0
D59V3, multiclass
                  clus
vv                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  OMENTUM                        1                 2
  OVARY                        277               281
  PERITONEUM OVARY               2                 0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V4, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED   271   2
  9Q LOSS WILD-TYPE 270   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    271    2
  9Q LOSS WILD-TYPE  270    3
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO              271               270
  YES               2                 3
[1] 2 2
[1] FALSE
D59V5, continuous
                   vv
clus                R0 R1 R2 RX
  9Q LOSS MUTATED    9 12  3  2
  9Q LOSS WILD-TYPE  6 14  2  1
D59V6, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0               9                 6
  R1              12                14
  R2               3                 2
  RX               2                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     5 159
  9Q LOSS WILD-TYPE   5 168
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      5  159
  9Q LOSS WILD-TYPE    5  168
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 5
  NOT HISPANIC OR LATINO             159               168
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    37  57
  10P LOSS WILD-TYPE 191 274
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                94                465 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                57                274 
$`10P LOSS MUTATED`
TCGA-59-A5PD TCGA-04-1341 TCGA-04-1364 TCGA-04-1371 TCGA-04-1648 TCGA-09-2043 
       20.52         1.08        33.67        82.39        28.64         6.18 
TCGA-09-2053 TCGA-13-1408 TCGA-13-1484 TCGA-13-1489 TCGA-13-1500 TCGA-13-1507 
       39.75        55.23       124.44        83.93        13.97        65.52 
TCGA-13-2057 TCGA-13-2065 TCGA-20-1684 TCGA-23-1114 TCGA-23-1809 TCGA-23-2072 
       80.02        65.52        19.10        68.68         0.53        24.95 
TCGA-23-2078 TCGA-24-0979 TCGA-24-1104 TCGA-24-1416 TCGA-24-1425 TCGA-24-1435 
       87.48        41.56        63.55         6.38         5.95        43.53 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1471 TCGA-24-1474 TCGA-24-1557 TCGA-24-1558 
       45.14       105.99         1.18        22.22        39.88        19.53 
TCGA-24-1614 TCGA-24-1842 TCGA-24-1844 TCGA-24-1923 TCGA-24-2019 TCGA-24-2026 
       48.33         8.32         3.72        22.68         4.87        34.82 
TCGA-24-2030 TCGA-24-2254 TCGA-24-2280 TCGA-24-2288 TCGA-24-2297 TCGA-24-2298 
       55.92        57.07        70.45         0.82        55.86        53.26 
TCGA-25-1313 TCGA-25-1323 TCGA-25-1625 TCGA-25-1632 TCGA-25-2393 TCGA-25-2398 
       26.96        12.99        27.62        59.15        38.04        45.01 
TCGA-25-2399 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1707 TCGA-29-1761 
       19.99        31.20        68.32        36.36        41.98        17.36 
TCGA-29-1769 TCGA-30-1714 TCGA-30-1855 TCGA-30-1860 TCGA-31-1944 TCGA-31-1951 
       22.98        38.07         2.47        44.91        45.57        22.49 
TCGA-31-1959 TCGA-36-2532 TCGA-36-2534 TCGA-36-2538 TCGA-36-2542 TCGA-36-2544 
        2.20        29.49        29.82        25.08        21.60        20.98 
TCGA-36-2545 TCGA-36-2547 TCGA-42-2589 TCGA-61-1724 TCGA-61-1734 TCGA-61-1737 
       18.31        20.52        42.02        20.94        28.47        44.84 
TCGA-61-1743 TCGA-61-1913 TCGA-61-1914 TCGA-61-2092 TCGA-61-2094 TCGA-61-2113 
       43.69        48.92        56.61        51.72        71.74        22.22 
TCGA-09-0364 TCGA-09-0366 TCGA-09-0367 TCGA-10-0935 TCGA-10-0938 TCGA-13-0724 
       29.16        57.76        17.98        35.44        20.91         2.73 
TCGA-13-0760 TCGA-13-0764 TCGA-13-0794 TCGA-13-0800 TCGA-13-0803 TCGA-13-0889 
       11.54        61.84        63.09        87.48        43.86        95.15 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0904 TCGA-13-0921 
      102.84        43.36        50.37        48.76 

$`10P LOSS WILD-TYPE`
TCGA-3P-A9WA TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 
       13.81        11.87        43.92        41.00         1.81        49.15 
TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 
        2.01        46.62        18.51        11.87        65.52        63.09 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 
       48.76        21.57        63.98        65.46         0.53        49.28 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 TCGA-04-1516 
       32.52        44.32        76.57       103.40        56.55        41.59 
TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 
       19.99         0.79        38.37       119.08        29.10        84.20 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 
       55.43        48.89        27.88        64.64        36.23        31.86 
TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       47.70        45.37         9.99        38.43        89.33        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 
       41.62        57.60        61.87        55.36        30.51        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 
        5.85         3.02         8.55        97.55         6.12        35.15 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2054 TCGA-09-2055 
        4.54       112.41        71.11        63.09        20.94        26.93 
TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1409 
       12.46        77.10        81.17        28.54        83.31        57.27 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 
       81.01        17.46        32.35        54.64        87.06        61.71 
TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 
       29.42        20.68        22.39        70.82        52.44       125.56 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 
       93.90        90.38         4.24       127.27        66.15       115.07 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 
       43.20        34.82        65.69        34.16        80.15        44.68 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-A5FT 
       54.25        14.53        78.48        77.88        76.90        70.45 
TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 
        8.42        23.05        25.94        26.20        72.20        27.52 
TCGA-20-1683 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 
       25.38        16.70         2.93         2.66        47.54        49.68 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 
       40.54        15.39        26.83        32.09        49.41         8.81 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
       29.13        18.90         2.76        51.35        54.51         3.22 
TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 
       31.20        19.46        33.30        86.01       129.96         4.27 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2077 TCGA-23-2079 
        6.38        39.09        33.47        58.13       115.89        91.66 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 
       77.00        49.84         2.76         4.70         4.50         7.63 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1105 
       11.64        21.80         7.66        22.32        54.12        47.41 
TCGA-24-1413 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 
        6.31         7.82         7.99         7.86         0.76         6.25 
TCGA-24-1424 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 
        6.02         5.36         4.83        17.39        28.37        18.64 
TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1469 TCGA-24-1470 
       18.67         8.55        72.92        12.46         9.11         3.45 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 
       26.96        57.40        64.27        16.21        56.58        41.06 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1560 
       51.91        41.39        58.09        88.50        70.62        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       45.50        47.70        25.87        10.26        17.23        90.15 
TCGA-24-1604 TCGA-24-1616 TCGA-24-1843 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 
       88.37        38.24         3.48         3.81         4.37        11.28 
TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 
        5.79         5.52         9.80        30.21        16.44        11.05 
TCGA-24-1930 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 
       81.11       152.02        44.84        58.16       109.71        14.43 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2260 TCGA-24-2261 
       18.48        28.18        64.01        44.52        36.16         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 TCGA-24-2289 TCGA-24-2290 
        0.36        47.54        31.63        44.61        67.36        36.23 
TCGA-24-2293 TCGA-24-2295 TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 
       16.64        33.11         1.02        33.01        52.04        42.05 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 
        2.01        34.98        65.00        37.97        33.96         2.99 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 
       15.02        18.58        17.03        12.95        20.61        38.20 
TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 
        0.30        62.17        35.87        52.04        14.96        24.99 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2396 
       24.00        85.05        13.02        49.05         1.02         3.02 
TCGA-25-2397 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       12.00        42.02         2.96        29.03        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 
       78.90        47.61        48.33       101.79        39.02        40.41 
TCGA-29-1696 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1710 
       33.93        16.93        23.93        59.67        18.25        31.27 
TCGA-29-1711 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 
       34.62        86.60        66.81        62.93        39.42        31.30 
TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 
       24.36        22.55        17.33        12.36        11.84        12.30 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 
       14.93         8.38         7.23         5.36        36.30        86.17 
TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 
       65.00        62.47        45.11        13.84        42.25        21.47 
TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1853 TCGA-30-1856 
       11.47         9.76        35.77        51.91        36.26        15.68 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 
        0.26        48.10        34.78         6.12        36.62         1.22 
TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1946 TCGA-31-1950 
       57.57        24.26        30.05        48.79        30.18        18.77 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
        6.71        42.51        44.12        28.77        29.10        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 
       22.85        22.55         8.55        30.08        25.74        27.85 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2537 TCGA-36-2540 
       24.23        24.69        35.05        33.01        25.91        23.80 
TCGA-36-2543 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 
        2.24        14.17         6.05        16.18        11.47        47.57 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 
       23.74        28.93        10.42        40.77         1.48        24.03 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 
       11.38        21.14         1.74        22.32        29.00        25.08 
TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       25.02       180.20        80.12        22.32       116.12         9.40 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 
       34.39         2.14         5.42        44.81        11.11         8.09 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 
       31.43        18.54        27.88         4.34        31.79        48.79 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
       35.80         2.43        33.67         1.45         8.42         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 
       11.41        13.02         9.07        34.13        31.30        37.05 
TCGA-61-1911 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 
       42.51        67.76        43.43        15.75        38.17         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 
        5.52        14.50        17.98         4.01        30.64        39.85 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
       30.64         1.18        45.96        45.40         4.80         4.77 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 
       61.64        58.39        60.62        65.52        55.50         6.48 
TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2612 TCGA-61-2613 
       76.87        20.68        44.52       125.75         6.35        31.07 
TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0365 
        8.61        39.68        18.94         0.79         9.99         9.47 
TCGA-09-0369 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       35.57        54.31        25.91        81.86        18.51        34.19 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 TCGA-13-0714 
       32.88        14.66         6.71        36.92        19.99         6.21 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 
       24.59        44.55        39.58        12.39        31.20        15.19 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0761 
       17.82        55.17         2.50        11.18        11.38        38.01 
TCGA-13-0762 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
      111.78        56.71        58.65        40.24       118.42       107.28 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 
       20.35        69.73        83.34        45.99        51.02        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 
       35.31        13.61        68.94       107.18       111.39       153.37 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       66.67        92.42       145.45        71.74        66.15       134.04 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
       19.36       127.79       123.16       118.98        60.59       116.65 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       44.55        37.64       109.32        58.68        84.53        48.79 
TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       83.74        85.94        25.41 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.53               0.26 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            124.44             180.20 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             37.20              31.86 
[1] "0.5 - 124.4 (37.2)" "0.3 - 180.2 (31.9)"
[1] "hr=" "1"  
D60V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  10P LOSS MUTATED         0    95                0
  10P LOSS WILD-TYPE       3   463                2
D60V3, multiclass
                  clus
vv                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  OMENTUM                         0                  3
  OVARY                          95                463
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V4, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    92   0
  10P LOSS WILD-TYPE 449   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     92    0
  10P LOSS WILD-TYPE  449    5
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                92                449
  YES                0                  5
[1] 2 2
[1] FALSE
D60V5, continuous
                    vv
clus                 R0 R1 R2 RX
  10P LOSS MUTATED    4  4  0  0
  10P LOSS WILD-TYPE 11 22  5  3
D60V6, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0                4                 11
  R1                4                 22
  R2                0                  5
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     2  49
  10P LOSS WILD-TYPE   8 278
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      2   49
  10P LOSS WILD-TYPE    8  278
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO               49                278
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    48  74
  10Q LOSS WILD-TYPE 180 257
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               122                437 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                74                257 
$`10Q LOSS MUTATED`
TCGA-04-1343 TCGA-04-1364 TCGA-04-1648 TCGA-04-1649 TCGA-09-1667 TCGA-09-1673 
       11.87        33.67        28.64        64.64        61.87         3.02 
TCGA-09-2043 TCGA-09-2053 TCGA-13-1407 TCGA-13-1408 TCGA-13-1489 TCGA-13-1492 
        6.18        39.75        83.31        55.23        83.93       125.56 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1507 TCGA-13-2057 TCGA-13-2065 TCGA-20-1684 
        4.24       127.27        65.52        80.02        65.52        19.10 
TCGA-20-1686 TCGA-23-1114 TCGA-23-1809 TCGA-23-2072 TCGA-24-0979 TCGA-24-1104 
        2.93        68.68         0.53        24.95        41.56        63.55 
TCGA-24-1416 TCGA-24-1418 TCGA-24-1430 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
        6.38         7.99        28.37        18.67        43.53         8.55 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1471 TCGA-24-1474 TCGA-24-1557 TCGA-24-1614 
       45.14       105.99         1.18        22.22        39.88        48.33 
TCGA-24-1842 TCGA-24-1844 TCGA-24-1850 TCGA-24-1928 TCGA-24-2026 TCGA-24-2030 
        8.32         3.72         5.52        11.05        34.82        55.92 
TCGA-24-2254 TCGA-24-2280 TCGA-24-2288 TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 
       57.07        70.45         0.82        55.86        53.26        26.96 
TCGA-25-1320 TCGA-25-1323 TCGA-25-1632 TCGA-25-1635 TCGA-25-2398 TCGA-25-2399 
       37.97        12.99        59.15        52.04        45.01        19.99 
TCGA-25-2400 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 
       42.02        31.20        68.32        36.36        16.93        59.67 
TCGA-29-1761 TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 TCGA-29-1778 TCGA-30-1714 
       17.36        39.42        22.98        24.36        14.93        38.07 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 TCGA-30-1860 TCGA-31-1944 TCGA-31-1951 
        2.47        15.68        48.10        44.91        45.57        22.49 
TCGA-31-1953 TCGA-31-1959 TCGA-36-1577 TCGA-36-1581 TCGA-36-2532 TCGA-36-2534 
        6.71         2.20        25.74        24.69        29.49        29.82 
TCGA-36-2538 TCGA-36-2542 TCGA-36-2543 TCGA-36-2545 TCGA-36-2547 TCGA-42-2589 
       25.08        21.60         2.24        18.31        20.52        42.02 
TCGA-61-1724 TCGA-61-1728 TCGA-61-1734 TCGA-61-1737 TCGA-61-1741 TCGA-61-1743 
       20.94        27.88        28.47        44.84        33.67        43.69 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1918 TCGA-61-2012 TCGA-61-2088 TCGA-61-2092 
       48.92        56.61        15.75        30.64         4.77        51.72 
TCGA-61-2094 TCGA-61-2102 TCGA-61-2113 TCGA-OY-A56P TCGA-09-0364 TCGA-09-0366 
       71.74         6.48        22.22        39.68        29.16        57.76 
TCGA-09-0367 TCGA-09-0369 TCGA-10-0935 TCGA-10-0938 TCGA-13-0724 TCGA-13-0751 
       17.98        35.57        35.44        20.91         2.73        55.17 
TCGA-13-0760 TCGA-13-0764 TCGA-13-0794 TCGA-13-0800 TCGA-13-0803 TCGA-13-0807 
       11.54        61.84        63.09        87.48        43.86        13.61 
TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 TCGA-13-0904 TCGA-13-0911 
       95.15       102.84        43.36        66.15        50.37        44.55 
TCGA-13-0916 TCGA-13-0921 
       58.68        48.76 

$`10Q LOSS WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1346 
       49.15         2.01        46.62         1.08        18.51        65.52 
TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 
       63.09        48.76        21.57        63.98        65.46         0.53 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 
       49.28        32.52        44.32        76.57       103.40        82.39 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 
       56.55        41.59        19.99         0.79        38.37       119.08 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1651 
       29.10        84.20        55.43        48.89        27.88        36.23 
TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       31.86        47.70        45.37         9.99        38.43        89.33 
TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 
       74.93        41.62        57.60        55.36        30.51        17.98 
TCGA-09-1672 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 
        5.85         8.55        97.55         6.12        35.15         4.54 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 
      112.41        71.11        63.09        20.94        26.93        12.46 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
       77.10        81.17        28.54        57.27        81.01        17.46 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
       32.35        54.64        87.06        61.71        29.42       124.44 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 
       20.68        22.39        70.82        52.44        93.90        90.38 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 
       66.15       115.07        13.97        43.20        34.82        65.69 
TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 
       34.16        80.15        44.68        54.25        14.53        78.48 
TCGA-13-2060 TCGA-13-2061 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
       77.88        76.90        70.45         8.42        23.05        25.94 
TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1685 TCGA-20-1687 
       26.20        72.20        27.52        25.38        16.70         2.66 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
       47.54        49.68        40.54        15.39        26.83        32.09 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 
       49.41         8.81        29.13        18.90         2.76        51.35 
TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
       54.51         3.22        31.20        19.46        33.30        86.01 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 
      129.96         4.27         6.38        39.09        33.47        58.13 
TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
      115.89        87.48        91.66        77.00        49.84         2.76 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 
        4.70         4.50         7.63        11.64        21.80         7.66 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 TCGA-24-1417 TCGA-24-1419 
       22.32        54.12        47.41         6.31         7.82         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        0.76         6.25         6.02         5.95         5.36         4.83 
TCGA-24-1428 TCGA-24-1431 TCGA-24-1463 TCGA-24-1464 TCGA-24-1469 TCGA-24-1470 
       17.39        18.64        72.92        12.46         9.11         3.45 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 
       26.96        57.40        64.27        16.21        56.58        41.06 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1558 
       51.91        41.39        58.09        88.50        70.62        19.53 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 
       44.09        45.50        47.70        25.87        10.26        17.23 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-1843 TCGA-24-1845 TCGA-24-1846 
       90.15        88.37        38.24         3.48         3.81         4.37 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 
       11.28         5.79         9.80        22.68        30.21        16.44 
TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 
       81.11         4.87       152.02        44.84        58.16       109.71 
TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2260 
       14.43        18.48        28.18        64.01        44.52        36.16 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 TCGA-24-2289 
        0.79         0.36        47.54        31.63        44.61        67.36 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 
       36.23        16.64        33.11         1.02        33.01        52.04 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 TCGA-25-1322 
       42.05         2.01        34.98        65.00        33.96         2.99 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 
       15.02        18.58        27.62        17.03        12.95        20.61 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 
       38.20         0.30        62.17        35.87        14.96        24.99 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 
       24.00        85.05        13.02        49.05         1.02        38.04 
TCGA-25-2396 TCGA-25-2397 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
        3.02        12.00         2.96        29.03        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 
       78.90        47.61        48.33       101.79        39.02        40.41 
TCGA-29-1696 TCGA-29-1702 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 
       33.93        23.93        18.25        41.98        31.27        34.62 
TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1768 TCGA-29-1771 TCGA-29-1774 
       86.60        66.81        62.93        31.30        22.55        17.33 
TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
       12.36        11.84        12.30         8.38         7.23         5.36 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 
       36.30        86.17        65.00        62.47        45.11        13.84 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1718 
       42.25        21.47        11.47         9.76        35.77        51.91 
TCGA-30-1853 TCGA-30-1857 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 
       36.26         0.26        34.78         6.12        36.62         1.22 
TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1946 TCGA-31-1950 
       57.57        24.26        30.05        48.79        30.18        18.77 
TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 
       42.51        44.12        28.77        29.10        21.53        22.85 
TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1578 TCGA-36-1580 TCGA-36-2529 
       22.55         8.55        30.08        27.85        24.23        35.05 
TCGA-36-2530 TCGA-36-2537 TCGA-36-2540 TCGA-36-2544 TCGA-36-2548 TCGA-36-2549 
       33.01        25.91        23.80        20.98        14.17         6.05 
TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 
       16.18        11.47        47.57        23.74        28.93        10.42 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 
       40.77         1.48        24.03        11.38        21.14         1.74 
TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 
       22.32        29.00        25.08        25.02       180.20        80.12 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       22.32       116.12         9.40        34.39         2.14         5.42 
TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 TCGA-61-1730 
       44.81        11.11         8.09        31.43        18.54         4.34 
TCGA-61-1733 TCGA-61-1736 TCGA-61-1738 TCGA-61-1740 TCGA-61-1895 TCGA-61-1899 
       31.79        48.79        35.80         2.43         1.45         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        5.79        11.41        13.02         9.07        34.13        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1915 TCGA-61-1917 TCGA-61-1919 TCGA-61-1995 
       37.05        42.51        67.76        43.43        38.17         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 
        5.52        14.50        17.98         4.01        30.64        39.85 
TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2095 TCGA-61-2096 
        1.18        45.96        45.40         4.80        61.64        58.39 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       60.62        65.52        55.50        76.87        20.68        44.52 
TCGA-61-2111 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56Q TCGA-VG-A8LO 
      125.75         6.35        31.07         8.61        18.94         0.79 
TCGA-WR-A838 TCGA-09-0365 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
        9.99         9.47        54.31        25.91        81.86        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 
       34.19        32.88        14.66         6.71        36.92        19.99 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 
        6.21        24.59        44.55        39.58        12.39        31.20 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0761 
       15.19        17.82         2.50        11.18        11.38        38.01 
TCGA-13-0762 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
      111.78        56.71        58.65        40.24       118.42       107.28 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 
       20.35        69.73        83.34        45.99        51.02        35.28 
TCGA-13-0805 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
       35.31        68.94       107.18       111.39       153.37        66.67 
TCGA-13-0888 TCGA-13-0890 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       92.42       145.45        71.74       134.04        19.36       127.79 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 
      123.16       118.98        60.59       116.65        37.64       109.32 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       84.53        48.79        83.74        85.94        25.41 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.53               0.26 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            127.27             180.20 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             35.13              32.09 
[1] "0.5 - 127.3 (35.1)" "0.3 - 180.2 (32.1)"
[1] "hr=" "1.1"
D61V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  10Q LOSS MUTATED         0   122                1
  10Q LOSS WILD-TYPE       3   436                1
D61V3, multiclass
                  clus
vv                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  OMENTUM                         0                  3
  OVARY                         122                436
  PERITONEUM OVARY                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V4, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED   118   2
  10Q LOSS WILD-TYPE 423   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED    118    2
  10Q LOSS WILD-TYPE  423    3
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO               118                423
  YES                2                  3
[1] 2 2
[1] FALSE
D61V5, continuous
                    vv
clus                 R0 R1 R2 RX
  10Q LOSS MUTATED    4  6  1  0
  10Q LOSS WILD-TYPE 11 20  4  3
D61V6, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0                4                 11
  R1                6                 20
  R2                1                  4
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     2  68
  10Q LOSS WILD-TYPE   8 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      2   68
  10Q LOSS WILD-TYPE    8  259
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO               68                259
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    74 117
  11P LOSS WILD-TYPE 154 214
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               191                368 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               117                214 
$`11P LOSS MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1338 TCGA-04-1341 TCGA-04-1347 
       13.81        20.52        43.92        46.62         1.08        63.09 
TCGA-04-1351 TCGA-04-1356 TCGA-04-1367 TCGA-04-1517 TCGA-04-1536 TCGA-04-1542 
       65.46        49.28       103.40        19.99        29.10        84.20 
TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1655 TCGA-09-1659 
       48.89        27.88        28.64        64.64        45.37         9.99 
TCGA-09-1661 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1670 TCGA-09-1674 
       38.43        57.60        61.87        55.36        17.98         8.55 
TCGA-09-2050 TCGA-09-2053 TCGA-13-1404 TCGA-13-1409 TCGA-13-1411 TCGA-13-1477 
       71.11        39.75        81.17        57.27        17.46        54.64 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1489 TCGA-13-1494 
       61.71        29.42       124.44        22.39        83.93        93.90 
TCGA-13-1495 TCGA-13-1500 TCGA-13-1505 TCGA-13-1507 TCGA-13-1512 TCGA-13-2060 
       90.38        13.97        65.69        65.52        14.53        77.88 
TCGA-13-2065 TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-1683 TCGA-20-1686 
       65.52         8.42        25.94        26.20        25.38         2.93 
TCGA-20-1687 TCGA-23-1022 TCGA-23-1027 TCGA-23-1031 TCGA-23-1113 TCGA-23-1114 
        2.66        49.68        32.09        18.90        31.20        68.68 
TCGA-23-1118 TCGA-23-1122 TCGA-23-2077 TCGA-23-2643 TCGA-24-0970 TCGA-24-1105 
       86.01        39.09       115.89         4.70        11.64        47.41 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1427 TCGA-24-1428 TCGA-24-1436 TCGA-24-1463 
        7.82         7.99         4.83        17.39         8.55        72.92 
TCGA-24-1466 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1549 TCGA-24-1562 
       45.14        22.22        26.96        57.40        56.58        45.50 
TCGA-24-1563 TCGA-24-1567 TCGA-24-1616 TCGA-24-1846 TCGA-24-1923 TCGA-24-1924 
       47.70        17.23        38.24         4.37        22.68        30.21 
TCGA-24-1930 TCGA-24-2019 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2254 
       81.11         4.87        34.82       109.71        14.43        57.07 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 TCGA-24-2280 TCGA-24-2293 TCGA-24-2295 
       36.16         0.79        47.54        70.45        16.64        33.11 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1323 TCGA-25-1329 TCGA-25-1628 
       34.98        65.00        37.97        12.99        15.02        20.61 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-2392 
       38.20         0.30        35.87        14.96        24.99         1.02 
TCGA-25-2393 TCGA-29-1688 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 
       38.04        78.90        40.41        33.93        31.20        68.32 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
       23.93        59.67        34.62        17.36        86.60        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 TCGA-29-1777 TCGA-29-2414 
       62.93        39.42        22.98        24.36        12.30        86.17 
TCGA-29-2425 TCGA-29-2428 TCGA-29-2434 TCGA-30-1853 TCGA-30-1861 TCGA-30-1866 
       65.00        45.11        11.47        36.26        34.78        36.62 
TCGA-30-1887 TCGA-31-1950 TCGA-31-1953 TCGA-36-1569 TCGA-36-1577 TCGA-36-1581 
       24.26        18.77         6.71        29.10        25.74        24.69 
TCGA-36-2529 TCGA-36-2538 TCGA-36-2543 TCGA-36-2549 TCGA-36-2552 TCGA-42-2589 
       35.05        25.08         2.24         6.05        11.47        42.02 
TCGA-57-1582 TCGA-57-1993 TCGA-59-2352 TCGA-59-2372 TCGA-61-1722 TCGA-61-1724 
       24.03        25.08         9.40        44.81         8.09        20.94 
TCGA-61-1725 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1738 TCGA-61-1741 
       31.43        27.88         4.34        31.79        35.80        33.67 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1910 TCGA-61-1917 TCGA-61-1919 TCGA-61-2002 
        9.07        34.13        37.05        43.43        38.17        17.98 
TCGA-61-2012 TCGA-61-2018 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2102 
       30.64        45.40         4.77        51.72        71.74         6.48 
TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56Q TCGA-VG-A8LO 
      125.75        22.22         6.35         8.61        18.94         0.79 
TCGA-WR-A838 TCGA-09-0366 TCGA-10-0926 TCGA-10-0928 TCGA-10-0930 TCGA-10-0937 
        9.99        57.76        25.91        18.51        34.19        19.99 
TCGA-10-0938 TCGA-13-0723 TCGA-13-0751 TCGA-13-0758 TCGA-13-0760 TCGA-13-0762 
       20.91        39.58        55.17        11.38        11.54       111.78 
TCGA-13-0768 TCGA-13-0802 TCGA-13-0804 TCGA-13-0886 TCGA-13-0899 TCGA-13-0901 
       58.65        51.02        35.28       153.37        66.15        19.36 
TCGA-13-0904 TCGA-13-0906 TCGA-13-0913 TCGA-13-0920 TCGA-13-0921 
       50.37       118.98       109.32        48.79        48.76 

$`11P LOSS WILD-TYPE`
TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 
       11.87        41.00         1.81        49.15         2.01        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1353 
       11.87        65.52        48.76        21.57        63.98         0.53 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1371 TCGA-04-1514 
       32.52        44.32        33.67        76.57        82.39        56.55 
TCGA-04-1516 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1638 TCGA-04-1651 
       41.59         0.79        38.37       119.08        55.43        36.23 
TCGA-04-1652 TCGA-04-1654 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1669 
       31.86        47.70        89.33        74.93        41.62        30.51 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 
        5.85         3.02        97.55         6.18         6.12        35.15 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2051 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 
        4.54       112.41        63.09        20.94        26.93        12.46 
TCGA-13-1403 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1412 
       77.10        28.54        83.31        55.23        81.01        32.35 
TCGA-13-1481 TCGA-13-1485 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 TCGA-13-1496 
       87.06        20.68        70.82        52.44       125.56         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1506 
      127.27        66.15       115.07        43.20        34.82        34.16 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-2057 TCGA-13-2059 TCGA-13-2061 
       80.15        44.68        54.25        80.02        78.48        76.90 
TCGA-13-A5FT TCGA-20-0987 TCGA-20-0996 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 
       70.45        23.05        72.20        27.52        19.10        16.70 
TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1028 TCGA-23-1029 
       47.54        40.54        15.39        26.83        49.41         8.81 
TCGA-23-1030 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1116 
       29.13         2.76        51.35        54.51         3.22        19.46 
TCGA-23-1117 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 
       33.30       129.96         4.27         6.38        33.47        58.13 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 
        0.53        24.95        87.48        91.66        77.00        49.84 
TCGA-23-2641 TCGA-23-2645 TCGA-24-0966 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        2.76         4.50         7.63        21.80        41.56         7.66 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1413 TCGA-24-1416 TCGA-24-1419 
       22.32        54.12        63.55         6.31         6.38         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1430 
        0.76         6.25         6.02         5.95         5.36        28.37 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1464 TCGA-24-1467 TCGA-24-1469 
       18.64        18.67        43.53        12.46       105.99         9.11 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1546 TCGA-24-1548 TCGA-24-1550 TCGA-24-1551 
        3.45         1.18        64.27        16.21        41.06        51.91 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 
       41.39        58.09        88.50        70.62        39.88        19.53 
TCGA-24-1560 TCGA-24-1564 TCGA-24-1565 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 
       44.09        25.87        10.26        90.15        88.37        48.33 
TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 TCGA-24-1849 
        8.32         3.48         3.72         3.81        11.28         5.79 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1927 TCGA-24-1928 TCGA-24-2020 TCGA-24-2023 
        5.52         9.80        16.44        11.05       152.02        44.84 
TCGA-24-2024 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
       58.16        55.92        18.48        28.18        64.01        44.52 
TCGA-24-2262 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 
        0.36        31.63        44.61         0.82        67.36        36.23 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 
       55.86        53.26         1.02        26.96        33.01        52.04 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1321 TCGA-25-1322 TCGA-25-1623 TCGA-25-1625 
       42.05         2.01        33.96         2.99        18.58        27.62 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 TCGA-25-1877 
       17.03        12.95        59.15        62.17        52.04        24.00 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 
       85.05        13.02        49.05         3.02        12.00        45.01 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       19.99        42.02         2.96        29.03        31.00        26.99 
TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1699 TCGA-29-1701 
       47.61        48.33       101.79        39.02        36.36        16.93 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1768 TCGA-29-1771 TCGA-29-1774 
       18.25        41.98        31.27        31.30        22.55        17.33 
TCGA-29-1775 TCGA-29-1776 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
       12.36        11.84        14.93         8.38         7.23         5.36 
TCGA-29-1785 TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2436 
       36.30        62.47        13.84        42.25        21.47         9.76 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 
       35.77        38.07        51.91         2.47        15.68         0.26 
TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1867 TCGA-30-1880 TCGA-30-1891 
       48.10        44.91         6.12         1.22        57.57        30.05 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1955 TCGA-31-1956 
       48.79        45.57        30.18        22.49        42.51        44.12 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 
        2.20        28.77        21.53        22.85        22.55         8.55 
TCGA-36-1576 TCGA-36-1578 TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       30.08        27.85        24.23        33.01        29.49        29.82 
TCGA-36-2537 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 
       25.91        23.80        21.60        20.98        18.31        20.52 
TCGA-36-2548 TCGA-36-2551 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 
       14.17        16.18        47.57        23.74        28.93        10.42 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 
       40.77         1.48        11.38        21.14         1.74        22.32 
TCGA-57-1992 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 
       29.00        25.02       180.20        80.12        22.32       116.12 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-61-1721 TCGA-61-1727 TCGA-61-1734 
       34.39         2.14         5.42        11.11        18.54        28.47 
TCGA-61-1736 TCGA-61-1737 TCGA-61-1740 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 
       48.79        44.84         2.43        43.69         1.45         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1907 TCGA-61-1911 TCGA-61-1913 
        5.79        11.41        13.02        31.30        42.51        48.92 
TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       56.61        67.76        15.75         2.01         5.52        14.50 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2087 
        4.01        30.64        39.85         1.18        45.96         4.80 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 
       61.64        58.39        60.62        65.52        55.50        76.87 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2613 TCGA-OY-A56P TCGA-09-0364 TCGA-09-0365 
       20.68        44.52        31.07        39.68        29.16         9.47 
TCGA-09-0367 TCGA-09-0369 TCGA-10-0925 TCGA-10-0927 TCGA-10-0931 TCGA-10-0933 
       17.98        35.57        54.31        81.86        32.88        14.66 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
        6.71        35.44        36.92         6.21        24.59        44.55 
TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 
        2.73        12.39        31.20        15.19        17.82         2.50 
TCGA-13-0757 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 
       11.18        38.01        61.84        56.71        40.24       118.42 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 
      107.28        63.09        20.35        69.73        83.34        87.48 
TCGA-13-0801 TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
       45.99        43.86        35.31        13.61        68.94       107.18 
TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 
      111.39        66.67        92.42        95.15       145.45       102.84 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0903 TCGA-13-0905 TCGA-13-0908 
       43.36        71.74       134.04       127.79       123.16        60.59 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 TCGA-13-0919 TCGA-13-0923 
      116.65        44.55        37.64        58.68        84.53        83.74 
TCGA-13-0924 TCGA-13-2071 
       85.94        25.41 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.30               0.26 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            153.37             180.20 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            34.130             31.745 
[1] "0.3 - 153.4 (34.1)" "0.3 - 180.2 (31.7)"
[1] "hr=" "1.1"
D62V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  11P LOSS MUTATED         1   191                2
  11P LOSS WILD-TYPE       2   367                0
D62V3, multiclass
                  clus
vv                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  OMENTUM                         1                  2
  OVARY                         191                367
  PERITONEUM OVARY                2                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V4, binary
                    cls
clus                   0   1
  11P LOSS MUTATED   187   3
  11P LOSS WILD-TYPE 354   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED    187    3
  11P LOSS WILD-TYPE  354    2
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO               187                354
  YES                3                  2
[1] 2 2
[1] FALSE
D62V5, continuous
                    vv
clus                 R0 R1 R2 RX
  11P LOSS MUTATED    6  9  2  2
  11P LOSS WILD-TYPE  9 17  3  1
D62V6, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0                6                  9
  R1                9                 17
  R2                2                  3
  RX                2                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     2 104
  11P LOSS WILD-TYPE   8 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      2  104
  11P LOSS WILD-TYPE    8  223
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO              104                223
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    53  91
  11Q LOSS WILD-TYPE 175 240
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               144                415 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                91                240 
$`11Q LOSS MUTATED`
TCGA-59-A5PD TCGA-04-1331 TCGA-04-1338 TCGA-04-1341 TCGA-04-1356 TCGA-04-1367 
       20.52        43.92        46.62         1.08        49.28       103.40 
TCGA-04-1517 TCGA-04-1536 TCGA-04-1648 TCGA-04-1649 TCGA-04-1655 TCGA-09-1666 
       19.99        29.10        28.64        64.64        45.37        57.60 
TCGA-09-1670 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-13-1404 TCGA-13-1409 
       17.98        71.11        63.09        39.75        81.17        57.27 
TCGA-13-1411 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1487 TCGA-13-1489 
       17.46        54.64        61.71        29.42        22.39        83.93 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1501 TCGA-13-1505 TCGA-13-1512 TCGA-13-2060 
       93.90        90.38        43.20        65.69        14.53        77.88 
TCGA-13-2065 TCGA-13-A5FU TCGA-20-0991 TCGA-20-1683 TCGA-20-1686 TCGA-23-1113 
       65.52         8.42        26.20        25.38         2.93        31.20 
TCGA-23-1114 TCGA-23-1118 TCGA-23-1122 TCGA-23-2077 TCGA-24-0970 TCGA-24-0982 
       68.68        86.01        39.09       115.89        11.64        22.32 
TCGA-24-1105 TCGA-24-1417 TCGA-24-1428 TCGA-24-1463 TCGA-24-1466 TCGA-24-1544 
       47.41         7.82        17.39        72.92        45.14        26.96 
TCGA-24-1562 TCGA-24-1567 TCGA-24-1923 TCGA-24-1924 TCGA-24-2019 TCGA-24-2254 
       45.50        17.23        22.68        30.21         4.87        57.07 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2280 TCGA-24-2293 TCGA-24-2295 TCGA-25-1319 
       36.16         0.79        70.45        16.64        33.11        65.00 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1329 TCGA-25-1628 TCGA-25-1870 TCGA-25-1871 
       37.97        33.96        15.02        20.61        14.96        24.99 
TCGA-25-2392 TCGA-25-2393 TCGA-29-1688 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 
        1.02        38.04        78.90        40.41        33.93        31.20 
TCGA-29-1698 TCGA-29-1703 TCGA-29-1711 TCGA-29-1761 TCGA-29-1766 TCGA-29-1769 
       68.32        59.67        34.62        17.36        39.42        22.98 
TCGA-29-1770 TCGA-29-1775 TCGA-29-1777 TCGA-29-2414 TCGA-29-2428 TCGA-29-2434 
       24.36        12.36        12.30        86.17        45.11        11.47 
TCGA-30-1853 TCGA-30-1861 TCGA-30-1866 TCGA-31-1953 TCGA-36-1571 TCGA-36-1581 
       36.26        34.78        36.62         6.71        22.85        24.69 
TCGA-36-2529 TCGA-36-2538 TCGA-36-2543 TCGA-36-2549 TCGA-36-2552 TCGA-42-2589 
       35.05        25.08         2.24         6.05        11.47        42.02 
TCGA-57-1582 TCGA-57-1993 TCGA-59-2348 TCGA-59-2352 TCGA-61-1724 TCGA-61-1725 
       24.03        25.08       180.20         9.40        20.94        31.43 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1738 TCGA-61-1741 TCGA-61-1743 
       27.88         4.34        31.79        35.80        33.67        43.69 
TCGA-61-1904 TCGA-61-1910 TCGA-61-1911 TCGA-61-1917 TCGA-61-1919 TCGA-61-2012 
        9.07        37.05        42.51        43.43        38.17        30.64 
TCGA-61-2018 TCGA-61-2092 TCGA-61-2102 TCGA-61-2111 TCGA-61-2113 TCGA-61-2614 
       45.40        51.72         6.48       125.75        22.22         8.61 
TCGA-OY-A56Q TCGA-WR-A838 TCGA-09-0366 TCGA-10-0926 TCGA-10-0928 TCGA-10-0930 
       18.94         9.99        57.76        25.91        18.51        34.19 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0723 TCGA-13-0724 TCGA-13-0730 TCGA-13-0751 
       19.99        20.91        39.58         2.73        17.82        55.17 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0762 TCGA-13-0768 TCGA-13-0795 
       11.18        11.38        11.54       111.78        58.65        20.35 
TCGA-13-0804 TCGA-13-0899 TCGA-13-0904 TCGA-13-0906 TCGA-13-0920 TCGA-13-0921 
       35.28        66.15        50.37       118.98        48.79        48.76 

