[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/15085780/OV-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/OV-TP/15096464/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 
              168               405 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              168               405 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              219               354 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              219               354 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              184               389 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              184               389 
[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 
              160               413 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              160               413 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              272               301 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              272               301 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               60               513 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               60               513 
[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 
               60               513 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               60               513 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              168               405 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              168               405 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               97               476 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               97               476 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              179               394 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              179               394 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              199               374 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              199               374 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              118               455 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              118               455 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              240               333 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              240               333 
[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 
               186                387 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               186                387 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               109                464 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               109                464 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                76                497 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                76                497 
[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 
               254                319 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               254                319 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               176                397 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               176                397 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                60                513 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                60                513 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                58                515 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                58                515 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                39                534 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                39                534 
[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 
                31                542 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                31                542 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                22                551 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                22                551 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                47                526 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                47                526 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               120                453 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               120                453 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                72                501 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                72                501 
[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 
               160                413 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               160                413 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               287                286 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               287                286 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               326                247 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               326                247 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               109                464 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               109                464 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                24                549 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                24                549 
[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 
               64               509 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               64               509 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               43               530 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               43               530 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               53               520 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               53               520 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               59               514 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               59               514 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               94               479 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               94               479 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               43               530 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               43               530 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              313               260 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              313               260 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              359               214 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              359               214 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              131               442 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              131               442 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              221               352 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              221               352 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              163               410 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              163               410 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              238               335 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              238               335 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
              120               453 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
              120               453 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               81               492 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               81               492 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              273               300 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              273               300 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               89               484 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               89               484 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              262               311 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              262               311 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              286               287 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              286               287 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                96                477 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                96                477 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               124                449 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               124                449 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               196                377 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               196                377 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               148                425 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               148                425 
[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 
               103                470 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               103                470 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               306                267 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               306                267 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               214                359 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               214                359 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               276                297 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               276                297 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               331                242 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               331                242 
[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 
               380                193 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               380                193 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               231                342 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               231                342 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               289                284 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               289                284 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               184                389 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               184                389 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               176                397 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               176                397 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                49                524 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                49                524 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                32                541 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                32                541 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               195                378 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               195                378 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               428                145 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               428                145 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              322               251 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              322               251 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              277               296 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              277               296 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                                    
 [2] "VITAL_STATUS"                                      
 [3] "DAYS_TO_DEATH"                                     
 [4] "DAYS_TO_LAST_FOLLOWUP"                             
 [5] "PRIMARY_SITE_OF_DISEASE"                           
 [6] "NEOPLASM_DISEASESTAGE"                             
 [7] "PATHOLOGY_T_STAGE"                                 
 [8] "PATHOLOGY_N_STAGE"                                 
 [9] "PATHOLOGY_M_STAGE"                                 
[10] "DCC_UPLOAD_DATE"                                   
[11] "GENDER"                                            
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"              
[13] "RADIATION_THERAPY"                                 
[14] "KARNOFSKY_PERFORMANCE_SCORE"                       
[15] "EXAMINATIONS_EXAMINATION_KARNOFSKYPERFORMANCESCORE"
[16] "HISTOLOGICAL_TYPE"                                 
[17] "TUMOR_GRADE"                                       
[18] "TUMOR_STAGE"                                       
[19] "PATIENT_TUMOR_RECURRENCE_STATUS"                   
[20] "DAYS_TO_TUMOR_RECURRENCE"                          
[21] "CHEMOTHERAPY"                                      
[22] "RADIATIONS_RADIATION_REGIMENINDICATION"            
[23] "COMPLETENESS_OF_RESECTION"                         
[24] "RACE"                                              
[25] "ETHNICITY"                                         
[26] "BATCH_NUMBER"                                      

Input Data has 26 rows and 573 columns.

[1] "Batch" "26"   
[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=268,	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=452,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "NEOPLASM_DISEASESTAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_T_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_N_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "GENDER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 14:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'EXAMINATIONS_EXAMINATION_KARNOFSKYPERFORMANCESCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "EXAMINATIONS_EXAMINATION_KARNOFSKYPERFORMANCESCORE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 16:'HISTOLOGICAL_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HISTOLOGICAL_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 17:'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 18:'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 19:'PATIENT_TUMOR_RECURRENCE_STATUS':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATIENT_TUMOR_RECURRENCE_STATUS is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 20:'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 21:'CHEMOTHERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "CHEMOTHERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 22:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 24:'RACE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 25:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 26:'BATCH_NUMBER':	nDistinctValues=16,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 573 columns, 1 survival variables, and 7 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"                        
[2] "PRIMARY_SITE_OF_DISEASE"               
[3] "KARNOFSKY_PERFORMANCE_SCORE"           
[4] "RADIATIONS_RADIATION_REGIMENINDICATION"
[5] "COMPLETENESS_OF_RESECTION"             
[6] "RACE"                                  
[7] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=55, binary=FALSE, numeric=TRUE
PRIMARY_SITE_OF_DISEASE, nv=3, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=6, binary=FALSE, numeric=TRUE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS_OF_RESECTION, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=5, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED    69  95
  1P GAIN WILD-TYPE 199 197
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              164               396 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               95               197 
$`1P GAIN MUTATED`
TCGA-04-1336 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1364 
       49.15        18.51        11.87        65.52        63.09        33.67 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1649 TCGA-04-1655 TCGA-09-0365 
       38.37       119.08        29.10        64.64        45.37         9.47 
TCGA-09-0366 TCGA-09-0369 TCGA-09-1659 TCGA-09-1667 TCGA-09-1670 TCGA-09-2045 
       57.76        35.57         9.99        61.87        17.98        35.15 
TCGA-09-2048 TCGA-09-2051 TCGA-10-0925 TCGA-10-0930 TCGA-13-0717 TCGA-13-0723 
        4.54        63.09        54.31        34.19        24.59        39.58 
TCGA-13-0724 TCGA-13-0726 TCGA-13-0751 TCGA-13-0757 TCGA-13-0760 TCGA-13-0795 
        2.73        31.20        55.17        11.18        11.54        19.59 
TCGA-13-0803 TCGA-13-0885 TCGA-13-0888 TCGA-13-0893 TCGA-13-0897 TCGA-13-0911 
       43.86        91.40        70.39        43.36        57.47        27.72 
TCGA-13-0919 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1495 TCGA-13-1496 
       14.89         6.05         5.92         4.70        49.25         4.24 
TCGA-13-1504 TCGA-13-1506 TCGA-13-1512 TCGA-13-2061 TCGA-13-A5FU TCGA-20-0987 
       16.57         4.41         3.09        10.78         8.42        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-23-1031 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 
       25.94        26.20        18.90        33.30        86.01       129.96 
TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2079 TCGA-23-2084 
       58.13         0.53        24.95       115.89        91.66        49.84 
TCGA-24-1104 TCGA-24-1417 TCGA-24-1418 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 
       63.55         7.82         7.99        19.17        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-25-1633 TCGA-25-1635 TCGA-25-2392 TCGA-25-2400 TCGA-29-1698 
       12.95        62.17        52.04         1.02        42.02        68.32 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1707 TCGA-29-1710 TCGA-29-1761 TCGA-29-1764 
       16.93        23.93        41.98        31.27        17.36        62.93 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1775 TCGA-29-1777 TCGA-29-1783 TCGA-29-1784 
       22.98        24.36        12.36        12.30         7.23         5.36 
TCGA-29-2425 TCGA-29-2432 TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 
       65.00        21.47        38.07        51.91         2.47        15.68 
TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-31-1959 TCGA-36-1577 TCGA-36-1581 
        6.12        36.62         1.22         2.20        25.74        24.69 
TCGA-36-2529 TCGA-36-2551 TCGA-42-2582 TCGA-42-2587 TCGA-57-1582 TCGA-57-1994 
       35.05        16.18        47.57        23.74        24.03        25.02 
TCGA-59-2351 TCGA-59-2355 TCGA-5X-AA5U TCGA-61-1722 TCGA-61-1730 TCGA-61-1733 
      116.12         2.14        11.87         8.09         4.34        31.79 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1899 TCGA-61-1906 
       35.80         2.43        33.67        43.69         8.42        34.13 
TCGA-61-1911 TCGA-61-1914 TCGA-61-1919 TCGA-61-2008 TCGA-61-2009 TCGA-61-2088 
       42.51        56.61        38.17        30.64        39.85         4.77 
TCGA-61-2092 TCGA-61-2097 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2111 
       51.72        60.62         6.48        76.87        20.68       125.75 
TCGA-61-2614 TCGA-OY-A56P 
        8.61        39.68 

$`1P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 
       43.92        41.00         1.81         2.01        46.62         1.08 
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-04-1371 TCGA-04-1514 
       32.52        44.32        76.57       103.40        82.39        56.55 
TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 
       41.59        19.99         0.79        84.20        55.43        48.89 
TCGA-04-1646 TCGA-04-1648 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-09-0364 
       27.88        28.64        36.23        31.86        47.70        29.16 
TCGA-09-0367 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 
       17.98        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-09-2049 TCGA-09-2050 TCGA-09-2053 TCGA-09-2054 
        6.18         6.12       112.41        71.11        39.75        20.94 
TCGA-09-2055 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 
       26.93        12.46        25.91        81.86        18.51        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-13-0720 TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 
        6.21        44.55        12.39        15.19        17.82         2.50 
TCGA-13-0758 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 
       11.38        34.06        32.25        31.04        21.40         8.45 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 
       38.93        36.72        28.70        30.35         8.71         7.79 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
        8.12         8.28         8.19        35.28        35.31        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 
       68.94       107.18        74.27        66.67        61.84        67.99 
TCGA-13-0891 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 
       69.01        56.15        57.07        19.36        47.38        48.33 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 
       47.84        44.94        44.84        37.08        34.06        29.98 
TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 
       21.17        13.81         4.64         6.41         6.08        10.88 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1409 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 
        6.61         7.36         6.84         4.21         5.33        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        98.04        20.68        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1497 
       70.82        82.88        52.44        73.55        38.20        54.31 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1505 TCGA-13-1507 
       37.61        38.40        13.97        32.84         4.21         4.77 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
        4.18         2.56         3.91        14.24        12.23         8.61 
TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 
        8.75         6.28        54.77        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-23-1024 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-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 
       29.13         2.76        51.35        54.51         3.22        31.20 
TCGA-23-1114 TCGA-23-1116 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 
       68.68         4.57         4.27         6.38        39.09        33.47 
TCGA-23-2078 TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 
       87.48        77.00         2.76         4.70         4.50         7.63 
TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
       19.66        11.64        21.80        41.56         7.66        22.32 
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-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1634 TCGA-25-1870 
       20.61        38.20         0.30        59.15        35.87        14.96 
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-25-2397 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-29-1699 TCGA-29-1703 
       39.02        40.41        33.93        31.20        36.36        59.67 
TCGA-29-1705 TCGA-29-1711 TCGA-29-1762 TCGA-29-1763 TCGA-29-1766 TCGA-29-1768 
       18.25        34.62        86.60        66.81        39.42        31.30 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 TCGA-29-1778 TCGA-29-1781 TCGA-29-1785 
       22.55        17.33        11.84        14.93         8.38        36.30 
TCGA-29-2414 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 
       86.17        62.47        45.11        13.84        42.25        11.47 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1853 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 
        9.76        35.77        36.26         0.26        48.10        44.91 
TCGA-30-1861 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 
       34.78        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-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-36-1578 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-36-2538 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-36-2552 TCGA-3P-A9WA 
       18.31        20.52        14.17         6.05        11.47        13.81 
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-59-2348 
       21.14         1.74        22.32        29.00        25.08       180.20 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 TCGA-59-2372 
       80.12        22.32         9.40        34.39         5.42        44.81 
TCGA-59-A5PD TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 
       20.52        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 

  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 
           26.070            29.015 
[1] "0.5 - 130.0 (26.1)" "0.3 - 180.2 (29.0)"
[1] "hr=" "1.2"
D1V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  1P GAIN MUTATED         1   162                1
  1P GAIN WILD-TYPE       2   396                1
D1V3, multiclass
                  clus
vv                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  OMENTUM                        1                 2
  OVARY                        162               396
  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, continuous
D1V5, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     2 166
  1P GAIN WILD-TYPE   1 404
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2  166
  1P GAIN WILD-TYPE    1  404
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                2                 1
  YES             166               404
[1] 2 2
[1] FALSE
                   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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  0     5
  1P GAIN WILD-TYPE                                3    14
                   vv
clus                BLACK OR AFRICAN AMERICAN
  1P GAIN MUTATED                           9
  1P GAIN WILD-TYPE                        25
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1P GAIN MUTATED                                           0   147
  1P GAIN WILD-TYPE                                         1   329
D1V7, multiclass
                                           clus
vv                                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   5                14
  BLACK OR AFRICAN AMERICAN                               9                25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 147               329
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     1  83
  1P GAIN WILD-TYPE   9 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1   83
  1P GAIN WILD-TYPE    9  244
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              83               244
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    94 117
  1Q GAIN WILD-TYPE 174 175
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              211               349 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              117               175 
$`1Q GAIN MUTATED`
TCGA-04-1336 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1356 
       49.15        18.51        11.87        65.52        63.09        49.28 
TCGA-04-1364 TCGA-04-1514 TCGA-04-1516 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 
       33.67        56.55        41.59        38.37       119.08        29.10 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1649 TCGA-04-1652 TCGA-04-1655 TCGA-09-0365 
       84.20        55.43        64.64        31.86        45.37         9.47 
TCGA-09-0366 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1667 TCGA-09-1668 
       57.76        35.57         9.99        38.43        61.87        55.36 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 
       17.98         5.85         8.55         6.12        35.15         4.54 
TCGA-09-2049 TCGA-09-2051 TCGA-09-2056 TCGA-10-0925 TCGA-10-0930 TCGA-10-0933 
      112.41        63.09        12.46        54.31        34.19        14.66 
TCGA-10-0935 TCGA-10-0938 TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 TCGA-13-0727 
       35.44        20.91        24.59        39.58         2.73        15.19 
TCGA-13-0751 TCGA-13-0757 TCGA-13-0760 TCGA-13-0762 TCGA-13-0795 TCGA-13-0799 
       55.17        11.18        11.54        32.25        19.59         7.79 
TCGA-13-0800 TCGA-13-0803 TCGA-13-0888 TCGA-13-0890 TCGA-13-0897 TCGA-13-0901 
        8.12        43.86        70.39        67.99        57.47        19.36 
TCGA-13-0911 TCGA-13-0919 TCGA-13-0921 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
       27.72        14.89         4.64         5.92         6.84         4.70 
TCGA-13-1481 TCGA-13-1484 TCGA-13-1495 TCGA-13-1504 TCGA-13-1506 TCGA-13-1512 
       87.06        98.04        49.25        16.57         4.41         3.09 
TCGA-13-2061 TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1683 
       10.78         8.42        23.05        25.94        26.20        25.38 
TCGA-20-1684 TCGA-23-1031 TCGA-23-1114 TCGA-23-1118 TCGA-23-1119 TCGA-23-1124 
       19.10        18.90        68.68        86.01       129.96        58.13 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-24-0982 TCGA-24-1104 TCGA-24-1413 
        0.53        24.95       115.89        22.32        63.55         6.31 
TCGA-24-1418 TCGA-24-1422 TCGA-24-1423 TCGA-24-1431 TCGA-24-1436 TCGA-24-1464 
        7.99         0.76         6.25        19.17         8.55        12.46 
TCGA-24-1466 TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1548 
       45.14         9.11         1.18        22.22        26.96        16.21 
TCGA-24-1549 TCGA-24-1553 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1564 
       56.58        58.09        39.88        19.53        44.09        25.87 
TCGA-24-1565 TCGA-24-1604 TCGA-24-1614 TCGA-24-1842 TCGA-24-1843 TCGA-24-1845 
       10.26        88.37        48.33         8.32         3.48         3.81 
TCGA-24-1924 TCGA-24-1930 TCGA-24-2026 TCGA-24-2029 TCGA-24-2038 TCGA-24-2254 
       30.21        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-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 
       26.96        42.05         2.01        34.98        65.00        37.97 
TCGA-25-1321 TCGA-25-1323 TCGA-25-1329 TCGA-25-1626 TCGA-25-1627 TCGA-25-1633 
       33.96        12.99        15.02        17.03        12.95        62.17 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1871 TCGA-25-2392 TCGA-25-2396 TCGA-25-2400 
       35.87        52.04        24.99         1.02         3.02        42.02 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1695 TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 
       78.90        47.61        40.41        68.32        16.93        23.93 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1764 TCGA-29-1766 TCGA-29-1769 
       41.98        31.27        34.62        62.93        39.42        22.98 
TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1777 TCGA-29-1783 TCGA-29-1784 
       24.36        17.33        12.36        12.30         7.23         5.36 
TCGA-29-2425 TCGA-29-2432 TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 
       65.00        21.47        11.47        35.77        38.07        51.91 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-31-1959 
        2.47        15.68         6.12        36.62         1.22         2.20 
TCGA-36-1569 TCGA-36-1571 TCGA-36-1576 TCGA-36-1581 TCGA-36-2529 TCGA-36-2551 
       29.10        22.85        30.08        24.69        35.05        16.18 
TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-57-1582 TCGA-57-1586 TCGA-57-1994 
       11.47        47.57        23.74        24.03        22.32        25.02 
TCGA-59-2351 TCGA-59-2355 TCGA-5X-AA5U TCGA-61-1722 TCGA-61-1730 TCGA-61-1733 
      116.12         2.14        11.87         8.09         4.34        31.79 
TCGA-61-1734 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1899 
       28.47        35.80         2.43        33.67        43.69         8.42 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1911 TCGA-61-1914 TCGA-61-1919 TCGA-61-2003 
        9.07        34.13        42.51        56.61        38.17         4.01 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2088 TCGA-61-2092 TCGA-61-2097 TCGA-61-2098 
       30.64        39.85         4.77        51.72        60.62        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2111 TCGA-61-2614 
       55.50         6.48        76.87        20.68       125.75         8.61 
TCGA-OY-A56P 
       39.68 

$`1Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 
       43.92        41.00         1.81         2.01        46.62         1.08 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1361 
       48.76        21.57        63.98        65.46         0.53        32.52 
TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1517 TCGA-04-1519 
       44.32        76.57       103.40        82.39        19.99         0.79 
TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1651 TCGA-04-1654 TCGA-09-0364 
       48.89        27.88        28.64        36.23        47.70        29.16 
TCGA-09-0367 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 
       17.98        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-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0934 
       26.93        25.91        81.86        18.51        32.88         6.71 
TCGA-10-0936 TCGA-10-0937 TCGA-13-0714 TCGA-13-0720 TCGA-13-0725 TCGA-13-0726 
       36.92        19.99         6.21        44.55        12.39        31.20 
TCGA-13-0730 TCGA-13-0755 TCGA-13-0758 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 
       17.82         2.50        11.38        34.06        31.04        21.40 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 
        8.45        38.93        36.72        28.70        30.35         8.71 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
        8.28         8.19        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        91.40        74.27        66.67        61.84        69.01 
TCGA-13-0893 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       43.36        56.15        57.07        47.38        48.33        47.84 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       44.94        44.84        37.08        34.06        29.98        21.17 
TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
       13.81         6.41         6.08        10.88         6.61         7.36 
TCGA-13-1407 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 
        6.05         4.21         5.33        54.64        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        82.88        52.44        73.55 
TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 
       38.20         4.24        54.31        37.61        38.40        13.97 
TCGA-13-1501 TCGA-13-1505 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
       32.84         4.21         4.77         4.18         2.56         3.91 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT 
       14.24        12.23         8.61         8.75         6.28        54.77 
TCGA-20-0996 TCGA-20-1682 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 
       72.20        27.52        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-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
        8.81        29.13         2.76        51.35        54.51         3.22 
TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 
       31.20         4.57        33.30         4.27         6.38        39.09 
TCGA-23-1123 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
       33.47        87.48        91.66        77.00        49.84         2.76 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 
        4.70         4.50         7.63        19.66        11.64        21.80 
TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 TCGA-24-1105 TCGA-24-1416 TCGA-24-1417 
       41.56         7.66        54.12        47.41         6.38         7.82 
TCGA-24-1419 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        7.86         6.02         5.95         5.36         4.83        17.39 
TCGA-24-1430 TCGA-24-1434 TCGA-24-1435 TCGA-24-1463 TCGA-24-1467 TCGA-24-1470 
       28.37        18.67        43.53        72.92       105.99         3.45 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 
       57.40        64.27        41.06        51.91        41.39        88.50 
TCGA-24-1556 TCGA-24-1562 TCGA-24-1563 TCGA-24-1567 TCGA-24-1603 TCGA-24-1616 
       70.62        45.50        47.70        17.23        90.15        38.24 
TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 
        3.72         4.37        11.28         5.79         5.52         9.80 
TCGA-24-1923 TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 
       22.68        16.44        11.05         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-25-1322 
       16.64        33.11        53.26        33.01        52.04         2.99 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 
       18.58        27.62        20.61        38.20         0.30        59.15 
TCGA-25-1870 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 
       14.96        24.00        85.05        13.02        49.05        38.04 
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-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 
       26.99        48.33       101.79        39.02        33.93        31.20 
TCGA-29-1699 TCGA-29-1703 TCGA-29-1705 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
       36.36        59.67        18.25        17.36        86.60        66.81 
TCGA-29-1768 TCGA-29-1771 TCGA-29-1776 TCGA-29-1778 TCGA-29-1781 TCGA-29-1785 
       31.30        22.55        11.84        14.93         8.38        36.30 
TCGA-29-2414 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2436 
       86.17        62.47        45.11        13.84        42.25         9.76 
TCGA-30-1853 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1880 
       36.26         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-31-1950 
       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-36-1570 
       22.49         6.71        42.51        44.12        28.77        21.53 
TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-2530 
       22.55         8.55        25.74        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-3P-A9WA TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 
       13.81        28.93        42.02        10.42        40.77         1.48 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 TCGA-57-1993 TCGA-59-2348 
       11.38        21.14         1.74        29.00        25.08       180.20 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 TCGA-59-2372 
       80.12        22.32         9.40        34.39         5.42        44.81 
TCGA-59-A5PD TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 
       20.52        11.11        20.94        31.43        18.54        27.88 
TCGA-61-1736 TCGA-61-1737 TCGA-61-1895 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 
       48.79        44.84         1.45         5.79        11.41        13.02 
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-61-1995 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-61-2094 TCGA-61-2095 TCGA-61-2096 
       45.96        45.40         4.80        71.74        61.64        58.39 
TCGA-61-2110 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-OY-A56Q TCGA-VG-A8LO 
       44.52        22.22         6.35        31.07        18.94         0.79 
TCGA-WR-A838 
        9.99 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.53              0.26 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           129.96            180.20 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            27.72             28.77 
[1] "0.5 - 130.0 (27.7)" "0.3 - 180.2 (28.8)"
[1] "hr=" "1.1"
D2V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  1Q GAIN MUTATED         2   208                2
  1Q GAIN WILD-TYPE       1   350                0
D2V3, multiclass
                  clus
vv                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  OMENTUM                        2                 1
  OVARY                        208               350
  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, continuous
D2V5, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     1 218
  1Q GAIN WILD-TYPE   2 352
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      1  218
  1Q GAIN WILD-TYPE    2  352
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO                1                 2
  YES             218               352
[1] 2 2
[1] FALSE
                   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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  0     6
  1Q GAIN WILD-TYPE                                3    13
                   vv
clus                BLACK OR AFRICAN AMERICAN
  1Q GAIN MUTATED                          12
  1Q GAIN WILD-TYPE                        22
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1Q GAIN MUTATED                                           0   188
  1Q GAIN WILD-TYPE                                         1   288
D2V7, multiclass
                                           clus
vv                                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   6                13
  BLACK OR AFRICAN AMERICAN                              12                22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 188               288
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, 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    83  95
  2P GAIN WILD-TYPE 185 197
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              178               382 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               95               197 
$`2P GAIN MUTATED`
TCGA-04-1336 TCGA-04-1342 TCGA-04-1347 TCGA-04-1350 TCGA-04-1356 TCGA-04-1364 
       49.15        18.51        63.09        63.98        49.28        33.67 
TCGA-04-1371 TCGA-04-1525 TCGA-04-1542 TCGA-04-1646 TCGA-04-1655 TCGA-09-0364 
       82.39        38.37        84.20        27.88        45.37        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0369 TCGA-09-1661 TCGA-09-1670 TCGA-09-1672 
        9.47        57.76        35.57        38.43        17.98         5.85 
TCGA-09-1674 TCGA-09-2043 TCGA-09-2048 TCGA-10-0927 TCGA-10-0933 TCGA-10-0935 
        8.55         6.18         4.54        81.86        14.66        35.44 
TCGA-10-0938 TCGA-13-0724 TCGA-13-0730 TCGA-13-0757 TCGA-13-0760 TCGA-13-0800 
       20.91         2.73        17.82        11.18        11.54         8.12 
TCGA-13-0802 TCGA-13-0884 TCGA-13-0888 TCGA-13-0893 TCGA-13-0899 TCGA-13-0901 
        8.19       107.18        70.39        43.36        56.15        19.36 
TCGA-13-0906 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-1407 TCGA-13-1409 
       44.94        14.89        13.81         4.64         6.05         6.84 
TCGA-13-1410 TCGA-13-1412 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-2057 
        4.70         5.33        32.84        16.57         4.21        14.24 
TCGA-13-2060 TCGA-13-A5FU TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1024 
        8.61         8.42         2.93         2.66        47.54        15.39 
TCGA-23-1114 TCGA-23-1118 TCGA-23-1119 TCGA-23-1121 TCGA-23-1122 TCGA-23-1809 
       68.68        86.01       129.96         6.38        39.09         0.53 
TCGA-23-2072 TCGA-23-2078 TCGA-23-2643 TCGA-24-0970 TCGA-24-0982 TCGA-24-1417 
       24.95        87.48         4.70        11.64        22.32         7.82 
TCGA-24-1418 TCGA-24-1422 TCGA-24-1424 TCGA-24-1434 TCGA-24-1436 TCGA-24-1467 
        7.99         0.76         6.02        18.67         8.55       105.99 
TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1552 TCGA-24-1553 
        9.11         1.18        22.22        26.96        41.39        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-24-1845 TCGA-24-1850 TCGA-24-1924 TCGA-24-1928 TCGA-24-2019 TCGA-24-2029 
        3.81         5.52        30.21        11.05         4.87        14.43 
TCGA-24-2033 TCGA-24-2261 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2295 
       18.48         0.79        44.61         0.82        67.36        33.11 
TCGA-25-1312 TCGA-25-1315 TCGA-25-1317 TCGA-25-1319 TCGA-25-1329 TCGA-25-1623 
        1.02        52.04         2.01        65.00        15.02        18.58 
TCGA-25-1626 TCGA-25-1628 TCGA-25-1631 TCGA-25-1634 TCGA-25-1870 TCGA-25-1877 
       17.03        20.61         0.30        35.87        14.96        24.00 
TCGA-25-2391 TCGA-25-2393 TCGA-25-2398 TCGA-25-2400 TCGA-25-2409 TCGA-29-1691 
       49.05        38.04        45.01        42.02        26.99        48.33 
TCGA-29-1695 TCGA-29-1701 TCGA-29-1702 TCGA-29-1763 TCGA-29-1764 TCGA-29-1769 
       40.41        16.93        23.93        66.81        62.93        22.98 
TCGA-29-1774 TCGA-29-1775 TCGA-29-1778 TCGA-29-2425 TCGA-29-2429 TCGA-29-A5NZ 
       17.33        12.36        14.93        65.00        13.84        35.77 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1859 TCGA-30-1862 TCGA-31-1950 TCGA-31-1953 
       38.07        51.91        48.10         6.12        18.77         6.71 
TCGA-31-1959 TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1578 TCGA-36-1581 
        2.20        22.85         8.55        30.08        27.85        24.69 
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-59-A5PD TCGA-5X-AA5U TCGA-61-1722 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 
       20.52        11.87         8.09        27.88         4.34        31.79 
TCGA-61-1741 TCGA-61-1899 TCGA-61-1900 TCGA-61-1906 TCGA-61-1919 TCGA-61-2000 
       33.67         8.42         5.79        34.13        38.17        14.50 
TCGA-61-2003 TCGA-61-2009 TCGA-61-2018 TCGA-61-2088 TCGA-61-2097 TCGA-61-2098 
        4.01        39.85        45.40         4.77        60.62        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 
       55.50         6.48        76.87       125.75        22.22         6.35 
TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-WR-A838 
        8.61        39.68        18.94         9.99 