$`11Q LOSS WILD-TYPE`
TCGA-3P-A9WA TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 
       13.81        11.87        41.00         1.81        49.15         2.01 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 
       18.51        11.87        65.52        63.09        48.76        21.57 
TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 
       63.98        65.46         0.53        32.52        44.32        33.67 
TCGA-04-1365 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1519 TCGA-04-1525 
       76.57        82.39        56.55        41.59         0.79        38.37 
TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1651 
      119.08        84.20        55.43        48.89        27.88        36.23 
TCGA-04-1652 TCGA-04-1654 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       31.86        47.70         9.99        38.43        89.33        74.93 
TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1672 TCGA-09-1673 
       41.62        61.87        55.36        30.51         5.85         3.02 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 
        8.55        97.55         6.18         6.12        35.15         4.54 
TCGA-09-2049 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1405 
      112.41        20.94        26.93        12.46        77.10        28.54 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1412 TCGA-13-1481 TCGA-13-1484 
       83.31        55.23        81.01        32.35        87.06       124.44 
TCGA-13-1485 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 TCGA-13-1496 TCGA-13-1497 
       20.68        70.82        52.44       125.56         4.24       127.27 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 
       66.15       115.07        13.97        34.82        34.16        65.52 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-2057 TCGA-13-2059 TCGA-13-2061 
       80.15        44.68        54.25        80.02        78.48        76.90 
TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 TCGA-20-0996 TCGA-20-1682 TCGA-20-1684 
       70.45        23.05        25.94        72.20        27.52        19.10 
TCGA-20-1685 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 
       16.70         2.66        47.54        49.68        40.54        15.39 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 
       26.83        32.09        49.41         8.81        29.13        18.90 
TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1116 TCGA-23-1117 
        2.76        51.35        54.51         3.22        19.46        33.30 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 
      129.96         4.27         6.38        33.47        58.13         0.53 
TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
       24.95        87.48        91.66        77.00        49.84         2.76 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        4.70         4.50         7.63        21.80        41.56         7.66 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1413 TCGA-24-1416 TCGA-24-1418 TCGA-24-1419 
       54.12        63.55         6.31         6.38         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        0.76         6.25         6.02         5.95         5.36         4.83 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1464 
       28.37        18.64        18.67        43.53         8.55        12.46 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1545 
      105.99         9.11         3.45         1.18        22.22        57.40 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
       64.27        16.21        56.58        41.06        51.91        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 
       58.09        88.50        70.62        39.88        19.53        44.09 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 
       47.70        25.87        10.26        90.15        88.37        48.33 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 
       38.24         8.32         3.48         3.72         3.81         4.37 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1927 TCGA-24-1928 
       11.28         5.79         5.52         9.80        16.44        11.05 
TCGA-24-1930 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 
       81.11       152.02        44.84        58.16        34.82       109.71 
TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
       14.43        55.92        18.48        28.18        64.01        44.52 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 
        0.36        47.54        31.63        44.61         0.82        67.36 
TCGA-24-2290 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 
       36.23        55.86        53.26         1.02        26.96        33.01 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1322 TCGA-25-1323 
       52.04        42.05         2.01        34.98         2.99        12.99 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 
       18.58        27.62        17.03        12.95        38.20         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1877 TCGA-25-1878 
       59.15        62.17        35.87        52.04        24.00        85.05 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 
       13.02        49.05         3.02        12.00        45.01        19.99 
TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1690 
       42.02         2.96        29.03        31.00        26.99        47.61 
TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 
       48.33       101.79        39.02        36.36        16.93        23.93 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 
       18.25        41.98        31.27        86.60        66.81        62.93 
TCGA-29-1768 TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 TCGA-29-1778 TCGA-29-1781 
       31.30        22.55        17.33        11.84        14.93         8.38 
TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2425 TCGA-29-2427 TCGA-29-2429 
        7.23         5.36        36.30        65.00        62.47        13.84 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 
       42.25        21.47         9.76        35.77        38.07        51.91 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 
        2.47        15.68         0.26        48.10        44.91         6.12 
TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 
        1.22        57.57        24.26        30.05        48.79        45.57 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 
       30.18        18.77        22.49        42.51        44.12         2.20 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 
       28.77        29.10        21.53        22.55         8.55        30.08 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       25.74        27.85        24.23        33.01        29.49        29.82 
TCGA-36-2537 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 
       25.91        23.80        21.60        20.98        18.31        20.52 
TCGA-36-2548 TCGA-36-2551 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 
       14.17        16.18        47.57        23.74        28.93        10.42 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 
       40.77         1.48        11.38        21.14         1.74        22.32 
TCGA-57-1992 TCGA-57-1994 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2354 
       29.00        25.02        80.12        22.32       116.12        34.39 
TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1727 
        2.14         5.42        44.81        11.11         8.09        18.54 
TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1740 TCGA-61-1895 TCGA-61-1899 
       28.47        48.79        44.84         2.43         1.45         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1906 TCGA-61-1907 TCGA-61-1913 
        5.79        11.41        13.02        34.13        31.30        48.92 
TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       56.61        67.76        15.75         2.01         5.52        14.50 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 
       17.98         4.01        30.64        39.85         1.18        45.96 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 
        4.80         4.77        71.74        61.64        58.39        60.62 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2612 
       65.52        55.50        76.87        20.68        44.52         6.35 
TCGA-61-2613 TCGA-OY-A56P TCGA-VG-A8LO TCGA-09-0364 TCGA-09-0365 TCGA-09-0367 
       31.07        39.68         0.79        29.16         9.47        17.98 
TCGA-09-0369 TCGA-10-0925 TCGA-10-0927 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       35.57        54.31        81.86        32.88        14.66         6.71 
TCGA-10-0935 TCGA-10-0936 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0725 
       35.44        36.92         6.21        24.59        44.55        12.39 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0755 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 
       31.20        15.19         2.50        38.01        61.84        56.71 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 
       40.24       118.42       107.28        63.09        69.73        83.34 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 
       87.48        45.99        51.02        43.86        35.31        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 
       68.94       107.18       111.39       153.37        66.67        92.42 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 
       95.15       145.45       102.84        43.36        71.74       134.04 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0905 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       19.36       127.79       123.16        60.59       116.65        44.55 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0923 TCGA-13-0924 
       37.64       109.32        58.68        84.53        83.74        85.94 
TCGA-13-2071 
       25.41 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.79               0.26 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            180.20             153.37 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             33.80              32.35 
[1] "0.8 - 180.2 (33.8)" "0.3 - 153.4 (32.4)"
[1] "hr=" "1.1"
D63V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  11Q LOSS MUTATED         1   142                2
  11Q LOSS WILD-TYPE       2   416                0
D63V3, multiclass
                  clus
vv                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  OMENTUM                         1                  2
  OVARY                         142                416
  PERITONEUM OVARY                2                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V4, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED   138   2
  11Q LOSS WILD-TYPE 403   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED    138    2
  11Q LOSS WILD-TYPE  403    3
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO               138                403
  YES                2                  3
[1] 2 2
[1] FALSE
D63V5, continuous
                    vv
clus                 R0 R1 R2 RX
  11Q LOSS MUTATED    5  6  1  1
  11Q LOSS WILD-TYPE 10 20  4  2
D63V6, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0                5                 10
  R1                6                 20
  R2                1                  4
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     3  78
  11Q LOSS WILD-TYPE   7 249
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3   78
  11Q LOSS WILD-TYPE    7  249
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  7
  NOT HISPANIC OR LATINO               78                249
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    29  48
  12P LOSS WILD-TYPE 199 283
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                77                482 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                48                283 
$`12P LOSS MUTATED`
TCGA-59-A5PD TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1364 TCGA-04-1638 
       20.52         1.81        49.15         2.01        33.67        55.43 
TCGA-09-1667 TCGA-09-1675 TCGA-09-2044 TCGA-13-1403 TCGA-13-1405 TCGA-13-1483 
       61.87        97.55         6.12        77.10        28.54        29.42 
TCGA-13-1488 TCGA-13-1494 TCGA-13-1497 TCGA-13-1501 TCGA-13-1507 TCGA-13-1512 
       70.82        93.90       127.27        43.20        65.52        14.53 
TCGA-20-0987 TCGA-23-1120 TCGA-23-1122 TCGA-23-2072 TCGA-23-2078 TCGA-24-0979 
       23.05         4.27        39.09        24.95        87.48        41.56 
TCGA-24-1105 TCGA-24-1425 TCGA-24-1428 TCGA-24-1435 TCGA-24-1471 TCGA-24-1550 
       47.41         5.95        17.39        43.53         1.18        41.06 
TCGA-24-1849 TCGA-24-2026 TCGA-24-2036 TCGA-24-2280 TCGA-24-2297 TCGA-25-1320 
        5.79        34.82        64.01        70.45        55.86        37.97 
TCGA-25-1632 TCGA-25-2397 TCGA-25-2404 TCGA-25-2409 TCGA-29-1688 TCGA-29-1691 
       59.15        12.00        29.03        26.99        78.90        48.33 
TCGA-29-1703 TCGA-29-1711 TCGA-29-1764 TCGA-29-1776 TCGA-29-2432 TCGA-30-1718 
       59.67        34.62        62.93        11.84        21.47        51.91 
TCGA-30-1853 TCGA-30-1857 TCGA-30-1861 TCGA-36-2538 TCGA-36-2549 TCGA-57-1584 
       36.26         0.26        34.78        25.08         6.05        21.14 
TCGA-57-1585 TCGA-61-1727 TCGA-61-1734 TCGA-61-1738 TCGA-61-1903 TCGA-61-1910 
        1.74        18.54        28.47        35.80        13.02        37.05 
TCGA-61-1913 TCGA-61-1919 TCGA-61-2008 TCGA-61-2102 TCGA-10-0936 TCGA-13-0724 
       48.92        38.17        30.64         6.48        36.92         2.73 
TCGA-13-0755 TCGA-13-0758 TCGA-13-0766 TCGA-13-0793 TCGA-13-0803 TCGA-13-0807 
        2.50        11.38        56.71       107.28        43.86        13.61 
TCGA-13-0885 TCGA-13-0891 TCGA-13-0905 TCGA-13-0908 TCGA-13-0919 
      111.39       102.84       123.16        60.59        84.53 

$`12P LOSS WILD-TYPE`
TCGA-3P-A9WA TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1338 TCGA-04-1341 
       13.81        11.87        43.92        41.00        46.62         1.08 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 
       18.51        11.87        65.52        63.09        48.76        21.57 
TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 
       63.98        65.46         0.53        49.28        32.52        44.32 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 
       76.57       103.40        82.39        56.55        41.59        19.99 
TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1644 
        0.79        38.37       119.08        29.10        84.20        48.89 
TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 
       27.88        28.64        64.64        36.23        31.86        47.70 
TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       45.37         9.99        38.43        89.33        74.93        41.62 
TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       57.60        55.36        30.51        17.98         5.85         3.02 
TCGA-09-1674 TCGA-09-2043 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 
        8.55         6.18        35.15         4.54       112.41        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1404 
       63.09        39.75        20.94        26.93        12.46        81.17 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
       83.31        55.23        57.27        81.01        17.46        32.35 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 
       54.64        87.06        61.71       124.44        20.68        22.39 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 
       83.93        52.44       125.56        90.38         4.24        66.15 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 
      115.07        13.97        34.82        65.69        34.16        80.15 
TCGA-13-1510 TCGA-13-1511 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 
       44.68        54.25        80.02        78.48        77.88        76.90 
TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 
       65.52        70.45         8.42        25.94        26.20        72.20 
TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 
       27.52        25.38        19.10        16.70         2.93         2.66 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
       47.54        49.68        40.54        15.39        26.83        32.09 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 
       49.41         8.81        29.13        18.90         2.76        51.35 
TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 
       54.51         3.22        31.20        68.68        19.46        33.30 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 
       86.01       129.96         6.38        33.47        58.13         0.53 
TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 
      115.89        91.66        77.00        49.84         2.76         4.70 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-0982 
        4.50         7.63        11.64        21.80         7.66        22.32 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 
       54.12        63.55         6.31         6.38         7.82         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1426 TCGA-24-1427 
        7.86         0.76         6.25         6.02         5.36         4.83 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 
       28.37        18.64        18.67         8.55        72.92        12.46 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1474 TCGA-24-1544 
       45.14       105.99         9.11         3.45        22.22        26.96 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 
       57.40        64.27        16.21        56.58        51.91        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 
       58.09        88.50        70.62        39.88        19.53        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       45.50        47.70        25.87        10.26        17.23        90.15 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
       88.37        48.33        38.24         8.32         3.48         3.72 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 
        3.81         4.37        11.28         5.52         9.80        22.68 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 
       30.21        16.44        11.05        81.11         4.87       152.02 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 
       44.84        58.16       109.71        14.43        55.92        18.48 
TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 
       28.18        44.52        57.07        36.16         0.79         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 
       47.54        31.63        44.61         0.82        67.36        36.23 
TCGA-24-2293 TCGA-24-2295 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 
       16.64        33.11        53.26         1.02        26.96        33.01 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 
       52.04        42.05         2.01        34.98        65.00        33.96 
TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 
        2.99        12.99        15.02        18.58        27.62        17.03 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 
       12.95        20.61        38.20         0.30        62.17        35.87 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 
       52.04        14.96        24.99        24.00        85.05        13.02 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 
       49.05         1.02        38.04         3.02        45.01        19.99 
TCGA-25-2400 TCGA-25-2401 TCGA-25-2408 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 
       42.02         2.96        31.00        47.61       101.79        39.02 
TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 
       40.41        33.93        31.20        68.32        36.36        16.93 
TCGA-29-1702 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1761 TCGA-29-1762 
       23.93        18.25        41.98        31.27        17.36        86.60 
TCGA-29-1763 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 
       66.81        39.42        31.30        22.98        24.36        22.55 
TCGA-29-1774 TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 
       17.33        12.36        12.30        14.93         8.38         7.23 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 
        5.36        36.30        86.17        65.00        62.47        45.11 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 
       13.84        42.25        11.47         9.76        35.77        38.07 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 
        2.47        15.68        48.10        44.91         6.12        36.62 
TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 
        1.22        57.57        24.26        30.05        48.79        45.57 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 
       30.18        18.77        22.49         6.71        42.51        44.12 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
        2.20        28.77        29.10        21.53        22.85        22.55 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 
        8.55        30.08        25.74        27.85        24.23        24.69 
TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2540 
       35.05        33.01        29.49        29.82        25.91        23.80 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 
       21.60         2.24        20.98        18.31        20.52        14.17 
TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 
       16.18        11.47        47.57        23.74        28.93        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1586 
       10.42        40.77         1.48        24.03        11.38        22.32 
TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 
       29.00        25.08        25.02       180.20        80.12        22.32 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 
      116.12         9.40        34.39         2.14         5.42        44.81 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1728 TCGA-61-1730 
       11.11         8.09        20.94        31.43        27.88         4.34 
TCGA-61-1733 TCGA-61-1736 TCGA-61-1737 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 
       31.79        48.79        44.84         2.43        33.67        43.69 
TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1904 TCGA-61-1906 
        1.45         8.42         5.79        11.41         9.07        34.13 
TCGA-61-1907 TCGA-61-1911 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 
       31.30        42.51        56.61        67.76        43.43        15.75 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2009 
        2.01         5.52        14.50        17.98         4.01        39.85 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
       30.64         1.18        45.96        45.40         4.80         4.77 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 
       51.72        71.74        61.64        58.39        60.62        65.52 
TCGA-61-2101 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
       55.50        76.87        20.68        44.52       125.75        22.22 
TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
        6.35        31.07         8.61        39.68        18.94         0.79 
TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 
        9.99        29.16         9.47        57.76        17.98        35.57 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       54.31        25.91        81.86        18.51        34.19        32.88 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
       14.66         6.71        35.44        19.99        20.91         6.21 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 
       24.59        44.55        39.58        12.39        31.20        15.19 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 
       17.82        55.17        11.18        11.54        38.01       111.78 
TCGA-13-0764 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0794 TCGA-13-0795 
       61.84        58.65        40.24       118.42        63.09        20.35 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 
       69.73        83.34        87.48        45.99        51.02        35.28 
TCGA-13-0805 TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 
       35.31        68.94       107.18       153.37        66.67        92.42 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       95.15       145.45        43.36        71.74        66.15       134.04 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 
       19.36       127.79        50.37       118.98       116.65        44.55 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 
       37.64       109.32        58.68        48.79        48.76        83.74 
TCGA-13-0924 TCGA-13-2071 
       85.94        25.41 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.26               0.30 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            127.27             180.20 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             36.26              31.71 
[1] "0.3 - 127.3 (36.3)" "0.3 - 180.2 (31.7)"
[1] "hr=" "1"  
D64V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  12P LOSS MUTATED         0    77                0
  12P LOSS WILD-TYPE       3   481                2
D64V3, multiclass
                  clus
vv                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  OMENTUM                         0                  3
  OVARY                          77                481
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V4, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    76   0
  12P LOSS WILD-TYPE 465   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     76    0
  12P LOSS WILD-TYPE  465    5
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                76                465
  YES                0                  5
[1] 2 2
[1] FALSE
D64V5, continuous
                    vv
clus                 R0 R1 R2 RX
  12P LOSS MUTATED    1  3  0  0
  12P LOSS WILD-TYPE 14 23  5  3
D64V6, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0                1                 14
  R1                3                 23
  R2                0                  5
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     1  49
  12P LOSS WILD-TYPE   9 278
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1   49
  12P LOSS WILD-TYPE    9  278
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO               49                278
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    41  61
  12Q LOSS WILD-TYPE 187 270
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               102                457 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                61                270 
$`12Q LOSS MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1335 TCGA-04-1356 TCGA-04-1371 TCGA-04-1542 
       13.81        20.52         1.81        49.28        82.39        84.20 
TCGA-04-1638 TCGA-09-1659 TCGA-09-1667 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 
       55.43         9.99        61.87         8.55        97.55         6.12 
TCGA-13-1405 TCGA-13-1408 TCGA-13-1411 TCGA-13-1483 TCGA-13-1488 TCGA-13-1489 
       28.54        55.23        17.46        29.42        70.82        83.93 
TCGA-13-1497 TCGA-13-1501 TCGA-13-1507 TCGA-13-1512 TCGA-13-2059 TCGA-20-0987 
      127.27        43.20        65.52        14.53        78.48        23.05 
TCGA-23-1120 TCGA-23-1122 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-24-0980 
        4.27        39.09        24.95       115.89        87.48         7.66 
TCGA-24-0982 TCGA-24-1104 TCGA-24-1105 TCGA-24-1425 TCGA-24-1428 TCGA-24-1431 
       22.32        63.55        47.41         5.95        17.39        18.64 
TCGA-24-1471 TCGA-24-1550 TCGA-24-1604 TCGA-24-1614 TCGA-24-1842 TCGA-24-1849 
        1.18        41.06        88.37        48.33         8.32         5.79 
TCGA-24-1920 TCGA-24-1927 TCGA-24-2023 TCGA-24-2026 TCGA-24-2036 TCGA-24-2254 
        9.80        16.44        44.84        34.82        64.01        57.07 
TCGA-24-2280 TCGA-24-2297 TCGA-25-1314 TCGA-25-1320 TCGA-25-1632 TCGA-25-1877 
       70.45        55.86        33.01        37.97        59.15        24.00 
TCGA-25-2397 TCGA-25-2409 TCGA-29-1691 TCGA-29-1703 TCGA-29-1711 TCGA-29-1776 
       12.00        26.99        48.33        59.67        34.62        11.84 
TCGA-29-2427 TCGA-29-2432 TCGA-30-1718 TCGA-30-1853 TCGA-30-1857 TCGA-30-1861 
       62.47        21.47        51.91        36.26         0.26        34.78 
TCGA-30-1891 TCGA-31-1956 TCGA-36-2538 TCGA-36-2549 TCGA-57-1584 TCGA-57-1585 
       30.05        44.12        25.08         6.05        21.14         1.74 
TCGA-59-2363 TCGA-61-1727 TCGA-61-1734 TCGA-61-1738 TCGA-61-1895 TCGA-61-1903 
        5.42        18.54        28.47        35.80         1.45        13.02 
TCGA-61-1904 TCGA-61-1913 TCGA-61-1917 TCGA-61-1919 TCGA-61-2008 TCGA-61-2087 
        9.07        48.92        43.43        38.17        30.64         4.80 
TCGA-61-2104 TCGA-61-2612 TCGA-13-0724 TCGA-13-0751 TCGA-13-0755 TCGA-13-0758 
       76.87         6.35         2.73        55.17         2.50        11.38 
TCGA-13-0760 TCGA-13-0766 TCGA-13-0793 TCGA-13-0803 TCGA-13-0807 TCGA-13-0885 
       11.54        56.71       107.28        43.86        13.61       111.39 
TCGA-13-0891 TCGA-13-0904 TCGA-13-0905 TCGA-13-0908 TCGA-13-0919 TCGA-13-0923 
      102.84        50.37       123.16        60.59        84.53        83.74 

$`12Q LOSS WILD-TYPE`
TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       11.87        43.92        41.00        49.15         2.01        46.62 
TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 
        1.08        18.51        11.87        65.52        63.09        48.76 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1361 TCGA-04-1362 
       21.57        63.98        65.46         0.53        32.52        44.32 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 
       33.67        76.57       103.40        56.55        41.59        19.99 
TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1644 TCGA-04-1646 
        0.79        38.37       119.08        29.10        48.89        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 
       28.64        64.64        36.23        31.86        47.70        45.37 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1668 
       38.43        89.33        74.93        41.62        57.60        55.36 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-2043 TCGA-09-2045 
       30.51        17.98         5.85         3.02         6.18        35.15 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 
        4.54       112.41        71.11        63.09        39.75        20.94 
TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1407 TCGA-13-1409 
       26.93        12.46        77.10        81.17        83.31        57.27 
TCGA-13-1410 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 
       81.01        32.35        54.64        87.06        61.71       124.44 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       20.68        22.39        52.44       125.56        93.90        90.38 
TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 TCGA-13-1505 
        4.24        66.15       115.07        13.97        34.82        65.69 
TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-2057 TCGA-13-2060 
       34.16        80.15        44.68        54.25        80.02        77.88 
TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 
       76.90        65.52        70.45         8.42        25.94        26.20 
TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 
       72.20        27.52        25.38        19.10        16.70         2.93 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
        2.66        47.54        49.68        40.54        15.39        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       32.09        49.41         8.81        29.13        18.90         2.76 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 
       51.35        54.51         3.22        31.20        68.68        19.46 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 
       33.30        86.01       129.96         6.38        33.47        58.13 
TCGA-23-1809 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 
        0.53        91.66        77.00        49.84         2.76         4.70 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-1103 
        4.50         7.63        11.64        21.80        41.56        54.12 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 
        6.31         6.38         7.82         7.99         7.86         0.76 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1426 TCGA-24-1427 TCGA-24-1430 TCGA-24-1434 
        6.25         6.02         5.36         4.83        28.37        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 
       43.53         8.55        72.92        12.46        45.14       105.99 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 
        9.11         3.45        22.22        26.96        57.40        64.27 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       16.21        56.58        51.91        41.39        58.09        88.50 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       70.62        39.88        19.53        44.09        45.50        47.70 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1616 TCGA-24-1843 
       25.87        10.26        17.23        90.15        38.24         3.48 
TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1850 TCGA-24-1923 
        3.72         3.81         4.37        11.28         5.52        22.68 
TCGA-24-1924 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2024 
       30.21        11.05        81.11         4.87       152.02        58.16 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2038 
      109.71        14.43        55.92        18.48        28.18        44.52 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 
       36.16         0.79         0.36        47.54        31.63        44.61 
TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2298 
        0.82        67.36        36.23        16.64        33.11        53.26 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
        1.02        26.96        52.04        42.05         2.01        34.98 
TCGA-25-1319 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
       65.00        33.96         2.99        12.99        15.02        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
       27.62        17.03        12.95        20.61        38.20         0.30 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 
       62.17        35.87        52.04        14.96        24.99        85.05 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 
       13.02        49.05         1.02        38.04         3.02        45.01 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-29-1688 
       19.99        42.02         2.96        29.03        31.00        78.90 
TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 
       47.61       101.79        39.02        40.41        33.93        31.20 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1705 TCGA-29-1707 
       68.32        36.36        16.93        23.93        18.25        41.98 
TCGA-29-1710 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 
       31.27        17.36        86.60        66.81        62.93        39.42 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 
       31.30        22.98        24.36        22.55        17.33        12.36 
TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 
       12.30        14.93         8.38         7.23         5.36        36.30 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 
       86.17        65.00        45.11        13.84        42.25        11.47 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 
        9.76        35.77        38.07         2.47        15.68        48.10 
TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 
       44.91         6.12        36.62         1.22        57.57        24.26 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 
       48.79        45.57        30.18        18.77        22.49         6.71 
TCGA-31-1955 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 
       42.51         2.20        28.77        29.10        21.53        22.85 
TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 
       22.55         8.55        30.08        25.74        27.85        24.23 
TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       24.69        35.05        33.01        29.49        29.82        25.91 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 
       23.80        21.60         2.24        20.98        18.31        20.52 
TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
       14.17        16.18        11.47        47.57        23.74        28.93 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 
       42.02        10.42        40.77         1.48        24.03        11.38 
TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 
       22.32        29.00        25.08        25.02       180.20        80.12 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2372 
       22.32       116.12         9.40        34.39         2.14        44.81 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1728 TCGA-61-1730 
       11.11         8.09        20.94        31.43        27.88         4.34 
TCGA-61-1733 TCGA-61-1736 TCGA-61-1737 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 
       31.79        48.79        44.84         2.43        33.67        43.69 
TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 
        8.42         5.79        11.41        34.13        31.30        37.05 
TCGA-61-1911 TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 
       42.51        56.61        67.76        15.75         2.01         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 
       14.50        17.98         4.01        39.85        30.64         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       45.96        45.40         4.77        51.72        71.74        61.64 
TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2109 
       58.39        60.62        65.52        55.50         6.48        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P 
       44.52       125.75        22.22        31.07         8.61        39.68 
TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 
       18.94         0.79         9.99        29.16         9.47        57.76 
TCGA-09-0367 TCGA-09-0369 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       17.98        35.57        54.31        25.91        81.86        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 
       34.19        32.88        14.66         6.71        35.44        36.92 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 
       19.99        20.91         6.21        24.59        44.55        39.58 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0757 TCGA-13-0761 
       12.39        31.20        15.19        17.82        11.18        38.01 
TCGA-13-0762 TCGA-13-0764 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0794 
      111.78        61.84        58.65        40.24       118.42        63.09 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 
       20.35        69.73        83.34        87.48        45.99        51.02 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 TCGA-13-0887 
       35.28        35.31        68.94       107.18       153.37        66.67 
TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 
       92.42        95.15       145.45        43.36        71.74        66.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 
      134.04        19.36       127.79       118.98       116.65        44.55 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0924 
       37.64       109.32        58.68        48.79        48.76        85.94 
TCGA-13-2071 
       25.41 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.26               0.30 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            127.27             180.20 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             34.80              32.09 
[1] "0.3 - 127.3 (34.8)" "0.3 - 180.2 (32.1)"
[1] "hr=" "1.1"
D65V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  12Q LOSS MUTATED         0   103                0
  12Q LOSS WILD-TYPE       3   455                2
D65V3, multiclass
                  clus
vv                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  OMENTUM                         0                  3
  OVARY                         103                455
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V4, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED   102   0
  12Q LOSS WILD-TYPE 439   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED    102    0
  12Q LOSS WILD-TYPE  439    5
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO               102                439
  YES                0                  5
[1] 2 2
[1] FALSE
D65V5, continuous
                    vv
clus                 R0 R1 R2 RX
  12Q LOSS MUTATED    2  5  0  1
  12Q LOSS WILD-TYPE 13 21  5  2
D65V6, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0                2                 13
  R1                5                 21
  R2                0                  5
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     2  64
  12Q LOSS WILD-TYPE   8 263
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2   64
  12Q LOSS WILD-TYPE    8  263
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO               64                263
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED   127 166
  13Q LOSS WILD-TYPE 101 165
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               293                266 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               166                165 
$`13Q LOSS MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1332 TCGA-04-1335 TCGA-04-1341 TCGA-04-1342 
       13.81        20.52        41.00         1.81         1.08        18.51 
TCGA-04-1343 TCGA-04-1347 TCGA-04-1349 TCGA-04-1353 TCGA-04-1361 TCGA-04-1365 
       11.87        63.09        21.57         0.53        32.52        76.57 
TCGA-04-1367 TCGA-04-1514 TCGA-04-1516 TCGA-04-1525 TCGA-04-1530 TCGA-04-1638 
      103.40        56.55        41.59        38.37       119.08        55.43 
TCGA-04-1646 TCGA-04-1648 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 
       27.88        28.64        36.23        31.86        47.70        45.37 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1670 
        9.99        38.43        57.60        61.87        55.36        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-2044 TCGA-09-2050 TCGA-09-2051 
        5.85         3.02         8.55         6.12        71.11        63.09 
TCGA-09-2054 TCGA-09-2055 TCGA-13-1403 TCGA-13-1404 TCGA-13-1409 TCGA-13-1482 
       20.94        26.93        77.10        81.17        57.27        61.71 
TCGA-13-1483 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1492 TCGA-13-1494 
       29.42        22.39        70.82        83.93       125.56        93.90 
TCGA-13-1495 TCGA-13-1497 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 
       90.38       127.27       115.07        13.97        43.20        34.82 
TCGA-13-1505 TCGA-13-1509 TCGA-13-1511 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FU 
       65.69        80.15        54.25        76.90        65.52         8.42 
TCGA-20-0991 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 TCGA-23-1021 TCGA-23-1023 
       26.20        27.52        19.10        16.70        47.54        40.54 
TCGA-23-1024 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1031 TCGA-23-1032 
       15.39        32.09        49.41         8.81        18.90         2.76 
TCGA-23-1114 TCGA-23-1116 TCGA-23-1118 TCGA-23-1119 TCGA-23-1121 TCGA-23-1123 
       68.68        19.46        86.01       129.96         6.38        33.47 
TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
       58.13         0.53       115.89        77.00        49.84         2.76 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0975 TCGA-24-0980 TCGA-24-1103 TCGA-24-1105 
        4.70         4.50        21.80         7.66        54.12        47.41 
TCGA-24-1413 TCGA-24-1417 TCGA-24-1419 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 
        6.31         7.82         7.86         6.02         5.95         5.36 
TCGA-24-1428 TCGA-24-1430 TCGA-24-1435 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 
       17.39        28.37        43.53        12.46        45.14         9.11 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 TCGA-24-1552 
       22.22        26.96        57.40        16.21        56.58        41.39 
TCGA-24-1555 TCGA-24-1558 TCGA-24-1560 TCGA-24-1563 TCGA-24-1564 TCGA-24-1603 
       88.50        19.53        44.09        47.70        25.87        90.15 
TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 
       48.33        38.24         8.32         3.48         3.72         3.81 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1850 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 
        4.37        11.28         5.52        30.21        16.44        11.05 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2030 
        4.87       152.02        44.84        58.16        34.82        55.92 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2290 
       57.07        36.16         0.79         0.36        47.54        36.23 
TCGA-25-1313 TCGA-25-1315 TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 TCGA-25-1329 
       26.96        52.04        34.98        65.00        33.96        15.02 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 
       12.95        20.61         0.30        62.17        35.87        52.04 
TCGA-25-1878 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 
       85.05        49.05         1.02        38.04         3.02        12.00 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2409 TCGA-29-1693 
       19.99        42.02         2.96        29.03        26.99       101.79 
TCGA-29-1694 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 
       39.02        31.20        68.32        36.36        16.93        23.93 
TCGA-29-1703 TCGA-29-1707 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 
       59.67        41.98        66.81        62.93        39.42        31.30 
TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1784 
       22.55        12.36        11.84        12.30        14.93         5.36 
TCGA-29-2427 TCGA-29-2431 TCGA-29-2432 TCGA-30-1860 TCGA-30-1861 TCGA-30-1866 
       62.47        42.25        21.47        44.91        34.78        36.62 
TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 TCGA-36-1569 
       30.05        18.77         6.71        42.51         2.20        29.10 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 
       22.85        22.55         8.55        24.23        24.69        35.05 
TCGA-36-2534 TCGA-36-2542 TCGA-36-2543 TCGA-36-2545 TCGA-36-2551 TCGA-42-2587 
       29.82        21.60         2.24        18.31        16.18        23.74 
TCGA-42-2590 TCGA-57-1584 TCGA-57-1992 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       10.42        21.14        29.00        22.32       116.12         9.40 
TCGA-59-2354 TCGA-59-2372 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
       34.39        44.81         8.09        20.94        31.43        18.54 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 
        4.34        31.79        28.47        44.84        35.80         2.43 
TCGA-61-1743 TCGA-61-1899 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 
       43.69         8.42        11.41        13.02         9.07        34.13 
TCGA-61-1907 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 TCGA-61-1919 
       31.30        48.92        56.61        67.76        15.75        38.17 
TCGA-61-1995 TCGA-61-2002 TCGA-61-2012 TCGA-61-2016 TCGA-61-2018 TCGA-61-2087 
        2.01        17.98        30.64         1.18        45.40         4.80 
TCGA-61-2088 TCGA-61-2094 TCGA-61-2097 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
        4.77        71.74        60.62        44.52       125.75        22.22 
TCGA-61-2612 TCGA-OY-A56P TCGA-OY-A56Q TCGA-09-0366 TCGA-09-0367 TCGA-10-0925 
        6.35        39.68        18.94        57.76        17.98        54.31 
TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 
       81.86        34.19        32.88        36.92        19.99        20.91 
TCGA-13-0717 TCGA-13-0724 TCGA-13-0726 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 
       24.59         2.73        31.20        17.82        55.17         2.50 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 
       61.84        56.71        58.65       118.42       107.28        20.35 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
       69.73        83.34        87.48        35.28        35.31        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0888 TCGA-13-0890 TCGA-13-0891 
       68.94       107.18       111.39        92.42       145.45       102.84 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 TCGA-13-0910 
      134.04        19.36       127.79        50.37       118.98       116.65 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0924 TCGA-13-2071 
       58.68        84.53        48.79        85.94        25.41 

$`13Q LOSS WILD-TYPE`
TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1346 
       11.87        43.92        49.15         2.01        46.62        65.52 
TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 
       48.76        63.98        65.46        49.28        44.32        33.67 
TCGA-04-1371 TCGA-04-1517 TCGA-04-1519 TCGA-04-1536 TCGA-04-1542 TCGA-04-1644 
       82.39        19.99         0.79        29.10        84.20        48.89 
TCGA-04-1649 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1669 TCGA-09-1675 
       64.64        89.33        74.93        41.62        30.51        97.55 
TCGA-09-2043 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2053 TCGA-09-2056 
        6.18        35.15         4.54       112.41        39.75        12.46 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
       28.54        83.31        55.23        81.01        17.46        32.35 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1484 TCGA-13-1485 TCGA-13-1491 TCGA-13-1496 
       54.64        87.06       124.44        20.68        52.44         4.24 
TCGA-13-1498 TCGA-13-1506 TCGA-13-1507 TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 
       66.15        34.16        65.52        44.68        14.53        80.02 
TCGA-13-2059 TCGA-13-2060 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 TCGA-20-0996 
       78.48        77.88        70.45        23.05        25.94        72.20 
TCGA-20-1683 TCGA-20-1686 TCGA-20-1687 TCGA-23-1022 TCGA-23-1026 TCGA-23-1030 
       25.38         2.93         2.66        49.68        26.83        29.13 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1117 TCGA-23-1120 
       51.35        54.51         3.22        31.20        33.30         4.27 
TCGA-23-1122 TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 TCGA-24-0966 TCGA-24-0970 
       39.09        24.95        87.48        91.66         7.63        11.64 
TCGA-24-0979 TCGA-24-0982 TCGA-24-1104 TCGA-24-1416 TCGA-24-1418 TCGA-24-1422 
       41.56        22.32        63.55         6.38         7.99         0.76 
TCGA-24-1423 TCGA-24-1427 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 
        6.25         4.83        18.64        18.67         8.55        72.92 
TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1546 TCGA-24-1550 TCGA-24-1551 
      105.99         3.45         1.18        64.27        41.06        51.91 
TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 TCGA-24-1562 TCGA-24-1565 TCGA-24-1567 
       58.09        70.62        39.88        45.50        10.26        17.23 
TCGA-24-1604 TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 TCGA-24-1930 TCGA-24-2027 
       88.37         5.79         9.80        22.68        81.11       109.71 
TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2271 
       14.43        18.48        28.18        64.01        44.52        31.63 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2293 TCGA-24-2295 
       70.45        44.61         0.82        67.36        16.64        33.11 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1314 TCGA-25-1316 TCGA-25-1317 
       55.86        53.26         1.02        33.01        42.05         2.01 
TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 
       37.97         2.99        12.99        18.58        27.62        17.03 
TCGA-25-1630 TCGA-25-1632 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-2042 
       38.20        59.15        14.96        24.99        24.00        13.02 
TCGA-25-2398 TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1695 
       45.01        31.00        78.90        47.61        48.33        40.41 
TCGA-29-1696 TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 
       33.93        18.25        31.27        34.62        17.36        86.60 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1774 TCGA-29-1781 TCGA-29-1783 TCGA-29-1785 
       22.98        24.36        17.33         8.38         7.23        36.30 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 TCGA-29-2434 TCGA-29-2436 
       86.17        65.00        45.11        13.84        11.47         9.76 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 
       35.77        38.07        51.91        36.26         2.47        15.68 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1862 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 
        0.26        48.10         6.12         1.22        57.57        24.26 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1956 TCGA-36-1568 
       48.79        45.57        30.18        22.49        44.12        28.77 
TCGA-36-1570 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-2530 TCGA-36-2532 
       21.53        30.08        25.74        27.85        33.01        29.49 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2544 TCGA-36-2547 TCGA-36-2548 
       25.91        25.08        23.80        20.98        20.52        14.17 
TCGA-36-2549 TCGA-36-2552 TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 TCGA-42-2591 
        6.05        11.47        47.57        28.93        42.02        40.77 
TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1585 TCGA-57-1586 TCGA-57-1993 
        1.48        24.03        11.38         1.74        22.32        25.08 
TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2355 TCGA-59-2363 TCGA-61-1721 
       25.02       180.20        80.12         2.14         5.42        11.11 
TCGA-61-1728 TCGA-61-1736 TCGA-61-1741 TCGA-61-1895 TCGA-61-1900 TCGA-61-1910 
       27.88        48.79        33.67         1.45         5.79        37.05 
TCGA-61-1911 TCGA-61-1917 TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 
       42.51        43.43         5.52        14.50         4.01        30.64 
TCGA-61-2009 TCGA-61-2017 TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 
       39.85        45.96        51.72        61.64        58.39        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2613 TCGA-61-2614 
       55.50         6.48        76.87        20.68        31.07         8.61 
TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0369 TCGA-10-0926 
        0.79         9.99        29.16         9.47        35.57        25.91 
TCGA-10-0928 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-13-0714 TCGA-13-0720 
       18.51        14.66         6.71        35.44         6.21        44.55 
TCGA-13-0723 TCGA-13-0725 TCGA-13-0727 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 
       39.58        12.39        15.19        11.18        11.38        11.54 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0791 TCGA-13-0794 TCGA-13-0801 TCGA-13-0802 
       38.01       111.78        40.24        63.09        45.99        51.02 
TCGA-13-0803 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0893 TCGA-13-0897 
       43.86       153.37        66.67        95.15        43.36        71.74 
TCGA-13-0899 TCGA-13-0905 TCGA-13-0908 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
       66.15       123.16        60.59        44.55        37.64       109.32 
TCGA-13-0921 TCGA-13-0923 
       48.76        83.74 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.30               0.26 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            152.02             180.20 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             32.09              33.06 
[1] "0.3 - 152.0 (32.1)" "0.3 - 180.2 (33.1)"
[1] "hr=" "1.1"
D66V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  13Q LOSS MUTATED         1   294                2
  13Q LOSS WILD-TYPE       2   264                0
D66V3, multiclass
                  clus
vv                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  OMENTUM                         1                  2
  OVARY                         294                264
  PERITONEUM OVARY                2                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V4, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED   284   2
  13Q LOSS WILD-TYPE 257   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED    284    2
  13Q LOSS WILD-TYPE  257    3
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO               284                257
  YES                2                  3
[1] 2 2
[1] FALSE
D66V5, continuous
                    vv
clus                 R0 R1 R2 RX
  13Q LOSS MUTATED    4 11  2  2
  13Q LOSS WILD-TYPE 11 15  3  1
D66V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0                4                 11
  R1               11                 15
  R2                2                  3
  RX                2                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     4 176
  13Q LOSS WILD-TYPE   6 151
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4  176
  13Q LOSS WILD-TYPE    6  151
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  6
  NOT HISPANIC OR LATINO              176                151
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    79 131
  14Q LOSS WILD-TYPE 149 200
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               210                349 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               131                200 
$`14Q LOSS MUTATED`
TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1341 
       20.52        11.87        41.00         1.81         2.01         1.08 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 
       11.87        65.52        65.46         0.53        49.28        32.52 
TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 
       44.32        33.67        76.57        38.37       119.08        84.20 
TCGA-04-1638 TCGA-04-1648 TCGA-04-1649 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 
       55.43        28.64        64.64        45.37         9.99        38.43 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-2048 TCGA-09-2051 TCGA-09-2053 
       17.98         5.85         3.02         4.54        63.09        39.75 
TCGA-09-2056 TCGA-13-1405 TCGA-13-1407 TCGA-13-1411 TCGA-13-1481 TCGA-13-1487 
       12.46        28.54        83.31        17.46        87.06        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1496 TCGA-13-1497 TCGA-13-1499 
       70.82        83.93        52.44         4.24       127.27       115.07 
TCGA-13-1504 TCGA-13-1507 TCGA-13-1510 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FU 
       34.82        65.52        44.68        76.90        65.52         8.42 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1687 TCGA-23-1024 TCGA-23-1027 TCGA-23-1028 
       25.38        19.10         2.66        15.39        32.09        49.41 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 
       29.13        18.90        51.35        54.51         3.22        68.68 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1122 TCGA-23-1123 TCGA-23-2072 
       33.30        86.01       129.96        39.09        33.47        24.95 
TCGA-23-2077 TCGA-23-2081 TCGA-23-2643 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
      115.89        77.00         4.70        11.64        21.80        41.56 
TCGA-24-0982 TCGA-24-1105 TCGA-24-1424 TCGA-24-1427 TCGA-24-1434 TCGA-24-1436 
       22.32        47.41         6.02         4.83        18.67         8.55 
TCGA-24-1463 TCGA-24-1466 TCGA-24-1469 TCGA-24-1471 TCGA-24-1544 TCGA-24-1546 
       72.92        45.14         9.11         1.18        26.96        64.27 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 TCGA-24-1564 TCGA-24-1565 
       16.21        56.58        51.91        41.39        25.87        10.26 
TCGA-24-1604 TCGA-24-1843 TCGA-24-1846 TCGA-24-1924 TCGA-24-2019 TCGA-24-2020 
       88.37         3.48         4.37        30.21         4.87       152.02 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2029 TCGA-24-2260 TCGA-24-2267 
       44.84        58.16        34.82        14.43        36.16        47.54 
TCGA-24-2280 TCGA-24-2288 TCGA-24-2295 TCGA-25-1320 TCGA-25-1321 TCGA-25-1323 
       70.45         0.82        33.11        37.97        33.96        12.99 
TCGA-25-1626 TCGA-25-1631 TCGA-25-1632 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 
       17.03         0.30        59.15        35.87        52.04        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-2391 TCGA-25-2393 TCGA-25-2400 TCGA-25-2404 
       24.99        24.00        49.05        38.04        42.02        29.03 
TCGA-29-1693 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1707 TCGA-29-1710 
      101.79        40.41        31.20        68.32        41.98        31.27 
TCGA-29-1761 TCGA-29-1763 TCGA-29-1766 TCGA-29-1769 TCGA-29-1771 TCGA-29-1775 
       17.36        66.81        39.42        22.98        22.55        12.36 
TCGA-29-1777 TCGA-29-2425 TCGA-29-2427 TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1718 
       12.30        65.00        62.47        11.47        35.77        51.91 
TCGA-30-1855 TCGA-30-1859 TCGA-30-1861 TCGA-30-1887 TCGA-31-1944 TCGA-31-1950 
        2.47        48.10        34.78        24.26        45.57        18.77 
TCGA-31-1951 TCGA-31-1953 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 
       22.49         6.71        22.85        22.55         8.55        30.08 
TCGA-36-2534 TCGA-36-2543 TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 TCGA-42-2589 
       29.82         2.24        16.18        11.47        23.74        42.02 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2372 
       40.77         1.48        29.00        25.08        25.02        44.81 
TCGA-61-1728 TCGA-61-1733 TCGA-61-1736 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 
       27.88        31.79        48.79         2.43        33.67        43.69 
TCGA-61-1901 TCGA-61-1904 TCGA-61-1906 TCGA-61-1917 TCGA-61-2000 TCGA-61-2009 
       11.41         9.07        34.13        43.43        14.50        39.85 
TCGA-61-2088 TCGA-61-2102 TCGA-61-2109 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
        4.77         6.48        20.68         8.61        39.68        18.94 
TCGA-09-0369 TCGA-10-0925 TCGA-10-0926 TCGA-10-0928 TCGA-10-0938 TCGA-13-0717 
       35.57        54.31        25.91        18.51        20.91        24.59 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
       39.58         2.73        31.20        15.19        17.82        55.17 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0766 TCGA-13-0792 
       11.18        11.38        11.54        38.01        56.71       118.42 
TCGA-13-0794 TCGA-13-0803 TCGA-13-0884 TCGA-13-0885 TCGA-13-0888 TCGA-13-0891 
       63.09        43.86       107.18       111.39        92.42       102.84 
TCGA-13-0906 TCGA-13-0913 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-2071 
      118.98       109.32        84.53        48.79        48.76        25.41 

$`14Q LOSS WILD-TYPE`
TCGA-3P-A9WA TCGA-04-1331 TCGA-04-1336 TCGA-04-1338 TCGA-04-1342 TCGA-04-1347 
       13.81        43.92        49.15        46.62        18.51        63.09 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 
       48.76        21.57        63.98       103.40        82.39        56.55 
TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1536 TCGA-04-1644 TCGA-04-1646 
       41.59        19.99         0.79        29.10        48.89        27.88 
TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       36.23        31.86        47.70        89.33        74.93        41.62 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1674 TCGA-09-1675 
       57.60        61.87        55.36        30.51         8.55        97.55 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2054 
        6.18         6.12        35.15       112.41        71.11        20.94 
TCGA-09-2055 TCGA-13-1403 TCGA-13-1404 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
       26.93        77.10        81.17        55.23        57.27        81.01 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 
       32.35        54.64        61.71        29.42       124.44        20.68 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 
      125.56        93.90        90.38        66.15        13.97        43.20 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 
       65.69        34.16        80.15        54.25        14.53        80.02 
TCGA-13-2059 TCGA-13-2060 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
       78.48        77.88        70.45        23.05        25.94        26.20 
TCGA-20-0996 TCGA-20-1682 TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 TCGA-23-1022 
       72.20        27.52        16.70         2.93        47.54        49.68 
TCGA-23-1023 TCGA-23-1026 TCGA-23-1029 TCGA-23-1032 TCGA-23-1113 TCGA-23-1116 
       40.54        26.83         8.81         2.76        31.20        19.46 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1124 TCGA-23-1809 TCGA-23-2078 TCGA-23-2079 
        4.27         6.38        58.13         0.53        87.48        91.66 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2645 TCGA-24-0966 TCGA-24-0980 TCGA-24-1103 
       49.84         2.76         4.50         7.63         7.66        54.12 
TCGA-24-1104 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       63.55         6.31         6.38         7.82         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 
        0.76         6.25         5.95         5.36        17.39        28.37 
TCGA-24-1431 TCGA-24-1435 TCGA-24-1464 TCGA-24-1467 TCGA-24-1470 TCGA-24-1474 
       18.64        43.53        12.46       105.99         3.45        22.22 
TCGA-24-1545 TCGA-24-1550 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       57.40        41.06        58.09        88.50        70.62        39.88 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1567 TCGA-24-1603 
       19.53        44.09        45.50        47.70        17.23        90.15 
TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 
       48.33        38.24         8.32         3.72         3.81        11.28 
TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1927 TCGA-24-1928 
        5.79         5.52         9.80        22.68        16.44        11.05 
TCGA-24-1930 TCGA-24-2027 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 
       81.11       109.71        55.92        18.48        28.18        64.01 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2261 TCGA-24-2262 TCGA-24-2271 TCGA-24-2281 
       44.52        57.07         0.79         0.36        31.63        44.61 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 
       67.36        36.23        16.64        55.86        53.26         1.02 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
       26.96        33.01        52.04        42.05         2.01        34.98 
TCGA-25-1319 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1627 
       65.00         2.99        15.02        18.58        27.62        12.95 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1633 TCGA-25-1878 TCGA-25-2042 TCGA-25-2392 
       20.61        38.20        62.17        85.05        13.02         1.02 
TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2401 TCGA-25-2408 
        3.02        12.00        45.01        19.99         2.96        31.00 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1694 TCGA-29-1696 
       26.99        78.90        47.61        48.33        39.02        33.93 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1711 
       36.36        16.93        23.93        59.67        18.25        34.62 
TCGA-29-1762 TCGA-29-1764 TCGA-29-1768 TCGA-29-1770 TCGA-29-1774 TCGA-29-1776 
       86.60        62.93        31.30        24.36        17.33        11.84 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 
       14.93         8.38         7.23         5.36        36.30        86.17 
TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2436 TCGA-30-1714 
       45.11        13.84        42.25        21.47         9.76        38.07 
TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 
       36.26        15.68         0.26        44.91         6.12        36.62 
TCGA-30-1867 TCGA-30-1880 TCGA-30-1891 TCGA-30-1892 TCGA-31-1946 TCGA-31-1955 
        1.22        57.57        30.05        48.79        30.18        42.51 
TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1577 
       44.12         2.20        28.77        29.10        21.53        25.74 
TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 
       27.85        24.23        24.69        35.05        33.01        29.49 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 
       25.91        25.08        23.80        21.60        20.98        18.31 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-42-2582 TCGA-42-2588 TCGA-42-2590 
       20.52        14.17         6.05        47.57        28.93        10.42 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-59-2348 
       24.03        11.38        21.14         1.74        22.32       180.20 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 
       80.12        22.32       116.12         9.40        34.39         2.14 
TCGA-59-2363 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
        5.42        11.11         8.09        20.94        31.43        18.54 
TCGA-61-1730 TCGA-61-1734 TCGA-61-1737 TCGA-61-1738 TCGA-61-1895 TCGA-61-1899 
        4.34        28.47        44.84        35.80         1.45         8.42 
TCGA-61-1900 TCGA-61-1903 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 
        5.79        13.02        31.30        37.05        42.51        48.92 
TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
       56.61        67.76        15.75        38.17         2.01         5.52 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 
       17.98         4.01        30.64        30.64         1.18        45.96 
TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 
       45.40         4.80        51.72        71.74        61.64        58.39 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 
       60.62        65.52        55.50        76.87        44.52       125.75 
TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 
       22.22         6.35        31.07         0.79         9.99        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 
        9.47        57.76        17.98        81.86        34.19        32.88 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-13-0714 
       14.66         6.71        35.44        36.92        19.99         6.21 
TCGA-13-0720 TCGA-13-0725 TCGA-13-0755 TCGA-13-0762 TCGA-13-0764 TCGA-13-0768 
       44.55        12.39         2.50       111.78        61.84        58.65 
TCGA-13-0791 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 
       40.24       107.28        20.35        69.73        83.34        87.48 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
       45.99        51.02        35.28        35.31        13.61        68.94 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 
      153.37        66.67        95.15       145.45        43.36        71.74 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       66.15       134.04        19.36       127.79        50.37       123.16 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 TCGA-13-0923 
       60.59       116.65        44.55        37.64        58.68        83.74 
TCGA-13-0924 
       85.94 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.30               0.26 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            152.02             180.20 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            32.815             32.880 
[1] "0.3 - 152.0 (32.8)" "0.3 - 180.2 (32.9)"
[1] "hr=" "1.1"
D67V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  14Q LOSS MUTATED         1   210                1
  14Q LOSS WILD-TYPE       2   348                1
D67V3, multiclass
                  clus
vv                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  OMENTUM                         1                  2
  OVARY                         210                348
  PERITONEUM OVARY                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V4, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   205   2
  14Q LOSS WILD-TYPE 336   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    205    2
  14Q LOSS WILD-TYPE  336    3
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO               205                336
  YES                2                  3
[1] 2 2
[1] FALSE
D67V5, continuous
                    vv
clus                 R0 R1 R2 RX
  14Q LOSS MUTATED    6  7  3  1
  14Q LOSS WILD-TYPE  9 19  2  2
D67V6, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0                6                  9
  R1                7                 19
  R2                3                  2
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     6 124
  14Q LOSS WILD-TYPE   4 203
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      6  124
  14Q LOSS WILD-TYPE    4  203
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                  4
  NOT HISPANIC OR LATINO              124                203
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    98 172
  15Q LOSS WILD-TYPE 130 159
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               270                289 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               172                159 
$`15Q LOSS MUTATED`
TCGA-04-1331 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1347 TCGA-04-1350 
       43.92        46.62         1.08        18.51        63.09        63.98 
TCGA-04-1356 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 TCGA-04-1519 
       49.28       103.40        82.39        56.55        19.99         0.79 
TCGA-04-1525 TCGA-04-1536 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1652 
       38.37        29.10        27.88        28.64        64.64        31.86 
TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 
       45.37         9.99        38.43        61.87        55.36        30.51 
TCGA-09-1670 TCGA-09-1674 TCGA-09-2050 TCGA-09-2051 TCGA-09-2054 TCGA-13-1405 
       17.98         8.55        71.11        63.09        20.94        28.54 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1482 
       83.31        55.23        57.27        81.01        17.46        61.71 
TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 
      124.44        22.39        70.82        83.93        52.44        93.90 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
       90.38         4.24        34.82        65.69        34.16        65.52 
TCGA-13-1510 TCGA-13-2057 TCGA-13-2061 TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 
       44.68        80.02        76.90         8.42        25.94        26.20 
TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1686 TCGA-23-1022 TCGA-23-1030 
       27.52        25.38        19.10         2.93        49.68        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 
       18.90         2.76        51.35        54.51        31.20        68.68 
TCGA-23-1116 TCGA-23-1123 TCGA-23-2077 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 
       19.46        33.47       115.89        49.84         2.76         4.70 
TCGA-23-2645 TCGA-24-0979 TCGA-24-0982 TCGA-24-1104 TCGA-24-1105 TCGA-24-1417 
        4.50        41.56        22.32        63.55        47.41         7.82 
TCGA-24-1418 TCGA-24-1422 TCGA-24-1424 TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 
        7.99         0.76         6.02         5.36        17.39        28.37 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 TCGA-24-1469 
       18.64        18.67         8.55        72.92        45.14         9.11 
TCGA-24-1471 TCGA-24-1544 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1552 
        1.18        26.96        16.21        56.58        41.06        41.39 
TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 TCGA-24-1564 TCGA-24-1603 TCGA-24-1614 
       58.09        70.62        39.88        25.87        90.15        48.33 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1850 
       38.24         8.32         3.48         3.72         3.81         5.52 
TCGA-24-1920 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 TCGA-24-2020 
        9.80        30.21        16.44        11.05         4.87       152.02 
TCGA-24-2026 TCGA-24-2030 TCGA-24-2036 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 
       34.82        55.92        64.01        57.07        36.16         0.79 
TCGA-24-2280 TCGA-24-2288 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 
       70.45         0.82        16.64        33.11        55.86        53.26 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1316 TCGA-25-1318 TCGA-25-1319 
        1.02        26.96        33.01        42.05        34.98        65.00 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
       37.97        33.96         2.99        12.99        15.02        18.58 
TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1871 
       20.61         0.30        59.15        62.17        35.87        24.99 
TCGA-25-1877 TCGA-25-2396 TCGA-25-2397 TCGA-25-2404 TCGA-29-1693 TCGA-29-1695 
       24.00         3.02        12.00        29.03       101.79        40.41 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 TCGA-29-1710 
       68.32        36.36        23.93        59.67        41.98        31.27 
TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 
       34.62        17.36        86.60        66.81        62.93        39.42 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1774 TCGA-29-1777 TCGA-29-1783 TCGA-29-1784 
       22.98        24.36        17.33        12.30         7.23         5.36 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 TCGA-29-2432 TCGA-29-2434 
       86.17        65.00        45.11        13.84        21.47        11.47 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 TCGA-30-1860 
       38.07        51.91         2.47        15.68        48.10        44.91 
TCGA-30-1866 TCGA-30-1867 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1950 
       36.62         1.22        24.26        30.05        48.79        18.77 
TCGA-31-1953 TCGA-36-1581 TCGA-36-2529 TCGA-36-2543 TCGA-36-2545 TCGA-36-2548 
        6.71        24.69        35.05         2.24        18.31        14.17 
TCGA-36-2551 TCGA-36-2552 TCGA-42-2589 TCGA-42-2593 TCGA-57-1583 TCGA-57-1586 
       16.18        11.47        42.02         1.48        11.38        22.32 
TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-61-1724 TCGA-61-1727 
       25.08       180.20        22.32       116.12        20.94        18.54 
TCGA-61-1728 TCGA-61-1733 TCGA-61-1734 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 
       27.88        31.79        28.47        44.84        35.80         2.43 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1901 TCGA-61-1904 TCGA-61-1906 TCGA-61-1914 
       33.67        43.69        11.41         9.07        34.13        56.61 
TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 
       43.43        15.75        38.17         4.01        30.64        30.64 
TCGA-61-2016 TCGA-61-2092 TCGA-61-2094 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 
        1.18        51.72        71.74        58.39        60.62        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
       55.50         6.48        76.87        44.52       125.75        22.22 
TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-09-0364 TCGA-09-0365 
        6.35         8.61        39.68        18.94        29.16         9.47 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0936 TCGA-13-0717 TCGA-13-0723 
       54.31        25.91        81.86        36.92        24.59        39.58 
TCGA-13-0724 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 
        2.73        17.82        55.17        11.18        11.38        11.54 
TCGA-13-0762 TCGA-13-0793 TCGA-13-0794 TCGA-13-0802 TCGA-13-0803 TCGA-13-0807 
      111.78       107.28        63.09        51.02        43.86        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 
       68.94       107.18       111.39        66.67        92.42        95.15 
TCGA-13-0891 TCGA-13-0899 TCGA-13-0910 TCGA-13-0911 TCGA-13-0921 TCGA-13-0923 
      102.84        66.15       116.65        44.55        48.76        83.74 