$`2P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 
       43.92        41.00         1.81         2.01        46.62         1.08 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 TCGA-04-1349 TCGA-04-1351 TCGA-04-1353 
       11.87        65.52        48.76        21.57        65.46         0.53 
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-04-1530 TCGA-04-1536 TCGA-04-1638 TCGA-04-1644 
       19.99         0.79       119.08        29.10        55.43        48.89 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-09-0367 
       28.64        64.64        36.23        31.86        47.70        17.98 
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-09-2054 TCGA-09-2055 
      112.41        71.11        63.09        39.75        20.94        26.93 
TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       12.46        54.31        25.91        18.51        34.19        32.88 
TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
        6.71        36.92        19.99         6.21        24.59        44.55 
TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0751 TCGA-13-0755 
       39.58        12.39        31.20        15.19        55.17         2.50 
TCGA-13-0758 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 
       11.38        34.06        32.25        31.04        21.40         8.45 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 
       38.93        36.72        28.70        30.35        19.59         8.71 
TCGA-13-0799 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
        7.79         8.28        43.86        35.28        35.31        13.61 
TCGA-13-0883 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 
       68.94        91.40        74.27        66.67        61.84        67.99 
TCGA-13-0891 TCGA-13-0897 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       69.01        57.47        57.07        47.38        48.33        47.84 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       44.84        37.08        27.72        34.06        29.98        21.17 
TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 
        6.41         6.08        10.88         6.61         7.36         5.92 
TCGA-13-1411 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
        4.21        54.64        87.06        61.71        29.42        98.04 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
       20.68        22.39        70.82        82.88        52.44        73.55 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 
       38.20        49.25         4.24        54.31        37.61        38.40 
TCGA-13-1500 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
       13.97         4.41         4.77         4.18         2.56         3.91 
TCGA-13-1512 TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT 
        3.09        12.23        10.78         8.75         6.28        54.77 
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-23-1022 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 
       19.10        16.70        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-23-1120 
       54.51         3.22        31.20         4.57        33.30         4.27 
TCGA-23-1123 TCGA-23-1124 TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 
       33.47        58.13       115.89        91.66        77.00        49.84 
TCGA-23-2641 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0975 TCGA-24-0979 
        2.76         4.50         7.63        19.66        21.80        41.56 
TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
        7.66        54.12        63.55        47.41         6.31         6.38 
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-24-1430 TCGA-24-1431 TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 
       28.37        19.17        43.53        72.92        12.46        45.14 
TCGA-24-1470 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 
        3.45        57.40        64.27        16.21        56.58        41.06 
TCGA-24-1551 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1562 TCGA-24-1563 
       51.91        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-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 TCGA-24-1927 
        4.37        11.28         5.79         9.80        22.68        16.44 
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-24-2030 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 
       55.92        28.18        64.01        44.52        57.07        36.16 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2290 TCGA-24-2293 
        0.36        47.54        31.63        70.45        36.23        16.64 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1314 TCGA-25-1316 TCGA-25-1318 
       55.86        53.26        26.96        33.01        42.05        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-25-1630 TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 TCGA-25-1871 TCGA-25-1878 
       38.20        59.15        62.17        52.04        24.99        85.05 
TCGA-25-2042 TCGA-25-2392 TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 TCGA-25-2401 
       13.02         1.02         3.02        12.00        19.99         2.96 
TCGA-25-2404 TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 
       29.03        31.00        78.90        47.61       101.79        39.02 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1703 TCGA-29-1705 
       33.93        31.20        68.32        36.36        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-29-1776 TCGA-29-1777 TCGA-29-1781 
       31.30        24.36        22.55        11.84        12.30         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-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-30-1853 TCGA-30-1855 
       42.25        21.47        11.47         9.76        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-30-1880 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-31-1955 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-36-1574 TCGA-36-1577 TCGA-36-1580 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 
       22.55        25.74        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-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-3P-A9WA 
       20.98        18.31        14.17         6.05        16.18        13.81 
TCGA-42-2582 TCGA-42-2588 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1584 
       47.57        28.93        10.42        40.77         1.48        21.14 
TCGA-57-1992 TCGA-57-1993 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2354 
       29.00        25.08        80.12        22.32       116.12        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-61-1734 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 
       20.68        44.52        31.07         0.79 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.30              0.26 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           180.20            152.02 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           20.565            31.055 
[1] "0.3 - 180.2 (20.6)" "0.3 - 152.0 (31.1)"
[1] "hr=" "1.3"
D3V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  2P GAIN MUTATED         1   178                0
  2P GAIN WILD-TYPE       2   380                2
D3V3, multiclass
                  clus
vv                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  OMENTUM                        1                 2
  OVARY                        178               380
  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, continuous
D3V5, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     1 183
  2P GAIN WILD-TYPE   2 387
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      1  183
  2P GAIN WILD-TYPE    2  387
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                1                 2
  YES             183               387
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  2P GAIN MUTATED    5  6  2  1
  2P GAIN WILD-TYPE 10 20  3  2
D3V6, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0               5                10
  R1               6                20
  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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P GAIN MUTATED                                  0     4
  2P GAIN WILD-TYPE                                3    15
                   vv
clus                BLACK OR AFRICAN AMERICAN
  2P GAIN MUTATED                          14
  2P GAIN WILD-TYPE                        20
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2P GAIN MUTATED                                           0   154
  2P GAIN WILD-TYPE                                         1   322
D3V7, multiclass
                                           clus
vv                                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   4                15
  BLACK OR AFRICAN AMERICAN                              14                20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 154               322
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     3  96
  2P GAIN WILD-TYPE   7 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      3   96
  2P GAIN WILD-TYPE    7  231
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 7
  NOT HISPANIC OR LATINO              96               231
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    67  82
  2Q GAIN WILD-TYPE 201 210
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              149               411 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               82               210 
$`2Q GAIN MUTATED`
TCGA-04-1347 TCGA-04-1350 TCGA-04-1356 TCGA-04-1364 TCGA-04-1516 TCGA-04-1536 
       63.09        63.98        49.28        33.67        41.59        29.10 
TCGA-04-1542 TCGA-04-1646 TCGA-04-1649 TCGA-04-1655 TCGA-09-0365 TCGA-09-0366 
       84.20        27.88        64.64        45.37         9.47        57.76 
TCGA-09-0369 TCGA-09-1661 TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 TCGA-09-2043 
       35.57        38.43        17.98         5.85         8.55         6.18 
TCGA-09-2048 TCGA-10-0927 TCGA-10-0933 TCGA-10-0935 TCGA-10-0938 TCGA-13-0724 
        4.54        81.86        14.66        35.44        20.91         2.73 
TCGA-13-0730 TCGA-13-0757 TCGA-13-0760 TCGA-13-0800 TCGA-13-0883 TCGA-13-0884 
       17.82        11.18        11.54         8.12        68.94       107.18 
TCGA-13-0888 TCGA-13-0893 TCGA-13-0901 TCGA-13-0906 TCGA-13-0919 TCGA-13-0920 
       70.39        43.36        19.36        44.94        14.89        13.81 
TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 TCGA-13-1412 TCGA-13-1488 TCGA-13-1496 
        6.05         6.84         4.70         5.33        70.82         4.24 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-2057 TCGA-13-2060 TCGA-20-1687 
       32.84        16.57         4.21        14.24         8.61         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-29-1778 TCGA-29-2425 TCGA-29-2429 TCGA-30-1714 TCGA-30-1718 
       12.36        14.93        65.00        13.84        38.07        51.91 
TCGA-30-1859 TCGA-30-1862 TCGA-31-1950 TCGA-31-1959 TCGA-36-1576 TCGA-36-1578 
       48.10         6.12        18.77         2.20        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-59-A5PD 
        1.74        22.32        25.02       180.20         9.40        20.52 
TCGA-5X-AA5U TCGA-61-1722 TCGA-61-1730 TCGA-61-1733 TCGA-61-1741 TCGA-61-1743 
       11.87         8.09         4.34        31.79        33.67        43.69 
TCGA-61-1899 TCGA-61-1906 TCGA-61-1919 TCGA-61-2003 TCGA-61-2012 TCGA-61-2018 
        8.42        34.13        38.17         4.01        30.64        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-61-2113 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
       22.22         6.35         8.61        39.68        18.94 

$`2Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       43.92        41.00         1.81        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-04-1351 TCGA-04-1353 TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 
       65.46         0.53        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-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 
       55.43        48.89        28.64        36.23        31.86        47.70 
TCGA-09-0364 TCGA-09-0367 TCGA-09-1659 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       29.16        17.98         9.99        89.33        74.93        41.62 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1673 TCGA-09-1675 
       57.60        61.87        55.36        30.51         3.02        97.55 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 
        6.12        35.15       112.41        71.11        63.09        39.75 
TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0928 
       20.94        26.93        12.46        54.31        25.91        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 TCGA-13-0714 
       34.19        32.88         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-13-0751 TCGA-13-0755 TCGA-13-0758 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 
       55.17         2.50        11.38        34.06        32.25        31.04 
TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 
       21.40         8.45        38.93        36.72        28.70        30.35 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 
       19.59         8.71         7.79         8.28         8.19        43.86 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
       35.28        35.31        13.61        91.40        74.27        66.67 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       61.84        67.99        69.01        57.47        56.15        57.07 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       47.38        48.33        47.84        44.84        37.08        27.72 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       34.06        29.98        21.17         4.64         6.41         6.08 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1411 TCGA-13-1477 
       10.88         6.61         7.36         5.92         4.21        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        98.04        20.68        22.39 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1497 
       82.88        52.44        73.55        38.20        49.25        54.31 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       37.61        38.40        13.97         4.41         4.77         4.18 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 
        2.56         3.91         3.09        12.23        10.78         8.75 
TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
        6.28        54.77         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-23-1022 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 
       49.68        40.54        26.83        32.09        49.41         8.81 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 
       29.13        18.90         2.76        51.35        54.51        31.20 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1120 TCGA-23-1123 TCGA-23-1124 TCGA-23-2077 
        4.57        33.30         4.27        33.47        58.13       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-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        7.63        19.66        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 
       19.17        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-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 
        8.38         7.23         5.36        36.30        86.17        62.47 
TCGA-29-2428 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ 
       45.11        42.25        21.47        11.47         9.76        35.77 
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-31-1953 TCGA-31-1955 TCGA-31-1956 
       45.57        30.18        22.49         6.71        42.51        44.12 
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-36-1580 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-3P-A9WA TCGA-42-2582 
       18.31        14.17         6.05        16.18        13.81        47.57 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1584 
       28.93        42.02        10.42        40.77         1.48        21.14 
TCGA-57-1992 TCGA-57-1993 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2354 
       29.00        25.08        80.12        22.32       116.12        34.39 
TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 
        2.14         5.42        44.81        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-61-1895 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 
       31.07         0.79         9.99 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.53              0.26 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           180.20            152.02 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            22.22             30.18 
[1] "0.5 - 180.2 (22.2)" "0.3 - 152.0 (30.2)"
[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, continuous
D4V5, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     2 151
  2Q GAIN WILD-TYPE   1 419
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2  151
  2Q GAIN WILD-TYPE    1  419
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                2                 1
  YES             151               419
[1] 2 2
[1] FALSE
                   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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q GAIN MUTATED                                  0     2
  2Q GAIN WILD-TYPE                                3    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  2Q GAIN MUTATED                          11
  2Q GAIN WILD-TYPE                        23
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2Q GAIN MUTATED                                           0   131
  2Q GAIN WILD-TYPE                                         1   345
D4V7, multiclass
                                           clus
vv                                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   2                17
  BLACK OR AFRICAN AMERICAN                              11                23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 131               345
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, 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    74  82
  3P GAIN WILD-TYPE 194 210
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              156               404 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               82               210 
$`3P GAIN MUTATED`
TCGA-04-1332 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1343 TCGA-04-1349 
       41.00         2.01        46.62         1.08        11.87        21.57 
TCGA-04-1371 TCGA-04-1516 TCGA-04-1517 TCGA-04-1536 TCGA-04-1646 TCGA-04-1655 
       82.39        41.59        19.99        29.10        27.88        45.37 
TCGA-09-0364 TCGA-09-0367 TCGA-09-1659 TCGA-09-1665 TCGA-09-1668 TCGA-09-1670 
       29.16        17.98         9.99        41.62        55.36        17.98 
TCGA-09-1672 TCGA-09-1674 TCGA-09-2043 TCGA-10-0930 TCGA-10-0935 TCGA-10-0936 
        5.85         8.55         6.18        34.19        35.44        36.92 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0751 TCGA-13-0760 TCGA-13-0762 TCGA-13-0795 
       39.58         2.73        55.17        11.54        32.25        19.59 
TCGA-13-0800 TCGA-13-0803 TCGA-13-0884 TCGA-13-0911 TCGA-13-0921 TCGA-13-1403 
        8.12        43.86       107.18        27.72         4.64        10.88 
TCGA-13-1410 TCGA-13-1484 TCGA-13-1489 TCGA-13-1495 TCGA-13-1504 TCGA-13-1505 
        4.70        98.04        82.88        49.25        16.57         4.21 
TCGA-13-1507 TCGA-13-2061 TCGA-20-0991 TCGA-20-1683 TCGA-20-1684 TCGA-20-1686 
        4.77        10.78        26.20        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         4.57        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-59-A5PD 
       24.03         1.74        25.02       116.12         9.40        20.52 
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-61-1915 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2097 
       67.76        17.98         4.01        30.64        39.85        60.62 
TCGA-61-2102 TCGA-61-2111 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
        6.48       125.75         6.35         8.61        39.68        18.94 

$`3P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 
       43.92         1.81        49.15        18.51        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-04-1514 TCGA-04-1519 
       44.32        33.67        76.57       103.40        56.55         0.79 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 
       38.37       119.08        84.20        55.43        48.89        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-09-0365 TCGA-09-0366 
       64.64        36.23        31.86        47.70         9.47        57.76 
TCGA-09-0369 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 
       35.57        38.43        89.33        74.93        57.60        61.87 
TCGA-09-1669 TCGA-09-1673 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 
       30.51         3.02        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-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 
       12.46        54.31        25.91        81.86        18.51        32.88 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
       14.66         6.71        19.99        20.91         6.21        24.59 
TCGA-13-0720 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 
       44.55        12.39        31.20        15.19        17.82         2.50 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 
       11.18        11.38        34.06        31.04        21.40         8.45 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 
       38.93        36.72        28.70        30.35         8.71         7.79 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
        8.28         8.19        35.28        35.31        13.61        68.94 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 
       91.40        74.27        66.67        70.39        61.84        67.99 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
       69.01        43.36        57.47        56.15        57.07        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
       47.38        48.33        47.84        44.94        44.84        37.08 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 
       34.06        29.98        21.17        14.89        13.81         6.41 
TCGA-13-0924 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
        6.08         6.61         7.36         6.05         5.92         6.84 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
        4.21         5.33        54.64        87.06        61.71        29.42 
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        73.55        38.20 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 
        4.24        54.31        37.61        38.40        13.97        32.84 
TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 
        4.41         4.18         2.56         3.91         3.09        14.24 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU 
       12.23         8.61         8.75         6.28        54.77         8.42 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0996 TCGA-20-1682 TCGA-20-1685 TCGA-23-1021 
       23.05        25.94        72.20        27.52        16.70        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-23-1111 TCGA-23-1113 TCGA-23-1114 
       29.13        18.90         2.76         3.22        31.20        68.68 
TCGA-23-1118 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 
       86.01         4.27         6.38        39.09        33.47        58.13 
TCGA-23-1809 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2645 TCGA-24-0966 
        0.53        77.00        49.84         2.76         4.50         7.63 
TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 
       19.66        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        19.17        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-3P-A9WA TCGA-42-2582 TCGA-42-2588 
        6.05        16.18        11.47        13.81        47.57        28.93 
TCGA-42-2589 TCGA-42-2591 TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 
       42.02        40.77         1.48        11.38        21.14        22.32 
TCGA-57-1992 TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2354 
       29.00        25.08       180.20        80.12        22.32        34.39 
TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-5X-AA5U TCGA-61-1721 TCGA-61-1722 
        2.14         5.42        44.81        11.87        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-61-1740 TCGA-61-1741 
       28.47        48.79        44.84        35.80         2.43        33.67 
TCGA-61-1743 TCGA-61-1895 TCGA-61-1900 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 
       43.69         1.45         5.79        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-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
       14.50        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-61-2098 
        4.77        51.72        71.74        61.64        58.39        65.52 
TCGA-61-2101 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2113 TCGA-61-2613 
       55.50        76.87        20.68        44.52        22.22        31.07 
TCGA-VG-A8LO TCGA-WR-A838 
        0.79         9.99 

  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 
           24.655            29.900 
[1] "0.8 - 152.0 (24.7)" "0.3 - 180.2 (29.9)"
[1] "hr=" "1.1"
D5V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  3P GAIN MUTATED         0   156                1
  3P GAIN WILD-TYPE       3   402                1
D5V3, multiclass
                  clus
vv                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  OMENTUM                        0                 3
  OVARY                        156               402
  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, continuous
D5V5, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     0 160
  3P GAIN WILD-TYPE   3 410
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0  160
  3P GAIN WILD-TYPE    3  410
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                0                 3
  YES             160               410
[1] 2 2
[1] FALSE
                   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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P GAIN MUTATED                                  1     3
  3P GAIN WILD-TYPE                                2    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  3P GAIN MUTATED                           7
  3P GAIN WILD-TYPE                        27
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3P GAIN MUTATED                                           1   141
  3P GAIN WILD-TYPE                                         0   335
D5V7, multiclass
                                           clus
vv                                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 2
  ASIAN                                                   3                16
  BLACK OR AFRICAN AMERICAN                               7                27
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 141               335
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     2  86
  3P GAIN WILD-TYPE   8 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2   86
  3P GAIN WILD-TYPE    8  241
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 8
  NOT HISPANIC OR LATINO              86               241
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED   128 139
  3Q GAIN WILD-TYPE 140 153
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              267               293 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              139               153 
$`3Q GAIN MUTATED`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 
       41.00         1.81        49.15         2.01        46.62         1.08 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1361 
       11.87        65.52        63.09        21.57        63.98        32.52 
TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1371 TCGA-04-1516 TCGA-04-1517 
       44.32        33.67        76.57        82.39        41.59        19.99 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1646 TCGA-04-1655 
       38.37       119.08        29.10        84.20        27.88        45.37 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 
       29.16         9.47        57.76        17.98        35.57         9.99 
TCGA-09-1665 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 
       41.62        55.36        30.51        17.98         5.85         8.55 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2048 TCGA-09-2049 TCGA-09-2053 TCGA-10-0930 
        6.18         6.12         4.54       112.41        39.75        34.19 
TCGA-10-0933 TCGA-10-0935 TCGA-10-0936 TCGA-13-0723 TCGA-13-0724 TCGA-13-0727 
       14.66        35.44        36.92        39.58         2.73        15.19 
TCGA-13-0751 TCGA-13-0757 TCGA-13-0760 TCGA-13-0768 TCGA-13-0795 TCGA-13-0800 
       55.17        11.18        11.54         8.45        19.59         8.12 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0884 TCGA-13-0888 TCGA-13-0897 
        8.19        43.86        35.28       107.18        70.39        57.47 
TCGA-13-0901 TCGA-13-0911 TCGA-13-0920 TCGA-13-0921 TCGA-13-1403 TCGA-13-1409 
       19.36        27.72        13.81         4.64        10.88         6.84 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 TCGA-13-1484 TCGA-13-1487 TCGA-13-1489 
        4.70         4.21        87.06        98.04        22.39        82.88 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
       49.25         4.24        16.57         4.21         4.41         4.77 
TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FU TCGA-20-0990 
       14.24         8.61        10.78         8.75         8.42        25.94 
TCGA-20-0991 TCGA-20-1683 TCGA-20-1684 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 
       26.20        25.38        19.10         2.93         2.66        47.54 
TCGA-23-1026 TCGA-23-1029 TCGA-23-1031 TCGA-23-1109 TCGA-23-1110 TCGA-23-1114 
       26.83         8.81        18.90        51.35        54.51        68.68 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1119 TCGA-23-1122 TCGA-23-1123 TCGA-23-1809 
        4.57        33.30       129.96        39.09        33.47         0.53 
TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2084 TCGA-23-2643 
       24.95       115.89        87.48        91.66        49.84         4.70 
TCGA-24-0970 TCGA-24-0979 TCGA-24-0982 TCGA-24-1413 TCGA-24-1417 TCGA-24-1424 
       11.64        41.56        22.32         6.31         7.82         6.02 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1434 TCGA-24-1436 TCGA-24-1467 
        5.36         4.83        17.39        18.67         8.55       105.99 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1548 TCGA-24-1553 TCGA-24-1557 
        3.45         1.18        22.22        16.21        58.09        39.88 
TCGA-24-1558 TCGA-24-1564 TCGA-24-1567 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 
       19.53        25.87        17.23        88.37        48.33        38.24 
TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 
        8.32         3.48         3.72        11.28         5.52         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-24-2020 TCGA-24-2026 TCGA-24-2033 TCGA-24-2038 TCGA-24-2260 TCGA-24-2261 
      152.02        34.82        18.48        44.52        36.16         0.79 
TCGA-24-2267 TCGA-24-2280 TCGA-24-2295 TCGA-24-2298 TCGA-25-1312 TCGA-25-1317 
       47.54        70.45        33.11        53.26         1.02         2.01 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
       34.98        65.00        33.96        12.99        15.02        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1630 TCGA-25-1634 TCGA-25-1635 
       27.62        17.03        12.95        38.20        35.87        52.04 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2396 TCGA-25-2398 
       14.96        24.99        24.00        85.05         3.02        45.01 
TCGA-25-2400 TCGA-25-2404 TCGA-29-1693 TCGA-29-1694 TCGA-29-1698 TCGA-29-1701 
       42.02        29.03       101.79        39.02        68.32        16.93 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1710 TCGA-29-1761 TCGA-29-1764 
       23.93        59.67        18.25        31.27        17.36        62.93 
TCGA-29-1766 TCGA-29-1770 TCGA-29-1775 TCGA-29-1776 TCGA-29-1778 TCGA-29-1783 
       39.42        24.36        12.36        11.84        14.93         7.23 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 
       86.17        65.00        45.11        42.25        21.47        11.47 
TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1853 TCGA-30-1857 TCGA-30-1859 TCGA-30-1861 
       35.77        51.91        36.26         0.26        48.10        34.78 
TCGA-30-1866 TCGA-30-1867 TCGA-30-1887 TCGA-30-1892 TCGA-31-1950 TCGA-31-1956 
       36.62         1.22        24.26        48.79        18.77        44.12 
TCGA-36-1569 TCGA-36-1574 TCGA-36-1576 TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 
       29.10        22.55        30.08        27.85        24.69        35.05 
TCGA-36-2530 TCGA-36-2534 TCGA-36-2543 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 
       33.01        29.82         2.24        18.31        20.52        14.17 
TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 TCGA-42-2590 TCGA-42-2593 TCGA-57-1582 
       16.18        11.47        23.74        10.42         1.48        24.03 
TCGA-57-1585 TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2350 TCGA-59-2351 
        1.74        22.32        25.08        25.02        22.32       116.12 
TCGA-59-2352 TCGA-59-A5PD TCGA-5X-AA5U TCGA-61-1722 TCGA-61-1727 TCGA-61-1728 
        9.40        20.52        11.87         8.09        18.54        27.88 
TCGA-61-1733 TCGA-61-1899 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 
       31.79         8.42        11.41        13.02         9.07        34.13 
TCGA-61-1907 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 
       31.30        56.61        67.76        43.43        15.75        38.17 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2097 TCGA-61-2098 
       17.98         4.01        30.64        39.85        60.62        65.52 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2614 
        6.48        76.87       125.75        22.22         6.35         8.61 
TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
       39.68        18.94         0.79 

$`3Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1342 TCGA-04-1348 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 
       43.92        18.51        48.76        65.46         0.53        49.28 
TCGA-04-1367 TCGA-04-1514 TCGA-04-1519 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 
      103.40        56.55         0.79        55.43        48.89        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-09-1661 TCGA-09-1662 
       64.64        36.23        31.86        47.70        38.43        89.33 
TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 TCGA-09-1673 TCGA-09-1675 TCGA-09-2045 
       74.93        57.60        61.87         3.02        97.55        35.15 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 
       71.11        63.09        20.94        26.93        12.46        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0934 TCGA-10-0937 
       25.91        81.86        18.51        32.88         6.71        19.99 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0725 TCGA-13-0726 
       20.91         6.21        24.59        44.55        12.39        31.20 
TCGA-13-0730 TCGA-13-0755 TCGA-13-0758 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 
       17.82         2.50        11.38        34.06        32.25        31.04 
TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 
       21.40        38.93        36.72        28.70        30.35         8.71 
TCGA-13-0799 TCGA-13-0801 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0885 
        7.79         8.28        35.31        13.61        68.94        91.40 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
       74.27        66.67        61.84        67.99        69.01        43.36 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
       56.15        57.07        47.38        48.33        47.84        44.94 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
       44.84        37.08        34.06        29.98        21.17        14.89 
TCGA-13-0923 TCGA-13-0924 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 
        6.41         6.08         6.61         7.36         6.05         5.92 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 TCGA-13-1488 
        5.33        54.64        61.71        29.42        20.68        70.82 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 
       52.44        73.55        38.20        54.31        37.61        38.40 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
       13.97        32.84         4.18         2.56         3.91         3.09 
TCGA-13-2059 TCGA-13-2071 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0996 TCGA-20-1682 
       12.23         6.28        54.77        23.05        72.20        27.52 
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-24-0968 TCGA-24-0975 TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 
       19.66        21.80         7.66        54.12        63.55        47.41 
TCGA-24-1416 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 
        6.38         7.99         7.86         0.76         6.25         5.95 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 
       28.37        19.17        43.53        72.92        12.46        45.14 
TCGA-24-1469 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1549 TCGA-24-1550 
        9.11        26.96        57.40        64.27        56.58        41.06 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 TCGA-24-1556 TCGA-24-1560 TCGA-24-1562 
       51.91        41.39        88.50        70.62        44.09        45.50 
TCGA-24-1563 TCGA-24-1565 TCGA-24-1603 TCGA-24-1845 TCGA-24-1846 TCGA-24-1849 
       47.70        10.26        90.15         3.81         4.37         5.79 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2035 
       44.84        58.16       109.71        14.43        55.92        28.18 
TCGA-24-2036 TCGA-24-2254 TCGA-24-2262 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 
       64.01        57.07         0.36        31.63        44.61         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-25-1313 TCGA-25-1314 
       67.36        36.23        16.64        55.86        26.96        33.01 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1320 TCGA-25-1322 TCGA-25-1628 TCGA-25-1631 
       52.04        42.05        37.97         2.99        20.61         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 
       59.15        62.17        13.02        49.05         1.02        38.04 
TCGA-25-2397 TCGA-25-2399 TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 
       12.00        19.99         2.96        31.00        26.99        78.90 
TCGA-29-1690 TCGA-29-1691 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 
       47.61        48.33        40.41        33.93        31.20        36.36 
TCGA-29-1707 TCGA-29-1711 TCGA-29-1762 TCGA-29-1763 TCGA-29-1768 TCGA-29-1769 
       41.98        34.62        86.60        66.81        31.30        22.98 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1777 TCGA-29-1781 TCGA-29-1784 TCGA-29-1785 
       22.55        17.33        12.30         8.38         5.36        36.30 
TCGA-29-2427 TCGA-29-2429 TCGA-29-2436 TCGA-30-1714 TCGA-30-1855 TCGA-30-1856 
       62.47        13.84         9.76        38.07         2.47        15.68 
TCGA-30-1860 TCGA-30-1862 TCGA-30-1880 TCGA-30-1891 TCGA-31-1944 TCGA-31-1946 
       44.91         6.12        57.57        30.05        45.57        30.18 
TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 TCGA-36-1568 TCGA-36-1570 
       22.49         6.71        42.51         2.20        28.77        21.53 
TCGA-36-1571 TCGA-36-1575 TCGA-36-1577 TCGA-36-1580 TCGA-36-2532 TCGA-36-2537 
       22.85         8.55        25.74        24.23        29.49        25.91 
TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-36-2549 TCGA-3P-A9WA 
       25.08        23.80        21.60        20.98         6.05        13.81 
TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 TCGA-42-2591 TCGA-57-1583 TCGA-57-1584 
       47.57        28.93        42.02        40.77        11.38        21.14 
TCGA-57-1992 TCGA-59-2348 TCGA-59-2349 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       29.00       180.20        80.12        34.39         2.14         5.42 
TCGA-59-2372 TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1730 TCGA-61-1734 
       44.81        11.11        20.94        31.43         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-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1995 
        1.45         5.79        37.05        42.51        48.92         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
        5.52        14.50        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-61-2101 TCGA-61-2109 TCGA-61-2110 TCGA-61-2613 TCGA-WR-A838 
       55.50        20.68        44.52        31.07         9.99 