$`15Q LOSS WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 
       13.81        20.52        11.87        41.00         1.81        49.15 
TCGA-04-1337 TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 TCGA-04-1349 TCGA-04-1351 
        2.01        11.87        65.52        48.76        21.57        65.46 
TCGA-04-1353 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1516 
        0.53        32.52        44.32        33.67        76.57        41.59 
TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1651 TCGA-04-1654 
      119.08        84.20        55.43        48.89        36.23        47.70 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1672 TCGA-09-1673 
       89.33        74.93        41.62        57.60         5.85         3.02 
TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 
       97.55         6.18         6.12        35.15         4.54       112.41 
TCGA-09-2053 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1412 
       39.75        26.93        12.46        77.10        81.17        32.35 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1483 TCGA-13-1485 TCGA-13-1492 TCGA-13-1497 
       54.64        87.06        29.42        20.68       125.56       127.27 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1509 TCGA-13-1511 
       66.15       115.07        13.97        43.20        80.15        54.25 
TCGA-13-1512 TCGA-13-2059 TCGA-13-2060 TCGA-13-2065 TCGA-13-A5FT TCGA-20-0987 
       14.53        78.48        77.88        65.52        70.45        23.05 
TCGA-20-0996 TCGA-20-1685 TCGA-20-1687 TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 
       72.20        16.70         2.66        47.54        40.54        15.39 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1111 TCGA-23-1117 
       26.83        32.09        49.41         8.81         3.22        33.30 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1124 
       86.01       129.96         4.27         6.38        39.09        58.13 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-24-0966 
        0.53        24.95        87.48        91.66        77.00         7.63 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-1103 TCGA-24-1413 TCGA-24-1416 
       11.64        21.80         7.66        54.12         6.31         6.38 
TCGA-24-1419 TCGA-24-1423 TCGA-24-1425 TCGA-24-1427 TCGA-24-1435 TCGA-24-1464 
        7.86         6.25         5.95         4.83        43.53        12.46 
TCGA-24-1467 TCGA-24-1470 TCGA-24-1474 TCGA-24-1545 TCGA-24-1546 TCGA-24-1551 
      105.99         3.45        22.22        57.40        64.27        51.91 
TCGA-24-1555 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1565 
       88.50        19.53        44.09        45.50        47.70        10.26 
TCGA-24-1567 TCGA-24-1604 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1923 
       17.23        88.37         4.37        11.28         5.79        22.68 
TCGA-24-1930 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 
       81.11        44.84        58.16       109.71        14.43        18.48 
TCGA-24-2035 TCGA-24-2038 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 
       28.18        44.52         0.36        47.54        31.63        44.61 
TCGA-24-2289 TCGA-24-2290 TCGA-25-1315 TCGA-25-1317 TCGA-25-1625 TCGA-25-1626 
       67.36        36.23        52.04         2.01        27.62        17.03 
TCGA-25-1627 TCGA-25-1630 TCGA-25-1635 TCGA-25-1870 TCGA-25-1878 TCGA-25-2042 
       12.95        38.20        52.04        14.96        85.05        13.02 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 
       49.05         1.02        38.04        45.01        19.99        42.02 
TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 
        2.96        31.00        26.99        78.90        47.61        48.33 
TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1701 TCGA-29-1705 TCGA-29-1768 
       39.02        33.93        31.20        16.93        18.25        31.30 
TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 TCGA-29-1778 TCGA-29-1781 TCGA-29-1785 
       22.55        12.36        11.84        14.93         8.38        36.30 
TCGA-29-2427 TCGA-29-2431 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1853 TCGA-30-1857 
       62.47        42.25         9.76        35.77        36.26         0.26 
TCGA-30-1861 TCGA-30-1862 TCGA-30-1880 TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 
       34.78         6.12        57.57        45.57        30.18        22.49 
TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
       42.51        44.12         2.20        28.77        29.10        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 
       22.85        22.55         8.55        30.08        25.74        27.85 
TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
       24.23        33.01        29.49        29.82        25.91        25.08 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-36-2547 TCGA-36-2549 TCGA-42-2582 
       23.80        21.60        20.98        20.52         6.05        47.57 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 TCGA-57-1584 
       23.74        28.93        10.42        40.77        24.03        21.14 
TCGA-57-1585 TCGA-57-1992 TCGA-57-1994 TCGA-59-2349 TCGA-59-2352 TCGA-59-2354 
        1.74        29.00        25.02        80.12         9.40        34.39 
TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1725 
        2.14         5.42        44.81        11.11         8.09        31.43 
TCGA-61-1730 TCGA-61-1736 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1903 
        4.34        48.79         1.45         8.42         5.79        13.02 
TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1915 TCGA-61-1995 
       31.30        37.05        42.51        48.92        67.76         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2009 TCGA-61-2017 TCGA-61-2018 
        5.52        14.50        17.98        39.85        45.96        45.40 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2095 TCGA-61-2109 TCGA-61-2613 TCGA-VG-A8LO 
        4.80         4.77        61.64        20.68        31.07         0.79 
TCGA-WR-A838 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-10-0928 TCGA-10-0930 
        9.99        57.76        17.98        35.57        18.51        34.19 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 
       32.88        14.66         6.71        35.44        19.99        20.91 
TCGA-13-0714 TCGA-13-0720 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0755 
        6.21        44.55        12.39        31.20        15.19         2.50 
TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 
       38.01        61.84        56.71        58.65        40.24       118.42 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0804 
       20.35        69.73        83.34        87.48        45.99        35.28 
TCGA-13-0805 TCGA-13-0886 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 
       35.31       153.37       145.45        43.36        71.74       134.04 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 
       19.36       127.79        50.37       123.16       118.98        60.59 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0924 
       37.64       109.32        58.68        84.53        48.79        85.94 
TCGA-13-2071 
       25.41 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.30               0.26 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            180.20             153.37 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             33.57              32.09 
[1] "0.3 - 180.2 (33.6)" "0.3 - 153.4 (32.1)"
[1] "hr=" "1.1"
D68V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  15Q LOSS MUTATED         1   269                2
  15Q LOSS WILD-TYPE       2   289                0
D68V3, multiclass
                  clus
vv                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  OMENTUM                         1                  2
  OVARY                         269                289
  PERITONEUM OVARY                2                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V4, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   260   2
  15Q LOSS WILD-TYPE 281   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    260    2
  15Q LOSS WILD-TYPE  281    3
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO               260                281
  YES                2                  3
[1] 2 2
[1] FALSE
D68V5, continuous
                    vv
clus                 R0 R1 R2 RX
  15Q LOSS MUTATED    5 13  3  1
  15Q LOSS WILD-TYPE 10 13  2  2
D68V6, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0                5                 10
  R1               13                 13
  R2                3                  2
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     6 152
  15Q LOSS WILD-TYPE   4 175
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      6  152
  15Q LOSS WILD-TYPE    4  175
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                  4
  NOT HISPANIC OR LATINO              152                175
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED   124 200
  16P LOSS WILD-TYPE 104 131
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               324                235 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               200                131 
$`16P LOSS MUTATED`
TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1337 TCGA-04-1338 
       20.52        11.87        43.92        41.00         2.01        46.62 
TCGA-04-1341 TCGA-04-1343 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 
        1.08        11.87        63.09        21.57        63.98        49.28 
TCGA-04-1362 TCGA-04-1364 TCGA-04-1367 TCGA-04-1516 TCGA-04-1517 TCGA-04-1530 
       44.32        33.67       103.40        41.59        19.99       119.08 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1649 TCGA-04-1652 TCGA-09-1659 TCGA-09-1665 
       55.43        48.89        64.64        31.86         9.99        41.62 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 
       57.60        61.87        55.36        30.51        17.98         3.02 
TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2049 TCGA-09-2053 TCGA-09-2054 
       97.55         6.18         6.12       112.41        39.75        20.94 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 
       77.10        81.17        28.54        83.31        55.23        81.01 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 TCGA-13-1484 TCGA-13-1488 TCGA-13-1489 
       17.46        32.35        87.06       124.44        70.82        83.93 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 
       52.44       125.56        93.90        90.38         4.24       127.27 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
      115.07        13.97        65.69        34.16        65.52        80.15 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT 
       54.25        14.53        80.02        76.90        65.52        70.45 
TCGA-20-0990 TCGA-20-1683 TCGA-20-1687 TCGA-23-1022 TCGA-23-1024 TCGA-23-1027 
       25.94        25.38         2.66        49.68        15.39        32.09 
TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1111 
       49.41        29.13        18.90         2.76        51.35         3.22 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 
       31.20        68.68        19.46        33.30        86.01       129.96 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-2072 TCGA-23-2078 
        4.27         6.38        39.09        33.47        24.95        87.48 
TCGA-23-2645 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-1104 TCGA-24-1105 
        4.50        11.64        21.80        41.56        63.55        47.41 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1426 
        6.38         7.82         7.99         7.86         0.76         5.36 
TCGA-24-1428 TCGA-24-1431 TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 TCGA-24-1469 
       17.39        18.64         8.55        72.92        45.14         9.11 
TCGA-24-1471 TCGA-24-1474 TCGA-24-1545 TCGA-24-1548 TCGA-24-1552 TCGA-24-1555 
        1.18        22.22        57.40        16.21        41.39        88.50 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1567 
       19.53        44.09        45.50        47.70        25.87        17.23 
TCGA-24-1603 TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 TCGA-24-1850 
       90.15         3.48         3.72         4.37        11.28         5.52 
TCGA-24-1923 TCGA-24-1924 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 
       22.68        30.21        11.05        81.11         4.87       152.02 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2035 
       44.84        58.16        34.82       109.71        14.43        28.18 
TCGA-24-2036 TCGA-24-2260 TCGA-24-2262 TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 
       64.01        36.16         0.36        47.54        70.45        44.61 
TCGA-24-2288 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 
        0.82        36.23        16.64        33.11        55.86        53.26 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
       26.96        33.01        52.04        42.05         2.01        34.98 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1626 
       65.00        37.97         2.99        12.99        15.02        17.03 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1635 TCGA-25-1870 
       12.95        20.61         0.30        59.15        52.04        14.96 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 
       13.02        49.05         1.02        38.04         3.02        12.00 
TCGA-25-2398 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2409 TCGA-29-1688 
       45.01        42.02         2.96        29.03        26.99        78.90 
TCGA-29-1693 TCGA-29-1697 TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 
      101.79        31.20        36.36        16.93        59.67        18.25 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 
       17.36        86.60        62.93        39.42        22.98        24.36 
TCGA-29-1771 TCGA-29-1775 TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 TCGA-29-1785 
       22.55        12.36        12.30         8.38         7.23        36.30 
TCGA-29-2425 TCGA-29-2428 TCGA-29-2431 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 
       65.00        45.11        42.25        38.07        51.91        36.26 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1860 TCGA-30-1861 TCGA-30-1866 
        2.47        15.68         0.26        44.91        34.78        36.62 
TCGA-30-1867 TCGA-30-1887 TCGA-31-1944 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 
        1.22        24.26        45.57        18.77        22.49         6.71 
TCGA-31-1955 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 
       42.51         2.20        28.77        29.10        21.53        22.85 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-2532 TCGA-36-2534 
        8.55        30.08        25.74        27.85        29.49        29.82 
TCGA-36-2543 TCGA-36-2548 TCGA-36-2551 TCGA-42-2589 TCGA-42-2590 TCGA-42-2593 
        2.24        14.17        16.18        42.02        10.42         1.48 
TCGA-57-1582 TCGA-57-1584 TCGA-57-1992 TCGA-57-1993 TCGA-59-2350 TCGA-59-2351 
       24.03        21.14        29.00        25.08        22.32       116.12 
TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 TCGA-61-1722 TCGA-61-1725 TCGA-61-1730 
        9.40         2.14         5.42         8.09        31.43         4.34 
TCGA-61-1736 TCGA-61-1737 TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 TCGA-61-1904 
       48.79        44.84        33.67         1.45         8.42         9.07 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1914 TCGA-61-1919 TCGA-61-1995 
       34.13        31.30        37.05        56.61        38.17         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 TCGA-61-2088 
        5.52        14.50         4.01        30.64        30.64         4.77 
TCGA-61-2094 TCGA-61-2097 TCGA-61-2098 TCGA-61-2102 TCGA-61-2109 TCGA-61-2113 
       71.74        60.62        65.52         6.48        20.68        22.22 
TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-VG-A8LO TCGA-WR-A838 
        6.35        31.07         8.61        39.68         0.79         9.99 
TCGA-09-0367 TCGA-10-0925 TCGA-10-0926 TCGA-10-0928 TCGA-10-0935 TCGA-10-0937 
       17.98        54.31        25.91        18.51        35.44        19.99 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0727 
       20.91         6.21        24.59        44.55        39.58        15.19 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 
       17.82        55.17        11.18        11.38        11.54        38.01 
TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0793 TCGA-13-0794 
      111.78        61.84        56.71        40.24       107.28        63.09 
TCGA-13-0795 TCGA-13-0801 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
       20.35        45.99        35.31        13.61        68.94       107.18 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0891 TCGA-13-0893 
      111.39       153.37        66.67        92.42       102.84        43.36 
TCGA-13-0899 TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
       66.15       127.79        50.37       118.98        60.59       116.65 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 
       44.55        37.64        58.68        84.53        48.79        83.74 

$`16P LOSS WILD-TYPE`
TCGA-3P-A9WA TCGA-04-1335 TCGA-04-1336 TCGA-04-1342 TCGA-04-1346 TCGA-04-1348 
       13.81         1.81        49.15        18.51        65.52        48.76 
TCGA-04-1351 TCGA-04-1353 TCGA-04-1361 TCGA-04-1365 TCGA-04-1371 TCGA-04-1514 
       65.46         0.53        32.52        76.57        82.39        56.55 
TCGA-04-1519 TCGA-04-1525 TCGA-04-1536 TCGA-04-1542 TCGA-04-1646 TCGA-04-1648 
        0.79        38.37        29.10        84.20        27.88        28.64 
TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       36.23        47.70        45.37        38.43        89.33        74.93 
TCGA-09-1672 TCGA-09-1674 TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 TCGA-09-2051 
        5.85         8.55        35.15         4.54        71.11        63.09 
TCGA-09-2055 TCGA-09-2056 TCGA-13-1409 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 
       26.93        12.46        57.27        54.64        61.71        29.42 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1498 TCGA-13-1501 TCGA-13-1504 TCGA-13-1510 
       20.68        22.39        66.15        43.20        34.82        44.68 
TCGA-13-2059 TCGA-13-2060 TCGA-13-A5FU TCGA-20-0987 TCGA-20-0991 TCGA-20-0996 
       78.48        77.88         8.42        23.05        26.20        72.20 
TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 TCGA-23-1023 
       27.52        19.10        16.70         2.93        47.54        40.54 
TCGA-23-1026 TCGA-23-1029 TCGA-23-1110 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 
       26.83         8.81        54.51        58.13         0.53       115.89 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-24-0966 
       91.66        77.00        49.84         2.76         4.70         7.63 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1413 TCGA-24-1423 TCGA-24-1424 
        7.66        22.32        54.12         6.31         6.25         6.02 
TCGA-24-1425 TCGA-24-1427 TCGA-24-1430 TCGA-24-1434 TCGA-24-1435 TCGA-24-1464 
        5.95         4.83        28.37        18.67        43.53        12.46 
TCGA-24-1467 TCGA-24-1470 TCGA-24-1544 TCGA-24-1546 TCGA-24-1549 TCGA-24-1550 
      105.99         3.45        26.96        64.27        56.58        41.06 
TCGA-24-1551 TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 TCGA-24-1565 TCGA-24-1604 
       51.91        58.09        70.62        39.88        10.26        88.37 
TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1845 TCGA-24-1849 TCGA-24-1920 
       48.33        38.24         8.32         3.81         5.79         9.80 
TCGA-24-1927 TCGA-24-2030 TCGA-24-2033 TCGA-24-2038 TCGA-24-2254 TCGA-24-2261 
       16.44        55.92        18.48        44.52        57.07         0.79 
TCGA-24-2271 TCGA-24-2289 TCGA-25-1312 TCGA-25-1321 TCGA-25-1623 TCGA-25-1625 
       31.63        67.36         1.02        33.96        18.58        27.62 
TCGA-25-1630 TCGA-25-1633 TCGA-25-1634 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 
       38.20        62.17        35.87        24.99        24.00        85.05 
TCGA-25-2399 TCGA-25-2408 TCGA-29-1690 TCGA-29-1691 TCGA-29-1694 TCGA-29-1695 
       19.99        31.00        47.61        48.33        39.02        40.41 
TCGA-29-1696 TCGA-29-1698 TCGA-29-1702 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 
       33.93        68.32        23.93        41.98        31.27        34.62 
TCGA-29-1763 TCGA-29-1768 TCGA-29-1774 TCGA-29-1776 TCGA-29-1778 TCGA-29-1784 
       66.81        31.30        17.33        11.84        14.93         5.36 
TCGA-29-2414 TCGA-29-2427 TCGA-29-2429 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 
       86.17        62.47        13.84        21.47        11.47         9.76 
TCGA-29-A5NZ TCGA-30-1859 TCGA-30-1862 TCGA-30-1880 TCGA-30-1891 TCGA-30-1892 
       35.77        48.10         6.12        57.57        30.05        48.79 
TCGA-31-1946 TCGA-31-1956 TCGA-36-1574 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 
       30.18        44.12        22.55        24.23        24.69        35.05 
TCGA-36-2530 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 
       33.01        25.91        25.08        23.80        21.60        20.98 
TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 
       18.31        20.52         6.05        11.47        47.57        23.74 
TCGA-42-2588 TCGA-42-2591 TCGA-57-1583 TCGA-57-1585 TCGA-57-1586 TCGA-57-1994 
       28.93        40.77        11.38         1.74        22.32        25.02 
TCGA-59-2348 TCGA-59-2349 TCGA-59-2354 TCGA-59-2372 TCGA-61-1721 TCGA-61-1724 
      180.20        80.12        34.39        44.81        11.11        20.94 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 TCGA-61-1734 TCGA-61-1738 TCGA-61-1740 
       18.54        27.88        31.79        28.47        35.80         2.43 
TCGA-61-1743 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1911 TCGA-61-1913 
       43.69         5.79        11.41        13.02        42.51        48.92 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-2002 TCGA-61-2009 TCGA-61-2016 
       67.76        43.43        15.75        17.98        39.85         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 
       45.96        45.40         4.80        51.72        61.64        58.39 
TCGA-61-2101 TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 TCGA-OY-A56Q TCGA-09-0364 
       55.50        76.87        44.52       125.75        18.94        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0369 TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 
        9.47        57.76        35.57        81.86        34.19        32.88 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0936 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 
       14.66         6.71        36.92         2.73        12.39        31.20 
TCGA-13-0755 TCGA-13-0768 TCGA-13-0792 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 
        2.50        58.65       118.42        69.73        83.34        87.48 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0889 TCGA-13-0890 TCGA-13-0897 
       51.02        43.86        35.28        95.15       145.45        71.74 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0905 TCGA-13-0913 TCGA-13-0921 TCGA-13-0924 
      134.04        19.36       123.16       109.32        48.76        85.94 
TCGA-13-2071 
       25.41 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.26               0.53 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            153.37             180.20 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            31.975             33.930 
[1] "0.3 - 153.4 (32.0)" "0.5 - 180.2 (33.9)"
[1] "hr=" "1.1"
D69V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  16P LOSS MUTATED         2   322                1
  16P LOSS WILD-TYPE       1   236                1
D69V3, multiclass
                  clus
vv                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  OMENTUM                         2                  1
  OVARY                         322                236
  PERITONEUM OVARY                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V4, binary
                    cls
clus                   0   1
  16P LOSS MUTATED   311   5
  16P LOSS WILD-TYPE 230   0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED    311    5
  16P LOSS WILD-TYPE  230    0
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO               311                230
  YES                5                  0
[1] 2 2
[1] FALSE
D69V5, continuous
                    vv
clus                 R0 R1 R2 RX
  16P LOSS MUTATED    7 13  3  1
  16P LOSS WILD-TYPE  8 13  2  2
D69V6, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0                7                  8
  R1               13                 13
  R2                3                  2
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     3 197
  16P LOSS WILD-TYPE   7 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3  197
  16P LOSS WILD-TYPE    7  130
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  7
  NOT HISPANIC OR LATINO              197                130
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED   154 245
  16Q LOSS WILD-TYPE  74  86
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               399                160 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               245                 86 
$`16Q LOSS MUTATED`
TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 
       20.52        11.87        43.92        41.00        49.15         2.01 
TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 
       46.62         1.08        18.51        11.87        65.52        63.09 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
       21.57        63.98        49.28        44.32        33.67        76.57 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 
      103.40        82.39        41.59        19.99        38.37       119.08 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1649 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 
       55.43        48.89        64.64        31.86        47.70        45.37 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 
        9.99        38.43        89.33        41.62        57.60        61.87 
TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 
       55.36        30.51        17.98         8.55        97.55         6.18 
TCGA-09-2044 TCGA-09-2048 TCGA-09-2049 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 
        6.12         4.54       112.41        63.09        39.75        20.94 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 
       77.10        81.17        28.54        83.31        55.23        81.01 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 
       17.46        32.35        87.06        29.42       124.44        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       70.82        83.93        52.44       125.56        93.90        90.38 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1505 
        4.24       127.27        66.15       115.07        13.97        65.69 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 
       34.16        65.52        80.15        54.25        14.53        80.02 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
       77.88        76.90        65.52        70.45         8.42        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1685 TCGA-20-1686 
       25.94        26.20        27.52        25.38        16.70         2.93 
TCGA-20-1687 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1027 TCGA-23-1028 
        2.66        49.68        40.54        15.39        32.09        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1111 
        8.81        29.13        18.90         2.76        51.35         3.22 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 
       31.20        68.68        19.46        33.30        86.01       129.96 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-2072 TCGA-23-2078 
        4.27         6.38        39.09        33.47        24.95        87.48 
TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 
       77.00         2.76         4.70         4.50         7.63        11.64 
TCGA-24-0979 TCGA-24-0982 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
       41.56        22.32        63.55        47.41         6.31         6.38 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1425 TCGA-24-1426 
        7.82         7.99         7.86         0.76         5.95         5.36 
TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
       17.39        28.37        18.64        18.67        43.53         8.55 
TCGA-24-1463 TCGA-24-1466 TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
       72.92        45.14         9.11         1.18        22.22        26.96 
TCGA-24-1545 TCGA-24-1548 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 
       57.40        16.21        41.06        51.91        41.39        88.50 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 
       19.53        44.09        45.50        47.70        25.87        10.26 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 
       17.23        90.15         8.32         3.48         3.72         4.37 
TCGA-24-1847 TCGA-24-1850 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 
       11.28         5.52        22.68        30.21        16.44        11.05 
TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 
       81.11         4.87       152.02        44.84        58.16        34.82 
TCGA-24-2029 TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 TCGA-24-2260 TCGA-24-2261 
       14.43        55.92        28.18        64.01        36.16         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
        0.36        47.54        31.63        70.45        44.61         0.82 
TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 
       16.64        33.11        55.86        53.26         1.02        26.96 
TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 
       33.01        52.04        42.05         2.01        34.98        65.00 
TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1626 TCGA-25-1627 
       37.97         2.99        12.99        15.02        17.03        12.95 
TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 
       20.61         0.30        59.15        52.04        14.96        24.99 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 
       24.00        85.05        13.02        49.05         1.02        38.04 
TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 
        3.02        12.00        45.01        19.99        42.02         2.96 
TCGA-25-2404 TCGA-25-2409 TCGA-29-1691 TCGA-29-1693 TCGA-29-1696 TCGA-29-1697 
       29.03        26.99        48.33       101.79        33.93        31.20 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 
       68.32        36.36        16.93        23.93        59.67        18.25 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 
       17.36        86.60        62.93        39.42        31.30        22.98 
TCGA-29-1770 TCGA-29-1771 TCGA-29-1775 TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 
       24.36        22.55        12.36        12.30         8.38         7.23 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2431 
        5.36        36.30        86.17        65.00        45.11        42.25 
TCGA-29-2432 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 
       21.47        35.77        38.07        51.91        36.26         2.47 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1860 TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 
       15.68         0.26        44.91        34.78        36.62         1.22 
TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 
       24.26        48.79        45.57        18.77        22.49         6.71 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1575 
        2.20        28.77        29.10        21.53        22.85         8.55 
TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-2529 TCGA-36-2532 
       30.08        25.74        27.85        24.23        35.05        29.49 
TCGA-36-2534 TCGA-36-2542 TCGA-36-2543 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 
       29.82        21.60         2.24        14.17        16.18        11.47 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2593 TCGA-57-1582 TCGA-57-1584 TCGA-57-1992 
       42.02        10.42         1.48        24.03        21.14        29.00 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2350 TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 
       25.08        25.02        22.32         9.40         2.14         5.42 
TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 
        8.09        31.43        18.54         4.34        31.79        48.79 
TCGA-61-1737 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
       44.84        33.67        43.69         1.45         8.42         5.79 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 
        9.07        34.13        31.30        37.05        48.92        56.61 
TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 
       38.17         2.01         5.52        14.50         4.01        30.64 
TCGA-61-2012 TCGA-61-2087 TCGA-61-2088 TCGA-61-2094 TCGA-61-2097 TCGA-61-2098 
       30.64         4.80         4.77        71.74        60.62        65.52 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 
        6.48        76.87        20.68       125.75        22.22         6.35 
TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0366 
       31.07         8.61        39.68         0.79         9.99        57.76 
TCGA-09-0367 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 
       17.98        54.31        25.91        81.86        18.51        32.88 
TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
       35.44        36.92        19.99        20.91         6.21        24.59 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 
       44.55        39.58         2.73        31.20        15.19        17.82 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 
       55.17         2.50        11.18        11.38        11.54        38.01 
TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0793 TCGA-13-0794 
      111.78        61.84        56.71        40.24       107.28        63.09 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 
       20.35        69.73        45.99        51.02        35.28        35.31 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
       13.61        68.94       107.18       111.39       153.37        66.67 
TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 TCGA-13-0903 
       92.42        95.15       102.84        43.36        66.15       127.79 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 
      118.98        60.59       116.65        44.55        37.64        58.68 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 
       84.53        48.79        83.74 

$`16Q LOSS WILD-TYPE`
TCGA-3P-A9WA TCGA-04-1335 TCGA-04-1348 TCGA-04-1351 TCGA-04-1353 TCGA-04-1361 
       13.81         1.81        48.76        65.46         0.53        32.52 
TCGA-04-1514 TCGA-04-1519 TCGA-04-1536 TCGA-04-1542 TCGA-04-1646 TCGA-04-1648 
       56.55         0.79        29.10        84.20        27.88        28.64 
TCGA-04-1651 TCGA-09-1664 TCGA-09-1672 TCGA-09-1673 TCGA-09-2045 TCGA-09-2050 
       36.23        74.93         5.85         3.02        35.15        71.11 
TCGA-09-2055 TCGA-09-2056 TCGA-13-1409 TCGA-13-1477 TCGA-13-1482 TCGA-13-1485 
       26.93        12.46        57.27        54.64        61.71        20.68 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1510 TCGA-13-2059 TCGA-20-0996 TCGA-20-1684 
       43.20        34.82        44.68        78.48        72.20        19.10 
TCGA-23-1021 TCGA-23-1026 TCGA-23-1110 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 
       47.54        26.83        54.51        58.13         0.53       115.89 
TCGA-23-2079 TCGA-23-2084 TCGA-24-0975 TCGA-24-0980 TCGA-24-1103 TCGA-24-1423 
       91.66        49.84        21.80         7.66        54.12         6.25 
TCGA-24-1424 TCGA-24-1427 TCGA-24-1464 TCGA-24-1467 TCGA-24-1470 TCGA-24-1546 
        6.02         4.83        12.46       105.99         3.45        64.27 
TCGA-24-1549 TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 TCGA-24-1604 TCGA-24-1614 
       56.58        58.09        70.62        39.88        88.37        48.33 
TCGA-24-1616 TCGA-24-1845 TCGA-24-1849 TCGA-24-1920 TCGA-24-2027 TCGA-24-2033 
       38.24         3.81         5.79         9.80       109.71        18.48 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2289 TCGA-24-2290 TCGA-25-1321 TCGA-25-1623 
       44.52        57.07        67.36        36.23        33.96        18.58 
TCGA-25-1625 TCGA-25-1630 TCGA-25-1633 TCGA-25-1634 TCGA-25-2408 TCGA-29-1688 
       27.62        38.20        62.17        35.87        31.00        78.90 
TCGA-29-1690 TCGA-29-1694 TCGA-29-1695 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 
       47.61        39.02        40.41        41.98        31.27        34.62 
TCGA-29-1763 TCGA-29-1774 TCGA-29-1776 TCGA-29-1778 TCGA-29-2427 TCGA-29-2429 
       66.81        17.33        11.84        14.93        62.47        13.84 
TCGA-29-2434 TCGA-29-2436 TCGA-30-1859 TCGA-30-1862 TCGA-30-1880 TCGA-30-1891 
       11.47         9.76        48.10         6.12        57.57        30.05 
TCGA-31-1946 TCGA-31-1955 TCGA-31-1956 TCGA-36-1574 TCGA-36-1581 TCGA-36-2530 
       30.18        42.51        44.12        22.55        24.69        33.01 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 
       25.91        25.08        23.80        20.98        18.31        20.52 
TCGA-36-2549 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2591 TCGA-57-1583 
        6.05        47.57        23.74        28.93        40.77        11.38 
TCGA-57-1585 TCGA-57-1586 TCGA-59-2348 TCGA-59-2349 TCGA-59-2351 TCGA-59-2354 
        1.74        22.32       180.20        80.12       116.12        34.39 
TCGA-59-2372 TCGA-61-1721 TCGA-61-1724 TCGA-61-1728 TCGA-61-1734 TCGA-61-1738 
       44.81        11.11        20.94        27.88        28.47        35.80 
TCGA-61-1740 TCGA-61-1901 TCGA-61-1903 TCGA-61-1911 TCGA-61-1915 TCGA-61-1917 
        2.43        11.41        13.02        42.51        67.76        43.43 
TCGA-61-1918 TCGA-61-2002 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
       15.75        17.98        39.85         1.18        45.96        45.40 
TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 TCGA-61-2101 TCGA-61-2110 TCGA-OY-A56Q 
       51.72        61.64        58.39        55.50        44.52        18.94 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0369 TCGA-10-0930 TCGA-10-0933 TCGA-10-0934 
       29.16         9.47        35.57        34.19        14.66         6.71 
TCGA-13-0725 TCGA-13-0768 TCGA-13-0792 TCGA-13-0799 TCGA-13-0800 TCGA-13-0803 
       12.39        58.65       118.42        83.34        87.48        43.86 
TCGA-13-0890 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 TCGA-13-0904 TCGA-13-0905 
      145.45        71.74       134.04        19.36        50.37       123.16 
TCGA-13-0913 TCGA-13-0921 TCGA-13-0924 TCGA-13-2071 
      109.32        48.76        85.94        25.41 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.26               0.53 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            153.37             180.20 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            31.300             35.685 
[1] "0.3 - 153.4 (31.3)" "0.5 - 180.2 (35.7)"
[1] "hr=" "1.2"
D70V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  16Q LOSS MUTATED         2   396                2
  16Q LOSS WILD-TYPE       1   162                0
D70V3, multiclass
                  clus
vv                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  OMENTUM                         2                  1
  OVARY                         396                162
  PERITONEUM OVARY                2                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V4, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED   388   4
  16Q LOSS WILD-TYPE 153   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    388    4
  16Q LOSS WILD-TYPE  153    1
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO               388                153
  YES                4                  1
[1] 2 2
[1] FALSE
D70V5, continuous
                    vv
clus                 R0 R1 R2 RX
  16Q LOSS MUTATED    8 17  4  1
  16Q LOSS WILD-TYPE  7  9  1  2
D70V6, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0                8                  7
  R1               17                  9
  R2                4                  1
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     5 235
  16Q LOSS WILD-TYPE   5  92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      5  235
  16Q LOSS WILD-TYPE    5   92
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  5
  NOT HISPANIC OR LATINO              235                 92
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED   183 279
  17P LOSS WILD-TYPE  45  52
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               462                 97 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               279                 52 
$`17P LOSS MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 
       13.81        20.52        43.92         1.81        49.15        46.62 
TCGA-04-1343 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 
       11.87        63.09        48.76        21.57        63.98        65.46 
TCGA-04-1353 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
        0.53        32.52        44.32        33.67        76.57       103.40 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 
       82.39        56.55        19.99         0.79        38.37       119.08 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 
       29.10        84.20        55.43        48.89        27.88        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 
       64.64        36.23        31.86        47.70        45.37         9.99 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 
       89.33        74.93        57.60        61.87        55.36        30.51 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 
       17.98         5.85         3.02        97.55         6.12        35.15 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-13-1403 
      112.41        71.11        39.75        20.94        26.93        77.10 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
       81.17        28.54        83.31        55.23        57.27        81.01 
TCGA-13-1411 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 
       17.46        87.06        61.71        29.42       124.44        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       70.82        83.93        52.44       125.56        93.90        90.38 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 
        4.24       127.27        66.15       115.07        13.97        43.20 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
       34.82        65.69        34.16        80.15        44.68        54.25 
TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
       76.90        65.52        70.45         8.42        23.05        25.94 
TCGA-20-0991 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 
       26.20        27.52        19.10        16.70         2.93         2.66 
TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       47.54        40.54        15.39        26.83        32.09        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 
        8.81        29.13        18.90         2.76        51.35        54.51 
TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 
        3.22        31.20        19.46        33.30        86.01       129.96 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 
        4.27         6.38        39.09        33.47        58.13        24.95 
TCGA-23-2077 TCGA-23-2078 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 
      115.89        87.48        77.00        49.84         2.76         4.70 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        4.50         7.63        11.64        21.80        41.56         7.66 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
       22.32        54.12        63.55        47.41         6.31         6.38 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 
        7.82         7.99         0.76         6.25         6.02         5.95 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 
        5.36         4.83        17.39        28.37        18.64        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 
       43.53         8.55        72.92        12.46        45.14       105.99 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 
        9.11         3.45         1.18        26.96        57.40        64.27 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 
       16.21        56.58        41.06        51.91        41.39        88.50 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
       39.88        19.53        44.09        45.50        47.70        25.87 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 
       17.23        90.15        88.37        48.33        38.24         8.32 
TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 
        3.48         3.72         4.37        11.28         5.79         5.52 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 
        9.80        22.68        16.44        11.05        81.11         4.87 
TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 
      152.02        44.84        58.16        34.82       109.71        14.43 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2036 TCGA-24-2261 TCGA-24-2267 TCGA-24-2271 
       55.92        18.48        64.01         0.79        47.54        31.63 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 
       70.45        44.61         0.82        36.23        16.64        33.11 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 
       55.86        53.26         1.02        33.01        52.04        42.05 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 
        2.01        34.98        65.00        37.97        33.96         2.99 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1625 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 
       12.99        15.02        27.62        12.95        20.61        38.20 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 
        0.30        59.15        62.17        35.87        52.04        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 
       24.99        24.00        13.02        49.05         1.02        38.04 
TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 
        3.02        45.01        19.99        42.02         2.96        29.03 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 
       26.99        78.90        48.33       101.79        39.02        40.41 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 
       33.93        31.20        68.32        36.36        16.93        59.67 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 
       18.25        41.98        34.62        17.36        86.60        62.93 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 
       31.30        22.98        24.36        22.55        12.36        11.84 
TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 
       12.30        14.93         8.38         7.23         5.36        36.30 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2431 TCGA-29-2432 
       86.17        65.00        62.47        45.11        42.25        21.47 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 
       38.07        51.91        36.26         2.47        15.68         0.26 
TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 
       48.10        44.91        34.78        36.62         1.22        57.57 
TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 
       24.26        30.05        48.79        45.57        30.18        18.77 
TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 
       22.49         6.71        42.51        44.12         2.20        28.77 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-2529 
       21.53        22.85        22.55         8.55        30.08        35.05 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2543 
       33.01        29.49        29.82        25.91        25.08         2.24 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 
       20.98        18.31        20.52        14.17         6.05        16.18 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 
       47.57        23.74        42.02        10.42        40.77         1.48 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1993 TCGA-59-2348 
       24.03        11.38        21.14         1.74        25.08       180.20 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 
       22.32       116.12        34.39         2.14         5.42        44.81 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 
       20.94        31.43        18.54        27.88         4.34        31.79 
TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 
       28.47        48.79        44.84        35.80         2.43        33.67 
TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1901 TCGA-61-1903 TCGA-61-1906 
       43.69         1.45         8.42        11.41        13.02        34.13 
TCGA-61-1907 TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 
       31.30        37.05        48.92        56.61        67.76        43.43 
TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       15.75        38.17         2.01         5.52        14.50        17.98 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 TCGA-61-2016 TCGA-61-2087 TCGA-61-2088 
        4.01        30.64        30.64         1.18         4.80         4.77 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 
       71.74        61.64        58.39        60.62        65.52        55.50 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
        6.48        76.87        20.68        44.52       125.75        22.22 
TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
        6.35        31.07         8.61        39.68        18.94         0.79 
TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-10-0926 
        9.99        29.16         9.47        57.76        17.98        25.91 
TCGA-10-0927 TCGA-10-0930 TCGA-10-0933 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 
       81.86        34.19        14.66        36.92        19.99        20.91 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 
        6.21        24.59        44.55        39.58         2.73        12.39 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 
       31.20        15.19        17.82         2.50        11.18        11.38 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 
       11.54        38.01        56.71        58.65        40.24       118.42 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 
      107.28        63.09        20.35        69.73        83.34        45.99 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
       51.02        43.86        35.28        35.31        13.61        68.94 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 
      107.18       111.39       153.37        66.67        92.42        95.15 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
      145.45       102.84        43.36       134.04        19.36       127.79 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       50.37       123.16        60.59       116.65        44.55        37.64 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       58.68        84.53        48.76        83.74        85.94        25.41 

$`17P LOSS WILD-TYPE`
TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1337 TCGA-04-1341 TCGA-04-1342 TCGA-04-1346 
       11.87        41.00         2.01         1.08        18.51        65.52 
TCGA-04-1356 TCGA-04-1516 TCGA-09-1661 TCGA-09-1665 TCGA-09-1674 TCGA-09-2043 
       49.28        41.59        38.43        41.62         8.55         6.18 
TCGA-09-2048 TCGA-09-2051 TCGA-09-2056 TCGA-13-1412 TCGA-13-1477 TCGA-13-1485 
        4.54        63.09        12.46        32.35        54.64        20.68 
TCGA-13-1507 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-20-0996 
       65.52        14.53        80.02        78.48        77.88        72.20 
TCGA-20-1683 TCGA-23-1022 TCGA-23-1114 TCGA-23-1809 TCGA-23-2079 TCGA-24-1419 
       25.38        49.68        68.68         0.53        91.66         7.86 
TCGA-24-1474 TCGA-24-1553 TCGA-24-1556 TCGA-24-1565 TCGA-24-1845 TCGA-24-1924 
       22.22        58.09        70.62        10.26         3.81        30.21 
TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 TCGA-24-2289 
       28.18        44.52        57.07        36.16         0.36        67.36 
TCGA-25-1313 TCGA-25-1623 TCGA-25-1626 TCGA-25-1878 TCGA-25-2397 TCGA-25-2408 
       26.96        18.58        17.03        85.05        12.00        31.00 
TCGA-29-1690 TCGA-29-1702 TCGA-29-1710 TCGA-29-1763 TCGA-29-1766 TCGA-29-1774 
       47.61        23.93        31.27        66.81        39.42        17.33 
TCGA-29-2429 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1862 TCGA-36-1569 
       13.84        11.47         9.76        35.77         6.12        29.10 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2540 TCGA-36-2542 
       25.74        27.85        24.23        24.69        23.80        21.60 
TCGA-36-2552 TCGA-42-2588 TCGA-57-1586 TCGA-57-1992 TCGA-57-1994 TCGA-59-2349 
       11.47        28.93        22.32        29.00        25.02        80.12 
TCGA-59-2352 TCGA-61-1721 TCGA-61-1722 TCGA-61-1900 TCGA-61-1904 TCGA-61-1911 
        9.40        11.11         8.09         5.79         9.07        42.51 
TCGA-61-2009 TCGA-61-2017 TCGA-61-2018 TCGA-61-2092 TCGA-09-0369 TCGA-10-0925 
       39.85        45.96        45.40        51.72        35.57        54.31 
TCGA-10-0928 TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 TCGA-13-0751 TCGA-13-0762 
       18.51        32.88         6.71        35.44        55.17       111.78 
TCGA-13-0764 TCGA-13-0800 TCGA-13-0897 TCGA-13-0899 TCGA-13-0906 TCGA-13-0913 
       61.84        87.48        71.74        66.15       118.98       109.32 
TCGA-13-0920 
       48.79 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.26               0.36 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            180.20             118.98 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            33.205             31.000 
[1] "0.3 - 180.2 (33.2)" "0.4 - 119.0 (31.0)"
[1] "hr=" "1.1"
D71V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  17P LOSS MUTATED         2   463                1
  17P LOSS WILD-TYPE       1    95                1
D71V3, multiclass
                  clus
vv                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  OMENTUM                         2                  1
  OVARY                         463                 95
  PERITONEUM OVARY                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V4, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   449   4
  17P LOSS WILD-TYPE  92   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    449    4
  17P LOSS WILD-TYPE   92    1
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO               449                 92
  YES                4                  1
[1] 2 2
[1] FALSE
D71V5, continuous
                    vv
clus                 R0 R1 R2 RX
  17P LOSS MUTATED   10 23  4  3
  17P LOSS WILD-TYPE  5  3  1  0
D71V6, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0               10                  5
  R1               23                  3
  R2                4                  1
  RX                3                  0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     7 272
  17P LOSS WILD-TYPE   3  55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      7  272
  17P LOSS WILD-TYPE    3   55
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    7                  3
  NOT HISPANIC OR LATINO              272                 55
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED   154 218
  17Q LOSS WILD-TYPE  74 113
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               372                187 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               218                113 
$`17Q LOSS MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1338 
       13.81        20.52        43.92        41.00         1.81        46.62 
TCGA-04-1343 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 
       11.87        63.09        48.76        21.57        63.98        65.46 
TCGA-04-1353 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
        0.53        32.52        44.32        33.67        76.57       103.40 
TCGA-04-1371 TCGA-04-1517 TCGA-04-1519 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 
       82.39        19.99         0.79        29.10        84.20        55.43 
TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 
       48.89        27.88        28.64        64.64        36.23        31.86 
TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 
       47.70        45.37         9.99        74.93        57.60        61.87 
TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 
       55.36        30.51        17.98         5.85         3.02        97.55 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2053 TCGA-09-2054 
        6.12        35.15       112.41        71.11        39.75        20.94 
TCGA-09-2055 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1409 
       26.93        77.10        81.17        28.54        83.31        57.27 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 TCGA-13-1488 
       81.01        17.46        87.06        61.71       124.44        70.82 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1497 TCGA-13-1499 
       52.44       125.56        93.90        90.38       127.27       115.07 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 
       13.97        43.20        34.82        65.69        34.16        80.15 
TCGA-13-1510 TCGA-13-1511 TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FU 
       44.68        54.25        78.48        76.90        65.52         8.42 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 
       23.05        25.94        26.20        27.52        19.10        16.70 
TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1024 TCGA-23-1026 TCGA-23-1029 
        2.93         2.66        47.54        15.39        26.83         8.81 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1111 TCGA-23-1113 TCGA-23-1119 
       29.13        18.90         2.76         3.22        31.20       129.96 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 
        6.38        39.09        33.47        58.13        24.95       115.89 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0979 
       77.00        49.84         2.76         4.70         4.50        41.56 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 
        7.66        22.32        54.12        63.55        47.41         6.31 
TCGA-24-1416 TCGA-24-1418 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 
        6.38         7.99         0.76         6.25         6.02         5.95 
TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 
        4.83        17.39        28.37        18.64        18.67         8.55 
TCGA-24-1463 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 
       72.92        45.14       105.99         9.11         3.45         1.18 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 TCGA-24-1550 TCGA-24-1551 TCGA-24-1555 
       26.96        57.40        16.21        41.06        51.91        88.50 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
       39.88        19.53        44.09        45.50        47.70        25.87 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1844 
       90.15        88.37        48.33        38.24         8.32         3.72 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 
        4.37        11.28         5.79         9.80        22.68        30.21 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 TCGA-24-2026 TCGA-24-2029 
       11.05        81.11         4.87        44.84        34.82        14.43 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2036 TCGA-24-2254 TCGA-24-2267 TCGA-24-2280 
       55.92        18.48        64.01        57.07        47.54        70.45 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 
       44.61         0.82        36.23        16.64        33.11        55.86 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
        1.02        26.96        52.04        42.05         2.01        34.98 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1625 TCGA-25-1627 
       37.97        33.96         2.99        12.99        27.62        12.95 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
       20.61        38.20         0.30        59.15        62.17        35.87 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-2391 TCGA-25-2393 
       52.04        14.96        24.99        24.00        49.05        38.04 
TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2404 
        3.02        12.00        45.01        19.99        42.02        29.03 
TCGA-29-1688 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       78.90        48.33       101.79        39.02        40.41        33.93 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
       31.20        68.32        16.93        59.67        18.25        41.98 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1769 TCGA-29-1770 
       17.36        86.60        66.81        62.93        22.98        24.36 
TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 
       22.55        12.36        11.84        12.30        14.93         8.38 
TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2425 TCGA-29-2427 TCGA-29-2429 
        7.23         5.36        36.30        65.00        62.47        13.84 
TCGA-29-2431 TCGA-29-2432 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 
       42.25        21.47        38.07        51.91        36.26         2.47 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1866 
       15.68         0.26        48.10        44.91        34.78        36.62 
TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-31-1944 TCGA-31-1950 TCGA-31-1953 
       57.57        24.26        30.05        45.57        18.77         6.71 
TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 
       42.51        44.12        28.77        22.85         8.55        30.08 
TCGA-36-1577 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       25.74        35.05        33.01        29.49        29.82        25.91 
TCGA-36-2538 TCGA-36-2543 TCGA-36-2545 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 
       25.08         2.24        18.31        14.17         6.05        16.18 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 
       47.57        23.74        42.02        10.42        40.77        24.03 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1993 TCGA-59-2348 TCGA-59-2351 TCGA-59-2355 
       11.38        21.14        25.08       180.20       116.12         2.14 
TCGA-59-2372 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 
       44.81        20.94        31.43        18.54        27.88         4.34 
TCGA-61-1733 TCGA-61-1734 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 
       31.79        28.47         2.43        33.67        43.69         1.45 
TCGA-61-1899 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        8.42        11.41        13.02         9.07        34.13        31.30 
TCGA-61-1910 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 
       37.05        67.76        43.43        15.75        38.17         2.01 
TCGA-61-1998 TCGA-61-2003 TCGA-61-2012 TCGA-61-2016 TCGA-61-2018 TCGA-61-2087 
        5.52         4.01        30.64         1.18        45.40         4.80 
TCGA-61-2088 TCGA-61-2094 TCGA-61-2097 TCGA-61-2101 TCGA-61-2104 TCGA-61-2109 
        4.77        71.74        60.62        55.50        76.87        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2613 TCGA-OY-A56Q TCGA-VG-A8LO 
       44.52       125.75        22.22        31.07        18.94         0.79 
TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-10-0926 
        9.99        29.16         9.47        57.76        17.98        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
       81.86        18.51        34.19        20.91         6.21        24.59 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0730 TCGA-13-0758 TCGA-13-0762 
       44.55        39.58         2.73        17.82        11.38       111.78 
TCGA-13-0766 TCGA-13-0791 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 
       56.71        40.24       107.28        20.35        69.73        83.34 
TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0883 TCGA-13-0884 
       45.99        43.86        35.28        35.31        68.94       107.18 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
      111.39       153.37        66.67       145.45       102.84        43.36 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0908 TCGA-13-0910 
       19.36       127.79        50.37       123.16        60.59       116.65 
TCGA-13-0911 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0924 TCGA-13-2071 
       44.55        58.68        84.53        48.76        85.94        25.41 

$`17Q LOSS WILD-TYPE`
TCGA-5X-AA5U TCGA-04-1336 TCGA-04-1337 TCGA-04-1341 TCGA-04-1342 TCGA-04-1346 
       11.87        49.15         2.01         1.08        18.51        65.52 
TCGA-04-1356 TCGA-04-1514 TCGA-04-1516 TCGA-04-1525 TCGA-04-1530 TCGA-09-1661 
       49.28        56.55        41.59        38.37       119.08        38.43 
TCGA-09-1662 TCGA-09-1665 TCGA-09-1674 TCGA-09-2043 TCGA-09-2048 TCGA-09-2051 
       89.33        41.62         8.55         6.18         4.54        63.09 
TCGA-09-2056 TCGA-13-1408 TCGA-13-1412 TCGA-13-1477 TCGA-13-1483 TCGA-13-1485 
       12.46        55.23        32.35        54.64        29.42        20.68 
TCGA-13-1487 TCGA-13-1489 TCGA-13-1496 TCGA-13-1498 TCGA-13-1507 TCGA-13-1512 
       22.39        83.93         4.24        66.15        65.52        14.53 
TCGA-13-2057 TCGA-13-2060 TCGA-13-A5FT TCGA-20-0996 TCGA-20-1683 TCGA-23-1022 
       80.02        77.88        70.45        72.20        25.38        49.68 
TCGA-23-1023 TCGA-23-1027 TCGA-23-1028 TCGA-23-1109 TCGA-23-1110 TCGA-23-1114 
       40.54        32.09        49.41        51.35        54.51        68.68 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 TCGA-23-1809 TCGA-23-2078 
       19.46        33.30        86.01         4.27         0.53        87.48 
TCGA-23-2079 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-1417 TCGA-24-1419 
       91.66         7.63        11.64        21.80         7.82         7.86 
TCGA-24-1426 TCGA-24-1435 TCGA-24-1464 TCGA-24-1474 TCGA-24-1546 TCGA-24-1549 
        5.36        43.53        12.46        22.22        64.27        56.58 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1556 TCGA-24-1565 TCGA-24-1567 TCGA-24-1843 
       41.39        58.09        70.62        10.26        17.23         3.48 
TCGA-24-1845 TCGA-24-1850 TCGA-24-1927 TCGA-24-2020 TCGA-24-2024 TCGA-24-2027 
        3.81         5.52        16.44       152.02        58.16       109.71 
TCGA-24-2035 TCGA-24-2038 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2271 
       28.18        44.52        36.16         0.79         0.36        31.63 
TCGA-24-2289 TCGA-24-2298 TCGA-25-1314 TCGA-25-1319 TCGA-25-1329 TCGA-25-1623 
       67.36        53.26        33.01        65.00        15.02        18.58 
TCGA-25-1626 TCGA-25-1878 TCGA-25-2042 TCGA-25-2392 TCGA-25-2401 TCGA-25-2408 
       17.03        85.05        13.02         1.02         2.96        31.00 
TCGA-25-2409 TCGA-29-1690 TCGA-29-1699 TCGA-29-1702 TCGA-29-1710 TCGA-29-1711 
       26.99        47.61        36.36        23.93        31.27        34.62 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1774 TCGA-29-2414 TCGA-29-2428 TCGA-29-2434 
       39.42        31.30        17.33        86.17        45.11        11.47 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1862 TCGA-30-1867 TCGA-30-1892 TCGA-31-1946 
        9.76        35.77         6.12         1.22        48.79        30.18 
TCGA-31-1951 TCGA-31-1959 TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 TCGA-36-1578 
       22.49         2.20        29.10        21.53        22.55        27.85 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-36-2547 
       24.23        24.69        23.80        21.60        20.98        20.52 
TCGA-36-2552 TCGA-42-2588 TCGA-42-2593 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 
       11.47        28.93         1.48         1.74        22.32        29.00 
TCGA-57-1994 TCGA-59-2349 TCGA-59-2350 TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 
       25.02        80.12        22.32         9.40        34.39         5.42 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1900 
       11.11         8.09        48.79        44.84        35.80         5.79 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-2000 TCGA-61-2002 TCGA-61-2008 
       42.51        48.92        56.61        14.50        17.98        30.64 
TCGA-61-2009 TCGA-61-2017 TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 
       39.85        45.96        51.72        61.64        58.39        65.52 
TCGA-61-2102 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P TCGA-09-0369 TCGA-10-0925 
        6.48         6.35         8.61        39.68        35.57        54.31 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 
       32.88        14.66         6.71        35.44        36.92        19.99 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 
       12.39        31.20        15.19        55.17         2.50        11.18 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 TCGA-13-0768 TCGA-13-0792 TCGA-13-0794 
       11.54        38.01        61.84        58.65       118.42        63.09 
TCGA-13-0800 TCGA-13-0802 TCGA-13-0807 TCGA-13-0888 TCGA-13-0889 TCGA-13-0897 
       87.48        51.02        13.61        92.42        95.15        71.74 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0906 TCGA-13-0912 TCGA-13-0913 TCGA-13-0920 
       66.15       134.04       118.98        37.64       109.32        48.79 
TCGA-13-0923 
       83.74 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.26               0.36 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            180.20             152.02 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             33.29              32.09 
[1] "0.3 - 180.2 (33.3)" "0.4 - 152.0 (32.1)"
[1] "hr=" "1.1"
D72V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  17Q LOSS MUTATED         2   373                1
  17Q LOSS WILD-TYPE       1   185                1
D72V3, multiclass
                  clus
vv                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  OMENTUM                         2                  1
  OVARY                         373                185
  PERITONEUM OVARY                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V4, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED   362   4
  17Q LOSS WILD-TYPE 179   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED    362    4
  17Q LOSS WILD-TYPE  179    1
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO               362                179
  YES                4                  1
[1] 2 2
[1] FALSE
D72V5, continuous
                    vv
clus                 R0 R1 R2 RX
  17Q LOSS MUTATED    8 18  2  2
  17Q LOSS WILD-TYPE  7  8  3  1
D72V6, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0                8                  7
  R1               18                  8
  R2                2                  3
  RX                2                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     4 221
  17Q LOSS WILD-TYPE   6 106
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      4  221
  17Q LOSS WILD-TYPE    6  106
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  6
  NOT HISPANIC OR LATINO              221                106
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    83 143
  18P LOSS WILD-TYPE 145 188
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               226                333 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               143                188 
$`18P LOSS MUTATED`
TCGA-59-A5PD TCGA-04-1338 TCGA-04-1341 TCGA-04-1350 TCGA-04-1351 TCGA-04-1362 
       20.52        46.62         1.08        63.98        65.46        44.32 
TCGA-04-1364 TCGA-04-1514 TCGA-04-1517 TCGA-04-1519 TCGA-04-1530 TCGA-04-1649 
       33.67        56.55        19.99         0.79       119.08        64.64 
TCGA-04-1651 TCGA-04-1655 TCGA-09-1666 TCGA-09-1667 TCGA-09-1672 TCGA-09-1673 
       36.23        45.37        57.60        61.87         5.85         3.02 
TCGA-09-2044 TCGA-09-2053 TCGA-13-1403 TCGA-13-1405 TCGA-13-1409 TCGA-13-1411 
        6.12        39.75        77.10        28.54        57.27        17.46 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1495 TCGA-13-1498 
       29.42       124.44        22.39        70.82        90.38        66.15 
TCGA-13-1506 TCGA-13-2057 TCGA-13-2061 TCGA-13-2065 TCGA-20-0990 TCGA-20-0991 
       34.16        80.02        76.90        65.52        25.94        26.20 
TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1687 TCGA-23-1021 TCGA-23-1027 
       27.52        25.38        19.10         2.66        47.54        32.09 
TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1122 
        3.22        31.20        19.46        33.30        86.01        39.09 
TCGA-23-2072 TCGA-23-2079 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-24-0966 
       24.95        91.66        49.84         2.76         4.70         7.63 
TCGA-24-0970 TCGA-24-0979 TCGA-24-0982 TCGA-24-1104 TCGA-24-1413 TCGA-24-1416 
       11.64        41.56        22.32        63.55         6.31         6.38 
TCGA-24-1423 TCGA-24-1425 TCGA-24-1427 TCGA-24-1431 TCGA-24-1436 TCGA-24-1463 
        6.25         5.95         4.83        18.64         8.55        72.92 
TCGA-24-1464 TCGA-24-1470 TCGA-24-1471 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 
       12.46         3.45         1.18        26.96        57.40        64.27 
TCGA-24-1548 TCGA-24-1551 TCGA-24-1556 TCGA-24-1557 TCGA-24-1560 TCGA-24-1562 
       16.21        51.91        70.62        39.88        44.09        45.50 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1603 TCGA-24-1614 TCGA-24-1842 TCGA-24-1843 
       47.70        25.87        90.15        48.33         8.32         3.48 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 TCGA-24-1927 TCGA-24-1928 
       11.28         5.79         9.80        22.68        16.44        11.05 
TCGA-24-2023 TCGA-24-2027 TCGA-24-2260 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       44.84       109.71        36.16        47.54        31.63        70.45 
TCGA-24-2288 TCGA-24-2293 TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 
        0.82        16.64        53.26        26.96        52.04        42.05 
TCGA-25-1317 TCGA-25-1320 TCGA-25-1322 TCGA-25-1329 TCGA-25-1626 TCGA-25-1627 
        2.01        37.97         2.99        15.02        17.03        12.95 
TCGA-25-1630 TCGA-25-1632 TCGA-25-1634 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 
       38.20        59.15        35.87        24.00        85.05        13.02 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2398 TCGA-25-2401 TCGA-25-2404 TCGA-25-2409 
        1.02        38.04        45.01         2.96        29.03        26.99 
TCGA-29-1694 TCGA-29-1697 TCGA-29-1701 TCGA-29-1703 TCGA-29-1707 TCGA-29-1762 
       39.02        31.20        16.93        59.67        41.98        86.60 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1768 TCGA-29-1770 TCGA-29-1775 TCGA-29-1777 
       66.81        62.93        31.30        24.36        12.36        12.30 
TCGA-29-1783 TCGA-29-2414 TCGA-29-2427 TCGA-29-2428 TCGA-29-A5NZ TCGA-30-1714 
        7.23        86.17        62.47        45.11        35.77        38.07 
TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1860 TCGA-30-1861 TCGA-30-1880 
       51.91         2.47        15.68        44.91        34.78        57.57 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1946 TCGA-36-1568 TCGA-36-1569 TCGA-36-1571 
       30.05        48.79        30.18        28.77        29.10        22.85 
TCGA-36-1575 TCGA-36-1577 TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
        8.55        25.74        24.23        33.01        29.49        29.82 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2545 TCGA-36-2548 TCGA-36-2552 TCGA-42-2587 
       21.60         2.24        18.31        14.17        11.47        23.74 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1585 TCGA-57-1993 TCGA-59-2350 
       40.77         1.48        24.03         1.74        25.08        22.32 
TCGA-59-2351 TCGA-59-2354 TCGA-59-2363 TCGA-59-2372 TCGA-61-1727 TCGA-61-1741 
      116.12        34.39         5.42        44.81        18.54        33.67 
TCGA-61-1743 TCGA-61-1895 TCGA-61-1904 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
       43.69         1.45         9.07        38.17         2.01         5.52 
TCGA-61-2002 TCGA-61-2009 TCGA-61-2012 TCGA-61-2088 TCGA-61-2094 TCGA-61-2098 
       17.98        39.85        30.64         4.77        71.74        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2612 
       55.50         6.48        76.87        20.68        44.52         6.35 
TCGA-61-2613 TCGA-09-0367 TCGA-10-0926 TCGA-10-0927 TCGA-10-0931 TCGA-13-0714 
       31.07        17.98        25.91        81.86        32.88         6.21 
TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0751 
       44.55         2.73        12.39        31.20        15.19        55.17 
TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0764 TCGA-13-0766 
        2.50        11.18        11.38        11.54        61.84        56.71 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0800 TCGA-13-0803 TCGA-13-0804 
      118.42       107.28        63.09        87.48        43.86        35.28 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0891 TCGA-13-0903 TCGA-13-0910 
       13.61        68.94       107.18       102.84       127.79       116.65 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0924 TCGA-13-2071 
       44.55        37.64        85.94        25.41 

$`18P LOSS WILD-TYPE`
TCGA-3P-A9WA TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 
       13.81        11.87        43.92        41.00         1.81        49.15 
TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 
        2.01        18.51        11.87        65.52        63.09        48.76 
TCGA-04-1349 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1365 TCGA-04-1367 
       21.57         0.53        49.28        32.52        76.57       103.40 
TCGA-04-1371 TCGA-04-1516 TCGA-04-1525 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 
       82.39        41.59        38.37        29.10        84.20        55.43 
TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1652 TCGA-04-1654 TCGA-09-1659 
       48.89        27.88        28.64        31.86        47.70         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1668 TCGA-09-1669 
       38.43        89.33        74.93        41.62        55.36        30.51 
TCGA-09-1670 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2045 TCGA-09-2048 
       17.98         8.55        97.55         6.18        35.15         4.54 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 
      112.41        71.11        63.09        20.94        26.93        12.46 
TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1412 TCGA-13-1477 
       81.17        83.31        55.23        81.01        32.35        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1485 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
       87.06        61.71        20.68        83.93        52.44       125.56 
TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 
       93.90         4.24       127.27       115.07        13.97        43.20 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
       34.82        65.69        65.52        80.15        44.68        54.25 
TCGA-13-1512 TCGA-13-2059 TCGA-13-2060 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
       14.53        78.48        77.88        70.45         8.42        23.05 
TCGA-20-0996 TCGA-20-1685 TCGA-20-1686 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 
       72.20        16.70         2.93        49.68        40.54        15.39 
TCGA-23-1026 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       26.83        49.41         8.81        29.13        18.90         2.76 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1114 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 
       51.35        54.51        68.68       129.96         4.27         6.38 
TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2078 TCGA-23-2081 
       33.47        58.13         0.53       115.89        87.48        77.00 
TCGA-23-2645 TCGA-24-0975 TCGA-24-0980 TCGA-24-1103 TCGA-24-1105 TCGA-24-1417 
        4.50        21.80         7.66        54.12        47.41         7.82 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1424 TCGA-24-1426 TCGA-24-1428 
        7.99         7.86         0.76         6.02         5.36        17.39 
TCGA-24-1430 TCGA-24-1434 TCGA-24-1435 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 
       28.37        18.67        43.53        45.14       105.99         9.11 
TCGA-24-1474 TCGA-24-1549 TCGA-24-1550 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       22.22        56.58        41.06        41.39        58.09        88.50 
TCGA-24-1558 TCGA-24-1565 TCGA-24-1567 TCGA-24-1604 TCGA-24-1616 TCGA-24-1844 
       19.53        10.26        17.23        88.37        38.24         3.72 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1850 TCGA-24-1924 TCGA-24-1930 TCGA-24-2019 
        3.81         4.37         5.52        30.21        81.11         4.87 
TCGA-24-2020 TCGA-24-2024 TCGA-24-2026 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 
      152.02        58.16        34.82        14.43        55.92        18.48 
TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2261 TCGA-24-2262 
       28.18        64.01        44.52        57.07         0.79         0.36 
TCGA-24-2281 TCGA-24-2289 TCGA-24-2290 TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 
       44.61        67.36        36.23        33.11        55.86         1.02 
TCGA-25-1314 TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 TCGA-25-1323 TCGA-25-1623 
       33.01        34.98        65.00        33.96        12.99        18.58 
TCGA-25-1625 TCGA-25-1628 TCGA-25-1631 TCGA-25-1633 TCGA-25-1635 TCGA-25-1870 
       27.62        20.61         0.30        62.17        52.04        14.96 
TCGA-25-1871 TCGA-25-2391 TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 TCGA-25-2400 
       24.99        49.05         3.02        12.00        19.99        42.02 
TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1695 
       31.00        78.90        47.61        48.33       101.79        40.41 
TCGA-29-1696 TCGA-29-1698 TCGA-29-1699 TCGA-29-1702 TCGA-29-1705 TCGA-29-1710 
       33.93        68.32        36.36        23.93        18.25        31.27 
TCGA-29-1711 TCGA-29-1761 TCGA-29-1766 TCGA-29-1769 TCGA-29-1771 TCGA-29-1774 
       34.62        17.36        39.42        22.98        22.55        17.33 
TCGA-29-1776 TCGA-29-1778 TCGA-29-1781 TCGA-29-1784 TCGA-29-1785 TCGA-29-2425 
       11.84        14.93         8.38         5.36        36.30        65.00 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-30-1853 
       13.84        42.25        21.47        11.47         9.76        36.26 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1887 
        0.26        48.10         6.12        36.62         1.22        24.26 
TCGA-31-1944 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 
       45.57        18.77        22.49         6.71        42.51        44.12 
TCGA-31-1959 TCGA-36-1570 TCGA-36-1574 TCGA-36-1576 TCGA-36-1578 TCGA-36-1581 
        2.20        21.53        22.55        30.08        27.85        24.69 
TCGA-36-2529 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2544 TCGA-36-2547 
       35.05        25.91        25.08        23.80        20.98        20.52 
TCGA-36-2549 TCGA-36-2551 TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
        6.05        16.18        47.57        28.93        42.02        10.42 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1992 TCGA-57-1994 TCGA-59-2348 
       11.38        21.14        22.32        29.00        25.02       180.20 
TCGA-59-2349 TCGA-59-2352 TCGA-59-2355 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 
       80.12         9.40         2.14        11.11         8.09        20.94 
TCGA-61-1725 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 
       31.43        27.88         4.34        31.79        28.47        48.79 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 
       44.84        35.80         2.43         8.42         5.79        11.41 
TCGA-61-1903 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 
       13.02        34.13        31.30        37.05        42.51        48.92 
TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-2000 TCGA-61-2003 
       56.61        67.76        43.43        15.75        14.50         4.01 
TCGA-61-2008 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 
       30.64         1.18        45.96        45.40         4.80        51.72 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2111 TCGA-61-2113 TCGA-61-2614 
       61.64        58.39        60.62       125.75        22.22         8.61 
TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 
       39.68        18.94         0.79         9.99        29.16         9.47 
TCGA-09-0366 TCGA-09-0369 TCGA-10-0925 TCGA-10-0928 TCGA-10-0930 TCGA-10-0933 
       57.76        35.57        54.31        18.51        34.19        14.66 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0717 
        6.71        35.44        36.92        19.99        20.91        24.59 
TCGA-13-0723 TCGA-13-0730 TCGA-13-0761 TCGA-13-0762 TCGA-13-0768 TCGA-13-0791 
       39.58        17.82        38.01       111.78        58.65        40.24 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0805 
       20.35        69.73        83.34        45.99        51.02        35.31 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 
      111.39       153.37        66.67        92.42        95.15       145.45 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0904 
       43.36        71.74        66.15       134.04        19.36        50.37 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
      123.16       118.98        60.59       109.32        58.68        84.53 
TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 
       48.79        48.76        83.74 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.79               0.26 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            127.79             180.20 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            31.135             34.190 
[1] "0.8 - 127.8 (31.1)" "0.3 - 180.2 (34.2)"
[1] "hr=" "1.3"
D73V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  18P LOSS MUTATED         2   224                0
  18P LOSS WILD-TYPE       1   334                2
D73V3, multiclass
                  clus
vv                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  OMENTUM                         2                  1
  OVARY                         224                334
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V4, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   214   4
  18P LOSS WILD-TYPE 327   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    214    4
  18P LOSS WILD-TYPE  327    1
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO               214                327
  YES                4                  1
[1] 2 2
[1] FALSE
D73V5, continuous
                    vv
clus                 R0 R1 R2 RX
  18P LOSS MUTATED    6 13  1  0
  18P LOSS WILD-TYPE  9 13  4  3
D73V6, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0                6                  9
  R1               13                 13
  R2                1                  4
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     4 128
  18P LOSS WILD-TYPE   6 199
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      4  128
  18P LOSS WILD-TYPE    6  199
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  6
  NOT HISPANIC OR LATINO              128                199
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED   112 167
  18Q LOSS WILD-TYPE 116 164
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               279                280 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               167                164 
$`18Q LOSS MUTATED`
TCGA-59-A5PD TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1341 
       20.52        41.00         1.81        49.15        46.62         1.08 
TCGA-04-1347 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 
       63.09        63.98        65.46        49.28        44.32        33.67 
TCGA-04-1517 TCGA-04-1519 TCGA-04-1530 TCGA-04-1649 TCGA-04-1651 TCGA-04-1655 
       19.99         0.79       119.08        64.64        36.23        45.37 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 
       57.60        61.87         5.85         3.02        97.55         6.18 
TCGA-09-2044 TCGA-09-2048 TCGA-09-2050 TCGA-09-2053 TCGA-09-2054 TCGA-09-2056 
        6.12         4.54        71.11        39.75        20.94        12.46 
TCGA-13-1403 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1411 
       77.10        28.54        83.31        55.23        57.27        17.46 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1495 TCGA-13-1498 
       29.42       124.44        22.39        70.82        90.38        66.15 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1505 TCGA-13-1506 TCGA-13-2057 TCGA-13-2059 
      115.07        13.97        65.69        34.16        80.02        78.48 
TCGA-13-2061 TCGA-13-2065 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 
       76.90        65.52        23.05        25.94        26.20        27.52 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 
       25.38        19.10        16.70         2.93         2.66        47.54 
TCGA-23-1023 TCGA-23-1027 TCGA-23-1028 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 
       40.54        32.09        49.41         3.22        31.20        19.46 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1122 TCGA-23-1124 TCGA-23-2072 
       33.30        86.01       129.96        39.09        58.13        24.95 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-24-0966 
       91.66        77.00        49.84         2.76         4.70         7.63 
TCGA-24-0970 TCGA-24-0979 TCGA-24-0982 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 
       11.64        41.56        22.32        63.55        47.41         6.31 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 
        6.38         7.82         7.99         6.25         6.02         5.95 
TCGA-24-1427 TCGA-24-1428 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1470 
        4.83        17.39         8.55        72.92        12.46         3.45 
TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 
        1.18        22.22        26.96        57.40        64.27        16.21 
TCGA-24-1552 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 
       41.39        70.62        39.88        19.53        44.09        45.50 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1603 TCGA-24-1614 TCGA-24-1842 TCGA-24-1843 
       47.70        25.87        90.15        48.33         8.32         3.48 
TCGA-24-1844 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 
        3.72        11.28         5.79         5.52         9.80        22.68 
TCGA-24-1927 TCGA-24-1928 TCGA-24-2020 TCGA-24-2023 TCGA-24-2027 TCGA-24-2029 
       16.44        11.05       152.02        44.84       109.71        14.43 
TCGA-24-2035 TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 TCGA-24-2271 TCGA-24-2288 
       28.18        36.16         0.79        47.54        31.63         0.82 
TCGA-24-2289 TCGA-24-2293 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1315 
       67.36        16.64        53.26         1.02        26.96        52.04 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 
       42.05         2.01        33.96         2.99        12.99        15.02 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1632 TCGA-25-1634 TCGA-25-1877 TCGA-25-1878 
       27.62        17.03        59.15        35.87        24.00        85.05 
TCGA-25-2042 TCGA-25-2392 TCGA-25-2393 TCGA-25-2401 TCGA-25-2404 TCGA-25-2409 
       13.02         1.02        38.04         2.96        29.03        26.99 
TCGA-29-1694 TCGA-29-1697 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 
       39.02        31.20        16.93        23.93        59.67        41.98 
TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1768 TCGA-29-1770 TCGA-29-1775 
       86.60        66.81        62.93        31.30        24.36        12.36 
TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 
       12.30         8.38         7.23        86.17        65.00        62.47 
TCGA-29-2428 TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 
       45.11        11.47        35.77        38.07        51.91         2.47 
TCGA-30-1856 TCGA-30-1861 TCGA-30-1866 TCGA-30-1880 TCGA-30-1891 TCGA-31-1944 
       15.68        34.78        36.62        57.57        30.05        45.57 
TCGA-31-1946 TCGA-31-1959 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1575 
       30.18         2.20        29.10        21.53        22.85         8.55 
TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-2532 TCGA-36-2534 
       30.08        25.74        27.85        24.23        29.49        29.82 
TCGA-36-2538 TCGA-36-2542 TCGA-36-2543 TCGA-36-2545 TCGA-36-2548 TCGA-36-2552 
       25.08        21.60         2.24        18.31        14.17        11.47 
TCGA-42-2587 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1585 
       23.74        40.77         1.48        24.03        11.38         1.74 
TCGA-57-1992 TCGA-57-1993 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 
       29.00        25.08        22.32       116.12         9.40        34.39 
TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1724 TCGA-61-1730 TCGA-61-1737 
        2.14         5.42        44.81        20.94         4.34        44.84 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1904 TCGA-61-1906 TCGA-61-1995 
       33.67        43.69         1.45         9.07        34.13         2.01 
TCGA-61-2002 TCGA-61-2012 TCGA-61-2088 TCGA-61-2094 TCGA-61-2097 TCGA-61-2102 
       17.98        30.64         4.77        71.74        60.62         6.48 
TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2612 TCGA-61-2613 TCGA-WR-A838 
       76.87        20.68        44.52         6.35        31.07         9.99 
TCGA-09-0367 TCGA-10-0926 TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 TCGA-13-0714 
       17.98        25.91        81.86        34.19        32.88         6.21 
TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 
       44.55         2.73        12.39        31.20        15.19        17.82 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0764 
       55.17         2.50        11.18        11.38        11.54        61.84 
TCGA-13-0766 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0800 TCGA-13-0803 
       56.71       118.42       107.28        63.09        87.48        43.86 
TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 TCGA-13-0899 
       35.28        13.61        68.94       107.18       153.37        66.15 
TCGA-13-0903 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
      127.79       118.98        60.59       116.65        44.55        37.64 
TCGA-13-0913 TCGA-13-0924 TCGA-13-2071 
      109.32        85.94        25.41 