  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 
            24.26             31.20 
[1] "0.3 - 152.0 (24.3)" "0.3 - 180.2 (31.2)"
[1] "hr=" "1.1"
D6V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  3Q GAIN MUTATED         1   266                2
  3Q GAIN WILD-TYPE       2   292                0
D6V3, multiclass
                  clus
vv                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  OMENTUM                        1                 2
  OVARY                        266               292
  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, continuous
D6V5, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     0 272
  3Q GAIN WILD-TYPE   3 298
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      0  272
  3Q GAIN WILD-TYPE    3  298
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO                0                 3
  YES             272               298
[1] 2 2
[1] FALSE
                   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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q GAIN MUTATED                                  2     8
  3Q GAIN WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN
  3Q GAIN MUTATED                          15
  3Q GAIN WILD-TYPE                        19
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3Q GAIN MUTATED                                           1   230
  3Q GAIN WILD-TYPE                                         0   246
D6V7, multiclass
                                           clus
vv                                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        2                 1
  ASIAN                                                   8                11
  BLACK OR AFRICAN AMERICAN                              15                19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 230               246
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, 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    24  35
  4P GAIN WILD-TYPE 244 257
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               59               501 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               35               257 
$`4P GAIN MUTATED`
TCGA-04-1349 TCGA-04-1356 TCGA-04-1364 TCGA-04-1525 TCGA-04-1530 TCGA-04-1646 
       21.57        49.28        33.67        38.37       119.08        27.88 
TCGA-09-1668 TCGA-09-2048 TCGA-10-0926 TCGA-13-0714 TCGA-13-0794 TCGA-13-0802 
       55.36         4.54        25.91         6.21        30.35         8.19 
TCGA-13-0883 TCGA-13-0920 TCGA-13-1483 TCGA-13-1499 TCGA-13-1505 TCGA-13-2060 
       68.94        13.81        29.42        38.40         4.21         8.61 
TCGA-13-A5FU TCGA-23-1026 TCGA-23-1110 TCGA-23-1114 TCGA-23-2645 TCGA-24-1427 
        8.42        26.83        54.51        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-29-1761 TCGA-29-1770 TCGA-29-2432 
        3.02        45.01        48.33        17.36        24.36        21.47 
TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1855 TCGA-36-1569 TCGA-36-1570 TCGA-36-1575 
       35.77        51.91         2.47        29.10        21.53         8.55 
TCGA-36-2529 TCGA-5X-AA5U TCGA-61-1728 TCGA-61-1733 TCGA-61-1740 TCGA-61-1743 
       35.05        11.87        27.88        31.79         2.43        43.69 
TCGA-61-1915 TCGA-61-1918 TCGA-61-2009 TCGA-61-2012 TCGA-61-2614 
       67.76        15.75        39.85        30.64         8.61 

$`4P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       43.92        41.00         1.81        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-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 
       63.98        65.46         0.53        32.52        44.32        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-04-1536 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-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 
       36.23        31.86        47.70        45.37        29.16         9.47 
TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       57.76        17.98        35.57         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-09-2049 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-10-0925 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       26.93        12.46        54.31        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-13-0717 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        34.06        32.25        31.04        21.40 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 
        8.45        38.93        36.72        28.70        19.59         8.71 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 
        7.79         8.12         8.28        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        91.40        74.27        66.67        70.39 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 
       61.84        67.99        69.01        43.36        57.47        56.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
       57.07        19.36        47.38        48.33        47.84        44.94 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       44.84        37.08        27.72        34.06        29.98        21.17 
TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 
       14.89         4.64         6.41         6.08        10.88         6.61 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
        7.36         6.05         5.92         6.84         4.70         4.21 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 TCGA-13-1485 
        5.33        54.64        87.06        61.71        98.04        20.68 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       22.39        70.82        82.88        52.44        73.55        38.20 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 
       49.25         4.24        54.31        37.61        13.97        32.84 
TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
       16.57         4.41         4.77         4.18         2.56         3.91 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 
        3.09        14.24        12.23        10.78         8.75         6.28 
TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 
       54.77        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-23-1111 TCGA-23-1113 
       29.13        18.90         2.76        51.35         3.22        31.20 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 
        4.57        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-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        7.63        19.66        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        19.17        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-29-1705 
       68.32        36.36        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-29-2434 TCGA-29-2436 TCGA-30-1714 TCGA-30-1853 TCGA-30-1856 
       42.25        11.47         9.76        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-30-1887 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-36-1571 TCGA-36-1574 TCGA-36-1576 TCGA-36-1577 
        2.20        28.77        22.85        22.55        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-36-2543 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-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
       13.81        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-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
       44.81        20.52        11.11         8.09        20.94        31.43 
TCGA-61-1727 TCGA-61-1730 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
       18.54         4.34        28.47        48.79        44.84        35.80 
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-61-1917 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       56.61        43.43        38.17         2.01         5.52        14.50 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
       17.98         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-61-2097 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-OY-A56P 
       44.52       125.75        22.22         6.35        31.07        39.68 
TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       18.94         0.79         9.99 

  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 
            25.91             29.03 
[1] "1.0 - 119.1 (25.9)" "0.3 - 180.2 (29.0)"
[1] "hr=" "1.5"
D7V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  4P GAIN MUTATED         1    57                1
  4P GAIN WILD-TYPE       2   501                1
D7V3, multiclass
                  clus
vv                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  OMENTUM                        1                 2
  OVARY                         57               501
  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, continuous
D7V5, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     1  59
  4P GAIN WILD-TYPE   2 511
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1   59
  4P GAIN WILD-TYPE    2  511
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                1                 2
  YES              59               511
[1] 2 2
[1] FALSE
                   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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P GAIN MUTATED                                  0     3
  4P GAIN WILD-TYPE                                3    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  4P GAIN MUTATED                           3
  4P GAIN WILD-TYPE                        31
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4P GAIN MUTATED                                           0    50
  4P GAIN WILD-TYPE                                         1   426
D7V7, multiclass
                                           clus
vv                                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   3                16
  BLACK OR AFRICAN AMERICAN                               3                31
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  50               426
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     2  31
  4P GAIN WILD-TYPE   8 296
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2   31
  4P GAIN WILD-TYPE    8  296
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 8
  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    13  19
  4Q GAIN WILD-TYPE 255 273
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               32               528 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               19               273 
$`4Q GAIN MUTATED`
TCGA-04-1349 TCGA-04-1356 TCGA-04-1525 TCGA-04-1530 TCGA-09-1668 TCGA-10-0936 
       21.57        49.28        38.37       119.08        55.36        36.92 
TCGA-13-0714 TCGA-13-0794 TCGA-13-0802 TCGA-13-0883 TCGA-13-0920 TCGA-13-2060 
        6.21        30.35         8.19        68.94        13.81         8.61 
TCGA-13-A5FU TCGA-20-1682 TCGA-23-2645 TCGA-24-1427 TCGA-24-1558 TCGA-24-1843 
        8.42        27.52         4.50         4.83        19.53         3.48 
TCGA-24-2026 TCGA-25-1313 TCGA-25-1877 TCGA-25-2396 TCGA-29-1691 TCGA-29-1701 
       34.82        26.96        24.00         3.02        48.33        16.93 
TCGA-29-1702 TCGA-29-1770 TCGA-29-2432 TCGA-30-1855 TCGA-36-1575 TCGA-61-1728 
       23.93        24.36        21.47         2.47         8.55        27.88 
TCGA-61-1743 TCGA-61-2012 
       43.69        30.64 

$`4Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       43.92        41.00         1.81        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-04-1350 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-04-1367 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-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
        0.79        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-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 
       29.16         9.47        57.76        17.98        35.57         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-10-0925 
       63.09        39.75        20.94        26.93        12.46        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-13-0717 TCGA-13-0720 
        6.71        35.44        19.99        20.91        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-13-0761 
       55.17         2.50        11.18        11.38        11.54        34.06 
TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 
       32.25        31.04        21.40         8.45        38.93        36.72 
TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
       28.70        19.59         8.71         7.79         8.12         8.28 
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        91.40 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 
       74.27        66.67        70.39        61.84        67.99        69.01 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       43.36        57.47        56.15        57.07        19.36        47.38 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       48.33        47.84        44.94        44.84        37.08        27.72 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 
       34.06        29.98        21.17        14.89         4.64         6.41 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 
        6.08        10.88         6.61         7.36         6.05         5.92 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
        6.84         4.70         4.21         5.33        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        98.04        20.68        22.39        70.82 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
       82.88        52.44        73.55        38.20        49.25         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 
       54.31        37.61        38.40        13.97        32.84        16.57 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
        4.21         4.41         4.77         4.18         2.56         3.91 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 
        3.09        14.24        12.23        10.78         8.75         6.28 
TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 
       54.77        23.05        25.94        26.20        72.20        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-23-1024 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         4.57        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-23-2643 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 
        2.76         4.70         7.63        19.66        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-24-1417 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-24-1425 TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 
        6.25         6.02         5.95         5.36        17.39        28.37 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 
       19.17        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-24-1560 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-24-1844 
       90.15        88.37        48.33        38.24         8.32         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-24-1928 TCGA-24-1930 TCGA-24-2019 
       22.68        30.21        16.44        11.05        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-24-2033 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-25-1314 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-25-1323 
       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-25-1635 
       38.20         0.30        59.15        62.17        35.87        52.04 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 
       14.96        24.99        85.05        13.02        49.05         1.02 
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-29-1703 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-29-1763 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-29-1771 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-29-2429 TCGA-29-2431 TCGA-29-2434 TCGA-29-2436 
       62.47        45.11        13.84        42.25        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-30-1862 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-36-1576 
       28.77        29.10        21.53        22.85        22.55        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-36-2547 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-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
       16.18        11.47        13.81        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-59-A5PD TCGA-5X-AA5U TCGA-61-1721 
        2.14         5.42        44.81        20.52        11.87        11.11 
TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1730 TCGA-61-1733 
        8.09        20.94        31.43        18.54         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-61-1895 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 

  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 
           23.965            29.065 
[1] "2.5 - 119.1 (24.0)" "0.3 - 180.2 (29.1)"
[1] "hr=" "1.5"
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, continuous
D8V5, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1  31
  4Q GAIN WILD-TYPE   2 539
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1   31
  4Q GAIN WILD-TYPE    2  539
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                1                 2
  YES              31               539
[1] 2 2
[1] FALSE
                   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-04-1516        TCGA-04-1644        TCGA-13-0807        TCGA-13-0911 
"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-3P-A9WA        TCGA-42-2582 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-42-2587        TCGA-42-2588        TCGA-42-2589        TCGA-42-2590 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-42-2593        TCGA-57-1993        TCGA-59-2363        TCGA-59-2372 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-5X-AA5U        TCGA-61-2612        TCGA-61-2613        TCGA-61-2614 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-OY-A56P        TCGA-OY-A56Q        TCGA-VG-A8LO 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q GAIN MUTATED                                  0     2
  4Q GAIN WILD-TYPE                                3    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  4Q GAIN MUTATED                           2
  4Q GAIN WILD-TYPE                        32
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4Q GAIN MUTATED                                           0    26
  4Q GAIN WILD-TYPE                                         1   450
D8V7, multiclass
                                           clus
vv                                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   2                17
  BLACK OR AFRICAN AMERICAN                               2                32
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  26               450
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1  19
  4Q GAIN WILD-TYPE   9 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1   19
  4Q GAIN WILD-TYPE    9  308
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              19               308
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    99  92
  5P GAIN WILD-TYPE 169 200
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              191               369 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               92               200 
$`5P GAIN MUTATED`
TCGA-04-1337 TCGA-04-1341 TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 
        2.01         1.08        18.51        65.52        63.09        21.57 
TCGA-04-1350 TCGA-04-1353 TCGA-04-1364 TCGA-04-1530 TCGA-04-1542 TCGA-04-1646 
       63.98         0.53        33.67       119.08        84.20        27.88 
TCGA-04-1649 TCGA-04-1654 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1661 
       64.64        47.70        57.76        17.98        35.57        38.43 
TCGA-09-1666 TCGA-09-1670 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2054 
       57.60        17.98         8.55        97.55         6.18        20.94 
TCGA-09-2056 TCGA-10-0927 TCGA-10-0930 TCGA-10-0933 TCGA-10-0936 TCGA-13-0717 
       12.46        81.86        34.19        14.66        36.92        24.59 
TCGA-13-0723 TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 
       39.58        12.39        15.19        17.82        55.17        11.18 
TCGA-13-0760 TCGA-13-0766 TCGA-13-0768 TCGA-13-0792 TCGA-13-0794 TCGA-13-0801 
       11.54        21.40         8.45        36.72        30.35         8.28 
TCGA-13-0883 TCGA-13-0886 TCGA-13-0889 TCGA-13-0899 TCGA-13-0901 TCGA-13-0904 
       68.94        74.27        61.84        56.15        19.36        48.33 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0911 TCGA-13-1403 TCGA-13-1404 TCGA-13-1407 
       47.84        44.94        27.72        10.88         6.61         6.05 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1411 TCGA-13-1481 TCGA-13-1484 TCGA-13-1488 
        5.92         6.84         4.21        87.06        98.04        70.82 
TCGA-13-1492 TCGA-13-1498 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       73.55        37.61        32.84        16.57         4.21         4.41 
TCGA-13-1507 TCGA-13-1512 TCGA-13-2065 TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 
        4.77         3.09         8.75         8.42        25.94        26.20 
TCGA-20-1685 TCGA-20-1686 TCGA-23-1024 TCGA-23-1029 TCGA-23-1032 TCGA-23-1111 
       16.70         2.93        15.39         8.81         2.76         3.22 
TCGA-23-1116 TCGA-23-1119 TCGA-23-1121 TCGA-23-1809 TCGA-23-2079 TCGA-23-2084 
        4.57       129.96         6.38         0.53        91.66        49.84 
TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0975 TCGA-24-0979 TCGA-24-0982 
        2.76         4.70         4.50        21.80        41.56        22.32 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1423 TCGA-24-1425 TCGA-24-1428 TCGA-24-1434 
        7.82         7.99         6.25         5.95        17.39        18.67 
TCGA-24-1436 TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 TCGA-24-1549 TCGA-24-1553 
        8.55         9.11         1.18        22.22        56.58        58.09 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1604 TCGA-24-1616 TCGA-24-1844 
       88.50        70.62        39.88        88.37        38.24         3.72 
TCGA-24-1845 TCGA-24-1847 TCGA-24-1850 TCGA-24-1923 TCGA-24-1924 TCGA-24-1928 
        3.81        11.28         5.52        22.68        30.21        11.05 
TCGA-24-2020 TCGA-24-2026 TCGA-24-2030 TCGA-24-2260 TCGA-24-2267 TCGA-24-2280 
      152.02        34.82        55.92        36.16        47.54        70.45 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2295 TCGA-24-2298 TCGA-25-1318 
       44.61         0.82        67.36        33.11        53.26        34.98 
TCGA-25-1319 TCGA-25-1321 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1627 
       65.00        33.96         2.99        15.02        18.58        12.95 
TCGA-25-1631 TCGA-25-1634 TCGA-25-1877 TCGA-25-1878 TCGA-25-2392 TCGA-25-2396 
        0.30        35.87        24.00        85.05         1.02         3.02 
TCGA-25-2404 TCGA-29-1688 TCGA-29-1691 TCGA-29-1695 TCGA-29-1707 TCGA-29-1761 
       29.03        78.90        48.33        40.41        41.98        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-29-1774 TCGA-29-2425 TCGA-29-2432 TCGA-30-1718 TCGA-30-1853 TCGA-31-1950 
       17.33        65.00        21.47        51.91        36.26        18.77 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1576 TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 
       28.77        29.10        30.08        27.85        24.69        35.05 
TCGA-36-2543 TCGA-36-2548 TCGA-36-2551 TCGA-42-2582 TCGA-42-2588 TCGA-42-2593 
        2.24        14.17        16.18        47.57        28.93         1.48 
TCGA-57-1582 TCGA-57-1585 TCGA-57-1993 TCGA-59-A5PD TCGA-5X-AA5U TCGA-61-1725 
       24.03         1.74        25.08        20.52        11.87        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 
       55.50       125.75         6.35         8.61        39.68 

$`5P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1343 
       43.92        41.00         1.81        49.15        46.62        11.87 
TCGA-04-1348 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 
       48.76        65.46        49.28        32.52        44.32        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-04-1536 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1651 
       38.37        29.10        55.43        48.89        28.64        36.23 
TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-1659 TCGA-09-1662 
       31.86        45.37        29.16         9.47         9.99        89.33 
TCGA-09-1664 TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1672 
       74.93        41.62        61.87        55.36        30.51         5.85 
TCGA-09-1673 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 
        3.02         6.12        35.15         4.54       112.41        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2055 TCGA-10-0925 TCGA-10-0926 TCGA-10-0928 
       63.09        39.75        26.93        54.31        25.91        18.51 
TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
       32.88         6.71        35.44        19.99        20.91         6.21 
TCGA-13-0720 TCGA-13-0724 TCGA-13-0726 TCGA-13-0755 TCGA-13-0758 TCGA-13-0761 
       44.55         2.73        31.20         2.50        11.38        34.06 
TCGA-13-0762 TCGA-13-0764 TCGA-13-0791 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 
       32.25        31.04        38.93        28.70        19.59         8.71 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 
        7.79         8.12         8.19        43.86        35.28        35.31 
TCGA-13-0807 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 
       13.61       107.18        91.40        66.67        70.39        67.99 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0903 TCGA-13-0908 
       69.01        43.36        57.47        57.07        47.38        44.84 
TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       37.08        34.06        29.98        21.17        14.89        13.81 
TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1405 TCGA-13-1410 TCGA-13-1412 
        4.64         6.41         6.08         7.36         4.70         5.33 
TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 TCGA-13-1489 
       54.64        61.71        29.42        20.68        22.39        82.88 
TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1499 
       52.44        38.20        49.25         4.24        54.31        38.40 
TCGA-13-1500 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-2057 TCGA-13-2059 
       13.97         4.18         2.56         3.91        14.24        12.23 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2071 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0996 
        8.61        10.78         6.28        54.77        23.05        72.20 
TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 
       27.52        25.38        19.10         2.66        47.54        49.68 
TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 
       40.54        26.83        32.09        49.41        29.13        18.90 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 TCGA-23-1117 TCGA-23-1118 
       51.35        54.51        31.20        68.68        33.30        86.01 
TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 
        4.27        39.09        33.47        58.13        24.95       115.89 
TCGA-23-2078 TCGA-23-2081 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0980 
       87.48        77.00         7.63        19.66        11.64         7.66 
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-24-1424 TCGA-24-1426 TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 
        0.76         6.02         5.36         4.83        28.37        19.17 
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-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1550 TCGA-24-1551 
       26.96        57.40        64.27        16.21        41.06        51.91 
TCGA-24-1552 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
       41.39        19.53        44.09        45.50        47.70        25.87 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1614 TCGA-24-1842 TCGA-24-1843 
       10.26        17.23        90.15        48.33         8.32         3.48 
TCGA-24-1846 TCGA-24-1849 TCGA-24-1920 TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 
        4.37         5.79         9.80        16.44        81.11         4.87 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 
       44.84        58.16       109.71        14.43        18.48        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2261 TCGA-24-2262 TCGA-24-2271 
       64.01        44.52        57.07         0.79         0.36        31.63 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 
       36.23        16.64        55.86         1.02        26.96        33.01 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1320 TCGA-25-1323 TCGA-25-1625 
       52.04        42.05         2.01        37.97        12.99        27.62 
TCGA-25-1626 TCGA-25-1628 TCGA-25-1630 TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 
       17.03        20.61        38.20        59.15        62.17        52.04 
TCGA-25-1870 TCGA-25-1871 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2397 
       14.96        24.99        13.02        49.05        38.04        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-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 
       47.61       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-29-1710 
       36.36        16.93        23.93        59.67        18.25        31.27 
TCGA-29-1711 TCGA-29-1762 TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 
       34.62        86.60        22.55        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-29-2427 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-29-A5NZ TCGA-30-1714 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 
       35.77        38.07         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-31-1951 
       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-36-1570 TCGA-36-1571 
        6.71        42.51        44.12         2.20        21.53        22.85 
TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 
       22.55         8.55        25.74        24.23        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-3P-A9WA TCGA-42-2587 
       18.31        20.52         6.05        11.47        13.81        23.74 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 
       42.02        10.42        40.77        11.38        21.14        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-59-2352 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-61-1900 TCGA-61-1901 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        1.45         5.79        11.41         9.07        34.13        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1915 TCGA-61-1917 TCGA-61-1995 
       37.05        42.51        48.92        67.76        43.43         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
        5.52        14.50        17.98         1.18        45.96        45.40 
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-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2113 TCGA-61-2613 
        6.48        76.87        20.68        44.52        22.22        31.07 
TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       18.94         0.79         9.99 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.30              0.26 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           152.02            180.20 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            24.69             29.49 
[1] "0.3 - 152.0 (24.7)" "0.3 - 180.2 (29.5)"
[1] "hr=" "1.1"
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, continuous
D9V5, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     1 196
  5P GAIN WILD-TYPE   2 374
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      1  196
  5P GAIN WILD-TYPE    2  374
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                1                 2
  YES             196               374
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  5P GAIN MUTATED    3  9  4  0
  5P GAIN WILD-TYPE 12 17  1  3
D9V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0               3                12
  R1               9                17
  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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P GAIN MUTATED                                  2     6
  5P GAIN WILD-TYPE                                1    13
                   vv
clus                BLACK OR AFRICAN AMERICAN
  5P GAIN MUTATED                          11
  5P GAIN WILD-TYPE                        23
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5P GAIN MUTATED                                           1   162
  5P GAIN WILD-TYPE                                         0   314
D9V7, multiclass
                                           clus
vv                                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        2                 1
  ASIAN                                                   6                13
  BLACK OR AFRICAN AMERICAN                              11                23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 162               314
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     3 109
  5P GAIN WILD-TYPE   7 218
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      3  109
  5P GAIN WILD-TYPE    7  218
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 7
  NOT HISPANIC OR LATINO             109               218
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    30  27
  5Q GAIN WILD-TYPE 238 265
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               57               503 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               27               265 
$`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-09-0369 TCGA-09-1661 TCGA-09-1666 TCGA-09-1670 TCGA-10-0930 
       84.20        35.57        38.43        57.60        17.98        34.19 
TCGA-10-0936 TCGA-13-0751 TCGA-13-0768 TCGA-13-0792 TCGA-13-0911 TCGA-13-1409 
       36.92        55.17         8.45        36.72        27.72         6.84 
TCGA-13-1492 TCGA-13-1498 TCGA-13-1504 TCGA-13-2065 TCGA-13-A5FU TCGA-23-1111 
       73.55        37.61        16.57         8.75         8.42         3.22 
TCGA-23-1116 TCGA-23-2079 TCGA-23-2645 TCGA-24-1417 TCGA-24-1428 TCGA-24-1434 
        4.57        91.66         4.50         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-24-2298 TCGA-25-1329 TCGA-25-1631 TCGA-25-2392 
       22.68         0.82        53.26        15.02         0.30         1.02 
TCGA-29-1688 TCGA-29-1763 TCGA-29-1769 TCGA-29-1770 TCGA-29-2432 TCGA-30-1853 
       78.90        66.81        22.98        24.36        21.47        36.26 
TCGA-36-1569 TCGA-36-2529 TCGA-36-2543 TCGA-36-2551 TCGA-61-1725 TCGA-61-1733 
       29.10        35.05         2.24        16.18        31.43        31.79 
TCGA-61-2009 TCGA-61-2612 TCGA-61-2614 
       39.85         6.35         8.61 

$`5Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1341 
       43.92        41.00         1.81        49.15        46.62         1.08 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 
       18.51        11.87        65.52        48.76        63.98        65.46 
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-04-1536 
       56.55        41.59        19.99         0.79        38.37        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-09-0364 TCGA-09-0365 TCGA-09-0366 
       31.86        47.70        45.37        29.16         9.47        57.76 
TCGA-09-0367 TCGA-09-1659 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1667 
       17.98         9.99        89.33        74.93        41.62        61.87 
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-09-2045 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-10-0925 
       63.09        39.75        20.94        26.93        12.46        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       25.91        81.86        18.51        32.88        14.66         6.71 
TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
       35.44        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-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 
        2.50        11.18        11.38        11.54        34.06        32.25 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 
       31.04        21.40        38.93        28.70        30.35        19.59 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 
        8.71         7.79         8.12         8.28         8.19        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        91.40 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 
       74.27        66.67        70.39        61.84        67.99        69.01 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       43.36        57.47        56.15        57.07        19.36        47.38 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 
       48.33        47.84        44.94        44.84        37.08        34.06 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 
       29.98        21.17        14.89        13.81         4.64         6.41 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 
        6.08        10.88         6.61         7.36         6.05         5.92 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 
        4.70         4.21         5.33        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        98.04        20.68        22.39        70.82        82.88 
TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1499 
       52.44        38.20        49.25         4.24        54.31        38.40 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       13.97        32.84         4.21         4.41         4.77         4.18 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
        2.56         3.91         3.09        14.24        12.23         8.61 
TCGA-13-2061 TCGA-13-2071 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
       10.78         6.28        54.77        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-23-1110 TCGA-23-1113 TCGA-23-1114 TCGA-23-1117 TCGA-23-1118 
       51.35        54.51        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-23-2081 TCGA-23-2084 
        0.53        24.95       115.89        87.48        77.00        49.84 
TCGA-23-2641 TCGA-23-2643 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 
        2.76         4.70         7.63        19.66        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-24-1426 TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 
        6.02         5.95         5.36         4.83        28.37        19.17 
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-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-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1623 
       65.00        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-25-1632 
       27.62        17.03        12.95        20.61        38.20        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-25-2042 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-25-2400 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-29-1693 TCGA-29-1694 TCGA-29-1695 
       26.99        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-29-1771 TCGA-29-1774 
       86.60        62.93        39.42        31.30        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-29-2429 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-30-1718 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-36-1570 
        6.71        42.51        44.12         2.20        28.77        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-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       24.23        24.69        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-36-2548 TCGA-36-2549 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 
       14.17         6.05        11.47        13.81        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-59-A5PD TCGA-5X-AA5U 
       34.39         2.14         5.42        44.81        20.52        11.87 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 
       11.11         8.09        20.94        18.54        27.88         4.34 
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-61-1900 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-61-2012 
        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-61-2613 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       31.07        39.68        18.94         0.79         9.99 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.30              0.26 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           119.08            180.20 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            22.68             29.00 
[1] "0.3 - 119.1 (22.7)" "0.3 - 180.2 (29.0)"
[1] "hr=" "1"  
D10V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  5Q GAIN MUTATED         0    57                1
  5Q GAIN WILD-TYPE       3   501                1
D10V3, multiclass
                  clus
vv                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  OMENTUM                        0                 3
  OVARY                         57               501
  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, continuous
D10V5, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     0  60
  5Q GAIN WILD-TYPE   3 510
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0   60
  5Q GAIN WILD-TYPE    3  510
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                0                 3
  YES              60               510
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  5Q GAIN MUTATED    0  7  1  0
  5Q GAIN WILD-TYPE 15 19  4  3
D10V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0               0                15
  R1               7                19
  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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q GAIN MUTATED                                  0     2
  5Q GAIN WILD-TYPE                                3    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  5Q GAIN MUTATED                           4
  5Q GAIN WILD-TYPE                        30
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5Q GAIN MUTATED                                           0    49
  5Q GAIN WILD-TYPE                                         1   427
D10V7, multiclass
                                           clus
vv                                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   2                17
  BLACK OR AFRICAN AMERICAN                               4                30
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  49               427
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     0  28
  5Q GAIN WILD-TYPE  10 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0   28
  5Q GAIN WILD-TYPE   10  299
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              28               299
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    84  79
  6P GAIN WILD-TYPE 184 213
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              163               397 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               79               213 
$`6P GAIN MUTATED`
TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 TCGA-04-1353 TCGA-04-1362 
       18.51        65.52        63.09        21.57         0.53        44.32 
TCGA-04-1364 TCGA-04-1516 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-09-0364 
       33.67        41.59        38.37       119.08        29.10        29.16 
TCGA-09-0366 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 
       57.76        38.43        89.33        41.62        57.60        61.87 
TCGA-09-1668 TCGA-09-1669 TCGA-09-1674 TCGA-09-2049 TCGA-09-2051 TCGA-09-2054 
       55.36        30.51         8.55       112.41        63.09        20.94 
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        31.04 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0800 TCGA-13-0885 
       36.72        28.70        30.35        19.59         8.12        91.40 
TCGA-13-0886 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1407 TCGA-13-1408 
       74.27        13.81         6.41         6.08         6.05         5.92 
TCGA-13-1409 TCGA-13-1411 TCGA-13-1481 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 
        6.84         4.21        87.06        22.39        70.82        82.88 
TCGA-13-1496 TCGA-13-1499 TCGA-13-1510 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 
        4.24        38.40         2.56        14.24         8.61        10.78 
TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1685 TCGA-20-1686 TCGA-23-1023 
       25.94        26.20        27.52        16.70         2.93        40.54 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1114 TCGA-23-1116 
       18.90         2.76        51.35        54.51        68.68         4.57 
TCGA-23-1120 TCGA-23-1124 TCGA-23-1809 TCGA-23-2079 TCGA-24-0982 TCGA-24-1417 
        4.27        58.13         0.53        91.66        22.32         7.82 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1469 TCGA-24-1474 TCGA-24-1558 TCGA-24-1563 
        6.25         6.02         9.11        22.22        19.53        47.70 
TCGA-24-1564 TCGA-24-1604 TCGA-24-1614 TCGA-24-1850 TCGA-24-2020 TCGA-24-2026 
       25.87        88.37        48.33         5.52       152.02        34.82 
TCGA-24-2254 TCGA-24-2261 TCGA-24-2267 TCGA-24-2281 TCGA-25-1317 TCGA-25-1319 
       57.07         0.79        47.54        44.61         2.01        65.00 
TCGA-25-1321 TCGA-25-1323 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
       33.96        12.99        35.87        14.96        24.99        24.00 
TCGA-25-1878 TCGA-25-2392 TCGA-25-2398 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 
       85.05         1.02        45.01        42.02         2.96        29.03 
TCGA-29-1691 TCGA-29-1695 TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 TCGA-29-1710 
       48.33        40.41        68.32        16.93        23.93        31.27 
TCGA-29-1764 TCGA-29-1770 TCGA-29-1774 TCGA-29-1778 TCGA-29-2414 TCGA-29-2425 
       62.93        24.36        17.33        14.93        86.17        65.00 
TCGA-29-2432 TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1856 TCGA-30-1861 TCGA-31-1953 
       21.47        35.77        51.91        15.68        34.78         6.71 
TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 
       42.51        44.12         2.20        22.85         8.55        30.08 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2542 TCGA-36-2545 TCGA-36-2551 
       24.23        24.69        35.05        21.60        18.31        16.18 
TCGA-36-2552 TCGA-42-2593 TCGA-57-1582 TCGA-57-1585 TCGA-57-1586 TCGA-57-1993 
       11.47         1.48        24.03         1.74        22.32        25.08 
TCGA-57-1994 TCGA-5X-AA5U TCGA-61-1722 TCGA-61-1730 TCGA-61-1737 TCGA-61-1741 
       25.02        11.87         8.09         4.34        44.84        33.67 
TCGA-61-1743 TCGA-61-1907 TCGA-61-1915 TCGA-61-1918 TCGA-61-1919 TCGA-61-1998 
       43.69        31.30        67.76        15.75        38.17         5.52 
TCGA-61-2003 TCGA-61-2009 TCGA-61-2088 TCGA-61-2097 TCGA-61-2098 TCGA-61-2102 
        4.01        39.85         4.77        60.62        65.52         6.48 
TCGA-61-2104 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56Q 
       76.87       125.75        22.22         6.35         8.61        18.94 
TCGA-WR-A838 
        9.99 