$`18Q LOSS WILD-TYPE`
TCGA-3P-A9WA TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 
       13.81        11.87        43.92         2.01        18.51        11.87 
TCGA-04-1346 TCGA-04-1348 TCGA-04-1349 TCGA-04-1353 TCGA-04-1361 TCGA-04-1365 
       65.52        48.76        21.57         0.53        32.52        76.57 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1525 TCGA-04-1536 
      103.40        82.39        56.55        41.59        38.37        29.10 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1652 
       84.20        55.43        48.89        27.88        28.64        31.86 
TCGA-04-1654 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       47.70         9.99        38.43        89.33        74.93        41.62 
TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1674 TCGA-09-2045 TCGA-09-2049 
       55.36        30.51        17.98         8.55        35.15       112.41 
TCGA-09-2051 TCGA-09-2055 TCGA-13-1404 TCGA-13-1410 TCGA-13-1412 TCGA-13-1477 
       63.09        26.93        81.17        81.01        32.35        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1485 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
       87.06        61.71        20.68        83.93        52.44       125.56 
TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 TCGA-13-1501 TCGA-13-1504 TCGA-13-1507 
       93.90         4.24       127.27        43.20        34.82        65.52 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2060 TCGA-13-A5FT 
       80.15        44.68        54.25        14.53        77.88        70.45 
TCGA-13-A5FU TCGA-20-0996 TCGA-23-1022 TCGA-23-1024 TCGA-23-1026 TCGA-23-1029 
        8.42        72.20        49.68        15.39        26.83         8.81 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1114 
       29.13        18.90         2.76        51.35        54.51        68.68 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1123 TCGA-23-1809 TCGA-23-2077 TCGA-23-2078 
        4.27         6.38        33.47         0.53       115.89        87.48 
TCGA-23-2645 TCGA-24-0975 TCGA-24-0980 TCGA-24-1103 TCGA-24-1419 TCGA-24-1422 
        4.50        21.80         7.66        54.12         7.86         0.76 
TCGA-24-1426 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1466 
        5.36        28.37        18.64        18.67        43.53        45.14 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1553 
      105.99         9.11        56.58        41.06        51.91        58.09 
TCGA-24-1555 TCGA-24-1565 TCGA-24-1567 TCGA-24-1604 TCGA-24-1616 TCGA-24-1845 
       88.50        10.26        17.23        88.37        38.24         3.81 
TCGA-24-1846 TCGA-24-1924 TCGA-24-1930 TCGA-24-2019 TCGA-24-2024 TCGA-24-2026 
        4.37        30.21        81.11         4.87        58.16        34.82 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2262 
       55.92        18.48        64.01        44.52        57.07         0.36 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2290 TCGA-24-2295 TCGA-24-2297 TCGA-25-1314 
       70.45        44.61        36.23        33.11        55.86        33.01 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1623 TCGA-25-1627 TCGA-25-1628 
       34.98        65.00        37.97        18.58        12.95        20.61 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1633 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 
       38.20         0.30        62.17        52.04        14.96        24.99 
TCGA-25-2391 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 
       49.05         3.02        12.00        45.01        19.99        42.02 
TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1695 
       31.00        78.90        47.61        48.33       101.79        40.41 
TCGA-29-1696 TCGA-29-1698 TCGA-29-1699 TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 
       33.93        68.32        36.36        18.25        31.27        34.62 
TCGA-29-1761 TCGA-29-1766 TCGA-29-1769 TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 
       17.36        39.42        22.98        22.55        17.33        11.84 
TCGA-29-1778 TCGA-29-1784 TCGA-29-1785 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 
       14.93         5.36        36.30        13.84        42.25        21.47 
TCGA-29-2436 TCGA-30-1853 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 
        9.76        36.26         0.26        48.10        44.91         6.12 
TCGA-30-1867 TCGA-30-1887 TCGA-30-1892 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 
        1.22        24.26        48.79        18.77        22.49         6.71 
TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1574 TCGA-36-1581 TCGA-36-2529 
       42.51        44.12        28.77        22.55        24.69        35.05 
TCGA-36-2530 TCGA-36-2537 TCGA-36-2540 TCGA-36-2544 TCGA-36-2547 TCGA-36-2549 
       33.01        25.91        23.80        20.98        20.52         6.05 
TCGA-36-2551 TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-57-1584 
       16.18        47.57        28.93        42.02        10.42        21.14 
TCGA-57-1586 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-61-1721 TCGA-61-1722 
       22.32        25.02       180.20        80.12        11.11         8.09 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 
       31.43        18.54        27.88        31.79        28.47        48.79 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 
       35.80         2.43         8.42         5.79        11.41        13.02 
TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 
       31.30        37.05        42.51        48.92        56.61        67.76 
TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 
       43.43        15.75        38.17         5.52        14.50         4.01 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
       30.64        39.85         1.18        45.96        45.40         4.80 
TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 TCGA-61-2101 TCGA-61-2111 
       51.72        61.64        58.39        65.52        55.50       125.75 
TCGA-61-2113 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-09-0364 
       22.22         8.61        39.68        18.94         0.79        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0369 TCGA-10-0925 TCGA-10-0928 TCGA-10-0933 
        9.47        57.76        35.57        54.31        18.51        14.66 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0717 
        6.71        35.44        36.92        19.99        20.91        24.59 
TCGA-13-0723 TCGA-13-0761 TCGA-13-0762 TCGA-13-0768 TCGA-13-0791 TCGA-13-0795 
       39.58        38.01       111.78        58.65        40.24        20.35 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0805 TCGA-13-0885 
       69.73        83.34        45.99        51.02        35.31       111.39 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
       66.67        92.42        95.15       145.45       102.84        43.36 
TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 TCGA-13-0904 TCGA-13-0905 TCGA-13-0916 
       71.74       134.04        19.36        50.37       123.16        58.68 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 
       84.53        48.79        48.76        83.74 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.79               0.26 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            153.37             180.20 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            29.420             35.685 
[1] "0.8 - 153.4 (29.4)" "0.3 - 180.2 (35.7)"
[1] "hr=" "1.1"
D74V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  18Q LOSS MUTATED         2   277                0
  18Q LOSS WILD-TYPE       1   281                2
D74V3, multiclass
                  clus
vv                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  OMENTUM                         2                  1
  OVARY                         277                281
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V4, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   264   4
  18Q LOSS WILD-TYPE 277   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    264    4
  18Q LOSS WILD-TYPE  277    1
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO               264                277
  YES                4                  1
[1] 2 2
[1] FALSE
D74V5, continuous
                    vv
clus                 R0 R1 R2 RX
  18Q LOSS MUTATED    7 14  1  0
  18Q LOSS WILD-TYPE  8 12  4  3
D74V6, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0                7                  8
  R1               14                 12
  R2                1                  4
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     7 156
  18Q LOSS WILD-TYPE   3 171
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      7  156
  18Q LOSS WILD-TYPE    3  171
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    7                  3
  NOT HISPANIC OR LATINO              156                171
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    73 105
  19P LOSS WILD-TYPE 155 226
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               178                381 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               105                226 
$`19P LOSS MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1332 TCGA-04-1341 TCGA-04-1343 TCGA-04-1347 
       13.81        20.52        41.00         1.08        11.87        63.09 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
       21.57        63.98        49.28        44.32        33.67        76.57 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1517 TCGA-04-1530 TCGA-04-1638 TCGA-04-1644 
      103.40        82.39        19.99       119.08        55.43        48.89 
TCGA-04-1646 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1668 
       27.88        47.70        45.37         9.99        38.43        55.36 
TCGA-09-1672 TCGA-09-1673 TCGA-09-2049 TCGA-09-2051 TCGA-09-2053 TCGA-09-2055 
        5.85         3.02       112.41        63.09        39.75        26.93 
TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1411 TCGA-13-1412 
       12.46        77.10        81.17        28.54        17.46        32.35 
TCGA-13-1483 TCGA-13-1489 TCGA-13-1492 TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 
       29.42        83.93       125.56         4.24        66.15       115.07 
TCGA-13-1504 TCGA-13-1507 TCGA-13-2060 TCGA-13-2061 TCGA-23-1027 TCGA-23-1030 
       34.82        65.52        77.88        76.90        32.09        29.13 
TCGA-23-1110 TCGA-23-1113 TCGA-23-1119 TCGA-23-1120 TCGA-23-1123 TCGA-23-1124 
       54.51        31.20       129.96         4.27        33.47        58.13 
TCGA-23-2072 TCGA-23-2643 TCGA-24-0966 TCGA-24-0979 TCGA-24-1413 TCGA-24-1424 
       24.95         4.70         7.63        41.56         6.31         6.02 
TCGA-24-1434 TCGA-24-1463 TCGA-24-1464 TCGA-24-1470 TCGA-24-1544 TCGA-24-1549 
       18.67        72.92        12.46         3.45        26.96        56.58 
TCGA-24-1560 TCGA-24-1564 TCGA-24-1846 TCGA-24-2019 TCGA-24-2024 TCGA-24-2026 
       44.09        25.87         4.37         4.87        58.16        34.82 
TCGA-24-2260 TCGA-24-2288 TCGA-24-2290 TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 
       36.16         0.82        36.23        53.26        26.96        52.04 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1627 TCGA-25-1630 TCGA-25-1632 TCGA-25-1633 
       42.05         2.01        12.95        38.20        59.15        62.17 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1877 TCGA-25-1878 TCGA-25-2392 
       35.87        52.04        14.96        24.00        85.05         1.02 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2399 TCGA-25-2400 TCGA-25-2404 TCGA-25-2409 
       38.04         3.02        19.99        42.02        29.03        26.99 
TCGA-29-1691 TCGA-29-1694 TCGA-29-1697 TCGA-29-1699 TCGA-29-1701 TCGA-29-1705 
       48.33        39.02        31.20        36.36        16.93        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1761 TCGA-29-1763 TCGA-29-1769 TCGA-29-1771 
       41.98        31.27        17.36        66.81        22.98        22.55 
TCGA-29-1774 TCGA-29-1778 TCGA-29-2427 TCGA-29-2428 TCGA-30-1853 TCGA-30-1861 
       17.33        14.93        62.47        45.11        36.26        34.78 
TCGA-30-1866 TCGA-30-1891 TCGA-31-1944 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 
       36.62        30.05        45.57         6.71        42.51        44.12 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 
        2.20        28.77        29.10        22.85         8.55        30.08 
TCGA-36-1581 TCGA-36-2530 TCGA-36-2537 TCGA-36-2538 TCGA-36-2548 TCGA-36-2551 
       24.69        33.01        25.91        25.08        14.17        16.18 
TCGA-57-1584 TCGA-57-1585 TCGA-57-1993 TCGA-57-1994 TCGA-59-2372 TCGA-61-1722 
       21.14         1.74        25.08        25.02        44.81         8.09 
TCGA-61-1733 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1903 TCGA-61-1907 
       31.79        35.80         2.43        33.67        13.02        31.30 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1919 TCGA-61-2002 TCGA-61-2016 TCGA-61-2017 
       67.76        43.43        38.17        17.98         1.18        45.96 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2102 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P 
        4.80         4.77         6.48         6.35         8.61        39.68 
TCGA-09-0366 TCGA-10-0928 TCGA-10-0936 TCGA-10-0937 TCGA-13-0723 TCGA-13-0724 
       57.76        18.51        36.92        19.99        39.58         2.73 
TCGA-13-0730 TCGA-13-0762 TCGA-13-0768 TCGA-13-0797 TCGA-13-0800 TCGA-13-0803 
       17.82       111.78        58.65        69.73        87.48        43.86 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0899 TCGA-13-0908 TCGA-13-0911 TCGA-13-0919 
      111.39       153.37        66.15        60.59        44.55        84.53 
TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       48.79        48.76        83.74        85.94 

$`19P LOSS WILD-TYPE`
TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       11.87        43.92         1.81        49.15         2.01        46.62 
TCGA-04-1342 TCGA-04-1346 TCGA-04-1348 TCGA-04-1351 TCGA-04-1353 TCGA-04-1361 
       18.51        65.52        48.76        65.46         0.53        32.52 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1519 TCGA-04-1525 TCGA-04-1536 TCGA-04-1542 
       56.55        41.59         0.79        38.37        29.10        84.20 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-09-1662 TCGA-09-1664 
       28.64        64.64        36.23        31.86        89.33        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 TCGA-09-1670 TCGA-09-1674 
       41.62        57.60        61.87        30.51        17.98         8.55 
TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 
       97.55         6.18         6.12        35.15         4.54        71.11 
TCGA-09-2054 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1477 
       20.94        83.31        55.23        57.27        81.01        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 
       87.06        61.71       124.44        20.68        22.39        70.82 
TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1497 TCGA-13-1500 TCGA-13-1501 
       52.44        93.90        90.38       127.27        13.97        43.20 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
       65.69        34.16        80.15        44.68        54.25        14.53 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
       80.02        78.48        65.52        70.45         8.42        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 
       25.94        26.20        72.20        27.52        25.38        19.10 
TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 
       16.70         2.93         2.66        47.54        49.68        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1028 TCGA-23-1029 TCGA-23-1031 TCGA-23-1032 
       15.39        26.83        49.41         8.81        18.90         2.76 
TCGA-23-1109 TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
       51.35         3.22        68.68        19.46        33.30        86.01 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1809 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 
        6.38        39.09         0.53       115.89        87.48        91.66 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2645 TCGA-24-0970 TCGA-24-0975 
       77.00        49.84         2.76         4.50        11.64        21.80 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1416 
        7.66        22.32        54.12        63.55        47.41         6.38 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 
        7.82         7.99         7.86         0.76         6.25         5.95 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 
        5.36         4.83        17.39        28.37        18.64        43.53 
TCGA-24-1436 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 
        8.55        45.14       105.99         9.11         1.18        22.22 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
       57.40        64.27        16.21        41.06        51.91        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1562 
       58.09        88.50        70.62        39.88        19.53        45.50 
TCGA-24-1563 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 
       47.70        10.26        17.23        90.15        88.37        48.33 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 
       38.24         8.32         3.48         3.72         3.81        11.28 
TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 
        5.79         5.52         9.80        22.68        30.21        16.44 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2020 TCGA-24-2023 TCGA-24-2027 TCGA-24-2029 
       11.05        81.11       152.02        44.84       109.71        14.43 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 
       55.92        18.48        28.18        64.01        44.52        57.07 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 
        0.79         0.36        47.54        31.63        70.45        44.61 
TCGA-24-2289 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 TCGA-25-1314 
       67.36        16.64        33.11        55.86         1.02        33.01 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 
       34.98        65.00        37.97        33.96         2.99        12.99 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1628 TCGA-25-1631 
       15.02        18.58        27.62        17.03        20.61         0.30 
TCGA-25-1871 TCGA-25-2042 TCGA-25-2391 TCGA-25-2397 TCGA-25-2398 TCGA-25-2401 
       24.99        13.02        49.05        12.00        45.01         2.96 
TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1695 TCGA-29-1696 
       31.00        78.90        47.61       101.79        40.41        33.93 
TCGA-29-1698 TCGA-29-1702 TCGA-29-1703 TCGA-29-1711 TCGA-29-1762 TCGA-29-1764 
       68.32        23.93        59.67        34.62        86.60        62.93 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1770 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 
       39.42        31.30        24.36        12.36        11.84        12.30 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 
        8.38         7.23         5.36        36.30        86.17        65.00 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ 
       13.84        42.25        21.47        11.47         9.76        35.77 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 
       38.07        51.91         2.47        15.68         0.26        48.10 
TCGA-30-1860 TCGA-30-1862 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1892 
       44.91         6.12         1.22        57.57        24.26        48.79 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-36-1570 TCGA-36-1574 TCGA-36-1577 
       30.18        18.77        22.49        21.53        22.55        25.74 
TCGA-36-1578 TCGA-36-1580 TCGA-36-2529 TCGA-36-2532 TCGA-36-2534 TCGA-36-2540 
       27.85        24.23        35.05        29.49        29.82        23.80 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 
       21.60         2.24        20.98        18.31        20.52         6.05 
TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
       11.47        47.57        23.74        28.93        42.02        10.42 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1586 TCGA-57-1992 
       40.77         1.48        24.03        11.38        22.32        29.00 
TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 
      180.20        80.12        22.32       116.12         9.40        34.39 
TCGA-59-2355 TCGA-59-2363 TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
        2.14         5.42        11.11        20.94        31.43        18.54 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1743 
       27.88         4.34        28.47        48.79        44.84        43.69 
TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1904 TCGA-61-1906 
        1.45         8.42         5.79        11.41         9.07        34.13 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1918 TCGA-61-1995 
       37.05        42.51        48.92        56.61        15.75         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 
        5.52        14.50         4.01        30.64        39.85        30.64 
TCGA-61-2018 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 
       45.40        51.72        71.74        61.64        58.39        60.62 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       65.52        55.50        76.87        20.68        44.52       125.75 
TCGA-61-2113 TCGA-61-2613 TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 
       22.22        31.07        18.94         0.79         9.99        29.16 
TCGA-09-0365 TCGA-09-0367 TCGA-09-0369 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 
        9.47        17.98        35.57        54.31        25.91        81.86 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0938 
       34.19        32.88        14.66         6.71        35.44        20.91 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 
        6.21        24.59        44.55        12.39        31.20        15.19 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 
       55.17         2.50        11.18        11.38        11.54        38.01 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 
       61.84        56.71        40.24       118.42       107.28        63.09 
TCGA-13-0795 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 
       20.35        83.34        45.99        51.02        35.28        35.31 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 
       13.61        68.94       107.18        66.67        92.42        95.15 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 
      145.45       102.84        43.36        71.74       134.04        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0912 
      127.79        50.37       123.16       118.98       116.65        37.64 
TCGA-13-0913 TCGA-13-0916 TCGA-13-2071 
      109.32        58.68        25.41 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.82               0.26 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            153.37             180.20 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             33.67              31.63 
[1] "0.8 - 153.4 (33.7)" "0.3 - 180.2 (31.6)"
[1] "hr=" "1"  
D75V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  19P LOSS MUTATED         1   179                0
  19P LOSS WILD-TYPE       2   379                2
D75V3, multiclass
                  clus
vv                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  OMENTUM                         1                  2
  OVARY                         179                379
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V4, binary
                    cls
clus                   0   1
  19P LOSS MUTATED   174   1
  19P LOSS WILD-TYPE 367   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED    174    1
  19P LOSS WILD-TYPE  367    4
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO               174                367
  YES                1                  4
[1] 2 2
[1] FALSE
D75V5, continuous
                    vv
clus                 R0 R1 R2 RX
  19P LOSS MUTATED    2 11  1  1
  19P LOSS WILD-TYPE 13 15  4  2
D75V6, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0                2                 13
  R1               11                 15
  R2                1                  4
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     4 109
  19P LOSS WILD-TYPE   6 218
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      4  109
  19P LOSS WILD-TYPE    6  218
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  6
  NOT HISPANIC OR LATINO              109                218
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    73  95
  19Q LOSS WILD-TYPE 155 236
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               168                391 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                95                236 
$`19Q LOSS MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1341 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 
       13.81        20.52         1.08        63.09        21.57        63.98 
TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 
       49.28        44.32        33.67        76.57       103.40        82.39 
TCGA-04-1530 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1654 TCGA-04-1655 
      119.08        55.43        48.89        27.88        47.70        45.37 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1664 TCGA-09-1667 TCGA-09-1668 TCGA-09-1672 
        9.99        38.43        74.93        61.87        55.36         5.85 
TCGA-09-1673 TCGA-09-1675 TCGA-09-2049 TCGA-09-2051 TCGA-09-2053 TCGA-09-2055 
        3.02        97.55       112.41        63.09        39.75        26.93 
TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1411 
       12.46        77.10        81.17        28.54        83.31        17.46 
TCGA-13-1412 TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 TCGA-13-1496 TCGA-13-1498 
       32.35        83.93        52.44        93.90         4.24        66.15 
TCGA-13-1499 TCGA-13-1510 TCGA-13-2060 TCGA-13-2061 TCGA-23-1024 TCGA-23-1030 
      115.07        44.68        77.88        76.90        15.39        29.13 
TCGA-23-1110 TCGA-23-1113 TCGA-23-1119 TCGA-23-1120 TCGA-23-1123 TCGA-23-1124 
       54.51        31.20       129.96         4.27        33.47        58.13 
TCGA-23-2072 TCGA-23-2643 TCGA-24-0966 TCGA-24-0979 TCGA-24-0980 TCGA-24-1413 
       24.95         4.70         7.63        41.56         7.66         6.31 
TCGA-24-1424 TCGA-24-1434 TCGA-24-1463 TCGA-24-1464 TCGA-24-1467 TCGA-24-1470 
        6.02        18.67        72.92        12.46       105.99         3.45 
TCGA-24-1549 TCGA-24-1560 TCGA-24-1564 TCGA-24-1846 TCGA-24-2019 TCGA-24-2024 
       56.58        44.09        25.87         4.37         4.87        58.16 
TCGA-24-2026 TCGA-24-2260 TCGA-24-2290 TCGA-24-2293 TCGA-24-2298 TCGA-25-1315 
       34.82        36.16        36.23        16.64        53.26        52.04 
TCGA-25-1316 TCGA-25-1627 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 
       42.05        12.95        59.15        62.17        35.87        52.04 
TCGA-25-1870 TCGA-25-1877 TCGA-25-1878 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 
       14.96        24.00        85.05         1.02        38.04         3.02 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2409 TCGA-29-1694 TCGA-29-1697 TCGA-29-1699 
       19.99        42.02        26.99        39.02        31.20        36.36 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1761 TCGA-29-1763 TCGA-29-1769 
       18.25        41.98        31.27        17.36        66.81        22.98 
TCGA-29-1771 TCGA-29-1778 TCGA-29-2427 TCGA-29-2428 TCGA-30-1853 TCGA-30-1861 
       22.55        14.93        62.47        45.11        36.26        34.78 
TCGA-30-1866 TCGA-30-1891 TCGA-31-1944 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 
       36.62        30.05        45.57         6.71        42.51        44.12 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1580 
       28.77        29.10        22.85         8.55        30.08        24.23 
TCGA-36-1581 TCGA-36-2530 TCGA-36-2537 TCGA-36-2538 TCGA-36-2548 TCGA-36-2551 
       24.69        33.01        25.91        25.08        14.17        16.18 
TCGA-57-1584 TCGA-57-1585 TCGA-57-1993 TCGA-57-1994 TCGA-59-2372 TCGA-61-1725 
       21.14         1.74        25.08        25.02        44.81        31.43 
TCGA-61-1733 TCGA-61-1738 TCGA-61-1903 TCGA-61-1907 TCGA-61-1915 TCGA-61-1917 
       31.79        35.80        13.02        31.30        67.76        43.43 
TCGA-61-1919 TCGA-61-2002 TCGA-61-2016 TCGA-61-2017 TCGA-61-2087 TCGA-61-2088 
       38.17        17.98         1.18        45.96         4.80         4.77 
TCGA-61-2102 TCGA-61-2612 TCGA-OY-A56P TCGA-09-0366 TCGA-10-0928 TCGA-10-0936 
        6.48         6.35        39.68        57.76        18.51        36.92 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0723 TCGA-13-0724 TCGA-13-0762 TCGA-13-0768 
       19.99        20.91        39.58         2.73       111.78        58.65 
TCGA-13-0797 TCGA-13-0800 TCGA-13-0803 TCGA-13-0804 TCGA-13-0807 TCGA-13-0886 
       69.73        87.48        43.86        35.28        13.61       153.37 
TCGA-13-0899 TCGA-13-0908 TCGA-13-0911 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 
       66.15        60.59        44.55        84.53        48.76        83.74 

$`19Q LOSS WILD-TYPE`
TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 
       11.87        43.92        41.00         1.81        49.15         2.01 
TCGA-04-1338 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 TCGA-04-1351 
       46.62        18.51        11.87        65.52        48.76        65.46 
TCGA-04-1353 TCGA-04-1361 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 
        0.53        32.52        56.55        41.59        19.99         0.79 
TCGA-04-1525 TCGA-04-1536 TCGA-04-1542 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 
       38.37        29.10        84.20        28.64        64.64        36.23 
TCGA-04-1652 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 TCGA-09-1670 
       31.86        89.33        41.62        57.60        30.51        17.98 
TCGA-09-1674 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 
        8.55         6.18         6.12        35.15         4.54        71.11 
TCGA-09-2054 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1477 TCGA-13-1481 
       20.94        55.23        57.27        81.01        54.64        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 
       61.71        29.42       124.44        20.68        22.39        70.82 
TCGA-13-1492 TCGA-13-1495 TCGA-13-1497 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 
      125.56        90.38       127.27        13.97        43.20        34.82 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 
       65.69        34.16        65.52        80.15        54.25        14.53 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
       80.02        78.48        65.52        70.45         8.42        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 
       25.94        26.20        72.20        27.52        25.38        19.10 
TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 
       16.70         2.93         2.66        47.54        49.68        40.54 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1031 TCGA-23-1032 
       26.83        32.09        49.41         8.81        18.90         2.76 
TCGA-23-1109 TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
       51.35         3.22        68.68        19.46        33.30        86.01 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1809 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 
        6.38        39.09         0.53       115.89        87.48        91.66 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2645 TCGA-24-0970 TCGA-24-0975 
       77.00        49.84         2.76         4.50        11.64        21.80 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1416 TCGA-24-1417 
       22.32        54.12        63.55        47.41         6.38         7.82 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 
        7.99         7.86         0.76         6.25         5.95         5.36 
TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 TCGA-24-1436 
        4.83        17.39        28.37        18.64        43.53         8.55 
TCGA-24-1466 TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 
       45.14         9.11         1.18        22.22        26.96        57.40 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 
       64.27        16.21        41.06        51.91        41.39        58.09 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1562 TCGA-24-1563 
       88.50        70.62        39.88        19.53        45.50        47.70 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 
       10.26        17.23        90.15        88.37        48.33        38.24 
TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 TCGA-24-1849 
        8.32         3.48         3.72         3.81        11.28         5.79 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 
        5.52         9.80        22.68        30.21        16.44        11.05 
TCGA-24-1930 TCGA-24-2020 TCGA-24-2023 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 
       81.11       152.02        44.84       109.71        14.43        55.92 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2261 
       18.48        28.18        64.01        44.52        57.07         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
        0.36        47.54        31.63        70.45        44.61         0.82 
TCGA-24-2289 TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 
       67.36        33.11        55.86         1.02        26.96        33.01 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 
        2.01        34.98        65.00        37.97        33.96         2.99 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1628 
       12.99        15.02        18.58        27.62        17.03        20.61 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1871 TCGA-25-2042 TCGA-25-2391 TCGA-25-2397 
       38.20         0.30        24.99        13.02        49.05        12.00 
TCGA-25-2398 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 
       45.01         2.96        29.03        31.00        78.90        47.61 
TCGA-29-1691 TCGA-29-1693 TCGA-29-1695 TCGA-29-1696 TCGA-29-1698 TCGA-29-1701 
       48.33       101.79        40.41        33.93        68.32        16.93 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1711 TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 
       23.93        59.67        34.62        86.60        62.93        39.42 
TCGA-29-1768 TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 
       31.30        24.36        17.33        12.36        11.84        12.30 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 
        8.38         7.23         5.36        36.30        86.17        65.00 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ 
       13.84        42.25        21.47        11.47         9.76        35.77 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 
       38.07        51.91         2.47        15.68         0.26        48.10 
TCGA-30-1860 TCGA-30-1862 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1892 
       44.91         6.12         1.22        57.57        24.26        48.79 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1959 TCGA-36-1570 TCGA-36-1574 
       30.18        18.77        22.49         2.20        21.53        22.55 
TCGA-36-1577 TCGA-36-1578 TCGA-36-2529 TCGA-36-2532 TCGA-36-2534 TCGA-36-2540 
       25.74        27.85        35.05        29.49        29.82        23.80 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 
       21.60         2.24        20.98        18.31        20.52         6.05 
TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
       11.47        47.57        23.74        28.93        42.02        10.42 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1586 TCGA-57-1992 
       40.77         1.48        24.03        11.38        22.32        29.00 
TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 
      180.20        80.12        22.32       116.12         9.40        34.39 
TCGA-59-2355 TCGA-59-2363 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1727 
        2.14         5.42        11.11         8.09        20.94        18.54 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1740 
       27.88         4.34        28.47        48.79        44.84         2.43 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 
       33.67        43.69         1.45         8.42         5.79        11.41 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 
        9.07        34.13        37.05        42.51        48.92        56.61 
TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 
       15.75         2.01         5.52        14.50         4.01        30.64 
TCGA-61-2009 TCGA-61-2012 TCGA-61-2018 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       39.85        30.64        45.40        51.72        71.74        61.64 
TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 TCGA-61-2109 
       58.39        60.62        65.52        55.50        76.87        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56Q 
       44.52       125.75        22.22        31.07         8.61        18.94 
TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0367 TCGA-09-0369 
        0.79         9.99        29.16         9.47        17.98        35.57 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 
       54.31        25.91        81.86        34.19        32.88        14.66 
TCGA-10-0934 TCGA-10-0935 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0725 
        6.71        35.44         6.21        24.59        44.55        12.39 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 
       31.20        15.19        17.82        55.17         2.50        11.18 
TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 
       11.38        11.54        38.01        61.84        56.71        40.24 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0799 TCGA-13-0801 
      118.42       107.28        63.09        20.35        83.34        45.99 
TCGA-13-0802 TCGA-13-0805 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 
       51.02        35.31        68.94       107.18       111.39        66.67 
TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 
       92.42        95.15       145.45       102.84        43.36        71.74 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
      134.04        19.36       127.79        50.37       123.16       118.98 
TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0924 
      116.65        37.64       109.32        58.68        48.79        85.94 
TCGA-13-2071 
       25.41 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              1.02               0.26 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            153.37             180.20 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            35.835             31.070 
[1] "1.0 - 153.4 (35.8)" "0.3 - 180.2 (31.1)"
[1] "hr=" "1.1"
D76V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  19Q LOSS MUTATED         2   167                0
  19Q LOSS WILD-TYPE       1   391                2
D76V3, multiclass
                  clus
vv                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  OMENTUM                         2                  1
  OVARY                         167                391
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V4, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED   166   1
  19Q LOSS WILD-TYPE 375   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED    166    1
  19Q LOSS WILD-TYPE  375    4
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO               166                375
  YES                1                  4
[1] 2 2
[1] FALSE
D76V5, continuous
                    vv
clus                 R0 R1 R2 RX
  19Q LOSS MUTATED    2 11  1  1
  19Q LOSS WILD-TYPE 13 15  4  2
D76V6, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0                2                 13
  R1               11                 15
  R2                1                  4
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     4 102
  19Q LOSS WILD-TYPE   6 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      4  102
  19Q LOSS WILD-TYPE    6  225
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  6
  NOT HISPANIC OR LATINO              102                225
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    25  24
  20P LOSS WILD-TYPE 203 307
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                49                510 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                24                307 
$`20P LOSS MUTATED`
TCGA-04-1336 TCGA-04-1536 TCGA-09-1667 TCGA-09-2048 TCGA-13-1489 TCGA-13-1494 
       49.15        29.10        61.87         4.54        83.93        93.90 
TCGA-13-1495 TCGA-13-2059 TCGA-20-0987 TCGA-20-1682 TCGA-20-1687 TCGA-23-1028 
       90.38        78.48        23.05        27.52         2.66        49.41 
TCGA-23-1118 TCGA-23-1119 TCGA-23-2072 TCGA-24-1417 TCGA-24-1426 TCGA-24-1427 
       86.01       129.96        24.95         7.82         5.36         4.83 
TCGA-24-1428 TCGA-24-1463 TCGA-24-1471 TCGA-24-1552 TCGA-24-1603 TCGA-24-2298 
       17.39        72.92         1.18        41.39        90.15        53.26 
TCGA-25-2392 TCGA-29-1693 TCGA-29-1702 TCGA-29-1711 TCGA-29-1781 TCGA-29-2434 
        1.02       101.79        23.93        34.62         8.38        11.47 
TCGA-29-2436 TCGA-30-1853 TCGA-36-1577 TCGA-36-1578 TCGA-57-1993 TCGA-61-1725 
        9.76        36.26        25.74        27.85        25.08        31.43 
TCGA-61-1734 TCGA-61-1737 TCGA-61-1741 TCGA-61-2088 TCGA-WR-A838 TCGA-09-0364 
       28.47        44.84        33.67         4.77         9.99        29.16 
TCGA-10-0930 TCGA-13-0720 TCGA-13-0804 TCGA-13-0883 TCGA-13-0893 TCGA-13-0921 
       34.19        44.55        35.28        68.94        43.36        48.76 
TCGA-13-2071 
       25.41 