$`6P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       43.92        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1341 TCGA-04-1343 TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 
        1.08        11.87        48.76        63.98        65.46        49.28 
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-04-1519 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 
        0.79        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-09-0365 
       64.64        36.23        31.86        47.70        45.37         9.47 
TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1664 TCGA-09-1670 TCGA-09-1672 
       17.98        35.57         9.99        74.93        17.98         5.85 
TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 
        3.02        97.55         6.18         6.12        35.15         4.54 
TCGA-09-2050 TCGA-09-2053 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 
       71.11        39.75        26.93        12.46        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-13-0720 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        34.06        32.25        21.40         8.45        38.93 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 
        8.71         7.79         8.28         8.19        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        70.39 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 
       61.84        67.99        69.01        43.36        57.47        56.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
       57.07        19.36        47.38        48.33        47.84        44.94 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       44.84        37.08        27.72        34.06        29.98        21.17 
TCGA-13-0919 TCGA-13-0921 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1410 
       14.89         4.64        10.88         6.61         7.36         4.70 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 
        5.33        54.64        61.71        29.42        98.04        20.68 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1497 TCGA-13-1498 
       52.44        73.55        38.20        49.25        54.31        37.61 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
       13.97        32.84        16.57         4.21         4.41         4.77 
TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2065 TCGA-13-2071 
        4.18         3.91         3.09        12.23         8.75         6.28 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 
       54.77         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-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        4.50         7.63        19.66        11.64        21.80        41.56 
TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
        7.66        54.12        63.55        47.41         6.31         6.38 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        7.99         7.86         0.76         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        19.17        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-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1616 
       44.09        45.50        10.26        17.23        90.15        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-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 
        5.79         9.80        22.68        30.21        16.44        11.05 
TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 
       81.11         4.87        44.84        58.16       109.71        14.43 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2260 
       55.92        18.48        28.18        64.01        44.52        36.16 
TCGA-24-2262 TCGA-24-2271 TCGA-24-2280 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 
        0.36        31.63        70.45         0.82        67.36        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-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1318 TCGA-25-1320 TCGA-25-1322 
       33.01        52.04        42.05        34.98        37.97         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-25-1632 TCGA-25-1633 TCGA-25-1635 TCGA-25-2042 
       38.20         0.30        59.15        62.17        52.04        13.02 
TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 TCGA-25-2408 
       49.05        38.04         3.02        12.00        19.99        31.00 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 
       26.99        78.90        47.61       101.79        39.02        33.93 
TCGA-29-1697 TCGA-29-1699 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 
       31.20        36.36        59.67        18.25        41.98        34.62 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 
       17.36        86.60        66.81        39.42        31.30        22.98 
TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 
       22.55        12.36        11.84        12.30         8.38         7.23 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 
        5.36        36.30        62.47        45.11        13.84        42.25 
TCGA-29-2434 TCGA-29-2436 TCGA-30-1714 TCGA-30-1853 TCGA-30-1855 TCGA-30-1857 
       11.47         9.76        38.07        36.26         2.47         0.26 
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-30-1891 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-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 TCGA-36-1577 
       22.49        28.77        29.10        21.53        22.55        25.74 
TCGA-36-1578 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
       27.85        33.01        29.49        29.82        25.91        25.08 
TCGA-36-2540 TCGA-36-2543 TCGA-36-2544 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 
       23.80         2.24        20.98        20.52        14.17         6.05 
TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
       13.81        47.57        23.74        28.93        42.02        10.42 
TCGA-42-2591 TCGA-57-1583 TCGA-57-1584 TCGA-57-1992 TCGA-59-2348 TCGA-59-2349 
       40.77        11.38        21.14        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-59-A5PD TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
       44.81        20.52        11.11        20.94        31.43        18.54 
TCGA-61-1728 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1738 TCGA-61-1740 
       27.88        31.79        28.47        48.79        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-61-1910 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-61-1995 TCGA-61-2000 TCGA-61-2002 TCGA-61-2008 TCGA-61-2012 TCGA-61-2016 
        2.01        14.50        17.98        30.64        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-61-2101 TCGA-61-2109 TCGA-61-2110 TCGA-61-2613 TCGA-OY-A56P 
       58.39        55.50        20.68        44.52        31.07        39.68 
TCGA-VG-A8LO 
        0.79 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.53              0.26 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           152.02            180.20 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            25.02             29.42 
[1] "0.5 - 152.0 (25.0)" "0.3 - 180.2 (29.4)"
[1] "hr=" "1.1"
D11V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  6P GAIN MUTATED         1   163                1
  6P GAIN WILD-TYPE       2   395                1
D11V3, multiclass
                  clus
vv                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  OMENTUM                        1                 2
  OVARY                        163               395
  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, continuous
D11V5, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     0 168
  6P GAIN WILD-TYPE   3 402
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0  168
  6P GAIN WILD-TYPE    3  402
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                0                 3
  YES             168               402
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  6P GAIN MUTATED    5  8  1  1
  6P GAIN WILD-TYPE 10 18  4  2
D11V6, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0               5                10
  R1               8                18
  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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P GAIN MUTATED                                  2     3
  6P GAIN WILD-TYPE                                1    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  6P GAIN MUTATED                          10
  6P GAIN WILD-TYPE                        24
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6P GAIN MUTATED                                           0   142
  6P GAIN WILD-TYPE                                         1   334
D11V7, multiclass
                                           clus
vv                                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        2                 1
  ASIAN                                                   3                16
  BLACK OR AFRICAN AMERICAN                              10                24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 142               334
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, 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    49  44
  6Q GAIN WILD-TYPE 219 248
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               93               467 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               44               248 
$`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-09-0364 TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 
       29.10        29.16        41.62        61.87        55.36        30.51 
TCGA-09-1674 TCGA-09-2051 TCGA-10-0930 TCGA-10-0933 TCGA-13-0723 TCGA-13-0724 
        8.55        63.09        34.19        14.66        39.58         2.73 
TCGA-13-0760 TCGA-13-0764 TCGA-13-0794 TCGA-13-0795 TCGA-13-0800 TCGA-13-0885 
       11.54        31.04        30.35        19.59         8.12        91.40 
TCGA-13-0920 TCGA-13-0924 TCGA-13-1408 TCGA-13-1409 TCGA-13-1487 TCGA-13-1488 
       13.81         6.08         5.92         6.84        22.39        70.82 
TCGA-13-1496 TCGA-13-1499 TCGA-13-2057 TCGA-13-2061 TCGA-20-0991 TCGA-20-1682 
        4.24        38.40        14.24        10.78        26.20        27.52 
TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 TCGA-23-1120 TCGA-23-1124 
       54.51         3.22        68.68         4.57         4.27        58.13 
TCGA-23-1809 TCGA-23-2079 TCGA-24-1424 TCGA-24-1469 TCGA-24-1474 TCGA-24-1558 
        0.53        91.66         6.02         9.11        22.22        19.53 
TCGA-24-1563 TCGA-24-1604 TCGA-24-1614 TCGA-24-1850 TCGA-24-1928 TCGA-24-2267 
       47.70        88.37        48.33         5.52        11.05        47.54 
TCGA-24-2281 TCGA-25-1635 TCGA-25-1871 TCGA-25-1877 TCGA-25-2392 TCGA-25-2400 
       44.61        52.04        24.99        24.00         1.02        42.02 
TCGA-25-2404 TCGA-29-1691 TCGA-29-1695 TCGA-29-1698 TCGA-29-1702 TCGA-29-1710 
       29.03        48.33        40.41        68.32        23.93        31.27 
TCGA-29-1764 TCGA-29-1770 TCGA-29-1774 TCGA-29-1778 TCGA-29-2425 TCGA-30-1859 
       62.93        24.36        17.33        14.93        65.00        48.10 
TCGA-30-1861 TCGA-30-1862 TCGA-36-1575 TCGA-36-1576 TCGA-36-1581 TCGA-36-2551 
       34.78         6.12         8.55        30.08        24.69        16.18 
TCGA-36-2552 TCGA-57-1582 TCGA-57-1993 TCGA-57-1994 TCGA-61-1741 TCGA-61-1743 
       11.47        24.03        25.08        25.02        33.67        43.69 
TCGA-61-1915 TCGA-61-1919 TCGA-61-2003 TCGA-61-2088 TCGA-61-2102 TCGA-61-2111 
       67.76        38.17         4.01         4.77         6.48       125.75 
TCGA-61-2113 TCGA-61-2612 TCGA-WR-A838 
       22.22         6.35         9.99 

$`6Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       43.92        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1341 TCGA-04-1343 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 
        1.08        11.87        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-04-1542 
       82.39        56.55        19.99         0.79        38.37        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-09-0365 TCGA-09-0366 TCGA-09-0367 
       31.86        47.70        45.37         9.47        57.76        17.98 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 
       35.57         9.99        38.43        89.33        74.93        57.60 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 
       17.98         5.85         3.02        97.55         6.18         6.12 
TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2053 TCGA-09-2054 
       35.15         4.54       112.41        71.11        39.75        20.94 
TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       26.93        12.46        54.31        25.91        81.86        18.51 
TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 
       32.88         6.71        35.44        36.92        19.99        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-13-0730 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        34.06 
TCGA-13-0762 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       32.25        21.40         8.45        38.93        36.72        28.70 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 
        8.71         7.79         8.28         8.19        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        74.27        66.67 
TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 
       70.39        61.84        67.99        69.01        43.36        57.47 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       56.15        57.07        19.36        47.38        48.33        47.84 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
       44.94        44.84        37.08        27.72        34.06        29.98 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 TCGA-13-1403 TCGA-13-1404 
       21.17        14.89         4.64         6.41        10.88         6.61 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 
        7.36         6.05         4.70         4.21         5.33        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1489 
       87.06        61.71        29.42        98.04        20.68        82.88 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1497 TCGA-13-1498 
       52.44        73.55        38.20        49.25        54.31        37.61 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
       13.97        32.84        16.57         4.21         4.41         4.77 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2060 
        4.18         2.56         3.91         3.09        12.23         8.61 
TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
        8.75         6.28        54.77         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-23-1113 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1121 TCGA-23-1122 
       31.20        33.30        86.01       129.96         6.38        39.09 
TCGA-23-1123 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2081 TCGA-23-2084 
       33.47        24.95       115.89        87.48        77.00        49.84 
TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 
        2.76         4.70         4.50         7.63        19.66        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-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        0.76         6.25         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        19.17        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-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1616 
       45.50        25.87        10.26        17.23        90.15        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-24-1920 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-24-2030 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-24-2289 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-25-1870 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-25-2401 TCGA-25-2408 TCGA-25-2409 
       12.00        45.01        19.99         2.96        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-29-1701 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 
       36.36        16.93        59.67        18.25        41.98        34.62 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 
       17.36        86.60        66.81        39.42        31.30        22.98 
TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 
       22.55        12.36        11.84        12.30         8.38         7.23 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 
        5.36        36.30        86.17        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-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1860 
       51.91        36.26         2.47        15.68         0.26        44.91 
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-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-2529 TCGA-36-2530 
       22.55        25.74        27.85        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-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
       13.81        47.57        23.74        28.93        42.02        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-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-59-A5PD TCGA-5X-AA5U 
       34.39         2.14         5.42        44.81        20.52        11.87 
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-61-1895 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-61-1906 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-61-1917 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       56.61        43.43        15.75         2.01         5.52        14.50 
TCGA-61-2002 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 
       17.98        30.64        39.85        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-61-2109 TCGA-61-2110 
       60.62        65.52        55.50        76.87        20.68        44.52 
TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
       31.07         8.61        39.68        18.94         0.79 

  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 
            26.20             28.77 
[1] "0.5 - 125.8 (26.2)" "0.3 - 180.2 (28.8)"
[1] "hr=" "1.1"
D12V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  6Q GAIN MUTATED         0    94                0
  6Q GAIN WILD-TYPE       3   464                2
D12V3, multiclass
                  clus
vv                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  OMENTUM                        0                 3
  OVARY                         94               464
  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, continuous
D12V5, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     0  97
  6Q GAIN WILD-TYPE   3 473
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0   97
  6Q GAIN WILD-TYPE    3  473
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                0                 3
  YES              97               473
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  6Q GAIN MUTATED    3  3  0  0
  6Q GAIN WILD-TYPE 12 23  5  3
D12V6, multiclass
    clus
vv   6Q GAIN MUTATED 6Q 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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q GAIN MUTATED                                  1     0
  6Q GAIN WILD-TYPE                                2    19
                   vv
clus                BLACK OR AFRICAN AMERICAN
  6Q GAIN MUTATED                           5
  6Q GAIN WILD-TYPE                        29
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6Q GAIN MUTATED                                           0    84
  6Q GAIN WILD-TYPE                                         1   392
D12V7, multiclass
                                           clus
vv                                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 2
  ASIAN                                                   0                19
  BLACK OR AFRICAN AMERICAN                               5                29
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  84               392
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, 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    84  91
  7P GAIN WILD-TYPE 184 201
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              175               385 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               91               201 
$`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-04-1644 TCGA-04-1646 
      103.40        56.55        19.99        84.20        48.89        27.88 
TCGA-04-1649 TCGA-04-1652 TCGA-09-0365 TCGA-09-0367 TCGA-09-1661 TCGA-09-1665 
       64.64        31.86         9.47        17.98        38.43        41.62 
TCGA-09-1667 TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 TCGA-09-2043 TCGA-09-2045 
       61.87        17.98         5.85         8.55         6.18        35.15 
TCGA-09-2049 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-10-0926 TCGA-13-0717 
      112.41        63.09        39.75        20.94        25.91        24.59 
TCGA-13-0730 TCGA-13-0757 TCGA-13-0760 TCGA-13-0762 TCGA-13-0768 TCGA-13-0795 
       17.82        11.18        11.54        32.25         8.45        19.59 
TCGA-13-0803 TCGA-13-0807 TCGA-13-0883 TCGA-13-0888 TCGA-13-0899 TCGA-13-0901 
       43.86        13.61        68.94        70.39        56.15        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0912 TCGA-13-0921 TCGA-13-0923 TCGA-13-1407 
       47.38        48.33        34.06         4.64         6.41         6.05 
TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 
        5.92         4.70         4.21        87.06        61.71        98.04 
TCGA-13-1485 TCGA-13-1488 TCGA-13-1489 TCGA-13-1495 TCGA-13-1496 TCGA-13-1500 
       20.68        70.82        82.88        49.25         4.24        13.97 
TCGA-13-1504 TCGA-13-1509 TCGA-13-2059 TCGA-13-2060 TCGA-13-A5FU TCGA-20-0987 
       16.57         4.18        12.23         8.61         8.42        23.05 
TCGA-20-0991 TCGA-20-1682 TCGA-20-1686 TCGA-20-1687 TCGA-23-1024 TCGA-23-1032 
       26.20        27.52         2.93         2.66        15.39         2.76 
TCGA-23-1111 TCGA-23-1116 TCGA-23-1117 TCGA-23-1121 TCGA-23-1124 TCGA-23-1809 
        3.22         4.57        33.30         6.38        58.13         0.53 
TCGA-23-2072 TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-24-0980 TCGA-24-1413 
       24.95       115.89        91.66        77.00         7.66         6.31 
TCGA-24-1418 TCGA-24-1424 TCGA-24-1428 TCGA-24-1431 TCGA-24-1471 TCGA-24-1474 
        7.99         6.02        17.39        19.17         1.18        22.22 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1564 TCGA-24-1614 TCGA-24-1845 TCGA-24-1850 
       39.88        19.53        25.87        48.33         3.81         5.52 
TCGA-24-1928 TCGA-24-2020 TCGA-24-2026 TCGA-24-2030 TCGA-24-2038 TCGA-24-2261 
       11.05       152.02        34.82        55.92        44.52         0.79 
TCGA-24-2267 TCGA-24-2280 TCGA-24-2288 TCGA-24-2293 TCGA-24-2295 TCGA-25-1312 
       47.54        70.45         0.82        16.64        33.11         1.02 
TCGA-25-1313 TCGA-25-1318 TCGA-25-1320 TCGA-25-1323 TCGA-25-1626 TCGA-25-1627 
       26.96        34.98        37.97        12.99        17.03        12.95 
TCGA-25-1628 TCGA-25-1870 TCGA-25-1871 TCGA-25-2397 TCGA-25-2400 TCGA-29-1693 
       20.61        14.96        24.99        12.00        42.02       101.79 
TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1707 TCGA-29-1710 
       40.41        31.20        68.32        36.36        41.98        31.27 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1775 TCGA-29-1778 TCGA-29-1783 TCGA-29-2428 
       66.81        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-30-1856 
       13.84        21.47        11.47        35.77        36.26        15.68 
TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-31-1950 TCGA-31-1959 TCGA-36-1580 
        6.12        36.62         1.22        18.77         2.20        24.23 
TCGA-36-2547 TCGA-36-2548 TCGA-42-2582 TCGA-42-2587 TCGA-57-1993 TCGA-59-2348 
       20.52        14.17        47.57        23.74        25.08       180.20 
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 
        8.61 

$`7P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1341 
       43.92        41.00         1.81        49.15        46.62         1.08 
TCGA-04-1343 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 
       11.87        63.09        48.76        21.57        63.98        49.28 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 TCGA-04-1371 TCGA-04-1516 TCGA-04-1519 
       32.52        44.32        76.57        82.39        41.59         0.79 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1638 TCGA-04-1648 TCGA-04-1651 
       38.37       119.08        29.10        55.43        28.64        36.23 
TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0366 TCGA-09-0369 TCGA-09-1659 
       47.70        45.37        29.16        57.76        35.57         9.99 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 TCGA-09-1673 
       89.33        74.93        57.60        55.36        30.51         3.02 
TCGA-09-1675 TCGA-09-2044 TCGA-09-2048 TCGA-09-2050 TCGA-09-2055 TCGA-09-2056 
       97.55         6.12         4.54        71.11        26.93        12.46 
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-13-0764 TCGA-13-0766 
       55.17         2.50        11.38        34.06        31.04        21.40 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 
       38.93        36.72        28.70        30.35         8.71         7.79 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0884 
        8.12         8.28         8.19        35.28        35.31       107.18 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 
       91.40        74.27        66.67        61.84        67.99        69.01 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 
       43.36        57.47        57.07        47.84        44.94        44.84 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       37.08        27.72        29.98        21.17        14.89        13.81 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1409 TCGA-13-1412 
        6.08        10.88         6.61         7.36         6.84         5.33 
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        73.55        38.20 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 
       54.31        37.61        38.40        32.84         4.21         4.41 
TCGA-13-1507 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2061 
        4.77         2.56         3.91         3.09        14.24        10.78 
TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-20-0990 TCGA-20-0996 TCGA-20-1683 
        8.75         6.28        54.77        25.94        72.20        25.38 
TCGA-20-1684 TCGA-20-1685 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 
       19.10        16.70        47.54        49.68        40.54        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-23-1118 TCGA-23-1119 TCGA-23-1120 
       54.51        31.20        68.68        86.01       129.96         4.27 
TCGA-23-1122 TCGA-23-1123 TCGA-23-2078 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 
       39.09        33.47        87.48        49.84         2.76         4.70 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        4.50         7.63        19.66        11.64        21.80        41.56 
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-24-1419 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-24-1430 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 
       28.37        18.67        43.53         8.55        72.92        12.46 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1544 TCGA-24-1545 
       45.14       105.99         9.11         3.45        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-24-1560 TCGA-24-1562 TCGA-24-1563 
       58.09        88.50        70.62        44.09        45.50        47.70 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 
       10.26        17.23        90.15        88.37        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-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 
       22.68        30.21        16.44        81.11         4.87        44.84 
TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 
       58.16       109.71        14.43        18.48        28.18        64.01 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 TCGA-24-2271 TCGA-24-2281 TCGA-24-2289 
       57.07        36.16         0.36        31.63        44.61        67.36 
TCGA-24-2290 TCGA-24-2297 TCGA-24-2298 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 
       36.23        55.86        53.26        33.01        52.04        42.05 
TCGA-25-1317 TCGA-25-1319 TCGA-25-1321 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 
        2.01        65.00        33.96         2.99        15.02        18.58 
TCGA-25-1625 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
       27.62        38.20         0.30        59.15        62.17        35.87 
TCGA-25-1635 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 
       52.04        24.00        85.05        13.02        49.05         1.02 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 
       38.04         3.02        45.01        19.99         2.96        29.03 
TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1694 
       31.00        26.99        78.90        47.61        48.33        39.02 
TCGA-29-1696 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1711 
       33.93        16.93        23.93        59.67        18.25        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-29-1776 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-30-1857 TCGA-30-1859 TCGA-30-1860 
       38.07        51.91         2.47         0.26        48.10        44.91 
TCGA-30-1861 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 
       34.78        57.57        24.26        30.05        48.79        45.57 
TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 
       30.18        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-36-1581 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-36-2540 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-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA 
       20.98        18.31         6.05        16.18        11.47        13.81 
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-57-1994 
       11.38        21.14         1.74        22.32        29.00        25.02 
TCGA-59-2350 TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 TCGA-59-A5PD TCGA-5X-AA5U 
       22.32         9.40        34.39         5.42        20.52        11.87 
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-61-1736 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 TCGA-61-1900 
       48.79        35.80         2.43        33.67         1.45         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1906 TCGA-61-1910 TCGA-61-1913 TCGA-61-1915 
       11.41        13.02        34.13        37.05        48.92        67.76 
TCGA-61-1917 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2008 
       43.43         2.01         5.52        14.50        17.98        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-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2109 
       51.72        71.74        61.64        58.39        60.62        20.68 
TCGA-61-2111 TCGA-61-2612 TCGA-61-2613 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
      125.75         6.35        31.07        39.68        18.94         0.79 
TCGA-WR-A838 
        9.99 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.53              0.26 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           180.20            129.96 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            24.23             29.82 
[1] "0.5 - 180.2 (24.2)" "0.3 - 130.0 (29.8)"
[1] "hr=" "1"  
D13V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  7P GAIN MUTATED         2   174                0
  7P GAIN WILD-TYPE       1   384                2
D13V3, multiclass
                  clus
vv                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  OMENTUM                        2                 1
  OVARY                        174               384
  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, continuous
D13V5, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     0 179
  7P GAIN WILD-TYPE   3 391
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      0  179
  7P GAIN WILD-TYPE    3  391
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO                0                 3
  YES             179               391
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  7P GAIN MUTATED    5  8  1  0
  7P GAIN WILD-TYPE 10 18  4  3
D13V6, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0               5                10
  R1               8                18
  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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P GAIN MUTATED                                  0     3
  7P GAIN WILD-TYPE                                3    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  7P GAIN MUTATED                           7
  7P GAIN WILD-TYPE                        27
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7P GAIN MUTATED                                           1   157
  7P GAIN WILD-TYPE                                         0   319
D13V7, multiclass
                                           clus
vv                                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   3                16
  BLACK OR AFRICAN AMERICAN                               7                27
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 157               319
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V8, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     1 108
  7P GAIN WILD-TYPE   9 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      1  108
  7P GAIN WILD-TYPE    9  219
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO             108               219
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    88 104
  7Q GAIN WILD-TYPE 180 188
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              192               368 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              104               188 
$`7Q GAIN MUTATED`
TCGA-04-1337 TCGA-04-1341 TCGA-04-1342 TCGA-04-1347 TCGA-04-1351 TCGA-04-1353 
        2.01         1.08        18.51        63.09        65.46         0.53 
TCGA-04-1364 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1536 TCGA-04-1542 
       33.67        56.55        41.59        19.99        29.10        84.20 
TCGA-04-1644 TCGA-04-1646 TCGA-04-1649 TCGA-04-1652 TCGA-04-1655 TCGA-09-0365 
       48.89        27.88        64.64        31.86        45.37         9.47 
TCGA-09-0367 TCGA-09-1661 TCGA-09-1665 TCGA-09-1667 TCGA-09-1670 TCGA-09-1672 
       17.98        38.43        41.62        61.87        17.98         5.85 
TCGA-09-1674 TCGA-09-2043 TCGA-09-2045 TCGA-09-2051 TCGA-09-2053 TCGA-10-0926 
        8.55         6.18        35.15        63.09        39.75        25.91 
TCGA-10-0927 TCGA-13-0717 TCGA-13-0724 TCGA-13-0757 TCGA-13-0760 TCGA-13-0762 
       81.86        24.59         2.73        11.18        11.54        32.25 
TCGA-13-0768 TCGA-13-0795 TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
        8.45        19.59        43.86        35.31        13.61        68.94 
TCGA-13-0885 TCGA-13-0888 TCGA-13-0899 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 
       91.40        70.39        56.15        19.36        47.38        48.33 
TCGA-13-0912 TCGA-13-0921 TCGA-13-0923 TCGA-13-1407 TCGA-13-1410 TCGA-13-1411 
       34.06         4.64         6.41         6.05         4.70         4.21 
TCGA-13-1412 TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 TCGA-13-1485 TCGA-13-1488 
        5.33        87.06        61.71        98.04        20.68        70.82 
TCGA-13-1489 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1500 TCGA-13-1504 
       82.88        49.25         4.24        54.31        13.97        16.57 
TCGA-13-1509 TCGA-13-2059 TCGA-13-2060 TCGA-13-A5FU TCGA-20-0987 TCGA-20-0991 
        4.18        12.23         8.61         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-23-1809 
        2.76         3.22       129.96         6.38        39.09         0.53 
TCGA-23-2072 TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-24-1104 TCGA-24-1413 
       24.95       115.89        91.66        77.00        63.55         6.31 
TCGA-24-1418 TCGA-24-1424 TCGA-24-1428 TCGA-24-1431 TCGA-24-1436 TCGA-24-1471 
        7.99         6.02        17.39        19.17         8.55         1.18 
TCGA-24-1474 TCGA-24-1546 TCGA-24-1548 TCGA-24-1557 TCGA-24-1558 TCGA-24-1614 
       22.22        64.27        16.21        39.88        19.53        48.33 
TCGA-24-1844 TCGA-24-1845 TCGA-24-1850 TCGA-24-1928 TCGA-24-2019 TCGA-24-2020 
        3.72         3.81         5.52        11.05         4.87       152.02 
TCGA-24-2026 TCGA-24-2030 TCGA-24-2033 TCGA-24-2038 TCGA-24-2261 TCGA-24-2262 
       34.82        55.92        18.48        44.52         0.79         0.36 
TCGA-24-2267 TCGA-24-2280 TCGA-24-2295 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 
       47.54        70.45        33.11         1.02        26.96        33.01 
TCGA-25-1318 TCGA-25-1320 TCGA-25-1323 TCGA-25-1623 TCGA-25-1626 TCGA-25-1627 
       34.98        37.97        12.99        18.58        17.03        12.95 
TCGA-25-1628 TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 TCGA-25-2397 TCGA-25-2400 
       20.61        14.96        24.99        85.05        12.00        42.02 
TCGA-25-2401 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1707 
        2.96        40.41        31.20        68.32        36.36        41.98 
TCGA-29-1764 TCGA-29-1775 TCGA-29-1778 TCGA-29-1783 TCGA-29-2428 TCGA-29-2429 
       62.93        12.36        14.93         7.23        45.11        13.84 
TCGA-29-2432 TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1853 TCGA-30-1862 TCGA-30-1866 
       21.47        11.47        35.77        36.26         6.12        36.62 
TCGA-30-1867 TCGA-31-1950 TCGA-36-1580 TCGA-36-2529 TCGA-36-2545 TCGA-36-2547 
        1.22        18.77        24.23        35.05        18.31        20.52 
TCGA-36-2548 TCGA-42-2582 TCGA-42-2587 TCGA-42-2590 TCGA-57-1586 TCGA-57-1993 
       14.17        47.57        23.74        10.42        22.32        25.08 
TCGA-59-2348 TCGA-59-2349 TCGA-59-2351 TCGA-59-2355 TCGA-59-2372 TCGA-61-1725 
      180.20        80.12       116.12         2.14        44.81        31.43 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1737 TCGA-61-1740 TCGA-61-1743 TCGA-61-1899 
        4.34        31.79        44.84         2.43        43.69         8.42 
TCGA-61-1901 TCGA-61-1904 TCGA-61-1906 TCGA-61-1911 TCGA-61-1914 TCGA-61-1918 
       11.41         9.07        34.13        42.51        56.61        15.75 
TCGA-61-1919 TCGA-61-2003 TCGA-61-2088 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 
       38.17         4.01         4.77        55.50         6.48        76.87 
TCGA-61-2110 TCGA-61-2113 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-WR-A838 
       44.52        22.22         8.61        39.68        18.94         9.99 

$`7Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1343 
       43.92        41.00         1.81        49.15        46.62        11.87 
TCGA-04-1346 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 TCGA-04-1361 
       65.52        48.76        21.57        63.98        49.28        32.52 
TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1519 TCGA-04-1525 
       44.32        76.57       103.40        82.39         0.79        38.37 
TCGA-04-1530 TCGA-04-1638 TCGA-04-1648 TCGA-04-1651 TCGA-04-1654 TCGA-09-0364 
      119.08        55.43        28.64        36.23        47.70        29.16 
TCGA-09-0366 TCGA-09-0369 TCGA-09-1659 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 
       57.76        35.57         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-10-0925 
      112.41        71.11        20.94        26.93        12.46        54.31 
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-13-0720 TCGA-13-0723 
       36.92        19.99        20.91         6.21        44.55        39.58 
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-13-0758 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 
       11.38        34.06        31.04        21.40        38.93        36.72 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
       28.70        30.35         8.71         7.79         8.12         8.28 
TCGA-13-0802 TCGA-13-0804 TCGA-13-0884 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 
        8.19        35.28       107.18        74.27        66.67        61.84 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0905 
       67.99        69.01        43.36        57.47        57.07        47.84 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0913 TCGA-13-0916 
       44.94        44.84        37.08        27.72        29.98        21.17 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
       14.89        13.81         6.08        10.88         6.61         7.36 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1477 TCGA-13-1483 TCGA-13-1487 TCGA-13-1491 
        5.92         6.84        54.64        29.42        22.39        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1505 
       73.55        38.20        37.61        38.40        32.84         4.21 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 
        4.41         4.77         2.56         3.91         3.09        14.24 
TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-20-0990 TCGA-20-0996 
       10.78         8.75         6.28        54.77        25.94        72.20 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 
       25.38        19.10        16.70        49.68        40.54        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1109 TCGA-23-1110 
       32.09        49.41         8.81        29.13        51.35        54.51 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 
       31.20        68.68         4.57        33.30        86.01         4.27 
TCGA-23-1123 TCGA-23-1124 TCGA-23-2078 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 
       33.47        58.13        87.48        49.84         2.76         4.70 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        4.50         7.63        19.66        11.64        21.80        41.56 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1105 TCGA-24-1416 TCGA-24-1417 
        7.66        22.32        54.12        47.41         6.38         7.82 
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-24-1430 TCGA-24-1434 TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 
       28.37        18.67        43.53        72.92        12.46        45.14 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1544 TCGA-24-1545 TCGA-24-1549 
      105.99         9.11         3.45        26.96        57.40        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-24-1564 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-24-1842 TCGA-24-1843 TCGA-24-1846 
       90.15        88.37        38.24         8.32         3.48         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-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2035 
       81.11        44.84        58.16       109.71        14.43        28.18 
TCGA-24-2036 TCGA-24-2254 TCGA-24-2260 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 
       64.01        57.07        36.16        31.63        44.61         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 TCGA-25-1315 
       67.36        36.23        16.64        55.86        53.26        52.04 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1319 TCGA-25-1321 TCGA-25-1322 TCGA-25-1329 
       42.05         2.01        65.00        33.96         2.99        15.02 
TCGA-25-1625 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
       27.62        38.20         0.30        59.15        62.17        35.87 
TCGA-25-1635 TCGA-25-1877 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 
       52.04        24.00        13.02        49.05         1.02        38.04 
TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
        3.02        45.01        19.99        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-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 
       16.93        23.93        59.67        18.25        31.27        34.62 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 
       17.36        86.60        66.81        39.42        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-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2431 
        5.36        36.30        86.17        65.00        62.47        42.25 
TCGA-29-2436 TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 
        9.76        38.07        51.91         2.47        15.68         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-31-1951 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-36-1568 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-36-2530 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-36-2549 TCGA-36-2551 TCGA-36-2552 
       21.60         2.24        20.98         6.05        16.18        11.47 
TCGA-3P-A9WA TCGA-42-2588 TCGA-42-2589 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 
       13.81        28.93        42.02        40.77         1.48        24.03 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 TCGA-57-1994 TCGA-59-2350 
       11.38        21.14         1.74        29.00        25.02        22.32 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 TCGA-59-A5PD TCGA-5X-AA5U TCGA-61-1721 
        9.40        34.39         5.42        20.52        11.87        11.11 
TCGA-61-1722 TCGA-61-1724 TCGA-61-1727 TCGA-61-1728 TCGA-61-1734 TCGA-61-1736 
        8.09        20.94        18.54        27.88        28.47        48.79 
TCGA-61-1738 TCGA-61-1741 TCGA-61-1895 TCGA-61-1900 TCGA-61-1903 TCGA-61-1907 
       35.80        33.67         1.45         5.79        13.02        31.30 
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-61-2098 TCGA-61-2109 TCGA-61-2111 TCGA-61-2612 
       58.39        60.62        65.52        20.68       125.75         6.35 
TCGA-61-2613 TCGA-VG-A8LO 
       31.07         0.79 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.36              0.26 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           180.20            125.75 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           23.395            29.900 
[1] "0.4 - 180.2 (23.4)" "0.3 - 125.8 (29.9)"
[1] "hr=" "1.1"
D14V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  7Q GAIN MUTATED         1   193                1
  7Q GAIN WILD-TYPE       2   365                1
D14V3, multiclass
                  clus
vv                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  OMENTUM                        1                 2
  OVARY                        193               365
  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, continuous
D14V5, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     0 199
  7Q GAIN WILD-TYPE   3 371
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      0  199
  7Q GAIN WILD-TYPE    3  371
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO                0                 3
  YES             199               371
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  7Q GAIN MUTATED    7 11  2  1
  7Q GAIN WILD-TYPE  8 15  3  2
D14V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0               7                 8
  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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q GAIN MUTATED                                  0     3
  7Q GAIN WILD-TYPE                                3    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  7Q GAIN MUTATED                           9
  7Q GAIN WILD-TYPE                        25
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7Q GAIN MUTATED                                           1   169
  7Q GAIN WILD-TYPE                                         0   307
D14V7, multiclass
                                           clus
vv                                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   3                16
  BLACK OR AFRICAN AMERICAN                               9                25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 169               307
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V8, 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    52  64
  8P GAIN WILD-TYPE 216 228
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              116               444 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               64               228 
$`8P GAIN MUTATED`
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-04-1362 TCGA-04-1364 TCGA-04-1542 TCGA-09-0365 TCGA-09-0369 TCGA-09-1659 
       44.32        33.67        84.20         9.47        35.57         9.99 
TCGA-09-1665 TCGA-09-1667 TCGA-09-1672 TCGA-09-2043 TCGA-10-0935 TCGA-10-0937 
       41.62        61.87         5.85         6.18        35.44        19.99 
TCGA-13-0717 TCGA-13-0724 TCGA-13-0726 TCGA-13-0751 TCGA-13-0768 TCGA-13-0794 
       24.59         2.73        31.20        55.17         8.45        30.35 
TCGA-13-0800 TCGA-13-0884 TCGA-13-0893 TCGA-13-0897 TCGA-13-0903 TCGA-13-0908 
        8.12       107.18        43.36        57.47        47.38        44.84 
TCGA-13-0911 TCGA-13-1404 TCGA-13-1408 TCGA-13-1409 TCGA-13-1485 TCGA-13-1488 
       27.72         6.61         5.92         6.84        20.68        70.82 
TCGA-13-1497 TCGA-13-1506 TCGA-13-2057 TCGA-13-2060 TCGA-13-2071 TCGA-20-0987 
       54.31         4.41        14.24         8.61         6.28        23.05 
TCGA-20-1683 TCGA-20-1687 TCGA-23-1023 TCGA-23-1029 TCGA-23-1109 TCGA-23-1110 
       25.38         2.66        40.54         8.81        51.35        54.51 
TCGA-23-1111 TCGA-23-1119 TCGA-23-2079 TCGA-24-0979 TCGA-24-1103 TCGA-24-1418 
        3.22       129.96        91.66        41.56        54.12         7.99 
TCGA-24-1435 TCGA-24-1471 TCGA-24-1545 TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 
       43.53         1.18        57.40        58.09        70.62        39.88 
TCGA-24-1563 TCGA-24-1847 TCGA-24-1849 TCGA-24-1923 TCGA-24-2019 TCGA-24-2020 
       47.70        11.28         5.79        22.68         4.87       152.02 
TCGA-24-2262 TCGA-24-2271 TCGA-25-1312 TCGA-25-1317 TCGA-25-1320 TCGA-25-1329 
        0.36        31.63         1.02         2.01        37.97        15.02 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1628 TCGA-25-1632 TCGA-25-1877 TCGA-25-2392 
       18.58        27.62        20.61        59.15        24.00         1.02 
TCGA-25-2398 TCGA-25-2401 TCGA-29-1690 TCGA-29-1693 TCGA-29-1696 TCGA-29-1702 
       45.01         2.96        47.61       101.79        33.93        23.93 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1776 TCGA-29-1777 TCGA-29-1785 TCGA-29-2425 
       66.81        62.93        11.84        12.30        36.30        65.00 
TCGA-29-2431 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1861 TCGA-30-1892 
       42.25        38.07        51.91        36.26        34.78        48.79 
TCGA-31-1946 TCGA-31-1956 TCGA-31-1959 TCGA-36-1576 TCGA-36-2529 TCGA-36-2548 
       30.18        44.12         2.20        30.08        35.05        14.17 
TCGA-36-2551 TCGA-42-2582 TCGA-57-1582 TCGA-59-2354 TCGA-59-2355 TCGA-5X-AA5U 
       16.18        47.57        24.03        34.39         2.14        11.87 
TCGA-61-1743 TCGA-61-1899 TCGA-61-1906 TCGA-61-2009 TCGA-61-2111 TCGA-61-2612 
       43.69         8.42        34.13        39.85       125.75         6.35 
TCGA-61-2614 TCGA-OY-A56Q 
        8.61        18.94 

$`8P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       43.92        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1341 TCGA-04-1346 TCGA-04-1348 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 
        1.08        65.52        48.76         0.53        49.28        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-09-0364 TCGA-09-0366 TCGA-09-0367 TCGA-09-1661 TCGA-09-1662 
       45.37        29.16        57.76        17.98        38.43        89.33 
TCGA-09-1664 TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 
       74.93        57.60        55.36        30.51        17.98         3.02 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 
        8.55        97.55         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-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-10-0936 TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 
       14.66         6.71        36.92        20.91         6.21        44.55 
TCGA-13-0723 TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 
       39.58        12.39        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        34.06        32.25        31.04        21.40 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 
       38.93        36.72        28.70        19.59         8.71         7.79 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
        8.28         8.19        43.86        35.28        35.31        13.61 
TCGA-13-0883 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 
       68.94        91.40        74.27        66.67        70.39        61.84 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0904 
       67.99        69.01        56.15        57.07        19.36        48.33 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       47.84        44.94        37.08        34.06        29.98        21.17 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 
       14.89        13.81         4.64         6.41         6.08        10.88 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 
        7.36         6.05         4.70         4.21         5.33        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1489 
       87.06        61.71        29.42        98.04        22.39        82.88 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 
       52.44        73.55        38.20        49.25         4.24        37.61 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1507 
       38.40        13.97        32.84        16.57         4.21         4.77 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2061 
        4.18         2.56         3.91         3.09        12.23        10.78 
TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 
        8.75        54.77         8.42        25.94        26.20        72.20 
TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 TCGA-23-1022 
       27.52        19.10        16.70         2.93        47.54        49.68 
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-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
        2.76        31.20        68.68         4.57        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-23-2077 TCGA-23-2078 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
       24.95       115.89        87.48        77.00        49.84         2.76 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 
        4.70         4.50         7.63        19.66        11.64        21.80 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
        7.66        22.32        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        19.17        18.67 
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-24-1546 TCGA-24-1548 TCGA-24-1549 
        3.45        22.22        26.96        64.27        16.21        56.58 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 TCGA-24-1558 TCGA-24-1560 
       41.06        51.91        41.39        88.50        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-24-1614 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-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 
        4.37         5.52         9.80        30.21        16.44        11.05 
TCGA-24-1930 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 
       81.11        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-24-2267 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
       36.16         0.79        47.54        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-25-1323 TCGA-25-1626 TCGA-25-1627 TCGA-25-1630 
       33.96         2.99        12.99        17.03        12.95        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-25-1878 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-25-2399 TCGA-25-2400 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 
       19.99        42.02        29.03        31.00        26.99        78.90 
TCGA-29-1691 TCGA-29-1694 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
       48.33        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-29-1778 TCGA-29-1781 TCGA-29-1783 
       22.55        17.33        12.36        14.93         8.38         7.23 
TCGA-29-1784 TCGA-29-2414 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2432 
        5.36        86.17        62.47        45.11        13.84        21.47 
TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 
       11.47         9.76        35.77         2.47        15.68         0.26 
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-30-1891 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-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
       42.51        28.77        29.10        21.53        22.85        22.55 
TCGA-36-1575 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2530 
        8.55        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-36-2549 TCGA-36-2552 
        2.24        20.98        18.31        20.52         6.05        11.47 
TCGA-3P-A9WA TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
       13.81        23.74        28.93        42.02        10.42        40.77 
TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 
        1.48        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-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 
        9.40         5.42        44.81        20.52        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-61-1740 TCGA-61-1741 
       28.47        48.79        44.84        35.80         2.43        33.67 
TCGA-61-1895 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1907 
        1.45         5.79        11.41        13.02         9.07        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-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
        4.01        30.64        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-61-2113 TCGA-61-2613 TCGA-OY-A56P TCGA-VG-A8LO TCGA-WR-A838 
       44.52        22.22        31.07        39.68         0.79         9.99 

  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 
           30.775            28.275 
[1] "0.4 - 152.0 (30.8)" "0.3 - 180.2 (28.3)"
[1] "hr=" "1"  
D15V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  8P GAIN MUTATED         0   116                1
  8P GAIN WILD-TYPE       3   442                1
D15V3, multiclass
                  clus
vv                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  OMENTUM                        0                 3
  OVARY                        116               442
  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, continuous
D15V5, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     1 117
  8P GAIN WILD-TYPE   2 453
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1  117
  8P GAIN WILD-TYPE    2  453
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                1                 2
  YES             117               453
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  8P GAIN MUTATED    3  7  0  1
  8P GAIN WILD-TYPE 12 19  5  2
D15V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0               3                12
  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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0     1
  8P GAIN WILD-TYPE                                3    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  8P GAIN MUTATED                           7
  8P GAIN WILD-TYPE                        27
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8P GAIN MUTATED                                           0   104
  8P GAIN WILD-TYPE                                         1   372
D15V7, multiclass
                                           clus
vv                                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   1                18
  BLACK OR AFRICAN AMERICAN                               7                27
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 104               372
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V8, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     2  69
  8P GAIN WILD-TYPE   8 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      2   69
  8P GAIN WILD-TYPE    8  258
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 8
  NOT HISPANIC OR LATINO              69               258
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   105 130
  8Q GAIN WILD-TYPE 163 162
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              235               325 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              130               162 
$`8Q GAIN MUTATED`
TCGA-04-1335 TCGA-04-1338 TCGA-04-1342 TCGA-04-1343 TCGA-04-1347 TCGA-04-1349 
        1.81        46.62        18.51        11.87        63.09        21.57 
TCGA-04-1351 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1530 TCGA-04-1536 
       65.46        44.32        33.67        76.57       119.08        29.10 
TCGA-04-1542 TCGA-04-1646 TCGA-04-1652 TCGA-09-0365 TCGA-09-1659 TCGA-09-1661 
       84.20        27.88        31.86         9.47         9.99        38.43 
TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 
       41.62        61.87        55.36        17.98         5.85         8.55 
TCGA-09-2043 TCGA-10-0925 TCGA-10-0927 TCGA-10-0930 TCGA-10-0933 TCGA-10-0935 
        6.18        54.31        81.86        34.19        14.66        35.44 
TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0717 TCGA-13-0724 TCGA-13-0726 
       36.92        19.99        20.91        24.59         2.73        31.20 
TCGA-13-0751 TCGA-13-0761 TCGA-13-0768 TCGA-13-0792 TCGA-13-0794 TCGA-13-0800 
       55.17        34.06         8.45        36.72        30.35         8.12 
TCGA-13-0802 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0890 TCGA-13-0893 
        8.19        13.61        68.94       107.18        67.99        43.36 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0911 TCGA-13-0919 
       57.47        56.15        57.07        47.38        27.72        14.89 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
        6.08        10.88         6.61         5.92         6.84         4.70 
TCGA-13-1411 TCGA-13-1484 TCGA-13-1485 TCGA-13-1488 TCGA-13-1497 TCGA-13-1500 
        4.21        98.04        20.68        70.82        54.31        13.97 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-2059 
       32.84        16.57         4.21         4.41         4.77        12.23 
TCGA-13-2060 TCGA-13-2071 TCGA-20-0987 TCGA-20-0991 TCGA-20-1683 TCGA-20-1686 
        8.61         6.28        23.05        26.20        25.38         2.93 
TCGA-20-1687 TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 TCGA-23-1029 TCGA-23-1031 
        2.66        49.68        40.54        26.83         8.81        18.90 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1116 TCGA-23-1117 TCGA-23-1119 
       51.35        54.51         3.22         4.57        33.30       129.96 
TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2079 
        6.38        33.47        58.13        24.95       115.89        91.66 
TCGA-23-2084 TCGA-23-2643 TCGA-23-2645 TCGA-24-0975 TCGA-24-0979 TCGA-24-1103 
       49.84         4.70         4.50        21.80        41.56        54.12 
TCGA-24-1105 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 
       47.41         7.82         7.99         7.86         0.76         6.25 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1464 TCGA-24-1467 TCGA-24-1471 
       18.67        43.53         8.55        12.46       105.99         1.18 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1549 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       57.40        64.27        56.58        41.39        58.09        88.50 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1563 TCGA-24-1564 TCGA-24-1844 
       70.62        39.88        19.53        47.70        25.87         3.72 
TCGA-24-1847 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-2019 TCGA-24-2020 
       11.28        22.68        30.21        16.44         4.87       152.02 
TCGA-24-2027 TCGA-24-2033 TCGA-24-2035 TCGA-24-2262 TCGA-24-2271 TCGA-24-2290 
      109.71        18.48        28.18         0.36        31.63        36.23 
TCGA-24-2295 TCGA-25-1312 TCGA-25-1317 TCGA-25-1320 TCGA-25-1321 TCGA-25-1329 
       33.11         1.02         2.01        37.97        33.96        15.02 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1627 TCGA-25-1628 TCGA-25-1632 TCGA-25-1877 
       18.58        27.62        12.95        20.61        59.15        24.00 
TCGA-25-1878 TCGA-25-2392 TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2401 
       85.05         1.02         3.02        45.01        19.99         2.96 
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-29-1763 
       68.32        36.36        16.93        23.93        59.67        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1774 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 
       62.93        39.42        17.33        11.84        12.30        14.93 
TCGA-29-1783 TCGA-29-1785 TCGA-29-2425 TCGA-29-2427 TCGA-29-2431 TCGA-29-2432 
        7.23        36.30        65.00        62.47        42.25        21.47 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1857 TCGA-30-1859 TCGA-30-1861 
       38.07        51.91        36.26         0.26        48.10        34.78 
TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 
       24.26        48.79        45.57        30.18        18.77        22.49 
TCGA-31-1956 TCGA-31-1959 TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 TCGA-36-1576 
       44.12         2.20        29.10        21.53        22.55        30.08 
TCGA-36-1580 TCGA-36-2529 TCGA-36-2543 TCGA-36-2548 TCGA-36-2551 TCGA-3P-A9WA 
       24.23        35.05         2.24        14.17        16.18        13.81 
TCGA-42-2582 TCGA-42-2588 TCGA-57-1582 TCGA-57-1585 TCGA-57-1586 TCGA-59-2348 
       47.57        28.93        24.03         1.74        22.32       180.20 
TCGA-59-2354 TCGA-59-2355 TCGA-5X-AA5U TCGA-61-1725 TCGA-61-1728 TCGA-61-1736 
       34.39         2.14        11.87        31.43        27.88        48.79 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1899 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 
       33.67        43.69         8.42        34.13        31.30        37.05 
TCGA-61-1911 TCGA-61-1914 TCGA-61-1919 TCGA-61-1998 TCGA-61-2009 TCGA-61-2016 
       42.51        56.61        38.17         5.52        39.85         1.18 
TCGA-61-2088 TCGA-61-2109 TCGA-61-2111 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56Q 
        4.77        20.68       125.75         6.35         8.61        18.94 
TCGA-VG-A8LO 
        0.79 

$`8Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1341 TCGA-04-1346 
       43.92        41.00        49.15         2.01         1.08        65.52 
TCGA-04-1348 TCGA-04-1350 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1367 
       48.76        63.98         0.53        49.28        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-09-0364 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1662 
       45.37        29.16        57.76        17.98        35.57        89.33 
TCGA-09-1664 TCGA-09-1666 TCGA-09-1669 TCGA-09-1673 TCGA-09-1675 TCGA-09-2044 
       74.93        57.60        30.51         3.02        97.55         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-10-0926 TCGA-10-0928 TCGA-10-0931 
       20.94        26.93        12.46        25.91        18.51        32.88 
TCGA-10-0934 TCGA-13-0714 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0727 
        6.71         6.21        44.55        39.58        12.39        15.19 
TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0762 
       17.82         2.50        11.18        11.38        11.54        32.25 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 
       31.04        21.40        38.93        28.70        19.59         8.71 
TCGA-13-0799 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0885 
        7.79         8.28        43.86        35.28        35.31        91.40 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 TCGA-13-0901 
       74.27        66.67        70.39        61.84        69.01        19.36 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 
       48.33        47.84        44.94        44.84        37.08        34.06 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-1405 
       29.98        21.17        13.81         4.64         6.41         7.36 
TCGA-13-1407 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
        6.05         5.33        54.64        87.06        61.71        29.42 
TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       22.39        82.88        52.44        73.55        38.20        49.25 
TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
        4.24        37.61        38.40         4.18         2.56         3.91 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU 
        3.09        14.24        10.78         8.75        54.77         8.42 
TCGA-20-0990 TCGA-20-0996 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 TCGA-23-1021 
       25.94        72.20        27.52        19.10        16.70        47.54 
TCGA-23-1024 TCGA-23-1027 TCGA-23-1028 TCGA-23-1030 TCGA-23-1032 TCGA-23-1113 
       15.39        32.09        49.41        29.13         2.76        31.20 
TCGA-23-1114 TCGA-23-1118 TCGA-23-1120 TCGA-23-1122 TCGA-23-1809 TCGA-23-2078 
       68.68        86.01         4.27        39.09         0.53        87.48 
TCGA-23-2081 TCGA-23-2641 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0980 
       77.00         2.76         7.63        19.66        11.64         7.66 
TCGA-24-0982 TCGA-24-1104 TCGA-24-1413 TCGA-24-1416 TCGA-24-1424 TCGA-24-1425 
       22.32        63.55         6.31         6.38         6.02         5.95 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1463 
        5.36         4.83        17.39        28.37        19.17        72.92 
TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 TCGA-24-1474 TCGA-24-1544 TCGA-24-1548 
       45.14         9.11         3.45        22.22        26.96        16.21 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1560 TCGA-24-1562 TCGA-24-1565 TCGA-24-1567 
       41.06        51.91        44.09        45.50        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-24-1845 TCGA-24-1846 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1928 
        3.81         4.37         5.79         5.52         9.80        11.05 
TCGA-24-1930 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2029 TCGA-24-2030 
       81.11        44.84        58.16        34.82        14.43        55.92 
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-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2293 TCGA-24-2297 
       70.45        44.61         0.82        67.36        16.64        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-25-1322 TCGA-25-1323 TCGA-25-1626 TCGA-25-1630 TCGA-25-1631 
       65.00         2.99        12.99        17.03        38.20         0.30 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-2042 
       62.17        35.87        52.04        14.96        24.99        13.02 
TCGA-25-2391 TCGA-25-2393 TCGA-25-2397 TCGA-25-2400 TCGA-25-2404 TCGA-25-2408 
       49.05        38.04        12.00        42.02        29.03        31.00 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1691 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 
       26.99        78.90        48.33        18.25        41.98        31.27 
TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 
       34.62        17.36        86.60        31.30        22.98        24.36 
TCGA-29-1771 TCGA-29-1775 TCGA-29-1781 TCGA-29-1784 TCGA-29-2414 TCGA-29-2428 
       22.55        12.36         8.38         5.36        86.17        45.11 
TCGA-29-2429 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1855 TCGA-30-1856 
       13.84        11.47         9.76        35.77         2.47        15.68 
TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1891 
       44.91         6.12        36.62         1.22        57.57        30.05 
TCGA-31-1953 TCGA-31-1955 TCGA-36-1568 TCGA-36-1571 TCGA-36-1575 TCGA-36-1577 
        6.71        42.51        28.77        22.85         8.55        25.74 
TCGA-36-1578 TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       27.85        24.69        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-36-2552 TCGA-42-2587 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
        6.05        11.47        23.74        42.02        10.42        40.77 
TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 
        1.48        11.38        21.14        29.00        25.08        25.02 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2363 TCGA-59-2372 
       80.12        22.32       116.12         9.40         5.42        44.81 
TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1727 TCGA-61-1730 
       20.52        11.11         8.09        20.94        18.54         4.34 
TCGA-61-1733 TCGA-61-1734 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1895 
       31.79        28.47        44.84        35.80         2.43         1.45 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1913 TCGA-61-1915 
        5.79        11.41        13.02         9.07        48.92        67.76 
TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 
       43.43        15.75         2.01        14.50        17.98         4.01 
TCGA-61-2008 TCGA-61-2012 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 
       30.64        30.64        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-61-2110 TCGA-61-2113 TCGA-61-2613 TCGA-OY-A56P 
        6.48        76.87        44.52        22.22        31.07        39.68 
TCGA-WR-A838 
        9.99 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.26              0.30 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           180.20            116.12 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            27.88             28.77 
[1] "0.3 - 180.2 (27.9)" "0.3 - 116.1 (28.8)"
[1] "hr=" "1.1"
D16V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  8Q GAIN MUTATED         1   235                2
  8Q GAIN WILD-TYPE       2   323                0
D16V3, multiclass
                  clus
vv                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  OMENTUM                        1                 2
  OVARY                        235               323
  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, continuous
D16V5, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     1 239
  8Q GAIN WILD-TYPE   2 331
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1  239
  8Q GAIN WILD-TYPE    2  331
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                1                 2
  YES             239               331
[1] 2 2
[1] FALSE
                   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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q GAIN MUTATED                                  0     4
  8Q GAIN WILD-TYPE                                3    15
                   vv
clus                BLACK OR AFRICAN AMERICAN
  8Q GAIN MUTATED                          15
  8Q GAIN WILD-TYPE                        19
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8Q GAIN MUTATED                                           0   207
  8Q GAIN WILD-TYPE                                         1   269
D16V7, multiclass
                                           clus
vv                                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   4                15
  BLACK OR AFRICAN AMERICAN                              15                19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 207               269
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V8, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     3 139
  8Q GAIN WILD-TYPE   7 188
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      3  139
  8Q GAIN WILD-TYPE    7  188
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 7
  NOT HISPANIC OR LATINO             139               188
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    38  49
  9P GAIN WILD-TYPE 230 243
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               87               473 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               49               243 
$`9P GAIN MUTATED`
TCGA-04-1362 TCGA-04-1516 TCGA-04-1655 TCGA-09-1668 TCGA-09-2045 TCGA-09-2051 
       44.32        41.59        45.37        55.36        35.15        63.09 
TCGA-10-0933 TCGA-10-0935 TCGA-10-0936 TCGA-13-0723 TCGA-13-0730 TCGA-13-0751 
       14.66        35.44        36.92        39.58        17.82        55.17 
TCGA-13-0803 TCGA-13-0807 TCGA-13-0884 TCGA-13-0893 TCGA-13-0911 TCGA-13-0919 
       43.86        13.61       107.18        43.36        27.72        14.89 
TCGA-13-0923 TCGA-13-1488 TCGA-13-1504 TCGA-13-1505 TCGA-13-1507 TCGA-13-1511 
        6.41        70.82        16.57         4.21         4.77         3.91 
TCGA-20-0990 TCGA-20-1683 TCGA-20-1686 TCGA-20-1687 TCGA-23-1024 TCGA-23-1026 
       25.94        25.38         2.93         2.66        15.39        26.83 
TCGA-23-1032 TCGA-23-1121 TCGA-23-1122 TCGA-23-1809 TCGA-23-2077 TCGA-23-2084 
        2.76         6.38        39.09         0.53       115.89        49.84 
TCGA-24-0968 TCGA-24-1424 TCGA-24-1428 TCGA-24-1434 TCGA-24-1436 TCGA-24-1466 
       19.66         6.02        17.39        18.67         8.55        45.14 
TCGA-24-1469 TCGA-24-1471 TCGA-24-1544 TCGA-24-1548 TCGA-24-1552 TCGA-24-1553 
        9.11         1.18        26.96        16.21        41.39        58.09 
TCGA-24-1556 TCGA-24-1842 TCGA-24-1844 TCGA-24-1847 TCGA-24-1850 TCGA-24-1924 
       70.62         8.32         3.72        11.28         5.52        30.21 
TCGA-24-1928 TCGA-24-2020 TCGA-24-2026 TCGA-24-2288 TCGA-24-2298 TCGA-25-1319 
       11.05       152.02        34.82         0.82        53.26        65.00 
TCGA-25-1320 TCGA-25-1329 TCGA-25-1628 TCGA-25-1635 TCGA-25-1878 TCGA-25-2396 
       37.97        15.02        20.61        52.04        85.05         3.02 
TCGA-25-2404 TCGA-29-1762 TCGA-29-1763 TCGA-29-1777 TCGA-29-1784 TCGA-30-1855 
       29.03        86.60        66.81        12.30         5.36         2.47 
TCGA-30-1859 TCGA-30-1862 TCGA-30-1867 TCGA-36-1577 TCGA-36-1581 TCGA-36-2532 
       48.10         6.12         1.22        25.74        24.69        29.49 
TCGA-36-2543 TCGA-5X-AA5U TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1906 
        2.24        11.87        33.67        43.69         1.45        34.13 
TCGA-61-2087 TCGA-61-2094 TCGA-61-2111 
        4.80        71.74       125.75 