$`20P LOSS WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 
        2.01        46.62         1.08        18.51        11.87        65.52 
TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 
       63.09        48.76        21.57        63.98        65.46         0.53 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       49.28        32.52        44.32        33.67        76.57       103.40 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 
       82.39        56.55        41.59        19.99         0.79        38.37 
TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 
      119.08        84.20        55.43        48.89        27.88        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 
       64.64        36.23        31.86        47.70        45.37         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1668 
       38.43        89.33        74.93        41.62        57.60        55.36 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 
       30.51        17.98         5.85         3.02         8.55        97.55 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
        6.18         6.12        35.15       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 
       39.75        20.94        26.93        12.46        77.10        81.17 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
       28.54        83.31        55.23        57.27        81.01        17.46 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
       32.35        54.64        87.06        61.71        29.42       124.44 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 TCGA-13-1496 
       20.68        22.39        70.82        52.44       125.56         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 
      127.27        66.15       115.07        13.97        43.20        34.82 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
       65.69        34.16        65.52        80.15        44.68        54.25 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT 
       14.53        80.02        77.88        76.90        65.52        70.45 
TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 
        8.42        25.94        26.20        72.20        25.38        19.10 
TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 
       16.70         2.93        47.54        49.68        40.54        15.39 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       26.83        32.09         8.81        29.13        18.90         2.76 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 
       51.35        54.51         3.22        31.20        68.68        19.46 
TCGA-23-1117 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 
       33.30         4.27         6.38        39.09        33.47        58.13 
TCGA-23-1809 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 
        0.53       115.89        87.48        91.66        77.00        49.84 
TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 
        2.76         4.70         4.50         7.63        11.64        21.80 
TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 
       41.56         7.66        22.32        54.12        63.55        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 
        6.31         6.38         7.99         7.86         0.76         6.25 
TCGA-24-1424 TCGA-24-1425 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 
        6.02         5.95        28.37        18.64        18.67        43.53 
TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 
        8.55        12.46        45.14       105.99         9.11         3.45 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 
       22.22        26.96        57.40        64.27        16.21        56.58 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       41.06        51.91        58.09        88.50        70.62        39.88 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 
       19.53        44.09        45.50        47.70        25.87        10.26 
TCGA-24-1567 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 
       17.23        88.37        48.33        38.24         8.32         3.48 
TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 
        3.72         3.81         4.37        11.28         5.79         5.52 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 
        9.80        22.68        30.21        16.44        11.05        81.11 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 
        4.87       152.02        44.84        58.16        34.82       109.71 
TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
       14.43        55.92        18.48        28.18        64.01        44.52 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 
       57.07        36.16         0.79         0.36        47.54        31.63 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 
       70.45        44.61         0.82        67.36        36.23        16.64 
TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 
       33.11        55.86         1.02        26.96        33.01        52.04 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 
       42.05         2.01        34.98        65.00        37.97        33.96 
TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 
        2.99        12.99        15.02        18.58        27.62        17.03 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
       12.95        20.61        38.20         0.30        59.15        62.17 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 
       35.87        52.04        14.96        24.99        24.00        85.05 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 
       13.02        49.05        38.04         3.02        12.00        45.01 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       19.99        42.02         2.96        29.03        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       78.90        47.61        48.33        39.02        40.41        33.93 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 
       31.20        68.32        36.36        16.93        59.67        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 
       41.98        31.27        17.36        86.60        66.81        62.93 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
       39.42        31.30        22.98        24.36        22.55        17.33 
TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1783 TCGA-29-1784 
       12.36        11.84        12.30        14.93         7.23         5.36 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 
       36.30        86.17        65.00        62.47        45.11        13.84 
TCGA-29-2431 TCGA-29-2432 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 
       42.25        21.47        35.77        38.07        51.91         2.47 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 
       15.68         0.26        48.10        44.91        34.78         6.12 
TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 
       36.62         1.22        57.57        24.26        30.05        48.79 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 
       45.57        30.18        18.77        22.49         6.71        42.51 
TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 
       44.12         2.20        28.77        29.10        21.53        22.85 
TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 
       22.55         8.55        30.08        24.23        24.69        35.05 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       33.01        29.49        29.82        25.91        25.08        23.80 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 
       21.60         2.24        20.98        18.31        20.52        14.17 
TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
        6.05        16.18        11.47        47.57        23.74        28.93 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 
       42.02        10.42        40.77         1.48        24.03        11.38 
TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1994 TCGA-59-2348 
       21.14         1.74        22.32        29.00        25.02       180.20 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 
       80.12        22.32       116.12         9.40        34.39         2.14 
TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1727 
        5.42        44.81        11.11         8.09        20.94        18.54 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 TCGA-61-1738 TCGA-61-1740 
       27.88         4.34        31.79        48.79        35.80         2.43 
TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 
       43.69         1.45         8.42         5.79        11.41        13.02 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 
        9.07        34.13        31.30        37.05        42.51        48.92 
TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 
       56.61        67.76        43.43        15.75        38.17         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 
        5.52        14.50        17.98         4.01        30.64        39.85 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 
       30.64         1.18        45.96        45.40         4.80        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 
       71.74        61.64        58.39        60.62        65.52        55.50 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
        6.48        76.87        20.68        44.52       125.75        22.22 
TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
        6.35        31.07         8.61        39.68        18.94         0.79 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-10-0925 TCGA-10-0926 
        9.47        57.76        17.98        35.57        54.31        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 
       81.86        18.51        32.88        14.66         6.71        35.44 
TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0723 
       36.92        19.99        20.91         6.21        24.59        39.58 
TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
        2.73        12.39        31.20        15.19        17.82        55.17 
TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 
        2.50        11.18        11.38        11.54        38.01       111.78 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       61.84        56.71        58.65        40.24       118.42       107.28 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
       63.09        20.35        69.73        83.34        87.48        45.99 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 TCGA-13-0884 TCGA-13-0885 
       51.02        43.86        35.31        13.61       107.18       111.39 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 
      153.37        66.67        92.42        95.15       145.45       102.84 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 
       71.74        66.15       134.04        19.36       127.79        50.37 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
      123.16       118.98        60.59       116.65        44.55        37.64 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 
      109.32        58.68        84.53        48.79        83.74        85.94 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              1.02               0.26 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            129.96             180.20 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            31.430             32.945 
[1] "1.0 - 130.0 (31.4)" "0.3 - 180.2 (32.9)"
[1] "hr=" "1.2"
D77V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  20P LOSS MUTATED         0    49                0
  20P LOSS WILD-TYPE       3   509                2
D77V3, multiclass
                  clus
vv                 20P LOSS MUTATED 20P LOSS WILD-TYPE
  OMENTUM                         0                  3
  OVARY                          49                509
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V4, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    48   1
  20P LOSS WILD-TYPE 493   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     48    1
  20P LOSS WILD-TYPE  493    4
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                48                493
  YES                1                  4
[1] 2 2
[1] FALSE
D77V5, continuous
                    vv
clus                 R0 R1 R2 RX
  20P LOSS MUTATED    3  0  0  0
  20P LOSS WILD-TYPE 12 26  5  3
D77V6, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0                3                 12
  R1                0                 26
  R2                0                  5
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     2  30
  20P LOSS WILD-TYPE   8 297
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2   30
  20P LOSS WILD-TYPE    8  297
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO               30                297
[1] 2 2
[1] FALSE

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED    14  18
  20Q LOSS WILD-TYPE 214 313
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                32                527 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                18                313 
$`20Q LOSS MUTATED`
TCGA-04-1336 TCGA-09-1667 TCGA-09-2048 TCGA-13-1489 TCGA-13-1494 TCGA-13-1495 
       49.15        61.87         4.54        83.93        93.90        90.38 
TCGA-13-2059 TCGA-20-0987 TCGA-23-1028 TCGA-23-1118 TCGA-23-1119 TCGA-23-2072 
       78.48        23.05        49.41        86.01       129.96        24.95 
TCGA-24-1428 TCGA-24-1463 TCGA-24-1471 TCGA-24-1552 TCGA-24-2030 TCGA-24-2298 
       17.39        72.92         1.18        41.39        55.92        53.26 
TCGA-25-2392 TCGA-29-1695 TCGA-29-1702 TCGA-29-1711 TCGA-29-1781 TCGA-30-1853 
        1.02        40.41        23.93        34.62         8.38        36.26 
TCGA-36-1578 TCGA-61-1734 TCGA-61-2002 TCGA-61-2088 TCGA-WR-A838 TCGA-13-0720 
       27.85        28.47        17.98         4.77         9.99        44.55 
TCGA-13-0804 TCGA-13-0883 
       35.28        68.94 

$`20Q LOSS WILD-TYPE`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 
       13.81        20.52        11.87        43.92        41.00         1.81 
TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 
        2.01        46.62         1.08        18.51        11.87        65.52 
TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 
       63.09        48.76        21.57        63.98        65.46         0.53 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       49.28        32.52        44.32        33.67        76.57       103.40 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 
       82.39        56.55        41.59        19.99         0.79        38.37 
TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
      119.08        29.10        84.20        55.43        48.89        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 
       28.64        64.64        36.23        31.86        47.70        45.37 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 
        9.99        38.43        89.33        74.93        41.62        57.60 
TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 
       55.36        30.51        17.98         5.85         3.02         8.55 
TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 
       97.55         6.18         6.12        35.15       112.41        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 
       63.09        39.75        20.94        26.93        12.46        77.10 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
       81.17        28.54        83.31        55.23        57.27        81.01 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
       17.46        32.35        54.64        87.06        61.71        29.42 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 
      124.44        20.68        22.39        70.82        52.44       125.56 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 
        4.24       127.27        66.15       115.07        13.97        43.20 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 
       34.82        65.69        34.16        65.52        80.15        44.68 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 
       54.25        14.53        80.02        77.88        76.90        65.52 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 
       70.45         8.42        25.94        26.20        72.20        27.52 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 
       25.38        19.10        16.70         2.93         2.66        47.54 
TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1029 
       49.68        40.54        15.39        26.83        32.09         8.81 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
       29.13        18.90         2.76        51.35        54.51         3.22 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1120 TCGA-23-1121 
       31.20        68.68        19.46        33.30         4.27         6.38 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2078 
       39.09        33.47        58.13         0.53       115.89        87.48 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 
       91.66        77.00        49.84         2.76         4.70         4.50 
TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
        7.63        11.64        21.80        41.56         7.66        22.32 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 
       54.12        63.55        47.41         6.31         6.38         7.82 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 
        7.99         7.86         0.76         6.25         6.02         5.95 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 
        5.36         4.83        28.37        18.64        18.67        43.53 
TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 
        8.55        12.46        45.14       105.99         9.11         3.45 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 
       22.22        26.96        57.40        64.27        16.21        56.58 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       41.06        51.91        58.09        88.50        70.62        39.88 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 
       19.53        44.09        45.50        47.70        25.87        10.26 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 
       17.23        90.15        88.37        48.33        38.24         8.32 
TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 
        3.48         3.72         3.81         4.37        11.28         5.79 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 
        5.52         9.80        22.68        30.21        16.44        11.05 
TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 
       81.11         4.87       152.02        44.84        58.16        34.82 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
      109.71        14.43        18.48        28.18        64.01        44.52 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 
       57.07        36.16         0.79         0.36        47.54        31.63 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 
       70.45        44.61         0.82        67.36        36.23        16.64 
TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 
       33.11        55.86         1.02        26.96        33.01        52.04 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 
       42.05         2.01        34.98        65.00        37.97        33.96 
TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 
        2.99        12.99        15.02        18.58        27.62        17.03 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
       12.95        20.61        38.20         0.30        59.15        62.17 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 
       35.87        52.04        14.96        24.99        24.00        85.05 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 
       13.02        49.05        38.04         3.02        12.00        45.01 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       19.99        42.02         2.96        29.03        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 
       78.90        47.61        48.33       101.79        39.02        33.93 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 
       31.20        68.32        36.36        16.93        59.67        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 
       41.98        31.27        17.36        86.60        66.81        62.93 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
       39.42        31.30        22.98        24.36        22.55        17.33 
TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1783 TCGA-29-1784 
       12.36        11.84        12.30        14.93         7.23         5.36 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 
       36.30        86.17        65.00        62.47        45.11        13.84 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 
       42.25        21.47        11.47         9.76        35.77        38.07 
TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 
       51.91         2.47        15.68         0.26        48.10        44.91 
TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 
       34.78         6.12        36.62         1.22        57.57        24.26 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 
       30.05        48.79        45.57        30.18        18.77        22.49 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 
        6.71        42.51        44.12         2.20        28.77        29.10 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 
       21.53        22.85        22.55         8.55        30.08        25.74 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       24.23        24.69        35.05        33.01        29.49        29.82 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 
       25.91        25.08        23.80        21.60         2.24        20.98 
TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 
       18.31        20.52        14.17         6.05        16.18        11.47 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
       47.57        23.74        28.93        42.02        10.42        40.77 
TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 
        1.48        24.03        11.38        21.14         1.74        22.32 
TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 
       29.00        25.08        25.02       180.20        80.12        22.32 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 
      116.12         9.40        34.39         2.14         5.42        44.81 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 
       11.11         8.09        20.94        31.43        18.54        27.88 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 
        4.34        31.79        48.79        44.84        35.80         2.43 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 
       33.67        43.69         1.45         8.42         5.79        11.41 
TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 
       13.02         9.07        34.13        31.30        37.05        42.51 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 
       48.92        56.61        67.76        43.43        15.75        38.17 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 
        2.01         5.52        14.50         4.01        30.64        39.85 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 
       30.64         1.18        45.96        45.40         4.80        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 
       71.74        61.64        58.39        60.62        65.52        55.50 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
        6.48        76.87        20.68        44.52       125.75        22.22 
TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
        6.35        31.07         8.61        39.68        18.94         0.79 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-10-0925 
       29.16         9.47        57.76        17.98        35.57        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 
       25.91        81.86        18.51        34.19        32.88        14.66 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
        6.71        35.44        36.92        19.99        20.91         6.21 
TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 
       24.59        39.58         2.73        12.39        31.20        15.19 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 
       17.82        55.17         2.50        11.18        11.38        11.54 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 
       38.01       111.78        61.84        56.71        58.65        40.24 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 
      118.42       107.28        63.09        20.35        69.73        83.34 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 
       87.48        45.99        51.02        43.86        35.31        13.61 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 
      107.18       111.39       153.37        66.67        92.42        95.15 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
      145.45       102.84        43.36        71.74        66.15       134.04 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 
       19.36       127.79        50.37       123.16       118.98        60.59 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
      116.65        44.55        37.64       109.32        58.68        84.53 
TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       48.79        48.76        83.74        85.94        25.41 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              1.02               0.26 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            129.96             180.20 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            38.335             32.090 
[1] "1.0 - 130.0 (38.3)" "0.3 - 180.2 (32.1)"
[1] "hr=" "1.3"
D78V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  20Q LOSS MUTATED         0    32                0
  20Q LOSS WILD-TYPE       3   526                2
D78V3, multiclass
                  clus
vv                 20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  OMENTUM                         0                  3
  OVARY                          32                526
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V4, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    32   0
  20Q LOSS WILD-TYPE 509   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     32    0
  20Q LOSS WILD-TYPE  509    5
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                32                509
  YES                0                  5
[1] 2 2
[1] FALSE
D78V5, continuous
                    vv
clus                 R0 R1 R2 RX
  20Q LOSS MUTATED    0  0  0  0
  20Q LOSS WILD-TYPE 15 26  5  3
D78V6, multiclass
D78V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     1  21
  20Q LOSS WILD-TYPE   9 306
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1   21
  20Q LOSS WILD-TYPE    9  306
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO               21                306
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    77 117
  21Q LOSS WILD-TYPE 151 214
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               194                365 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               117                214 
$`21Q LOSS MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1335 TCGA-04-1347 TCGA-04-1350 TCGA-04-1351 
       13.81        20.52         1.81        63.09        63.98        65.46 
TCGA-04-1353 TCGA-04-1356 TCGA-04-1362 TCGA-04-1365 TCGA-04-1638 TCGA-04-1644 
        0.53        49.28        44.32        76.57        55.43        48.89 
TCGA-04-1648 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 
       28.64        36.23        31.86        47.70        45.37         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1667 TCGA-09-1669 TCGA-09-1675 TCGA-09-2049 
       38.43        89.33        61.87        30.51        97.55       112.41 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-13-1404 TCGA-13-1407 TCGA-13-1409 
       63.09        39.75        12.46        81.17        83.31        57.27 
TCGA-13-1411 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1494 
       17.46        29.42       124.44        22.39        70.82        93.90 
TCGA-13-1495 TCGA-13-1497 TCGA-13-1501 TCGA-13-1507 TCGA-13-2061 TCGA-13-2065 
       90.38       127.27        43.20        65.52        76.90        65.52 
TCGA-20-1682 TCGA-20-1684 TCGA-20-1686 TCGA-20-1687 TCGA-23-1022 TCGA-23-1030 
       27.52        19.10         2.93         2.66        49.68        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1113 TCGA-23-1114 TCGA-23-1124 TCGA-23-2072 
       18.90         2.76        31.20        68.68        58.13        24.95 
TCGA-23-2077 TCGA-23-2641 TCGA-24-0975 TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 
      115.89         2.76        21.80        54.12        47.41         6.31 
TCGA-24-1418 TCGA-24-1422 TCGA-24-1425 TCGA-24-1431 TCGA-24-1434 TCGA-24-1471 
        7.99         0.76         5.95        18.64        18.67         1.18 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1557 TCGA-24-1567 TCGA-24-1604 TCGA-24-1614 
       16.21        56.58        39.88        17.23        88.37        48.33 
TCGA-24-1846 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-1930 
        4.37         5.79         5.52         9.80        30.21        81.11 
TCGA-24-2023 TCGA-24-2026 TCGA-24-2029 TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 
       44.84        34.82        14.43        47.54        70.45        44.61 
TCGA-24-2288 TCGA-24-2298 TCGA-25-1316 TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 
        0.82        53.26        42.05        34.98        37.97        33.96 
TCGA-25-1625 TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
       27.62        12.95        38.20         0.30        59.15        62.17 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-2396 TCGA-29-1691 
       35.87        52.04        14.96        24.99         3.02        48.33 
TCGA-29-1695 TCGA-29-1699 TCGA-29-1705 TCGA-29-1711 TCGA-29-1761 TCGA-29-1763 
       40.41        36.36        18.25        34.62        17.36        66.81 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1784 TCGA-29-1785 
       22.98        24.36        17.33        12.36         5.36        36.30 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 
       86.17        65.00        62.47        35.77        38.07        51.91 
TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 TCGA-30-1866 TCGA-30-1891 
       36.26         2.47        15.68        48.10        36.62        30.05 
TCGA-30-1892 TCGA-31-1950 TCGA-31-1956 TCGA-36-1569 TCGA-36-1575 TCGA-36-1581 
       48.79        18.77        44.12        29.10         8.55        24.69 
TCGA-36-2530 TCGA-36-2538 TCGA-36-2545 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 
       33.01        25.08        18.31        14.17        16.18        11.47 
TCGA-42-2587 TCGA-42-2593 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2351 
       23.74         1.48        25.08        25.02       180.20       116.12 
TCGA-59-2372 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 
       44.81        18.54        27.88         4.34        31.79        28.47 
TCGA-61-1741 TCGA-61-1899 TCGA-61-1904 TCGA-61-1913 TCGA-61-1918 TCGA-61-1919 
       33.67         8.42         9.07        48.92        15.75        38.17 
TCGA-61-2008 TCGA-61-2016 TCGA-61-2094 TCGA-61-2113 TCGA-WR-A838 TCGA-09-0367 
       30.64         1.18        71.74        22.22         9.99        17.98 
TCGA-09-0369 TCGA-10-0926 TCGA-10-0927 TCGA-10-0930 TCGA-10-0937 TCGA-13-0723 
       35.57        25.91        81.86        34.19        19.99        39.58 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 
       15.19        17.82        55.17        11.38        11.54        38.01 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0794 TCGA-13-0800 TCGA-13-0803 TCGA-13-0883 
       40.24       118.42        63.09        87.48        43.86        68.94 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0891 TCGA-13-0899 TCGA-13-0900 TCGA-13-0905 
      153.37        66.67       102.84        66.15       134.04       123.16 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
      118.98        60.59        37.64       109.32        58.68        84.53 
TCGA-13-0920 TCGA-13-0921 
       48.79        48.76 

$`21Q LOSS WILD-TYPE`
TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       11.87        43.92        41.00        49.15         2.01        46.62 
TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 TCGA-04-1349 
        1.08        18.51        11.87        65.52        48.76        21.57 
TCGA-04-1361 TCGA-04-1364 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 
       32.52        33.67       103.40        82.39        56.55        41.59 
TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 
       19.99         0.79        38.37       119.08        29.10        84.20 
TCGA-04-1646 TCGA-04-1649 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1668 
       27.88        64.64        74.93        41.62        57.60        55.36 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-2043 TCGA-09-2044 
       17.98         5.85         3.02         8.55         6.18         6.12 
TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 TCGA-09-2054 TCGA-09-2055 TCGA-13-1403 
       35.15         4.54        71.11        20.94        26.93        77.10 
TCGA-13-1405 TCGA-13-1408 TCGA-13-1410 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
       28.54        55.23        81.01        32.35        54.64        87.06 
TCGA-13-1482 TCGA-13-1485 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1496 
       61.71        20.68        83.93        52.44       125.56         4.24 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       66.15       115.07        13.97        34.82        65.69        34.16 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 
       80.15        44.68        54.25        14.53        80.02        78.48 
TCGA-13-2060 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
       77.88        70.45         8.42        23.05        25.94        26.20 
TCGA-20-0996 TCGA-20-1683 TCGA-20-1685 TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 
       72.20        25.38        16.70        47.54        40.54        15.39 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1109 TCGA-23-1110 
       26.83        32.09        49.41         8.81        51.35        54.51 
TCGA-23-1111 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 
        3.22        19.46        33.30        86.01       129.96         4.27 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1809 TCGA-23-2078 TCGA-23-2079 
        6.38        39.09        33.47         0.53        87.48        91.66 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 
       77.00        49.84         4.70         4.50         7.63        11.64 
TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1104 TCGA-24-1416 TCGA-24-1417 
       41.56         7.66        22.32        63.55         6.38         7.82 
TCGA-24-1419 TCGA-24-1423 TCGA-24-1424 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        7.86         6.25         6.02         5.36         4.83        17.39 
TCGA-24-1430 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 
       28.37        43.53         8.55        72.92        12.46        45.14 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 
      105.99         9.11         3.45        22.22        26.96        57.40 
TCGA-24-1546 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       64.27        41.06        51.91        41.39        58.09        88.50 
TCGA-24-1556 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
       70.62        19.53        44.09        45.50        47.70        25.87 
TCGA-24-1565 TCGA-24-1603 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
       10.26        90.15        38.24         8.32         3.48         3.72 
TCGA-24-1845 TCGA-24-1847 TCGA-24-1923 TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 
        3.81        11.28        22.68        16.44        11.05         4.87 
TCGA-24-2020 TCGA-24-2024 TCGA-24-2027 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 
      152.02        58.16       109.71        55.92        18.48        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 
       64.01        44.52        57.07        36.16         0.79         0.36 
TCGA-24-2271 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 
       31.63        67.36        36.23        16.64        33.11        55.86 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1317 TCGA-25-1319 
        1.02        26.96        33.01        52.04         2.01        65.00 
TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1628 
        2.99        12.99        15.02        18.58        17.03        20.61 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 
       24.00        85.05        13.02        49.05         1.02        38.04 
TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 
       12.00        45.01        19.99        42.02         2.96        29.03 
TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 
       31.00        26.99        78.90        47.61       101.79        39.02 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 
       33.93        31.20        68.32        16.93        23.93        59.67 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 
       41.98        31.27        86.60        62.93        39.42        31.30 
TCGA-29-1771 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 
       22.55        11.84        12.30        14.93         8.38         7.23 
TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 
       45.11        13.84        42.25        21.47        11.47         9.76 
TCGA-30-1857 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1867 TCGA-30-1880 
        0.26        44.91        34.78         6.12         1.22        57.57 
TCGA-30-1887 TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 
       24.26        45.57        30.18        22.49         6.71        42.51 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1576 
        2.20        28.77        21.53        22.85        22.55        30.08 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-2529 TCGA-36-2532 TCGA-36-2534 
       25.74        27.85        24.23        35.05        29.49        29.82 
TCGA-36-2537 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2547 
       25.91        23.80        21.60         2.24        20.98        20.52 
TCGA-36-2549 TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
        6.05        47.57        28.93        42.02        10.42        40.77 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 
       24.03        11.38        21.14         1.74        22.32        29.00 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       80.12        22.32         9.40        34.39         2.14         5.42 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1736 TCGA-61-1737 
       11.11         8.09        20.94        31.43        48.79        44.84 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1743 TCGA-61-1895 TCGA-61-1900 TCGA-61-1901 
       35.80         2.43        43.69         1.45         5.79        11.41 
TCGA-61-1903 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1914 
       13.02        34.13        31.30        37.05        42.51        56.61 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       67.76        43.43         2.01         5.52        14.50        17.98 
TCGA-61-2003 TCGA-61-2009 TCGA-61-2012 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
        4.01        39.85        30.64        45.96        45.40         4.80 
TCGA-61-2088 TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 
        4.77        51.72        61.64        58.39        60.62        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       55.50         6.48        76.87        20.68        44.52       125.75 
TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
        6.35        31.07         8.61        39.68        18.94         0.79 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-10-0925 TCGA-10-0928 TCGA-10-0931 
       29.16         9.47        57.76        54.31        18.51        32.88 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0938 TCGA-13-0714 
       14.66         6.71        35.44        36.92        20.91         6.21 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0755 
       24.59        44.55         2.73        12.39        31.20         2.50 
TCGA-13-0757 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0793 
       11.18       111.78        61.84        56.71        58.65       107.28 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 
       20.35        69.73        83.34        45.99        51.02        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0884 TCGA-13-0885 TCGA-13-0888 TCGA-13-0889 
       35.31        13.61       107.18       111.39        92.42        95.15 
TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 
      145.45        43.36        71.74        19.36       127.79        50.37 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
      116.65        44.55        83.74        85.94        25.41 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.30               0.26 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            180.20             152.02 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             36.05              31.20 
[1] "0.3 - 180.2 (36.0)" "0.3 - 152.0 (31.2)"
[1] "hr=" "1.1"
D79V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  21Q LOSS MUTATED         1   194                0
  21Q LOSS WILD-TYPE       2   364                2
D79V3, multiclass
                  clus
vv                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  OMENTUM                         1                  2
  OVARY                         194                364
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V4, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED   189   1
  21Q LOSS WILD-TYPE 352   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    189    1
  21Q LOSS WILD-TYPE  352    4
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO               189                352
  YES                1                  4
[1] 2 2
[1] FALSE
D79V5, continuous
                    vv
clus                 R0 R1 R2 RX
  21Q LOSS MUTATED    4  9  1  1
  21Q LOSS WILD-TYPE 11 17  4  2
D79V6, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0                4                 11
  R1                9                 17
  R2                1                  4
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     3 122
  21Q LOSS WILD-TYPE   7 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      3  122
  21Q LOSS WILD-TYPE    7  205
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  7
  NOT HISPANIC OR LATINO              122                205
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED   164 255
  22Q LOSS WILD-TYPE  64  76
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               419                140 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               255                 76 
$`22Q LOSS MUTATED`
TCGA-3P-A9WA TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       13.81        11.87        43.92        49.15         2.01        46.62 
TCGA-04-1341 TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 
        1.08        18.51        65.52        63.09        21.57        63.98 
TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 
       65.46        49.28        32.52        44.32        76.57       103.40 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 
       82.39        56.55        19.99         0.79        38.37       119.08 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 
       84.20        55.43        48.89        27.88        28.64        64.64 
TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       36.23        31.86        45.37         9.99        38.43        89.33 
TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 
       74.93        57.60        61.87        55.36        30.51        17.98 
TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2048 TCGA-09-2049 
        3.02         8.55        97.55         6.12         4.54       112.41 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2056 TCGA-13-1404 
       71.11        63.09        39.75        20.94        12.46        81.17 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
       83.31        55.23        57.27        81.01        17.46        32.35 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1489 
       87.06        61.71        29.42       124.44        22.39        83.93 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 
       52.44       125.56        93.90        90.38         4.24       127.27 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       66.15       115.07        13.97        34.82        65.69        34.16 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
       65.52        80.15        14.53        80.02        78.48        77.88 
TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 
       76.90        65.52        70.45         8.42        25.94        26.20 
TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1687 TCGA-23-1021 
       27.52        25.38        19.10        16.70         2.66        47.54 
TCGA-23-1022 TCGA-23-1024 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
       49.68        15.39        32.09        49.41         8.81        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 
       18.90         2.76        51.35        54.51        31.20        68.68 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1122 TCGA-23-1123 TCGA-23-2072 
       19.46        33.30        86.01        39.09        33.47        24.95 
TCGA-23-2078 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 
       87.48        77.00        49.84         2.76         4.70         4.50 
TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0982 TCGA-24-1104 
        7.63        11.64        21.80        41.56        22.32        63.55 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       47.41         6.31         6.38         7.82         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        0.76         6.25         6.02         5.95         5.36         4.83 
TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1464 
       17.39        18.64        18.67        43.53         8.55        12.46 
TCGA-24-1466 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 
       45.14         1.18        22.22        26.96        57.40        16.21 
TCGA-24-1549 TCGA-24-1550 TCGA-24-1552 TCGA-24-1555 TCGA-24-1557 TCGA-24-1560 
       56.58        41.06        41.39        88.50        39.88        44.09 
TCGA-24-1562 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 
       45.50        25.87        10.26        17.23        90.15        88.37 
TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 
       48.33        38.24         8.32         3.48         3.72         4.37 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1930 TCGA-24-2019 
        5.52         9.80        22.68        30.21        81.11         4.87 
TCGA-24-2020 TCGA-24-2023 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 
      152.02        44.84        34.82       109.71        14.43        55.92 
TCGA-24-2033 TCGA-24-2036 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 
       18.48        64.01        57.07        36.16         0.79         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2288 TCGA-24-2293 TCGA-24-2295 
       47.54        31.63        70.45         0.82        16.64        33.11 
TCGA-24-2298 TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
       53.26         1.02        33.01        52.04        42.05         2.01 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1329 
       34.98        65.00        37.97        33.96         2.99        15.02 
TCGA-25-1623 TCGA-25-1626 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
       18.58        17.03        20.61         0.30        59.15        62.17 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 
       35.87        52.04        14.96        24.99        24.00        85.05 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2397 TCGA-25-2398 
       13.02        49.05         1.02        38.04        12.00        45.01 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1693 
       19.99        42.02        29.03        31.00        26.99       101.79 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1701 
       39.02        40.41        33.93        31.20        68.32        16.93 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 TCGA-29-1761 
       23.93        59.67        18.25        41.98        34.62        17.36 
TCGA-29-1763 TCGA-29-1766 TCGA-29-1769 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 
       66.81        39.42        22.98        17.33        12.36        11.84 
TCGA-29-1778 TCGA-29-1783 TCGA-29-1785 TCGA-29-2428 TCGA-29-2429 TCGA-29-2432 
       14.93         7.23        36.30        45.11        13.84        21.47 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 
       35.77        38.07        51.91        36.26         2.47        15.68 
TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 
       48.10        44.91         6.12        36.62         1.22        57.57 
TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 
       24.26        48.79        45.57        22.49         6.71        42.51 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 
        2.20        28.77        29.10        22.85         8.55        30.08 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 
       25.74        27.85        24.23        24.69        33.01        29.49 
TCGA-36-2534 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 
       29.82        25.08        23.80        21.60         2.24        20.98 
TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
       14.17        16.18        11.47        28.93        42.02        10.42 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1992 
       40.77         1.48        24.03        11.38        21.14        29.00 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       25.08        25.02       180.20        22.32       116.12         9.40 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1722 TCGA-61-1725 
       34.39         2.14         5.42        44.81         8.09        31.43 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 TCGA-61-1738 TCGA-61-1740 
       27.88         4.34        31.79        48.79        35.80         2.43 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1906 
       33.67        43.69         8.42         5.79        11.41        34.13 
TCGA-61-1907 TCGA-61-1910 TCGA-61-1913 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 
       31.30        37.05        48.92        67.76        43.43        15.75 
TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 TCGA-61-2009 
       38.17         2.01         5.52        14.50         4.01        39.85 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2096 
       30.64         1.18        45.40         4.80         4.77        58.39 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       60.62        65.52         6.48        76.87        20.68        44.52 
TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P 
      125.75        22.22         6.35        31.07         8.61        39.68 
TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 
       18.94         0.79         9.99        29.16         9.47        57.76 
TCGA-09-0367 TCGA-09-0369 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       17.98        35.57        54.31        25.91        81.86        18.51 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
       32.88        14.66        19.99        20.91         6.21        24.59 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 
       44.55        39.58         2.73        12.39        15.19        17.82 
TCGA-13-0751 TCGA-13-0757 TCGA-13-0758 TCGA-13-0761 TCGA-13-0766 TCGA-13-0791 
       55.17        11.18        11.38        38.01        56.71        40.24 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 
       63.09        20.35        83.34        87.48        45.99        51.02 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
       43.86        35.28        35.31        13.61        68.94       107.18 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 
      111.39       153.37        66.67        92.42        95.15       145.45 
TCGA-13-0891 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0906 
      102.84        71.74       134.04        19.36       127.79       118.98 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       60.59       116.65        44.55        37.64       109.32        58.68 
TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       84.53        48.76        83.74        85.94        25.41 