$`9P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       43.92        41.00         1.81        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-04-1356 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-04-1530 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-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 
       47.70        29.16         9.47        57.76        17.98        35.57 
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-09-2048 TCGA-09-2049 TCGA-09-2050 
       97.55         6.18         6.12         4.54       112.41        71.11 
TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 
       39.75        20.94        26.93        12.46        54.31        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 TCGA-10-0937 
       81.86        18.51        34.19        32.88         6.71        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-13-0726 TCGA-13-0727 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 
       31.20        15.19         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 
       34.06        32.25        31.04        21.40         8.45        38.93 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 
       36.72        28.70        30.35        19.59         8.71         7.79 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0883 
        8.12         8.28         8.19        35.28        35.31        68.94 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 
       91.40        74.27        66.67        70.39        61.84        67.99 
TCGA-13-0891 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       69.01        57.47        56.15        57.07        19.36        47.38 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 
       48.33        47.84        44.94        44.84        37.08        34.06 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0924 TCGA-13-1403 
       29.98        21.17        13.81         4.64         6.08        10.88 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
        6.61         7.36         6.05         5.92         6.84         4.70 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
        4.21         5.33        54.64        87.06        61.71        29.42 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
       98.04        20.68        22.39        82.88        52.44        73.55 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 
       38.20        49.25         4.24        54.31        37.61        38.40 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 
       13.97        32.84         4.41         4.18         2.56         3.09 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 
       14.24        12.23         8.61        10.78         8.75         6.28 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 
       54.77         8.42        23.05        26.20        72.20        27.52 
TCGA-20-1684 TCGA-20-1685 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1027 
       19.10        16.70        47.54        49.68        40.54        32.09 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1109 TCGA-23-1110 
       49.41         8.81        29.13        18.90        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         4.57        33.30        86.01 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2078 
      129.96         4.27        33.47        58.13        24.95        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-24-1425 TCGA-24-1426 TCGA-24-1427 
        7.86         0.76         6.25         5.95         5.36         4.83 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 TCGA-24-1467 
       28.37        19.17        43.53        72.92        12.46       105.99 
TCGA-24-1470 TCGA-24-1474 TCGA-24-1545 TCGA-24-1546 TCGA-24-1549 TCGA-24-1550 
        3.45        22.22        57.40        64.27        56.58        41.06 
TCGA-24-1551 TCGA-24-1555 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 
       51.91        88.50        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-24-1849 
       48.33        38.24         3.48         3.81         4.37         5.79 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 
        9.80        22.68        16.44        81.11         4.87        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-24-2038 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-24-2289 TCGA-24-2290 
       47.54        31.63        70.45        44.61        67.36        36.23 
TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 
       16.64        33.11        55.86         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-25-1630 
       12.99        18.58        27.62        17.03        12.95        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-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2397 
       24.00        13.02        49.05         1.02        38.04        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-29-1764 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-29-1778 TCGA-29-1781 TCGA-29-1783 
       17.33        12.36        11.84        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-29-2432 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-30-1861 
       51.91        36.26        15.68         0.26        44.91        34.78 
TCGA-30-1866 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 
       36.62        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-36-1578 TCGA-36-1580 TCGA-36-2529 TCGA-36-2530 
        8.55        30.08        27.85        24.23        35.05        33.01 
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-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 
       18.31        20.52        14.17         6.05        16.18        11.47 
TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
       13.81        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-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
       44.81        20.52        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-61-1899 TCGA-61-1900 TCGA-61-1901 
       44.84        35.80         2.43         8.42         5.79        11.41 
TCGA-61-1903 TCGA-61-1904 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 
       13.02         9.07        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-61-2088 TCGA-61-2092 
       30.64         1.18        45.96        45.40         4.77        51.72 
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-61-2113 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-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
        8.61        39.68        18.94         0.79         9.99 

  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 
            25.74             29.10 
[1] "0.5 - 152.0 (25.7)" "0.3 - 180.2 (29.1)"
[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, continuous
D17V5, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     1  88
  9P GAIN WILD-TYPE   2 482
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1   88
  9P GAIN WILD-TYPE    2  482
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                1                 2
  YES              88               482
[1] 2 2
[1] FALSE
                   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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P GAIN MUTATED                                  1     3
  9P GAIN WILD-TYPE                                2    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  9P GAIN MUTATED                           6
  9P GAIN WILD-TYPE                        28
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9P GAIN MUTATED                                           0    73
  9P GAIN WILD-TYPE                                         1   403
D17V7, multiclass
                                           clus
vv                                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 2
  ASIAN                                                   3                16
  BLACK OR AFRICAN AMERICAN                               6                28
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  73               403
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V8, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     0  50
  9P GAIN WILD-TYPE  10 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0   50
  9P GAIN WILD-TYPE   10  277
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              50               277
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    20  22
  9Q GAIN WILD-TYPE 248 270
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               42               518 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               22               270 
$`9Q GAIN MUTATED`
TCGA-04-1362 TCGA-04-1516 TCGA-09-1668 TCGA-13-0723 TCGA-13-0761 TCGA-13-0887 
       44.32        41.59        55.36        39.58        34.06        66.67 
TCGA-13-0893 TCGA-13-0911 TCGA-13-0919 TCGA-13-1505 TCGA-20-1683 TCGA-20-1687 
       43.36        27.72        14.89         4.21        25.38         2.66 
TCGA-23-1032 TCGA-23-1122 TCGA-23-1809 TCGA-23-2084 TCGA-24-1428 TCGA-24-1434 
        2.76        39.09         0.53        49.84        17.39        18.67 
TCGA-24-1436 TCGA-24-1466 TCGA-24-1552 TCGA-24-1842 TCGA-24-1844 TCGA-24-1847 
        8.55        45.14        41.39         8.32         3.72        11.28 
TCGA-24-1850 TCGA-24-2020 TCGA-24-2298 TCGA-25-1329 TCGA-25-1628 TCGA-25-1635 
        5.52       152.02        53.26        15.02        20.61        52.04 
TCGA-25-1878 TCGA-25-2404 TCGA-29-1762 TCGA-29-1784 TCGA-30-1855 TCGA-30-1862 
       85.05        29.03        86.60         5.36         2.47         6.12 
TCGA-31-1959 TCGA-36-1577 TCGA-36-2542 TCGA-42-2591 TCGA-61-1740 TCGA-61-2008 
        2.20        25.74        21.60        40.77         2.43        30.64 

$`9Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       43.92        41.00         1.81        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-04-1356 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-04-1530 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-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 
       47.70        45.37        29.16         9.47        57.76        17.98 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       35.57         9.99        38.43        89.33        74.93        41.62 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       57.60        61.87        30.51        17.98         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-09-2050 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-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       12.46        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-13-0724 TCGA-13-0725 
       20.91         6.21        24.59        44.55         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-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 
       11.38        11.54        32.25        31.04        21.40         8.45 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 
       38.93        36.72        28.70        30.35        19.59         8.71 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 
        7.79         8.12         8.28         8.19        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        91.40        74.27 
TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0897 TCGA-13-0899 
       70.39        61.84        67.99        69.01        57.47        56.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
       57.07        19.36        47.38        48.33        47.84        44.94 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 
       44.84        37.08        34.06        29.98        21.17        13.81 
TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
        4.64         6.41         6.08        10.88         6.61         7.36 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
        6.05         5.92         6.84         4.70         4.21         5.33 
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        98.04        20.68 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       22.39        70.82        82.88        52.44        73.55        38.20 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 
       49.25         4.24        54.31        37.61        38.40        13.97 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 
       32.84        16.57         4.41         4.77         4.18         2.56 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 
        3.91         3.09        14.24        12.23         8.61        10.78 
TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
        8.75         6.28        54.77         8.42        23.05        25.94 
TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 
       26.20        72.20        27.52        19.10        16.70         2.93 
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-23-1109 TCGA-23-1110 
       49.41         8.81        29.13        18.90        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         4.57        33.30        86.01 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 
      129.96         4.27         6.38        33.47        58.13        24.95 
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-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        4.50         7.63        19.66        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-24-1430 TCGA-24-1431 
        6.02         5.95         5.36         4.83        28.37        19.17 
TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 
       43.53        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-24-1553 TCGA-24-1555 TCGA-24-1556 
       56.58        41.06        51.91        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-24-1843 TCGA-24-1845 TCGA-24-1846 TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 
        3.48         3.81         4.37         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-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1623 
       65.00        37.97        33.96         2.99        12.99        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 
       27.62        17.03        12.95        38.20         0.30        59.15 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-2042 
       62.17        35.87        14.96        24.99        24.00        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-25-2408 TCGA-25-2409 TCGA-29-1688 
       19.99        42.02         2.96        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-29-1697 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-29-1763 
       18.25        41.98        31.27        34.62        17.36        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-29-1778 TCGA-29-1781 
       17.33        12.36        11.84        12.30        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-30-1859 
       38.07        51.91        36.26        15.68         0.26        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-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-36-1578 TCGA-36-1580 
       22.85        22.55         8.55        30.08        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-36-2538 TCGA-36-2540 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 
       25.08        23.80         2.24        20.98        18.31        20.52 
TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 
       14.17         6.05        16.18        11.47        13.81        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-59-A5PD TCGA-5X-AA5U 
       34.39         2.14         5.42        44.81        20.52        11.87 
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-61-1741 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-61-2002 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-61-2102 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-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
       22.22         6.35        31.07         8.61        39.68        18.94 
TCGA-VG-A8LO TCGA-WR-A838 
        0.79         9.99 

  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 
            25.56             28.85 
[1] "0.5 - 152.0 (25.6)" "0.3 - 180.2 (28.9)"
[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, continuous
D18V5, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     1  42
  9Q GAIN WILD-TYPE   2 528
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1   42
  9Q GAIN WILD-TYPE    2  528
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                1                 2
  YES              42               528
[1] 2 2
[1] FALSE
                   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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q GAIN MUTATED                                  1     3
  9Q GAIN WILD-TYPE                                2    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  9Q GAIN MUTATED                           2
  9Q GAIN WILD-TYPE                        32
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9Q GAIN MUTATED                                           0    36
  9Q GAIN WILD-TYPE                                         1   440
D18V7, multiclass
                                           clus
vv                                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 2
  ASIAN                                                   3                16
  BLACK OR AFRICAN AMERICAN                               2                32
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  36               440
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     0  25
  9Q GAIN WILD-TYPE  10 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0   25
  9Q GAIN WILD-TYPE   10  302
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              25               302
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    86  96
  10P GAIN WILD-TYPE 182 196
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               182                378 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                96                196 
$`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-09-0365 
       84.20        27.88        64.64        31.86        45.37         9.47 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1667 TCGA-09-1668 TCGA-09-1670 
       35.57         9.99        38.43        61.87        55.36        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-2050 TCGA-09-2051 TCGA-10-0930 
        5.85         3.02         8.55        71.11        63.09        34.19 
TCGA-10-0933 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0762 
       14.66        15.19        17.82        55.17        11.18        32.25 
TCGA-13-0768 TCGA-13-0802 TCGA-13-0807 TCGA-13-0884 TCGA-13-0885 TCGA-13-0888 
        8.45         8.19        13.61       107.18        91.40        70.39 
TCGA-13-0890 TCGA-13-0911 TCGA-13-0919 TCGA-13-0923 TCGA-13-1407 TCGA-13-1409 
       67.99        27.72        14.89         6.41         6.05         6.84 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1492 TCGA-13-1495 
        4.21         5.33        54.64        87.06        73.55        49.25 
TCGA-13-1496 TCGA-13-1499 TCGA-13-1504 TCGA-13-2060 TCGA-13-2061 TCGA-20-0987 
        4.24        38.40        16.57         8.61        10.78        23.05 
TCGA-20-1682 TCGA-20-1683 TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 TCGA-23-1022 
       27.52        25.38        16.70         2.93        47.54        49.68 
TCGA-23-1024 TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1116 TCGA-23-1122 
       15.39        18.90         2.76        54.51         4.57        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-2077 TCGA-23-2643 TCGA-24-0982 TCGA-24-1417 
       33.47        58.13       115.89         4.70        22.32         7.82 
TCGA-24-1418 TCGA-24-1424 TCGA-24-1427 TCGA-24-1428 TCGA-24-1434 TCGA-24-1436 
        7.99         6.02         4.83        17.39        18.67         8.55 
TCGA-24-1469 TCGA-24-1544 TCGA-24-1548 TCGA-24-1564 TCGA-24-1565 TCGA-24-1616 
        9.11        26.96        16.21        25.87        10.26        38.24 
TCGA-24-1843 TCGA-24-1850 TCGA-24-1928 TCGA-24-2020 TCGA-24-2260 TCGA-24-2261 
        3.48         5.52        11.05       152.02        36.16         0.79 
TCGA-24-2281 TCGA-24-2293 TCGA-25-1312 TCGA-25-1317 TCGA-25-1320 TCGA-25-1321 
       44.61        16.64         1.02         2.01        37.97        33.96 
TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 
        2.99        15.02        18.58        17.03        12.95        20.61 
TCGA-25-1631 TCGA-25-1634 TCGA-25-1635 TCGA-25-1871 TCGA-25-1877 TCGA-25-2392 
        0.30        35.87        52.04        24.99        24.00         1.02 
TCGA-29-1691 TCGA-29-1693 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1710 
       48.33       101.79        16.93        23.93        59.67        31.27 
TCGA-29-1763 TCGA-29-1766 TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 TCGA-29-1783 
       66.81        39.42        12.36        12.30        14.93         7.23 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2432 TCGA-29-2436 
       36.30        86.17        65.00        45.11        21.47         9.76 
TCGA-29-A5NZ TCGA-30-1853 TCGA-30-1856 TCGA-30-1861 TCGA-30-1866 TCGA-30-1887 
       35.77        36.26        15.68        34.78        36.62        24.26 
TCGA-31-1950 TCGA-31-1953 TCGA-36-1569 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 
       18.77         6.71        29.10        25.74        27.85        24.23 
TCGA-36-1581 TCGA-36-2529 TCGA-36-2543 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 
       24.69        35.05         2.24        14.17        16.18        11.47 
TCGA-42-2588 TCGA-57-1582 TCGA-57-1583 TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 
       28.93        24.03        11.38        22.32        25.08        25.02 
TCGA-59-2348 TCGA-59-2352 TCGA-59-2372 TCGA-61-1722 TCGA-61-1728 TCGA-61-1730 
      180.20         9.40        44.81         8.09        27.88         4.34 
TCGA-61-1733 TCGA-61-1740 TCGA-61-1741 TCGA-61-1904 TCGA-61-1907 TCGA-61-1911 
       31.79         2.43        33.67         9.07        31.30        42.51 
TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-2003 TCGA-61-2012 TCGA-61-2018 
       43.43        15.75        38.17         4.01        30.64        45.40 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2111 TCGA-61-2612 TCGA-OY-A56P 
       65.52        55.50         6.48       125.75         6.35        39.68 
TCGA-OY-A56Q TCGA-WR-A838 
       18.94         9.99 

$`10P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1341 TCGA-04-1342 
       43.92         1.81        49.15         2.01         1.08        18.51 
TCGA-04-1348 TCGA-04-1351 TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       48.76        65.46        32.52        33.67        76.57       103.40 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1519 TCGA-04-1525 TCGA-04-1536 
       82.39        56.55        41.59         0.79        38.37        29.10 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1651 TCGA-04-1654 TCGA-09-0364 
       55.43        48.89        28.64        36.23        47.70        29.16 
TCGA-09-0366 TCGA-09-0367 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 
       57.76        17.98        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-10-0925 
      112.41        39.75        20.94        26.93        12.46        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 
       25.91        81.86        18.51        32.88         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-13-0755 TCGA-13-0758 
       39.58         2.73        12.39        31.20         2.50        11.38 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 
       11.54        34.06        31.04        21.40        38.93        36.72 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 
       28.70        30.35        19.59         8.71         7.79         8.12 
TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0883 TCGA-13-0886 
        8.28        43.86        35.28        35.31        68.94        74.27 
TCGA-13-0887 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 
       66.67        61.84        69.01        43.36        57.47        56.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
       57.07        19.36        47.38        48.33        47.84        44.94 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 
       44.84        37.08        34.06        29.98        21.17        13.81 
TCGA-13-0921 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 
        4.64         6.08        10.88         6.61         7.36         5.92 
TCGA-13-1410 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 
        4.70        61.71        29.42        98.04        20.68        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 TCGA-13-1497 TCGA-13-1498 
       70.82        82.88        52.44        38.20        54.31        37.61 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       13.97        32.84         4.21         4.41         4.77         4.18 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2065 
        2.56         3.91         3.09        14.24        12.23         8.75 
TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 
        6.28        54.77         8.42        25.94        26.20        72.20 
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-23-1109 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 
        8.81        29.13        51.35         3.22        31.20        68.68 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1809 
       33.30        86.01       129.96         4.27         6.38         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-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        4.50         7.63        19.66        11.64        21.80        41.56 
TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
        7.66        54.12        63.55        47.41         6.31         6.38 
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-24-1435 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 
       19.17        43.53        72.92        12.46        45.14       105.99 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1545 TCGA-24-1546 TCGA-24-1549 
        3.45         1.18        22.22        57.40        64.27        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-24-1567 
       39.88        19.53        44.09        45.50        47.70        17.23 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 
       90.15        88.37        48.33         8.32         3.72         3.81 
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-24-1927 TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 
       16.44        81.11         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-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       44.52        57.07         0.36        47.54        31.63        70.45 
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-25-1313 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-25-1625 TCGA-25-1630 TCGA-25-1632 TCGA-25-1633 TCGA-25-1870 
       12.99        27.62        38.20        59.15        62.17        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-25-2400 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-29-1694 TCGA-29-1695 TCGA-29-1696 
       26.99        78.90        47.61        39.02        40.41        33.93 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 
       31.20        68.32        36.36        18.25        41.98        34.62 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 
       17.36        86.60        62.93        31.30        22.98        24.36 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 TCGA-29-1781 TCGA-29-1784 TCGA-29-2427 
       22.55        17.33        11.84         8.38         5.36        62.47 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 
       13.84        42.25        11.47        38.07        51.91         2.47 
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-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1955 
       30.05        48.79        45.57        30.18        22.49        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-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
        8.55        30.08        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-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2589 TCGA-42-2590 
        6.05        13.81        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-59-A5PD 
       22.32       116.12        34.39         2.14         5.42        20.52 
TCGA-5X-AA5U TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1734 
       11.87        11.11        20.94        31.43        18.54        28.47 
TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 
       48.79        44.84        35.80        43.69         1.45         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1906 TCGA-61-1910 TCGA-61-1913 
        5.79        11.41        13.02        34.13        37.05        48.92 
TCGA-61-1914 TCGA-61-1915 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       56.61        67.76         2.01         5.52        14.50        17.98 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2087 TCGA-61-2088 
       30.64        39.85         1.18        45.96         4.80         4.77 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2104 
       51.72        71.74        61.64        58.39        60.62        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 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.30               0.26 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            180.20             129.96 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             24.13              30.28 
[1] "0.3 - 180.2 (24.1)" "0.3 - 130.0 (30.3)"
[1] "hr=" "1.1"
D19V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  10P GAIN MUTATED         2   180                2
  10P GAIN WILD-TYPE       1   378                0
D19V3, multiclass
                  clus
vv                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  OMENTUM                         2                  1
  OVARY                         180                378
  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, continuous
D19V5, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     2 184
  10P GAIN WILD-TYPE   1 386
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2  184
  10P GAIN WILD-TYPE    1  386
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 2                  1
  YES              184                386
[1] 2 2
[1] FALSE
                    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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P GAIN MUTATED                                  0     5
  10P GAIN WILD-TYPE                                3    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  10P GAIN MUTATED                           9
  10P GAIN WILD-TYPE                        25
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10P GAIN MUTATED                                           0   162
  10P GAIN WILD-TYPE                                         1   314
D19V7, multiclass
                                           clus
vv                                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    5                 14
  BLACK OR AFRICAN AMERICAN                                9                 25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                  162                314
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V8, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     2 109
  10P GAIN WILD-TYPE   8 218
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2  109
  10P GAIN WILD-TYPE    8  218
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO              109                218
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    47  60
  10Q GAIN WILD-TYPE 221 232
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               107                453 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                60                232 
$`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-09-0365 TCGA-09-1659 TCGA-09-1661 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 
        9.47         9.99        38.43        55.36        17.98         5.85 
TCGA-09-1674 TCGA-09-2055 TCGA-10-0930 TCGA-10-0933 TCGA-13-0727 TCGA-13-0730 
        8.55        26.93        34.19        14.66        15.19        17.82 
TCGA-13-0757 TCGA-13-0762 TCGA-13-0802 TCGA-13-0884 TCGA-13-0885 TCGA-13-0890 
       11.18        32.25         8.19       107.18        91.40        67.99 
TCGA-13-0919 TCGA-13-1477 TCGA-13-1481 TCGA-13-1484 TCGA-13-1495 TCGA-13-1504 
       14.89        54.64        87.06        98.04        49.25        16.57 
TCGA-13-2061 TCGA-20-0990 TCGA-20-1682 TCGA-20-1685 TCGA-23-1021 TCGA-23-1022 
       10.78        25.94        27.52        16.70        47.54        49.68 
TCGA-23-1110 TCGA-23-1123 TCGA-23-1124 TCGA-23-2077 TCGA-23-2643 TCGA-24-0982 
       54.51        33.47        58.13       115.89         4.70        22.32 
TCGA-24-1424 TCGA-24-1427 TCGA-24-1428 TCGA-24-1548 TCGA-24-1564 TCGA-24-1616 
        6.02         4.83        17.39        16.21        25.87        38.24 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2261 TCGA-24-2293 TCGA-25-1312 TCGA-25-1317 
        4.87       152.02         0.79        16.64         1.02         2.01 
TCGA-25-1318 TCGA-25-1321 TCGA-25-1623 TCGA-25-1626 TCGA-25-1631 TCGA-25-1634 
       34.98        33.96        18.58        17.03         0.30        35.87 
TCGA-25-1877 TCGA-25-2392 TCGA-29-1702 TCGA-29-1710 TCGA-29-1763 TCGA-29-1775 
       24.00         1.02        23.93        31.27        66.81        12.36 
TCGA-29-1777 TCGA-29-1783 TCGA-29-2425 TCGA-29-2428 TCGA-29-2432 TCGA-29-2436 
       12.30         7.23        65.00        45.11        21.47         9.76 
TCGA-29-A5NZ TCGA-30-1853 TCGA-30-1861 TCGA-30-1866 TCGA-31-1950 TCGA-36-1578 
       35.77        36.26        34.78        36.62        18.77        27.85 
TCGA-36-1580 TCGA-36-2529 TCGA-36-2548 TCGA-36-2552 TCGA-57-1582 TCGA-57-1583 
       24.23        35.05        14.17        11.47        24.03        11.38 
TCGA-57-1994 TCGA-59-2352 TCGA-59-2372 TCGA-61-1722 TCGA-61-1730 TCGA-61-1733 
       25.02         9.40        44.81         8.09         4.34        31.79 
TCGA-61-1741 TCGA-61-1904 TCGA-61-1907 TCGA-61-1915 TCGA-61-2003 TCGA-61-2098 
       33.67         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 
       55.50       125.75         6.35        18.94         9.99 

$`10Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 
       43.92         1.81        49.15         2.01        46.62         1.08 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1351 
       18.51        11.87        65.52        63.09        48.76        65.46 
TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 
       32.52        33.67        76.57       103.40        82.39        56.55 
TCGA-04-1516 TCGA-04-1519 TCGA-04-1525 TCGA-04-1536 TCGA-04-1638 TCGA-04-1644 
       41.59         0.79        38.37        29.10        55.43        48.89 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-09-0364 TCGA-09-0366 
       28.64        64.64        36.23        47.70        29.16        57.76 
TCGA-09-0367 TCGA-09-0369 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 
       17.98        35.57        89.33        74.93        41.62        57.60 
TCGA-09-1667 TCGA-09-1669 TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 
       61.87        30.51         3.02        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-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       20.94        12.46        54.31        25.91        81.86        18.51 
TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 
       32.88         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-13-0725 
        6.21        24.59        44.55        39.58         2.73        12.39 
TCGA-13-0726 TCGA-13-0751 TCGA-13-0755 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 
       31.20        55.17         2.50        11.38        11.54        34.06 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       31.04        21.40         8.45        38.93        36.72        28.70 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
       30.35        19.59         8.71         7.79         8.12         8.28 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0886 
       43.86        35.28        35.31        13.61        68.94        74.27 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 
       66.67        70.39        61.84        69.01        43.36        57.47 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       56.15        57.07        19.36        47.38        48.33        47.84 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
       44.94        44.84        37.08        27.72        34.06        29.98 
TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 
       21.17        13.81         4.64         6.41         6.08        10.88 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
        6.61         7.36         6.05         5.92         6.84         4.70 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 
        4.21         5.33        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        82.88        52.44        73.55        38.20         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1505 
       54.31        37.61        38.40        13.97        32.84         4.21 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
        4.41         4.77         4.18         2.56         3.91         3.09 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT 
       14.24        12.23         8.61         8.75         6.28        54.77 
TCGA-13-A5FU TCGA-20-0987 TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 
        8.42        23.05        26.20        72.20        25.38        19.10 
TCGA-20-1686 TCGA-20-1687 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
        2.93         2.66        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-23-1116 TCGA-23-1117 TCGA-23-1118 
        3.22        31.20        68.68         4.57        33.30        86.01 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1809 TCGA-23-2072 
      129.96         4.27         6.38        39.09         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-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        7.63        19.66        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-24-1418 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-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 
       28.37        19.17        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-24-1549 TCGA-24-1550 
       22.22        26.96        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-24-1565 TCGA-24-1567 
       19.53        44.09        45.50        47.70        10.26        17.23 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
       90.15        88.37        48.33         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-24-1928 TCGA-24-1930 TCGA-24-2023 
       22.68        30.21        16.44        11.05        81.11        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-24-2262 
       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-24-2289 
       47.54        31.63        70.45        44.61         0.82        67.36 
TCGA-24-2290 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1314 
       36.23        33.11        55.86        53.26        26.96        33.01 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 
       52.04        42.05        65.00        37.97         2.99        12.99 
TCGA-25-1329 TCGA-25-1625 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1632 
       15.02        27.62        12.95        20.61        38.20        59.15 
TCGA-25-1633 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 TCGA-25-2042 
       62.17        52.04        14.96        24.99        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-25-2409 TCGA-29-1688 
       42.02         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-29-1697 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-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 
       41.98        34.62        17.36        86.60        62.93        39.42 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 
       31.30        22.98        24.36        22.55        17.33        11.84 
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-29-2434 TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 
       13.84        42.25        11.47        38.07        51.91         2.47 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1867 
       15.68         0.26        48.10        44.91         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-31-1951 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-36-1581 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       25.74        24.69        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-36-2549 TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 
       20.52         6.05        16.18        13.81        47.57        23.74 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1584 
       28.93        42.02        10.42        40.77         1.48        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-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-A5PD 
       22.32       116.12        34.39         2.14         5.42        20.52 
TCGA-5X-AA5U TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 
       11.87        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-61-1743 
       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-61-1906 
        1.45         8.42         5.79        11.41        13.02        34.13 
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-61-2008 
       38.17         2.01         5.52        14.50        17.98        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-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2113 TCGA-61-2613 
        6.48        76.87        20.68        44.52        22.22        31.07 
TCGA-61-2614 TCGA-OY-A56P TCGA-VG-A8LO 
        8.61        39.68         0.79 

  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 
             25.02              29.10 
[1] "0.3 - 152.0 (25.0)" "0.3 - 180.2 (29.1)"
[1] "hr=" "1.1"
D20V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  10Q GAIN MUTATED         2   105                1
  10Q GAIN WILD-TYPE       1   453                1
D20V3, multiclass
                  clus
vv                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  OMENTUM                         2                  1
  OVARY                         105                453
  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, continuous
D20V5, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     0 109
  10Q GAIN WILD-TYPE   3 461
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0  109
  10Q GAIN WILD-TYPE    3  461
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 0                  3
  YES              109                461
[1] 2 2
[1] FALSE
                    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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q GAIN MUTATED                                  0     3
  10Q GAIN WILD-TYPE                                3    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  10Q GAIN MUTATED                           5
  10Q GAIN WILD-TYPE                        29
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10Q GAIN MUTATED                                           0    94
  10Q GAIN WILD-TYPE                                         1   382
D20V7, multiclass
                                           clus
vv                                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    3                 16
  BLACK OR AFRICAN AMERICAN                                5                 29
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   94                382
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V8, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     2  60
  10Q GAIN WILD-TYPE   8 267
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2   60
  10Q GAIN WILD-TYPE    8  267
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO               60                267
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    42  33
  11P GAIN WILD-TYPE 226 259
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                75                485 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                33                259 
$`11P GAIN MUTATED`
TCGA-04-1343 TCGA-04-1346 TCGA-04-1350 TCGA-04-1361 TCGA-04-1362 TCGA-04-1516 
       11.87        65.52        63.98        32.52        44.32        41.59 
TCGA-09-0369 TCGA-09-2043 TCGA-09-2051 TCGA-10-0931 TCGA-13-0724 TCGA-13-0727 
       35.57         6.18        63.09        32.88         2.73        15.19 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 
       19.59         8.71        91.40        66.67        70.39        67.99 
TCGA-13-1407 TCGA-13-1410 TCGA-13-1497 TCGA-13-1499 TCGA-13-2057 TCGA-23-1021 
        6.05         4.70        54.31        38.40        14.24        47.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1029 TCGA-23-1030 TCGA-23-1109 TCGA-23-1111 
       15.39        26.83         8.81        29.13        51.35         3.22 
TCGA-23-1116 TCGA-23-1119 TCGA-23-2072 TCGA-23-2084 TCGA-23-2645 TCGA-24-1417 
        4.57       129.96        24.95        49.84         4.50         7.82 
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-61-2012 TCGA-61-2097 TCGA-OY-A56P 
       30.64        60.62        39.68 

$`11P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       43.92        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1341 TCGA-04-1342 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1351 
        1.08        18.51        63.09        48.76        21.57        65.46 
TCGA-04-1353 TCGA-04-1356 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 
        0.53        49.28        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-09-0364 TCGA-09-0365 
       36.23        31.86        47.70        45.37        29.16         9.47 
TCGA-09-0366 TCGA-09-0367 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       57.76        17.98         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-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       12.46        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 
       34.06        32.25        31.04        21.40         8.45        38.93 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
       36.72        28.70        30.35         7.79         8.12         8.28 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
        8.19        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        74.27        61.84        69.01        43.36        57.47 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       56.15        57.07        19.36        47.38        48.33        47.84 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
       44.94        44.84        37.08        27.72        34.06        29.98 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       21.17        14.89        13.81         4.64         6.41         6.08 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1409 TCGA-13-1411 
       10.88         6.61         7.36         5.92         6.84         4.21 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
        5.33        54.64        87.06        61.71        29.42        98.04 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
       20.68        22.39        70.82        82.88        52.44        73.55 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 
       38.20        49.25         4.24        37.61        13.97        32.84 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 
       16.57         4.21         4.41         4.77         4.18         2.56 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 
        3.91         3.09        12.23         8.61        10.78         8.75 
TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
        6.28        54.77         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-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        7.63        19.66        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-24-1418 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        19.17        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-3P-A9WA TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
       11.47        13.81        47.57        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-59-2349 TCGA-59-2350 
       22.32        29.00        25.08        25.02        80.12        22.32 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD 
        9.40        34.39         2.14         5.42        44.81        20.52 
TCGA-5X-AA5U TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
       11.87        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-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
       35.80        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-61-2009 
        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-61-2088 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-61-2102 
       71.74        61.64        58.39        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-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       31.07         8.61        18.94         0.79         9.99 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.26               0.30 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            180.20             152.02 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             27.85              28.70 
[1] "0.3 - 180.2 (27.9)" "0.3 - 152.0 (28.7)"
[1] "hr=" "1.4"
D21V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  11P GAIN MUTATED         0    76                0
  11P GAIN WILD-TYPE       3   482                2
D21V3, multiclass
                  clus
vv                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  OMENTUM                         0                  3
  OVARY                          76                482
  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, continuous
D21V5, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1  75
  11P GAIN WILD-TYPE   2 495
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   75
  11P GAIN WILD-TYPE    2  495
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 1                  2
  YES               75                495
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  11P GAIN MUTATED    1  1  1  0
  11P GAIN WILD-TYPE 14 25  4  3
D21V6, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0                1                 14
  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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     3
  11P GAIN WILD-TYPE                                3    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  11P GAIN MUTATED                           1
  11P GAIN WILD-TYPE                        33
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11P GAIN MUTATED                                           0    70
  11P GAIN WILD-TYPE                                         1   406
D21V7, multiclass
                                           clus
vv                                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    3                 16
  BLACK OR AFRICAN AMERICAN                                1                 33
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   70                406
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V8, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1  46
  11P GAIN WILD-TYPE   9 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   46
  11P GAIN WILD-TYPE    9  281
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO               46                281
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    52  56
  11Q GAIN WILD-TYPE 216 236
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
               108                452 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                56                236 
$`11Q GAIN MUTATED`
TCGA-04-1343 TCGA-04-1346 TCGA-04-1350 TCGA-04-1361 TCGA-04-1516 TCGA-04-1646 
       11.87        65.52        63.98        32.52        41.59        27.88 
TCGA-04-1652 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1667 TCGA-09-1668 
       31.86        35.57         9.99        38.43        61.87        55.36 
TCGA-10-0931 TCGA-13-0726 TCGA-13-0764 TCGA-13-0797 TCGA-13-0885 TCGA-13-0887 
       32.88        31.20        31.04         8.71        91.40        66.67 
TCGA-13-0888 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-1407 TCGA-13-1410 
       70.39        67.99        43.36        57.47         6.05         4.70 
TCGA-13-1412 TCGA-13-1484 TCGA-13-1497 TCGA-13-1499 TCGA-13-1506 TCGA-13-2057 
        5.33        98.04        54.31        38.40         4.41        14.24 
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-24-1417 TCGA-24-1427 
       24.95        49.84         4.70         4.50         7.82         4.83 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1471 TCGA-24-1548 TCGA-24-1549 
       19.17        18.67         8.55         1.18        16.21        56.58 
TCGA-24-1551 TCGA-24-1556 TCGA-24-1558 TCGA-24-1563 TCGA-24-1564 TCGA-24-1604 
       51.91        70.62        19.53        47.70        25.87        88.37 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 TCGA-24-1850 TCGA-24-1928 
       38.24         8.32         3.72         3.81         5.52        11.05 
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 

$`11Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       43.92        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1341 TCGA-04-1342 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1351 
        1.08        18.51        63.09        48.76        21.57        65.46 
TCGA-04-1353 TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
        0.53        49.28        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-04-1648 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-09-0364 TCGA-09-0365 TCGA-09-0366 
       36.23        47.70        45.37        29.16         9.47        57.76 
TCGA-09-0367 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 
       17.98        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-10-0925 TCGA-10-0926 
       39.75        20.94        26.93        12.46        54.31        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 
       81.86        18.51        34.19        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-13-0727 TCGA-13-0730 TCGA-13-0751 
       39.58         2.73        12.39        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        34.06        32.25 
TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 
       21.40         8.45        38.93        36.72        28.70        30.35 
TCGA-13-0795 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 
       19.59         7.79         8.12         8.28         8.19        43.86 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 
       35.28        35.31        13.61        68.94       107.18        74.27 
TCGA-13-0889 TCGA-13-0891 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       61.84        69.01        56.15        57.07        19.36        47.38 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       48.33        47.84        44.94        44.84        37.08        27.72 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 
       34.06        29.98        21.17        14.89        13.81         4.64 
TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 
        6.41         6.08        10.88         6.61         7.36         5.92 
TCGA-13-1409 TCGA-13-1411 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
        6.84         4.21        54.64        87.06        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        82.88        52.44        73.55 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 
       38.20        49.25         4.24        37.61        13.97        32.84 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
       16.57         4.21         4.77         4.18         2.56         3.91 
TCGA-13-1512 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 
        3.09        12.23         8.61        10.78         8.75         6.28 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 
       54.77         8.42        23.05        25.94        26.20        72.20 
TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1686 TCGA-23-1023 TCGA-23-1026 
       27.52        25.38        19.10         2.93        40.54        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 
       32.09        49.41        54.51        31.20        68.68         4.57 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 
       33.30        86.01         4.27         6.38        39.09        33.47 
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-23-2641 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        2.76         7.63        19.66        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-24-1418 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-24-1426 TCGA-24-1428 TCGA-24-1430 TCGA-24-1435 TCGA-24-1463 
        5.95         5.36        17.39        28.37        43.53        72.92 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1474 
       12.46        45.14       105.99         9.11         3.45        22.22 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1550 TCGA-24-1552 TCGA-24-1553 
       26.96        57.40        64.27        41.06        41.39        58.09 
TCGA-24-1555 TCGA-24-1557 TCGA-24-1560 TCGA-24-1562 TCGA-24-1565 TCGA-24-1567 
       88.50        39.88        44.09        45.50        10.26        17.23 
TCGA-24-1603 TCGA-24-1614 TCGA-24-1843 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 
       90.15        48.33         3.48         4.37        11.28         5.79 
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-24-2026 TCGA-24-2029 TCGA-24-2030 
      152.02        44.84        58.16        34.82        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-3P-A9WA TCGA-42-2582 TCGA-42-2588 
       14.17         6.05        11.47        13.81        47.57        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-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 
        1.74        22.32        29.00        25.08        25.02       180.20 
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-59-2372 TCGA-59-A5PD TCGA-5X-AA5U TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 
       44.81        20.52        11.87        11.11        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-61-1741 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-61-1910 TCGA-61-1911 
        5.79        11.41        13.02         9.07        37.05        42.51 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
       48.92        56.61        43.43        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-61-2098 TCGA-61-2101 TCGA-61-2102 
       71.74        61.64        58.39        65.52        55.50         6.48 
TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2613 TCGA-61-2614 
       76.87        44.52       125.75        22.22        31.07         8.61 
TCGA-OY-A56Q TCGA-WR-A838 
       18.94         9.99 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.26               0.36 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            129.96             180.20 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            24.475             29.015 
[1] "0.3 - 130.0 (24.5)" "0.4 - 180.2 (29.0)"
[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, continuous
D22V5, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     0 112
  11Q GAIN WILD-TYPE   3 458
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0  112
  11Q GAIN WILD-TYPE    3  458
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 0                  3
  YES              112                458
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  11Q GAIN MUTATED    1  6  2  0
  11Q GAIN WILD-TYPE 14 20  3  3
D22V6, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0                1                 14
  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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q GAIN MUTATED                                  0     3
  11Q GAIN WILD-TYPE                                3    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  11Q GAIN MUTATED                           6
  11Q GAIN WILD-TYPE                        28
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11Q GAIN MUTATED                                           0    97
  11Q GAIN WILD-TYPE                                         1   379
D22V7, multiclass
                                           clus
vv                                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    3                 16
  BLACK OR AFRICAN AMERICAN                                6                 28
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   97                379
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V8, 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   113 131
  12P GAIN WILD-TYPE 155 161
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               244                316 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               131                161 
$`12P GAIN MUTATED`
TCGA-04-1332 TCGA-04-1341 TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 TCGA-04-1351 
       41.00         1.08        18.51        65.52        63.09        65.46 
TCGA-04-1356 TCGA-04-1362 TCGA-04-1371 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 
       49.28        44.32        82.39        41.59        19.99        38.37 
TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1646 TCGA-04-1652 TCGA-04-1655 
      119.08        29.10        84.20        27.88        31.86        45.37 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 
       29.16         9.47        57.76        17.98        35.57         9.99 
TCGA-09-1661 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 TCGA-09-2043 
       38.43        55.36        17.98         5.85         8.55         6.18 
TCGA-09-2049 TCGA-09-2051 TCGA-09-2053 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
      112.41        63.09        39.75        25.91        81.86        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0938 TCGA-13-0717 TCGA-13-0723 
       34.19        32.88        14.66        20.91        24.59        39.58 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0760 TCGA-13-0762 
       15.19        17.82        55.17        11.18        11.54        32.25 
TCGA-13-0764 TCGA-13-0792 TCGA-13-0794 TCGA-13-0795 TCGA-13-0800 TCGA-13-0802 
       31.04        36.72        30.35        19.59         8.12         8.19 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0888 TCGA-13-0890 TCGA-13-0899 TCGA-13-0901 
       68.94       107.18        70.39        67.99        56.15        19.36 
TCGA-13-0904 TCGA-13-0906 TCGA-13-0912 TCGA-13-0920 TCGA-13-0923 TCGA-13-1407 
       48.33        44.94        34.06        13.81         6.41         6.05 
TCGA-13-1411 TCGA-13-1481 TCGA-13-1484 TCGA-13-1485 TCGA-13-1489 TCGA-13-1495 
        4.21        87.06        98.04        20.68        82.88        49.25 
TCGA-13-1496 TCGA-13-1499 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-2057 
        4.24        38.40        16.57         4.21         4.41        14.24 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FU TCGA-20-1682 
       12.23         8.61        10.78         8.75         8.42        27.52 
TCGA-20-1686 TCGA-23-1021 TCGA-23-1024 TCGA-23-1030 TCGA-23-1032 TCGA-23-1111 
        2.93        47.54        15.39        29.13         2.76         3.22 
TCGA-23-1114 TCGA-23-1116 TCGA-23-1118 TCGA-23-1124 TCGA-23-1809 TCGA-23-2079 
       68.68         4.57        86.01        58.13         0.53        91.66 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0968 TCGA-24-0982 TCGA-24-1418 TCGA-24-1422 
        4.70         4.50        19.66        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-42-2587 TCGA-57-1582 
       20.52        14.17        16.18        11.47        23.74        24.03 
TCGA-57-1583 TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2351 
       11.38        22.32        25.08        25.02       180.20       116.12 
TCGA-59-2352 TCGA-59-2363 TCGA-59-2372 TCGA-5X-AA5U TCGA-61-1722 TCGA-61-1728 
        9.40         5.42        44.81        11.87         8.09        27.88 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 
        4.34        31.79         2.43        33.67        43.69         1.45 
TCGA-61-1900 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1915 TCGA-61-1917 
        5.79         9.07        34.13        31.30        67.76        43.43 
TCGA-61-2002 TCGA-61-2009 TCGA-61-2012 TCGA-61-2097 TCGA-61-2111 TCGA-61-2612 
       17.98        39.85        30.64        60.62       125.75         6.35 
TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-WR-A838 
        8.61        39.68        18.94         9.99 

$`12P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1343 
       43.92         1.81        49.15         2.01        46.62        11.87 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1353 TCGA-04-1361 TCGA-04-1364 
       48.76        21.57        63.98         0.53        32.52        33.67 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 TCGA-04-1519 TCGA-04-1638 TCGA-04-1644 
       76.57       103.40        56.55         0.79        55.43        48.89 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-09-1662 TCGA-09-1664 
       28.64        64.64        36.23        47.70        89.33        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 TCGA-09-1673 TCGA-09-1675 
       41.62        57.60        61.87        30.51         3.02        97.55 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 TCGA-09-2054 TCGA-09-2055 
        6.12        35.15         4.54        71.11        20.94        26.93 
TCGA-09-2056 TCGA-10-0925 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 
       12.46        54.31         6.71        35.44        36.92        19.99 
TCGA-13-0714 TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0755 
        6.21        44.55         2.73        12.39        31.20         2.50 
TCGA-13-0758 TCGA-13-0761 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0793 
       11.38        34.06        21.40         8.45        38.93        28.70 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 
        8.71         7.79         8.28        43.86        35.28        35.31 
TCGA-13-0807 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0891 
       13.61        91.40        74.27        66.67        61.84        69.01 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0903 TCGA-13-0905 TCGA-13-0908 
       43.36        57.47        57.07        47.38        47.84        44.84 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 
       37.08        27.72        29.98        21.17        14.89         4.64 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1409 
        6.08        10.88         6.61         7.36         5.92         6.84 
TCGA-13-1410 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1487 
        4.70         5.33        54.64        61.71        29.42        22.39 
TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1497 TCGA-13-1498 
       70.82        52.44        73.55        38.20        54.31        37.61 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
       13.97        32.84         4.77         4.18         2.56         3.91 
TCGA-13-1512 TCGA-13-2071 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
        3.09         6.28        54.77        23.05        25.94        26.20 
TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1687 TCGA-23-1022 
       72.20        25.38        19.10        16.70         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        19.17        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-3P-A9WA TCGA-42-2582 TCGA-42-2588 
       20.98        18.31         6.05        13.81        47.57        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-59-A5PD 
       29.00        80.12        22.32        34.39         2.14        20.52 
TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1734 TCGA-61-1736 
       11.11        20.94        31.43        18.54        28.47        48.79 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1899 TCGA-61-1901 TCGA-61-1903 TCGA-61-1910 
       44.84        35.80         8.42        11.41        13.02        37.05 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 
       42.51        48.92        56.61        15.75        38.17         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 TCGA-61-2016 TCGA-61-2017 
        5.52        14.50         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-61-2096 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-61-2113 TCGA-61-2613 TCGA-VG-A8LO 
       44.52        22.22        31.07         0.79 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.53               0.26 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            180.20             129.96 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            25.005             30.195 
[1] "0.5 - 180.2 (25.0)" "0.3 - 130.0 (30.2)"
[1] "hr=" "1.1"
D23V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  12P GAIN MUTATED         2   243                2
  12P GAIN WILD-TYPE       1   315                0
D23V3, multiclass
                  clus
vv                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  OMENTUM                         2                  1
  OVARY                         243                315
  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, continuous
D23V5, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     1 253
  12P GAIN WILD-TYPE   2 317
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1  253
  12P GAIN WILD-TYPE    2  317
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 1                  2
  YES              253                317
[1] 2 2
[1] FALSE
                    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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P GAIN MUTATED                                  1     5
  12P GAIN WILD-TYPE                                2    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  12P GAIN MUTATED                          17
  12P GAIN WILD-TYPE                        17
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12P GAIN MUTATED                                           1   209
  12P GAIN WILD-TYPE                                         0   267
D23V7, multiclass
                                           clus
vv                                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  2
  ASIAN                                                    5                 14
  BLACK OR AFRICAN AMERICAN                               17                 17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  209                267
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V8, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     2 129
  12P GAIN WILD-TYPE   8 198
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2  129
  12P GAIN WILD-TYPE    8  198
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO              129                198
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    74  94
  12Q GAIN WILD-TYPE 194 198
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               168                392 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                94                198 
$`12Q GAIN MUTATED`
TCGA-04-1332 TCGA-04-1337 TCGA-04-1341 TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 
       41.00         2.01         1.08        18.51        65.52        63.09 
TCGA-04-1362 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1646 TCGA-04-1652 
       44.32        38.37       119.08        29.10        27.88        31.86 
TCGA-04-1655 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1668 
       45.37         9.47        57.76        17.98        35.57        55.36 
TCGA-09-1670 TCGA-09-1672 TCGA-09-2048 TCGA-09-2049 TCGA-09-2053 TCGA-10-0926 
       17.98         5.85         4.54       112.41        39.75        25.91 
TCGA-10-0927 TCGA-10-0930 TCGA-10-0936 TCGA-13-0717 TCGA-13-0723 TCGA-13-0727 
       81.86        34.19        36.92        24.59        39.58        15.19 
TCGA-13-0762 TCGA-13-0795 TCGA-13-0800 TCGA-13-0804 TCGA-13-0883 TCGA-13-0884 
       32.25        19.59         8.12        35.28        68.94       107.18 
TCGA-13-0888 TCGA-13-0890 TCGA-13-0912 TCGA-13-0920 TCGA-13-1407 TCGA-13-1481 
       70.39        67.99        34.06        13.81         6.05        87.06 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1488 TCGA-13-1496 TCGA-13-1499 TCGA-13-1505 
       98.04        20.68        70.82         4.24        38.40         4.21 
TCGA-13-1506 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-20-1682 
        4.41        14.24         8.61        10.78         8.75        27.52 
TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 TCGA-23-1032 TCGA-23-1111 TCGA-23-1116 
       16.70         2.93        47.54         2.76         3.22         4.57 
TCGA-23-1809 TCGA-23-2643 TCGA-23-2645 TCGA-24-0968 TCGA-24-1418 TCGA-24-1419 
        0.53         4.70         4.50        19.66         7.99         7.86 
TCGA-24-1424 TCGA-24-1434 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1474 
        6.02        18.67        12.46        45.14         9.11        22.22 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 
       26.96        57.40        16.21        39.88        19.53        44.09 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1616 TCGA-24-1844 TCGA-24-1845 
       47.70        25.87        10.26        38.24         3.72         3.81 
TCGA-24-1847 TCGA-24-1850 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 
       11.28         5.52        11.05        81.11         4.87       152.02 
TCGA-24-2033 TCGA-24-2038 TCGA-24-2260 TCGA-24-2261 TCGA-24-2281 TCGA-24-2288 
       18.48        44.52        36.16         0.79        44.61         0.82 
TCGA-24-2293 TCGA-24-2295 TCGA-25-1312 TCGA-25-1313 TCGA-25-1315 TCGA-25-1318 
       16.64        33.11         1.02        26.96        52.04        34.98 
TCGA-25-1321 TCGA-25-1323 TCGA-25-1627 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 
       33.96        12.99        12.95        35.87        52.04        14.96 
TCGA-25-1871 TCGA-25-2392 TCGA-25-2398 TCGA-29-1690 TCGA-29-1695 TCGA-29-1698 
       24.99         1.02        45.01        47.61        40.41        68.32 
TCGA-29-1710 TCGA-29-1761 TCGA-29-1763 TCGA-29-1766 TCGA-29-1768 TCGA-29-1774 
       31.27        17.36        66.81        39.42        31.30        17.33 
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-31-1950 TCGA-31-1955 TCGA-31-1959 TCGA-36-1571 TCGA-36-1575 TCGA-36-2529 
       18.77        42.51         2.20        22.85         8.55        35.05 
TCGA-36-2543 TCGA-36-2547 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 
        2.24        20.52        14.17        16.18        11.47        23.74 
TCGA-57-1583 TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2351 
       11.38        22.32        25.08        25.02       180.20       116.12 
TCGA-59-2352 TCGA-59-2372 TCGA-5X-AA5U TCGA-61-1730 TCGA-61-1733 TCGA-61-1740 
        9.40        44.81        11.87         4.34        31.79         2.43 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1906 TCGA-61-1907 TCGA-61-2009 TCGA-61-2012 
       33.67        43.69        34.13        31.30        39.85        30.64 
TCGA-61-2088 TCGA-61-2097 TCGA-61-2102 TCGA-61-2111 TCGA-61-2612 TCGA-61-2614 
        4.77        60.62         6.48       125.75         6.35         8.61 

$`12Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1343 TCGA-04-1348 
       43.92         1.81        49.15        46.62        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-04-1516 
       33.67        76.57       103.40        82.39        56.55        41.59 
TCGA-04-1517 TCGA-04-1519 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 
       19.99         0.79        84.20        55.43        48.89        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-09-0364 TCGA-09-1659 TCGA-09-1661 
       64.64        36.23        47.70        29.16         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-09-1673 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-09-2050 TCGA-09-2051 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 
       71.11        63.09        20.94        26.93        12.46        54.31 
TCGA-10-0928 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 
       18.51        32.88        14.66         6.71        35.44        19.99 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 
       20.91         6.21        44.55         2.73        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-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 
       34.06        31.04        21.40         8.45        38.93        36.72 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 
       28.70        30.35         8.71         7.79         8.28         8.19 
TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
       43.86        35.31        13.61        91.40        74.27        66.67 
TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       61.84        69.01        43.36        57.47        56.15        57.07 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 
       19.36        47.38        48.33        47.84        44.94        44.84 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 
       37.08        27.72        29.98        21.17        14.89         4.64 
TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 
        6.41         6.08        10.88         6.61         7.36         5.92 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 
        6.84         4.70         4.21         5.33        54.64        61.71 
TCGA-13-1483 TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       29.42        22.39        82.88        52.44        73.55        38.20 
TCGA-13-1495 TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 
       49.25        54.31        37.61        13.97        32.84        16.57 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 
        4.77         4.18         2.56         3.91         3.09        12.23 
TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
        6.28        54.77         8.42        23.05        25.94        26.20 
TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 TCGA-20-1687 TCGA-23-1022 TCGA-23-1023 
       72.20        25.38        19.10         2.66        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-23-1109 TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 TCGA-23-1117 
       18.90        51.35        54.51        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-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-24-0982 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-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 
        6.38         7.82         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        19.17        43.53         8.55 
TCGA-24-1463 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1546 TCGA-24-1549 
       72.92       105.99         3.45         1.18        64.27        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-24-1562 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1842 
       45.50        17.23        90.15        88.37        48.33         8.32 
TCGA-24-1843 TCGA-24-1846 TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 
        3.48         4.37         5.79         9.80        22.68        30.21 
TCGA-24-1927 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 
       16.44        44.84        58.16        34.82       109.71        14.43 
TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 TCGA-24-2254 TCGA-24-2262 TCGA-24-2267 
       55.92        28.18        64.01        57.07         0.36        47.54 
TCGA-24-2271 TCGA-24-2280 TCGA-24-2289 TCGA-24-2290 TCGA-24-2297 TCGA-24-2298 
       31.63        70.45        67.36        36.23        55.86        53.26 
TCGA-25-1314 TCGA-25-1316 TCGA-25-1317 TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 
       33.01        42.05         2.01        65.00        37.97         2.99 
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-25-1877 TCGA-25-1878 TCGA-25-2042 
        0.30        59.15        62.17        24.00        85.05        13.02 
TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 TCGA-25-2400 
       49.05        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-29-1691 
        2.96        29.03        31.00        26.99        78.90        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-29-1705 TCGA-29-1707 TCGA-29-1711 TCGA-29-1762 
       23.93        59.67        18.25        41.98        34.62        86.60 
TCGA-29-1764 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 
       62.93        22.98        24.36        22.55        12.36        11.84 
TCGA-29-1777 TCGA-29-1781 TCGA-29-1785 TCGA-29-2427 TCGA-29-2429 TCGA-29-2432 
       12.30         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-30-1887 
        0.26        44.91        34.78         6.12        57.57        24.26 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 
       30.05        48.79        45.57        30.18        22.49         6.71 
TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 TCGA-36-1576 
       44.12        28.77        29.10        21.53        22.55        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-36-2537 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-36-2549 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 
       18.31         6.05        13.81        47.57        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-57-1992 TCGA-59-2349 TCGA-59-2350 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       29.00        80.12        22.32        34.39         2.14         5.42 
TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
       20.52        11.11         8.09        20.94        31.43        18.54 
TCGA-61-1728 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1895 
       27.88        28.47        48.79        44.84        35.80         1.45 
TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1910 
        8.42         5.79        11.41        13.02         9.07        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-61-2016 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-61-2613 TCGA-OY-A56P TCGA-OY-A56Q 
       20.68        44.52        22.22        31.07        39.68        18.94 
TCGA-VG-A8LO TCGA-WR-A838 
        0.79         9.99 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.53               0.26 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            180.20             129.96 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            25.005             29.290 
[1] "0.5 - 180.2 (25.0)" "0.3 - 130.0 (29.3)"
[1] "hr=" "1.2"
D24V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  12Q GAIN MUTATED         2   166                2
  12Q GAIN WILD-TYPE       1   392                0
D24V3, multiclass
                  clus
vv                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  OMENTUM                         2                  1
  OVARY                         166                392
  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, continuous
D24V5, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     1 175
  12Q GAIN WILD-TYPE   2 395
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1  175
  12Q GAIN WILD-TYPE    2  395
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 1                  2
  YES              175                395
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  12Q GAIN MUTATED    6 11  0  0
  12Q GAIN WILD-TYPE  9 15  5  3
D24V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0                6                  9
  R1               11                 15
  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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q GAIN MUTATED                                  0     2
  12Q GAIN WILD-TYPE                                3    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  12Q GAIN MUTATED                          12
  12Q GAIN WILD-TYPE                        22
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12Q GAIN MUTATED                                           1   145
  12Q GAIN WILD-TYPE                                         0   331
D24V7, multiclass
                                           clus
vv                                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    2                 17
  BLACK OR AFRICAN AMERICAN                               12                 22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  145                331
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V8, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     1  85
  12Q GAIN WILD-TYPE   9 242
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1   85
  12Q GAIN WILD-TYPE    9  242
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO               85                242
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    26  32
  13Q GAIN WILD-TYPE 242 260
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                58                502 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                32                260 
$`13Q GAIN MUTATED`
TCGA-04-1337 TCGA-04-1351 TCGA-04-1371 TCGA-09-0364 TCGA-09-0365 TCGA-09-0369 
        2.01        65.46        82.39        29.16         9.47        35.57 
TCGA-09-2049 TCGA-10-0933 TCGA-10-0935 TCGA-13-0727 TCGA-13-0757 TCGA-13-0899 
      112.41        14.66        35.44        15.19        11.18        56.15 
TCGA-13-0921 TCGA-13-1407 TCGA-13-1408 TCGA-13-1481 TCGA-13-1484 TCGA-13-1506 
        4.64         6.05         5.92        87.06        98.04         4.41 
TCGA-23-1030 TCGA-23-1109 TCGA-23-2072 TCGA-24-0970 TCGA-24-1418 TCGA-24-1422 
       29.13        51.35        24.95        11.64         7.99         0.76 
TCGA-24-1434 TCGA-24-1467 TCGA-24-1471 TCGA-24-1930 TCGA-25-1312 TCGA-25-1317 
       18.67       105.99         1.18        81.11         1.02         2.01 
TCGA-25-1320 TCGA-25-1323 TCGA-25-1626 TCGA-25-1870 TCGA-25-2398 TCGA-29-1695 
       37.97        12.99        17.03        14.96        45.01        40.41 
TCGA-29-1710 TCGA-29-1761 TCGA-29-1770 TCGA-29-1783 TCGA-29-2425 TCGA-29-2428 
       31.27        17.36        24.36         7.23        65.00        45.11 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1880 TCGA-36-1576 TCGA-36-2552 
       38.07        51.91        36.26        57.57        30.08        11.47 
TCGA-42-2591 TCGA-57-1993 TCGA-59-2355 TCGA-5X-AA5U TCGA-61-1911 TCGA-61-2003 
       40.77        25.08         2.14        11.87        42.51         4.01 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2098 TCGA-61-2102 
       30.64        39.85        65.52         6.48 