$`22Q LOSS WILD-TYPE`
TCGA-59-A5PD TCGA-04-1332 TCGA-04-1335 TCGA-04-1343 TCGA-04-1348 TCGA-04-1353 
       20.52        41.00         1.81        11.87        48.76         0.53 
TCGA-04-1364 TCGA-04-1516 TCGA-04-1536 TCGA-04-1654 TCGA-09-1665 TCGA-09-1672 
       33.67        41.59        29.10        47.70        41.62         5.85 
TCGA-09-2043 TCGA-09-2045 TCGA-09-2055 TCGA-13-1403 TCGA-13-1405 TCGA-13-1477 
        6.18        35.15        26.93        77.10        28.54        54.64 
TCGA-13-1485 TCGA-13-1488 TCGA-13-1501 TCGA-13-1510 TCGA-13-1511 TCGA-20-0987 
       20.68        70.82        43.20        44.68        54.25        23.05 
TCGA-20-0996 TCGA-20-1686 TCGA-23-1023 TCGA-23-1026 TCGA-23-1111 TCGA-23-1119 
       72.20         2.93        40.54        26.83         3.22       129.96 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2079 
        4.27         6.38        58.13         0.53       115.89        91.66 
TCGA-24-0980 TCGA-24-1103 TCGA-24-1430 TCGA-24-1463 TCGA-24-1467 TCGA-24-1469 
        7.66        54.12        28.37        72.92       105.99         9.11 
TCGA-24-1470 TCGA-24-1546 TCGA-24-1551 TCGA-24-1553 TCGA-24-1556 TCGA-24-1558 
        3.45        64.27        51.91        58.09        70.62        19.53 
TCGA-24-1563 TCGA-24-1845 TCGA-24-1847 TCGA-24-1849 TCGA-24-1927 TCGA-24-1928 
       47.70         3.81        11.28         5.79        16.44        11.05 
TCGA-24-2024 TCGA-24-2035 TCGA-24-2038 TCGA-24-2281 TCGA-24-2289 TCGA-24-2290 
       58.16        28.18        44.52        44.61        67.36        36.23 
TCGA-24-2297 TCGA-25-1313 TCGA-25-1323 TCGA-25-1625 TCGA-25-1627 TCGA-25-1630 
       55.86        26.96        12.99        27.62        12.95        38.20 
TCGA-25-2396 TCGA-25-2401 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1699 
        3.02         2.96        78.90        47.61        48.33        36.36 
TCGA-29-1710 TCGA-29-1762 TCGA-29-1764 TCGA-29-1768 TCGA-29-1770 TCGA-29-1771 
       31.27        86.60        62.93        31.30        24.36        22.55 
TCGA-29-1777 TCGA-29-1781 TCGA-29-1784 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 
       12.30         8.38         5.36        86.17        65.00        62.47 
TCGA-29-2431 TCGA-29-2434 TCGA-29-2436 TCGA-30-1857 TCGA-30-1861 TCGA-30-1891 
       42.25        11.47         9.76         0.26        34.78        30.05 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1956 TCGA-36-1570 TCGA-36-1574 TCGA-36-2529 
       30.18        18.77        44.12        21.53        22.55        35.05 
TCGA-36-2537 TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 TCGA-42-2582 TCGA-42-2587 
       25.91        18.31        20.52         6.05        47.57        23.74 
TCGA-57-1585 TCGA-57-1586 TCGA-59-2349 TCGA-61-1721 TCGA-61-1724 TCGA-61-1727 
        1.74        22.32        80.12        11.11        20.94        18.54 
TCGA-61-1734 TCGA-61-1737 TCGA-61-1895 TCGA-61-1903 TCGA-61-1904 TCGA-61-1911 
       28.47        44.84         1.45        13.02         9.07        42.51 
TCGA-61-1914 TCGA-61-2002 TCGA-61-2008 TCGA-61-2017 TCGA-61-2092 TCGA-61-2094 
       56.61        17.98        30.64        45.96        51.72        71.74 
TCGA-61-2095 TCGA-61-2101 TCGA-10-0930 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 
       61.64        55.50        34.19         6.71        35.44        36.92 
TCGA-13-0726 TCGA-13-0755 TCGA-13-0760 TCGA-13-0762 TCGA-13-0764 TCGA-13-0768 
       31.20         2.50        11.54       111.78        61.84        58.65 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0797 TCGA-13-0893 TCGA-13-0899 TCGA-13-0904 
      118.42       107.28        69.73        43.36        66.15        50.37 
TCGA-13-0905 TCGA-13-0920 
      123.16        48.79 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.30               0.26 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            180.20             129.96 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             32.52              33.93 
[1] "0.3 - 180.2 (32.5)" "0.3 - 130.0 (33.9)"
[1] "hr=" "1.1"
D80V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  22Q LOSS MUTATED         2   418                1
  22Q LOSS WILD-TYPE       1   140                1
D80V3, multiclass
                  clus
vv                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  OMENTUM                         2                  1
  OVARY                         418                140
  PERITONEUM OVARY                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V4, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   406   5
  22Q LOSS WILD-TYPE 135   0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    406    5
  22Q LOSS WILD-TYPE  135    0
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO               406                135
  YES                5                  0
[1] 2 2
[1] FALSE
D80V5, continuous
                    vv
clus                 R0 R1 R2 RX
  22Q LOSS MUTATED    7 20  5  3
  22Q LOSS WILD-TYPE  8  6  0  0
D80V6, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0                7                  8
  R1               20                  6
  R2                5                  0
  RX                3                  0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     8 249
  22Q LOSS WILD-TYPE   2  78
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      8  249
  22Q LOSS WILD-TYPE    2   78
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                  2
  NOT HISPANIC OR LATINO              249                 78
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED   129 187
  XP LOSS WILD-TYPE  99 144
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              316               243 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              187               144 
$`XP LOSS MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1346 
       13.81        20.52        43.92         1.81        49.15        65.52 
TCGA-04-1347 TCGA-04-1348 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
       63.09        48.76        32.52        44.32        33.67        76.57 
TCGA-04-1367 TCGA-04-1514 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 
      103.40        56.55        19.99         0.79        38.37       119.08 
TCGA-04-1536 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1651 TCGA-04-1652 
       29.10        55.43        48.89        28.64        36.23        31.86 
TCGA-04-1654 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       47.70        45.37         9.99        38.43        89.33        74.93 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 TCGA-09-1673 TCGA-09-1675 TCGA-09-2044 
       57.60        61.87        30.51         3.02        97.55         6.12 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 
      112.41        71.11        63.09        39.75        20.94        26.93 
TCGA-09-2056 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1412 TCGA-13-1482 
       12.46        81.17        28.54        83.31        32.35        61.71 
TCGA-13-1483 TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       29.42        22.39        83.93        52.44       125.56        93.90 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1500 TCGA-13-1504 TCGA-13-1505 
       90.38         4.24        66.15        13.97        34.82        65.69 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2059 TCGA-13-2061 TCGA-20-0987 
       80.15        44.68        14.53        78.48        76.90        23.05 
TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 
       26.20        27.52        25.38        19.10        16.70         2.93 
TCGA-20-1687 TCGA-23-1022 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
        2.66        49.68        32.09        49.41         8.81        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 TCGA-23-1120 
       18.90         2.76        51.35         3.22        31.20         4.27 
TCGA-23-1123 TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-23-2641 TCGA-24-0966 
       33.47       115.89        91.66        77.00         2.76         7.63 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 
       11.64        21.80        41.56         7.66        54.12        63.55 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       47.41         6.31         6.38         7.82         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        0.76         6.25         6.02         5.36         4.83        17.39 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 TCGA-24-1469 
       28.37        18.64        43.53        72.92        12.46         9.11 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1552 TCGA-24-1555 
       64.27        16.21        56.58        41.06        41.39        88.50 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1567 TCGA-24-1603 TCGA-24-1614 
       44.09        45.50        47.70        17.23        90.15        48.33 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1930 TCGA-24-2023 
        3.81         4.37        11.28         5.79        81.11        44.84 
TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 
       58.16       109.71        14.43        55.92        18.48        28.18 
TCGA-24-2036 TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 
       64.01        57.07        36.16         0.36        47.54        31.63 
TCGA-24-2280 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2297 TCGA-24-2298 
       70.45         0.82        67.36        36.23        55.86        53.26 
TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1320 TCGA-25-1322 TCGA-25-1625 
       33.01        52.04        42.05        37.97         2.99        27.62 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 
       38.20         0.30        59.15        52.04        14.96        24.99 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2396 TCGA-25-2397 
       85.05        13.02        49.05         1.02         3.02        12.00 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2409 TCGA-29-1688 TCGA-29-1693 TCGA-29-1694 
       19.99        42.02        26.99        78.90       101.79        39.02 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 
       33.93        31.20        36.36        23.93        59.67        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1769 
       41.98        31.27        34.62        17.36        86.60        22.98 
TCGA-29-1771 TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1784 
       22.55        12.36        12.30        14.93         8.38         5.36 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2431 TCGA-29-2432 TCGA-29-A5NZ 
       36.30        86.17        62.47        42.25        21.47        35.77 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1857 TCGA-30-1866 TCGA-30-1880 
       38.07        51.91        36.26         0.26        36.62        57.57 
TCGA-30-1887 TCGA-30-1891 TCGA-31-1944 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 
       24.26        30.05        45.57        18.77        22.49         6.71 
TCGA-31-1955 TCGA-31-1956 TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 TCGA-36-1575 
       42.51        44.12        29.10        21.53        22.55         8.55 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       25.74        27.85        24.23        33.01        29.49        29.82 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2542 TCGA-36-2545 TCGA-36-2547 TCGA-42-2582 
       25.91        25.08        21.60        18.31        20.52        47.57 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 
       40.77         1.48        21.14         1.74        22.32        29.00 
TCGA-57-1994 TCGA-59-2350 TCGA-59-2354 TCGA-59-2363 TCGA-61-1724 TCGA-61-1725 
       25.02        22.32        34.39         5.42        20.94        31.43 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
       18.54        27.88        31.79        48.79        44.84        35.80 
TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1901 TCGA-61-1903 TCGA-61-1913 
       43.69         1.45         8.42        11.41        13.02        48.92 
TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 TCGA-61-1919 TCGA-61-2002 TCGA-61-2003 
       56.61        67.76        15.75        38.17        17.98         4.01 
TCGA-61-2008 TCGA-61-2012 TCGA-61-2016 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
       30.64        30.64         1.18        45.40         4.80         4.77 
TCGA-61-2096 TCGA-61-2098 TCGA-61-2104 TCGA-61-2110 TCGA-61-2113 TCGA-61-2612 
       58.39        65.52        76.87        44.52        22.22         6.35 
TCGA-61-2613 TCGA-61-2614 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-10-0925 
       31.07         8.61        57.76        17.98        35.57        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0937 
       25.91        81.86        18.51        34.19        32.88        19.99 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 TCGA-13-0725 TCGA-13-0755 TCGA-13-0757 
       20.91         6.21        44.55        12.39         2.50        11.18 
TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0766 TCGA-13-0792 TCGA-13-0794 
       11.38        11.54        38.01        56.71       118.42        63.09 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 
       20.35        69.73        83.34        45.99        43.86        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0887 TCGA-13-0889 TCGA-13-0891 
       35.31        13.61        68.94        66.67        95.15       102.84 
TCGA-13-0900 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
      134.04       127.79       123.16       118.98        60.59       116.65 
TCGA-13-0913 TCGA-13-0919 TCGA-13-0920 TCGA-13-0924 
      109.32        84.53        48.79        85.94 

$`XP LOSS WILD-TYPE`
TCGA-5X-AA5U TCGA-04-1332 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 
       11.87        41.00         2.01        46.62         1.08        18.51 
TCGA-04-1343 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 
       11.87        21.57        63.98        65.46         0.53        49.28 
TCGA-04-1371 TCGA-04-1516 TCGA-04-1542 TCGA-04-1646 TCGA-04-1649 TCGA-09-1665 
       82.39        41.59        84.20        27.88        64.64        41.62 
TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 TCGA-09-2043 TCGA-09-2045 
       55.36        17.98         5.85         8.55         6.18        35.15 
TCGA-09-2048 TCGA-13-1403 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
        4.54        77.10        55.23        57.27        81.01        17.46 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1484 TCGA-13-1485 TCGA-13-1488 TCGA-13-1497 
       54.64        87.06       124.44        20.68        70.82       127.27 
TCGA-13-1499 TCGA-13-1501 TCGA-13-1506 TCGA-13-1507 TCGA-13-1511 TCGA-13-2057 
      115.07        43.20        34.16        65.52        54.25        80.02 
TCGA-13-2060 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-0996 
       77.88        65.52        70.45         8.42        25.94        72.20 
TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1110 TCGA-23-1114 
       47.54        40.54        15.39        26.83        54.51        68.68 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1121 TCGA-23-1122 
       19.46        33.30        86.01       129.96         6.38        39.09 
TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2078 TCGA-23-2084 TCGA-23-2643 
       58.13         0.53        24.95        87.48        49.84         4.70 
TCGA-23-2645 TCGA-24-0982 TCGA-24-1425 TCGA-24-1434 TCGA-24-1436 TCGA-24-1466 
        4.50        22.32         5.95        18.67         8.55        45.14 
TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 
      105.99         3.45         1.18        22.22        26.96        57.40 
TCGA-24-1551 TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1564 
       51.91        58.09        70.62        39.88        19.53        25.87 
TCGA-24-1565 TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
       10.26        88.37        38.24         8.32         3.48         3.72 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 
        5.52         9.80        22.68        30.21        16.44        11.05 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2026 TCGA-24-2038 TCGA-24-2261 TCGA-24-2281 
        4.87       152.02        34.82        44.52         0.79        44.61 
TCGA-24-2293 TCGA-24-2295 TCGA-25-1312 TCGA-25-1313 TCGA-25-1317 TCGA-25-1318 
       16.64        33.11         1.02        26.96         2.01        34.98 
TCGA-25-1319 TCGA-25-1321 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 
       65.00        33.96        12.99        15.02        18.58        17.03 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1633 TCGA-25-1634 TCGA-25-1877 TCGA-25-2393 
       12.95        20.61        62.17        35.87        24.00        38.04 
TCGA-25-2398 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-29-1690 TCGA-29-1691 
       45.01         2.96        29.03        31.00        47.61        48.33 
TCGA-29-1695 TCGA-29-1698 TCGA-29-1701 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 
       40.41        68.32        16.93        66.81        62.93        39.42 
TCGA-29-1768 TCGA-29-1770 TCGA-29-1774 TCGA-29-1776 TCGA-29-1783 TCGA-29-2425 
       31.30        24.36        17.33        11.84         7.23        65.00 
TCGA-29-2428 TCGA-29-2429 TCGA-29-2434 TCGA-29-2436 TCGA-30-1855 TCGA-30-1856 
       45.11        13.84        11.47         9.76         2.47        15.68 
TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1867 TCGA-30-1892 
       48.10        44.91        34.78         6.12         1.22        48.79 
TCGA-31-1946 TCGA-31-1959 TCGA-36-1568 TCGA-36-1571 TCGA-36-1576 TCGA-36-1581 
       30.18         2.20        28.77        22.85        30.08        24.69 
TCGA-36-2529 TCGA-36-2540 TCGA-36-2543 TCGA-36-2544 TCGA-36-2548 TCGA-36-2549 
       35.05        23.80         2.24        20.98        14.17         6.05 
TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
       16.18        11.47        23.74        28.93        42.02        10.42 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 TCGA-59-2351 
       24.03        11.38        25.08       180.20        80.12       116.12 
TCGA-59-2352 TCGA-59-2355 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1730 
        9.40         2.14        44.81        11.11         8.09         4.34 
TCGA-61-1734 TCGA-61-1740 TCGA-61-1741 TCGA-61-1900 TCGA-61-1904 TCGA-61-1906 
       28.47         2.43        33.67         5.79         9.07        34.13 
TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1917 TCGA-61-1995 TCGA-61-1998 
       31.30        37.05        42.51        43.43         2.01         5.52 
TCGA-61-2000 TCGA-61-2009 TCGA-61-2017 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       14.50        39.85        45.96        51.72        71.74        61.64 
TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 TCGA-61-2109 TCGA-61-2111 TCGA-OY-A56P 
       60.62        55.50         6.48        20.68       125.75        39.68 
TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-10-0933 
       18.94         0.79         9.99        29.16         9.47        14.66 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 
        6.71        35.44        36.92        24.59        39.58         2.73 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0762 TCGA-13-0764 
       31.20        15.19        17.82        55.17       111.78        61.84 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0793 TCGA-13-0800 TCGA-13-0802 TCGA-13-0884 
       58.65        40.24       107.28        87.48        51.02       107.18 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0888 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 
      111.39       153.37        92.42       145.45        43.36        71.74 
TCGA-13-0899 TCGA-13-0901 TCGA-13-0904 TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 
       66.15        19.36        50.37        44.55        37.64        58.68 
TCGA-13-0921 TCGA-13-0923 TCGA-13-2071 
       48.76        83.74        25.41 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.26              0.53 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           134.04            180.20 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           32.945            31.300 
[1] "0.3 - 134.0 (32.9)" "0.5 - 180.2 (31.3)"
[1] "hr=" "1"  
D81V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  XP LOSS MUTATED         2   314                0
  XP LOSS WILD-TYPE       1   244                2
D81V3, multiclass
                  clus
vv                 XP LOSS MUTATED XP LOSS WILD-TYPE
  OMENTUM                        2                 1
  OVARY                        314               244
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V4, binary
                   cls
clus                  0   1
  XP LOSS MUTATED   307   4
  XP LOSS WILD-TYPE 234   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED    307    4
  XP LOSS WILD-TYPE  234    1
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO              307               234
  YES               4                 1
[1] 2 2
[1] FALSE
D81V5, continuous
                   vv
clus                R0 R1 R2 RX
  XP LOSS MUTATED    6 14  1  1
  XP LOSS WILD-TYPE  9 12  4  2
D81V6, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  R0               6                 9
  R1              14                12
  R2               1                 4
  RX               1                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     5 180
  XP LOSS WILD-TYPE   5 147
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      5  180
  XP LOSS WILD-TYPE    5  147
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 5
  NOT HISPANIC OR LATINO             180               147
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED   110 163
  XQ LOSS WILD-TYPE 118 168
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              273               286 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              163               168 
$`XQ LOSS MUTATED`
TCGA-3P-A9WA TCGA-59-A5PD TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1341 
       13.81        20.52        43.92        41.00        49.15         1.08 
TCGA-04-1343 TCGA-04-1347 TCGA-04-1348 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 
       11.87        63.09        48.76        32.52        44.32        33.67 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 TCGA-04-1517 TCGA-04-1519 TCGA-04-1530 
       76.57       103.40        56.55        19.99         0.79       119.08 
TCGA-04-1536 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1651 TCGA-04-1654 
       29.10        55.43        48.89        28.64        36.23        47.70 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 
        9.99        38.43        89.33        74.93        57.60        61.87 
TCGA-09-1673 TCGA-09-1675 TCGA-09-2044 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
        3.02        97.55         6.12       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-13-1405 TCGA-13-1407 
       39.75        20.94        26.93        12.46        28.54        83.31 
TCGA-13-1408 TCGA-13-1412 TCGA-13-1482 TCGA-13-1483 TCGA-13-1487 TCGA-13-1489 
       55.23        32.35        61.71        29.42        22.39        83.93 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
       52.44       125.56        90.38         4.24       127.27        66.15 
TCGA-13-1500 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2059 
       13.97        65.52        80.15        44.68        14.53        78.48 
TCGA-13-2061 TCGA-20-1682 TCGA-20-1684 TCGA-23-1022 TCGA-23-1027 TCGA-23-1028 
       76.90        27.52        19.10        49.68        32.09        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1113 TCGA-23-1120 
        8.81        29.13        18.90         2.76        31.20         4.27 
TCGA-23-1122 TCGA-23-1123 TCGA-23-2081 TCGA-23-2641 TCGA-24-0966 TCGA-24-0970 
       39.09        33.47        77.00         2.76         7.63        11.64 
TCGA-24-0980 TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 
        7.66        54.12        47.41         6.31         6.38         7.82 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        7.99         7.86         6.25         5.95         5.36         4.83 
TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 
       17.39        28.37        18.64        43.53        72.92        12.46 
TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 
       45.14         9.11         3.45        64.27        16.21        56.58 
TCGA-24-1550 TCGA-24-1552 TCGA-24-1560 TCGA-24-1562 TCGA-24-1567 TCGA-24-1603 
       41.06        41.39        44.09        45.50        17.23        90.15 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1845 TCGA-24-1849 TCGA-24-1930 TCGA-24-2023 
       88.37        48.33         3.81         5.79        81.11        44.84 
TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 
       58.16       109.71        14.43        55.92        28.18        64.01 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 TCGA-24-2271 TCGA-24-2280 TCGA-24-2288 
       57.07        36.16         0.36        31.63        70.45         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2297 TCGA-24-2298 TCGA-25-1314 TCGA-25-1315 
       67.36        36.23        55.86        53.26        33.01        52.04 
TCGA-25-1316 TCGA-25-1322 TCGA-25-1625 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 
       42.05         2.99        27.62        38.20         0.30        59.15 
TCGA-25-1633 TCGA-25-1635 TCGA-25-1870 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 
       62.17        52.04        14.96        85.05        13.02        49.05 
TCGA-25-2392 TCGA-25-2396 TCGA-25-2399 TCGA-25-2409 TCGA-29-1688 TCGA-29-1693 
        1.02         3.02        19.99        26.99        78.90       101.79 
TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
       39.02        33.93        31.20        59.67        18.25        41.98 
TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1769 TCGA-29-1771 TCGA-29-1775 
       34.62        17.36        86.60        22.98        22.55        12.36 
TCGA-29-1777 TCGA-29-1781 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 
       12.30         8.38         5.36        36.30        86.17        62.47 
TCGA-29-2431 TCGA-29-2432 TCGA-30-1714 TCGA-30-1853 TCGA-30-1857 TCGA-30-1866 
       42.25        21.47        38.07        36.26         0.26        36.62 
TCGA-30-1880 TCGA-30-1891 TCGA-31-1944 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 
       57.57        30.05        45.57         6.71        42.51        44.12 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 TCGA-36-1578 
       29.10        21.53        22.55         8.55        25.74        27.85 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2542 
       33.01        29.49        29.82        25.91        25.08        21.60 
TCGA-36-2545 TCGA-36-2547 TCGA-42-2582 TCGA-42-2589 TCGA-42-2591 TCGA-42-2593 
       18.31        20.52        47.57        42.02        40.77         1.48 
TCGA-57-1585 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2350 TCGA-59-2354 
        1.74        29.00        25.08        25.02        22.32        34.39 
TCGA-59-2363 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1736 TCGA-61-1737 
        5.42        20.94        31.43        18.54        48.79        44.84 
TCGA-61-1738 TCGA-61-1743 TCGA-61-1901 TCGA-61-1903 TCGA-61-1913 TCGA-61-1918 
       35.80        43.69        11.41        13.02        48.92        15.75 
TCGA-61-1919 TCGA-61-1995 TCGA-61-2002 TCGA-61-2008 TCGA-61-2012 TCGA-61-2016 
       38.17         2.01        17.98        30.64        30.64         1.18 
TCGA-61-2018 TCGA-61-2088 TCGA-61-2094 TCGA-61-2096 TCGA-61-2098 TCGA-61-2104 
       45.40         4.77        71.74        58.39        65.52        76.87 
TCGA-61-2110 TCGA-61-2113 TCGA-61-2613 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 
       44.52        22.22        31.07        57.76        17.98        35.57 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0937 
       54.31        25.91        18.51        34.19        32.88        19.99 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0725 TCGA-13-0726 TCGA-13-0758 TCGA-13-0760 
       20.91         6.21        12.39        31.20        11.38        11.54 
TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0799 
       56.71        40.24       118.42       107.28        63.09        83.34 
TCGA-13-0801 TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0887 
       45.99        43.86        35.31        13.61        68.94        66.67 
TCGA-13-0889 TCGA-13-0891 TCGA-13-0900 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 
       95.15       102.84       134.04       127.79       123.16       118.98 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0919 TCGA-13-0920 
       60.59       116.65        37.64       109.32        84.53        48.79 
TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       83.74        85.94        25.41 

$`XQ LOSS WILD-TYPE`
TCGA-5X-AA5U TCGA-04-1335 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 TCGA-04-1346 
       11.87         1.81         2.01        46.62        18.51        65.52 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1371 
       21.57        63.98        65.46         0.53        49.28        82.39 
TCGA-04-1516 TCGA-04-1525 TCGA-04-1542 TCGA-04-1646 TCGA-04-1649 TCGA-04-1652 
       41.59        38.37        84.20        27.88        64.64        31.86 
TCGA-04-1655 TCGA-09-1665 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 
       45.37        41.62        55.36        30.51        17.98         5.85 
TCGA-09-1674 TCGA-09-2043 TCGA-09-2045 TCGA-09-2048 TCGA-13-1403 TCGA-13-1404 
        8.55         6.18        35.15         4.54        77.10        81.17 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1477 TCGA-13-1481 TCGA-13-1484 
       57.27        81.01        17.46        54.64        87.06       124.44 
TCGA-13-1485 TCGA-13-1488 TCGA-13-1494 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 
       20.68        70.82        93.90       115.07        43.20        34.82 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1511 TCGA-13-2057 TCGA-13-2060 TCGA-13-2065 
       65.69        34.16        54.25        80.02        77.88        65.52 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 
       70.45         8.42        23.05        25.94        26.20        72.20 
TCGA-20-1683 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1023 
       25.38        16.70         2.93         2.66        47.54        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 
       15.39        26.83        51.35        54.51         3.22        68.68 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1121 TCGA-23-1124 
       19.46        33.30        86.01       129.96         6.38        58.13 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2084 
        0.53        24.95       115.89        87.48        91.66        49.84 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0975 TCGA-24-0979 TCGA-24-0982 TCGA-24-1104 
        4.70         4.50        21.80        41.56        22.32        63.55 
TCGA-24-1422 TCGA-24-1424 TCGA-24-1434 TCGA-24-1436 TCGA-24-1467 TCGA-24-1471 
        0.76         6.02        18.67         8.55       105.99         1.18 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1551 TCGA-24-1553 TCGA-24-1555 
       22.22        26.96        57.40        51.91        58.09        88.50 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 
       70.62        39.88        19.53        47.70        25.87        10.26 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 
       38.24         8.32         3.48         3.72         4.37        11.28 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 
        5.52         9.80        22.68        30.21        16.44        11.05 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2026 TCGA-24-2033 TCGA-24-2038 TCGA-24-2261 
        4.87       152.02        34.82        18.48        44.52         0.79 
TCGA-24-2267 TCGA-24-2281 TCGA-24-2293 TCGA-24-2295 TCGA-25-1312 TCGA-25-1313 
       47.54        44.61        16.64        33.11         1.02        26.96 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1323 
        2.01        34.98        65.00        37.97        33.96        12.99 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1634 
       15.02        18.58        17.03        12.95        20.61        35.87 
TCGA-25-1871 TCGA-25-1877 TCGA-25-2393 TCGA-25-2397 TCGA-25-2398 TCGA-25-2400 
       24.99        24.00        38.04        12.00        45.01        42.02 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-29-1690 TCGA-29-1691 TCGA-29-1695 
        2.96        29.03        31.00        47.61        48.33        40.41 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1710 TCGA-29-1763 
       68.32        36.36        16.93        23.93        31.27        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1770 TCGA-29-1774 TCGA-29-1776 
       62.93        39.42        31.30        24.36        17.33        11.84 
TCGA-29-1778 TCGA-29-1783 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 TCGA-29-2434 
       14.93         7.23        65.00        45.11        13.84        11.47 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 
        9.76        35.77        51.91         2.47        15.68        48.10 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1867 TCGA-30-1887 TCGA-30-1892 
       44.91        34.78         6.12         1.22        24.26        48.79 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1959 TCGA-36-1568 TCGA-36-1571 
       30.18        18.77        22.49         2.20        28.77        22.85 
TCGA-36-1576 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2540 TCGA-36-2543 
       30.08        24.23        24.69        35.05        23.80         2.24 
TCGA-36-2544 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 
       20.98        14.17         6.05        16.18        11.47        23.74 
TCGA-42-2588 TCGA-42-2590 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 
       28.93        10.42        24.03        11.38        21.14        22.32 
TCGA-59-2348 TCGA-59-2349 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2372 
      180.20        80.12       116.12         9.40         2.14        44.81 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 
       11.11         8.09        27.88         4.34        31.79        28.47 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1904 
        2.43        33.67         1.45         8.42         5.79         9.07 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1914 TCGA-61-1915 
       34.13        31.30        37.05        42.51        56.61        67.76 
TCGA-61-1917 TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 TCGA-61-2009 TCGA-61-2017 
       43.43         5.52        14.50         4.01        39.85        45.96 
TCGA-61-2087 TCGA-61-2092 TCGA-61-2095 TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 
        4.80        51.72        61.64        60.62        55.50         6.48 
TCGA-61-2109 TCGA-61-2111 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
       20.68       125.75         6.35         8.61        39.68        18.94 
TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0364 TCGA-09-0365 TCGA-10-0927 TCGA-10-0933 
        0.79         9.99        29.16         9.47        81.86        14.66 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 
        6.71        35.44        36.92        24.59        44.55        39.58 
TCGA-13-0724 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 
        2.73        15.19        17.82        55.17         2.50        11.18 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0768 TCGA-13-0795 TCGA-13-0797 
       38.01       111.78        61.84        58.65        20.35        69.73 
TCGA-13-0800 TCGA-13-0802 TCGA-13-0804 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 
       87.48        51.02        35.28       107.18       111.39       153.37 
TCGA-13-0888 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0901 
       92.42       145.45        43.36        71.74        66.15        19.36 
TCGA-13-0904 TCGA-13-0911 TCGA-13-0916 TCGA-13-0921 
       50.37        44.55        58.68        48.76 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.26              0.53 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           134.04            180.20 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            35.31             30.13 
[1] "0.3 - 134.0 (35.3)" "0.5 - 180.2 (30.1)"
[1] "hr=" "1.1"
D82V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  XQ LOSS MUTATED         1   272                0
  XQ LOSS WILD-TYPE       2   286                2
D82V3, multiclass
                  clus
vv                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  OMENTUM                        1                 2
  OVARY                        272               286
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V4, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED   265   4
  XQ LOSS WILD-TYPE 276   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED    265    4
  XQ LOSS WILD-TYPE  276    1
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO              265               276
  YES               4                 1
[1] 2 2
[1] FALSE
D82V5, continuous
                   vv
clus                R0 R1 R2 RX
  XQ LOSS MUTATED    8 11  1  1
  XQ LOSS WILD-TYPE  7 15  4  2
D82V6, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0               8                 7
  R1              11                15
  R2               1                 4
  RX               1                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     4 159
  XQ LOSS WILD-TYPE   6 168
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      4  159
  XQ LOSS WILD-TYPE    6  168
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 6
  NOT HISPANIC OR LATINO             159               168
[1] 2 2
[1] FALSE