$`13Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1341 
       43.92        41.00         1.81        49.15        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-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 
       63.98         0.53        49.28        32.52        44.32        33.67 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 
       76.57       103.40        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-09-0366 TCGA-09-0367 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       45.37        57.76        17.98         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-10-0925 TCGA-10-0926 TCGA-10-0927 
       20.94        26.93        12.46        54.31        25.91        81.86 
TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 
       18.51        34.19        32.88         6.71        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-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0758 
       12.39        31.20        17.82        55.17         2.50        11.38 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 
       11.54        34.06        32.25        31.04        21.40         8.45 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 
       38.93        36.72        28.70        30.35        19.59         8.71 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 
        7.79         8.12         8.28         8.19        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        91.40        74.27 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
       66.67        70.39        61.84        67.99        69.01        43.36 
TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       57.47        57.07        19.36        47.38        48.33        47.84 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
       44.94        44.84        37.08        27.72        34.06        29.98 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 
       21.17        14.89        13.81         6.41         6.08        10.88 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
        6.61         7.36         6.84         4.70         4.21         5.33 
TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 
       54.64        61.71        29.42        20.68        22.39        70.82 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
       82.88        52.44        73.55        38.20        49.25         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 
       54.31        37.61        38.40        13.97        32.84        16.57 
TCGA-13-1505 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
        4.21         4.77         4.18         2.56         3.91         3.09 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 
       14.24        12.23         8.61        10.78         8.75         6.28 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 
       54.77         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-23-1021 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-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1111 
       49.41         8.81        18.90         2.76        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         4.57        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-23-2077 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-24-0968 TCGA-24-0975 TCGA-24-0979 
        4.70         4.50         7.63        19.66        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-24-1419 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 
        6.38         7.82         7.86         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        19.17        43.53 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 
        8.55        72.92        12.46        45.14         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-24-1552 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-24-1604 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-24-2019 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-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 
       44.52        57.07        36.16         0.79         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-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1314 
       16.64        33.11        55.86        53.26        26.96        33.01 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 TCGA-25-1322 
       52.04        42.05        34.98        65.00        33.96         2.99 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 
       15.02        18.58        27.62        12.95        20.61        38.20 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1871 
        0.30        59.15        62.17        35.87        52.04        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-29-1698 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-29-1707 TCGA-29-1711 TCGA-29-1762 
       23.93        59.67        18.25        41.98        34.62        86.60 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 
       66.81        62.93        39.42        31.30        22.98        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-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 
        5.36        36.30        86.17        62.47        13.84        42.25 
TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1855 TCGA-30-1856 
       21.47        11.47         9.76        35.77         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-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 
        1.22        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-36-1580 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-36-2547 TCGA-36-2548 TCGA-36-2549 
        2.24        20.98        18.31        20.52        14.17         6.05 
TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 
       16.18        13.81        47.57        23.74        28.93        42.02 
TCGA-42-2590 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 
       10.42         1.48        24.03        11.38        21.14         1.74 
TCGA-57-1586 TCGA-57-1992 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 
       22.32        29.00        25.02       180.20        80.12        22.32 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD 
      116.12         9.40        34.39         5.42        44.81        20.52 
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 
       39.68        18.94         0.79         9.99 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.76               0.26 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            112.41             180.20 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            27.105             28.670 
[1] "0.8 - 112.4 (27.1)" "0.3 - 180.2 (28.7)"
[1] "hr=" "1.1"
D25V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  13Q GAIN MUTATED         0    58                0
  13Q GAIN WILD-TYPE       3   500                2
D25V3, multiclass
                  clus
vv                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  OMENTUM                         0                  3
  OVARY                          58                500
  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, continuous
D25V5, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     1  59
  13Q GAIN WILD-TYPE   2 511
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1   59
  13Q GAIN WILD-TYPE    2  511
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 1                  2
  YES               59                511
[1] 2 2
[1] FALSE
                    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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q GAIN MUTATED                                  0     2
  13Q GAIN WILD-TYPE                                3    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  13Q GAIN MUTATED                           2
  13Q GAIN WILD-TYPE                        32
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  13Q GAIN MUTATED                                           0    52
  13Q GAIN WILD-TYPE                                         1   424
D25V7, multiclass
                                           clus
vv                                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    2                 17
  BLACK OR AFRICAN AMERICAN                                2                 32
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   52                424
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V8, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     0  38
  13Q GAIN WILD-TYPE  10 289
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0   38
  13Q GAIN WILD-TYPE   10  289
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               38                289
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    27  30
  14Q GAIN WILD-TYPE 241 262
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                57                503 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                30                262 
$`14Q GAIN MUTATED`
TCGA-04-1514 TCGA-04-1517 TCGA-04-1646 TCGA-04-1652 TCGA-09-0364 TCGA-09-1668 
       56.55        19.99        27.88        31.86        29.16        55.36 
TCGA-09-1669 TCGA-13-0762 TCGA-13-0768 TCGA-13-0795 TCGA-13-0899 TCGA-13-0901 
       30.51        32.25         8.45        19.59        56.15        19.36 
TCGA-13-1408 TCGA-13-1501 TCGA-13-1505 TCGA-13-2057 TCGA-13-2059 TCGA-20-0991 
        5.92        32.84         4.21        14.24        12.23        26.20 
TCGA-23-1116 TCGA-23-1809 TCGA-24-1103 TCGA-24-1417 TCGA-24-1422 TCGA-24-1545 
        4.57         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-25-1321 TCGA-25-1628 TCGA-25-1878 TCGA-25-2401 
       33.01         2.01        33.96        20.61        85.05         2.96 
TCGA-25-2408 TCGA-29-1701 TCGA-29-1702 TCGA-29-1784 TCGA-29-2428 TCGA-30-1714 
       31.00        16.93        23.93         5.36        45.11        38.07 
TCGA-30-1853 TCGA-30-1866 TCGA-31-1959 TCGA-36-1570 TCGA-36-2544 TCGA-36-2545 
       36.26        36.62         2.20        21.53        20.98        18.31 
TCGA-36-2548 TCGA-57-1583 TCGA-59-2352 TCGA-59-2355 TCGA-61-1730 TCGA-61-2012 
       14.17        11.38         9.40         2.14         4.34        30.64 
TCGA-61-2097 TCGA-61-2612 TCGA-WR-A838 
       60.62         6.35         9.99 

$`14Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       43.92        41.00         1.81        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-04-1356 TCGA-04-1361 
       21.57        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-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 
       48.89        28.64        64.64        36.23        47.70        45.37 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 
        9.47        57.76        17.98        35.57         9.99        38.43 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1670 
       89.33        74.93        41.62        57.60        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-10-0925 TCGA-10-0926 TCGA-10-0927 
       20.94        26.93        12.46        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-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-13-0761 
       55.17         2.50        11.18        11.38        11.54        34.06 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 
       31.04        21.40        38.93        36.72        28.70        30.35 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 
        8.71         7.79         8.12         8.28         8.19        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        91.40 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 
       74.27        66.67        70.39        61.84        67.99        69.01 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       43.36        57.47        57.07        47.38        48.33        47.84 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
       44.94        44.84        37.08        27.72        34.06        29.98 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       21.17        14.89        13.81         4.64         6.41         6.08 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 
       10.88         6.61         7.36         6.05         6.84         4.70 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
        4.21         5.33        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 
       98.04        20.68        22.39        70.82        82.88        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
       73.55        38.20        49.25         4.24        54.31        37.61 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       38.40        13.97        16.57         4.41         4.77         4.18 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 
        2.56         3.91         3.09         8.61        10.78         8.75 
TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0996 
        6.28        54.77         8.42        23.05        25.94        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-23-1117 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-23-2072 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-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 
        2.76         4.70         4.50         7.63        19.66        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        19.17 
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-25-1322 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-25-1630 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-25-1870 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-25-2392 TCGA-25-2393 TCGA-25-2396 
       24.00        13.02        49.05         1.02        38.04         3.02 
TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2404 TCGA-25-2409 
       12.00        45.01        19.99        42.02        29.03        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-29-1703 TCGA-29-1705 
       33.93        31.20        68.32        36.36        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-29-1774 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-29-1785 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-29-2432 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-30-1855 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-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 
        6.12         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-36-1571 TCGA-36-1574 TCGA-36-1575 
       44.12        28.77        29.10        22.85        22.55         8.55 
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-36-2547 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 
       21.60         2.24        20.52         6.05        16.18        11.47 
TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
       13.81        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-59-A5PD TCGA-5X-AA5U 
      116.12        34.39         5.42        44.81        20.52        11.87 
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-61-1741 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-61-2002 TCGA-61-2003 TCGA-61-2008 
        2.01         5.52        14.50        17.98         4.01        30.64 
TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
       39.85         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-61-2101 
       51.72        71.74        61.64        58.39        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-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
       31.07         8.61        39.68        18.94         0.79 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.53               0.26 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              88.5              180.2 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             20.61              29.10 
[1] "0.5 - 88.5 (20.6)"  "0.3 - 180.2 (29.1)"
[1] "hr=" "1.5"
D26V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  14Q GAIN MUTATED         0    58                0
  14Q GAIN WILD-TYPE       3   500                2
D26V3, multiclass
                  clus
vv                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  OMENTUM                         0                  3
  OVARY                          58                500
  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, continuous
D26V5, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     2  56
  14Q GAIN WILD-TYPE   1 514
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2   56
  14Q GAIN WILD-TYPE    1  514
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 2                  1
  YES               56                514
[1] 2 2
[1] FALSE
                    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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q GAIN MUTATED                                  0     1
  14Q GAIN WILD-TYPE                                3    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  14Q GAIN MUTATED                           4
  14Q GAIN WILD-TYPE                        30
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  14Q GAIN MUTATED                                           0    49
  14Q GAIN WILD-TYPE                                         1   427
D26V7, multiclass
                                           clus
vv                                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    1                 18
  BLACK OR AFRICAN AMERICAN                                4                 30
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   49                427
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V8, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     0  31
  14Q GAIN WILD-TYPE  10 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0   31
  14Q GAIN WILD-TYPE   10  296
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               31                296
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    23  14
  15Q GAIN WILD-TYPE 245 278
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                37                523 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                14                278 
$`15Q GAIN MUTATED`
TCGA-04-1349 TCGA-04-1351 TCGA-04-1361 TCGA-04-1362 TCGA-09-0369 TCGA-09-1675 
       21.57        65.46        32.52        44.32        35.57        97.55 
TCGA-09-2053 TCGA-10-0938 TCGA-13-0761 TCGA-13-0792 TCGA-13-0890 TCGA-13-0919 
       39.75        20.91        34.06        36.72        67.99        14.89 
TCGA-13-1412 TCGA-13-1499 TCGA-13-2059 TCGA-13-2065 TCGA-13-2071 TCGA-23-1021 
        5.33        38.40        12.23         8.75         6.28        47.54 
TCGA-23-2072 TCGA-23-2079 TCGA-24-1413 TCGA-24-1419 TCGA-24-1551 TCGA-24-1558 
       24.95        91.66         6.31         7.86        51.91        19.53 
TCGA-25-1627 TCGA-30-1853 TCGA-31-1959 TCGA-36-1571 TCGA-36-2542 TCGA-57-1582 
       12.95        36.26         2.20        22.85        21.60        24.03 
TCGA-57-1994 TCGA-61-1730 TCGA-61-1907 TCGA-61-1915 TCGA-61-2009 TCGA-61-2097 
       25.02         4.34        31.30        67.76        39.85        60.62 
TCGA-WR-A838 
        9.99 

$`15Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       43.92        41.00         1.81        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-04-1350 TCGA-04-1353 TCGA-04-1356 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       63.98         0.53        49.28        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-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-1659 TCGA-09-1661 
       29.16         9.47        57.76        17.98         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-09-2043 
       30.51        17.98         5.85         3.02         8.55         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-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 
       20.94        26.93        12.46        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-13-0730 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-13-0762 TCGA-13-0764 
        2.50        11.18        11.38        11.54        32.25        31.04 
TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 
       21.40         8.45        38.93        28.70        30.35        19.59 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 
        8.71         7.79         8.12         8.28         8.19        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        91.40 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 
       74.27        66.67        70.39        61.84        69.01        43.36 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 
       57.47        56.15        57.07        19.36        47.38        48.33 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       47.84        44.94        44.84        37.08        27.72        34.06 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       29.98        21.17        13.81         4.64         6.41         6.08 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
       10.88         6.61         7.36         6.05         5.92         6.84 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
        4.70         4.21        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 
       98.04        20.68        22.39        70.82        82.88        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
       73.55        38.20        49.25         4.24        54.31        37.61 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
       13.97        32.84        16.57         4.21         4.41         4.77 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2060 
        4.18         2.56         3.91         3.09        14.24         8.61 
TCGA-13-2061 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
       10.78        54.77         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-23-1024 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-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 
       54.51         3.22        31.20        68.68         4.57        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-23-2077 TCGA-23-2078 TCGA-23-2081 TCGA-23-2084 
       58.13         0.53       115.89        87.48        77.00        49.84 
TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 
        2.76         4.70         4.50         7.63        19.66        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-24-1422 TCGA-24-1423 
       47.41         6.38         7.82         7.99         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-24-1464 
       19.17        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-24-1552 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-24-1563 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-24-1928 TCGA-24-1930 TCGA-24-2019 
       22.68        30.21        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-24-2035 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-25-1316 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-25-1628 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-29-1763 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-29-1778 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-30-1855 
       11.47         9.76        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-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 TCGA-36-1575 
       44.12        28.77        29.10        21.53        22.55         8.55 
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-36-2543 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-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
       16.18        11.47        13.81        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-59-A5PD TCGA-5X-AA5U TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 
       44.81        20.52        11.87        11.11         8.09        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-61-1737 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-61-1910 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-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
       30.64        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-61-2098 
        4.77        51.72        71.74        61.64        58.39        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-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
       22.22         6.35        31.07         8.61        39.68        18.94 
TCGA-VG-A8LO 
        0.79 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              2.20               0.26 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             97.55             180.20 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             25.02              28.70 
[1] "2.2 - 97.5 (25.0)"  "0.3 - 180.2 (28.7)"
[1] "hr=" "1.4"
D27V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  15Q GAIN MUTATED         0    38                0
  15Q GAIN WILD-TYPE       3   520                2
D27V3, multiclass
                  clus
vv                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  OMENTUM                         0                  3
  OVARY                          38                520
  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, continuous
D27V5, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     0  39
  15Q GAIN WILD-TYPE   3 531
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0   39
  15Q GAIN WILD-TYPE    3  531
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 0                  3
  YES               39                531
[1] 2 2
[1] FALSE
                    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-04-1516         TCGA-04-1644         TCGA-13-0807 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-13-0911         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-3P-A9WA         TCGA-42-2582 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-42-2587         TCGA-42-2588         TCGA-42-2589 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-42-2590         TCGA-42-2593         TCGA-57-1993 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-59-2363         TCGA-59-2372         TCGA-5X-AA5U 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-61-2612         TCGA-61-2613         TCGA-61-2614 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-OY-A56P         TCGA-OY-A56Q         TCGA-VG-A8LO 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q GAIN MUTATED                                  0     1
  15Q GAIN WILD-TYPE                                3    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  15Q GAIN MUTATED                           2
  15Q GAIN WILD-TYPE                        32
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  15Q GAIN MUTATED                                           0    33
  15Q GAIN WILD-TYPE                                         1   443
D27V7, multiclass
                                           clus
vv                                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    1                 18
  BLACK OR AFRICAN AMERICAN                                2                 32
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   33                443
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V8, 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    28  30
  16P GAIN WILD-TYPE 240 262
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                58                502 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                30                262 
$`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-09-0364 TCGA-09-0365 TCGA-09-0369 TCGA-09-1672 
       28.64        45.37        29.16         9.47        35.57         5.85 
TCGA-09-2051 TCGA-10-0936 TCGA-13-0724 TCGA-13-0889 TCGA-13-0897 TCGA-13-0901 
       63.09        36.92         2.73        61.84        57.47        19.36 
TCGA-13-0921 TCGA-13-1487 TCGA-13-1510 TCGA-13-2059 TCGA-20-1682 TCGA-23-1021 
        4.64        22.39         2.56        12.23        27.52        47.54 
TCGA-23-1124 TCGA-23-1809 TCGA-23-2643 TCGA-24-0966 TCGA-24-1434 TCGA-24-1464 
       58.13         0.53         4.70         7.63        18.67        12.46 
TCGA-24-1565 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1845 
       10.26        88.37        48.33        38.24         8.32         3.81 
TCGA-25-1321 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-29-1691 TCGA-29-1774 
       33.96        24.99        24.00        85.05        48.33        17.33 
TCGA-29-1784 TCGA-29-2432 TCGA-36-1581 TCGA-36-2547 TCGA-36-2552 TCGA-59-2372 
        5.36        21.47        24.69        20.52        11.47        44.81 
TCGA-61-1733 TCGA-61-1738 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-2000 
       31.79        35.80        67.76        43.43        15.75        14.50 
TCGA-61-2009 TCGA-61-2101 TCGA-61-2111 TCGA-OY-A56Q 
       39.85        55.50       125.75        18.94 

$`16P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       43.92        41.00         1.81        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-04-1353 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-04-1514 TCGA-04-1516 TCGA-04-1517 
       33.67        76.57       103.40        56.55        41.59        19.99 
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-09-0366 TCGA-09-0367 TCGA-09-1659 TCGA-09-1661 
       31.86        47.70        57.76        17.98         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-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 
       30.51        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-09-2053 
        6.12        35.15         4.54       112.41        71.11        39.75 
TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 
       20.94        26.93        12.46        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-10-0937 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-13-0751 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-13-0762 TCGA-13-0764 
       11.18        11.38        11.54        34.06        32.25        31.04 
TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 
       21.40         8.45        38.93        36.72        28.70        30.35 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 
       19.59         8.71         7.79         8.12         8.28         8.19 
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-13-0890 TCGA-13-0891 
       91.40        74.27        66.67        70.39        67.99        69.01 
TCGA-13-0893 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       43.36        56.15        57.07        47.38        48.33        47.84 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
       44.94        44.84        37.08        27.72        34.06        29.98 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 
       21.17        14.89        13.81         6.41         6.08        10.88 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
        6.61         7.36         6.05         5.92         6.84         4.70 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
        4.21         5.33        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 
       98.04        20.68        70.82        82.88        52.44        73.55 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 
       38.20        49.25         4.24        54.31        37.61        38.40 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
       13.97        32.84        16.57         4.21         4.41         4.77 
TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 
        4.18         3.91         3.09        14.24         8.61        10.78 
TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
        8.75         6.28        54.77         8.42        23.05        25.94 
TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 
       26.20        72.20        25.38        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-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 
       54.51         3.22        31.20        68.68         4.57        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-23-2072 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-23-2645 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        2.76         4.50        19.66        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-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 TCGA-24-1467 
       19.17        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-24-1563 TCGA-24-1564 TCGA-24-1567 TCGA-24-1603 TCGA-24-1843 
       45.50        47.70        25.87        17.23        90.15         3.48 
TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 
        3.72         4.37        11.28         5.79         5.52         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-24-2020 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-24-2035 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-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 
       42.05         2.01        34.98        65.00        37.97         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-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 
       52.04        14.96        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-29-1693 
       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-29-1701 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-29-1763 TCGA-29-1764 TCGA-29-1766 
       34.62        17.36        86.60        66.81        62.93        39.42 
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-29-1785 TCGA-29-2414 
       12.30        14.93         8.38         7.23        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-30-1855 
        9.76        35.77        38.07        51.91        36.26         2.47 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 
       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-36-1577 TCGA-36-1578 TCGA-36-1580 
       22.55         8.55        30.08        25.74        27.85        24.23 
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-36-2548 
       23.80        21.60         2.24        20.98        18.31        14.17 
TCGA-36-2549 TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
        6.05        16.18        13.81        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-A5PD TCGA-5X-AA5U TCGA-61-1721 TCGA-61-1722 
        2.14         5.42        20.52        11.87        11.11         8.09 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1734 
       20.94        31.43        18.54        27.88         4.34        28.47 
TCGA-61-1736 TCGA-61-1737 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 
       48.79        44.84         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-61-1919 
       31.30        37.05        42.51        48.92        56.61        38.17 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 
        2.01         5.52        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 
        8.61        39.68         0.79         9.99 

  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 
             27.70              28.85 
[1] "0.5 - 125.8 (27.7)" "0.3 - 180.2 (28.9)"
[1] "hr=" "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, continuous
D28V5, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     0  59
  16P GAIN WILD-TYPE   3 511
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      0   59
  16P GAIN WILD-TYPE    3  511
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 0                  3
  YES               59                511
[1] 2 2
[1] FALSE
                    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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P GAIN MUTATED                                  0     1
  16P GAIN WILD-TYPE                                3    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  16P GAIN MUTATED                           4
  16P GAIN WILD-TYPE                        30
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16P GAIN MUTATED                                           0    50
  16P GAIN WILD-TYPE                                         1   426
D28V7, multiclass
                                           clus
vv                                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    1                 18
  BLACK OR AFRICAN AMERICAN                                4                 30
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   50                426
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V8, 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    15  15
  16Q GAIN WILD-TYPE 253 277
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                30                530 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                15                277 
$`16Q GAIN MUTATED`
TCGA-04-1519 TCGA-04-1542 TCGA-04-1646 TCGA-04-1648 TCGA-09-0364 TCGA-09-0369 
        0.79        84.20        27.88        28.64        29.16        35.57 
TCGA-09-1672 TCGA-13-0897 TCGA-13-0921 TCGA-13-1510 TCGA-13-2059 TCGA-23-1021 
        5.85        57.47         4.64         2.56        12.23        47.54 
TCGA-24-1464 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1845 TCGA-25-1321 
       12.46        88.37        48.33        38.24         3.81        33.96 
TCGA-29-1774 TCGA-36-1581 TCGA-36-2538 TCGA-36-2547 TCGA-59-2351 TCGA-59-2372 
       17.33        24.69        25.08        20.52       116.12        44.81 
TCGA-61-1738 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-2000 TCGA-OY-A56Q 
       35.80        67.76        43.43        15.75        14.50        18.94 

$`16Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       43.92        41.00         1.81        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-04-1356 TCGA-04-1361 
       21.57        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-04-1514 
       44.32        33.67        76.57       103.40        82.39        56.55 
TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1638 
       41.59        19.99        38.37       119.08        29.10        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-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
        9.47        57.76        17.98         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-10-0925 TCGA-10-0926 TCGA-10-0927 
       20.94        26.93        12.46        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-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-13-0761 
       55.17         2.50        11.18        11.38        11.54        34.06 
TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 
       32.25        31.04        21.40         8.45        38.93        36.72 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 
       28.70        30.35        19.59         8.71         7.79         8.12 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
        8.28         8.19        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        91.40        74.27        66.67        70.39 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 TCGA-13-0900 
       61.84        67.99        69.01        43.36        56.15        57.07 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 
       19.36        47.38        48.33        47.84        44.94        44.84 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
       37.08        27.72        34.06        29.98        21.17        14.89 
TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
       13.81         6.41         6.08        10.88         6.61         7.36 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
        6.05         5.92         6.84         4.70         4.21         5.33 
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        98.04        20.68 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       22.39        70.82        82.88        52.44        73.55        38.20 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 
       49.25         4.24        54.31        37.61        38.40        13.97 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       32.84        16.57         4.21         4.41         4.77         4.18 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 
        3.91         3.09        14.24         8.61        10.78         8.75 
TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
        6.28        54.77         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-23-1024 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-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 
       54.51         3.22        31.20        68.68         4.57        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-23-2645 TCGA-24-0966 
       77.00        49.84         2.76         4.70         4.50         7.63 
TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
       19.66        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        19.17        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 
       43.53         8.55        72.92        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-24-1842 
       47.70        25.87        10.26        17.23        90.15         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-24-1924 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-25-1322 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-25-2392 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-29-1775 TCGA-29-1776 TCGA-29-1777 
       22.98        24.36        22.55        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-30-1714 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-30-1861 
        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-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-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       24.23        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-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 
        6.05        16.18        11.47        13.81        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-59-2352 TCGA-59-2354 
       25.02       180.20        80.12        22.32         9.40        34.39 
TCGA-59-2355 TCGA-59-2363 TCGA-59-A5PD TCGA-5X-AA5U TCGA-61-1721 TCGA-61-1722 
        2.14         5.42        20.52        11.87        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-61-2002 TCGA-61-2003 TCGA-61-2008 
       38.17         2.01         5.52        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-VG-A8LO TCGA-WR-A838 
        0.79         9.99 

  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 
            28.260             28.735 
[1] "0.8 - 116.1 (28.3)" "0.3 - 180.2 (28.7)"
[1] "hr=" "1.1"
D29V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  16Q GAIN MUTATED         0    31                0
  16Q GAIN WILD-TYPE       3   527                2
D29V3, multiclass
                  clus
vv                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  OMENTUM                         0                  3
  OVARY                          31                527
  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, continuous
D29V5, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     0  31
  16Q GAIN WILD-TYPE   3 539
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0   31
  16Q GAIN WILD-TYPE    3  539
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 0                  3
  YES               31                539
[1] 2 2
[1] FALSE
                    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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q GAIN MUTATED                                  0     0
  16Q GAIN WILD-TYPE                                3    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  16Q GAIN MUTATED                           2
  16Q GAIN WILD-TYPE                        32
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16Q GAIN MUTATED                                           0    25
  16Q GAIN WILD-TYPE                                         1   451
D29V7, multiclass
                                           clus
vv                                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    0                 19
  BLACK OR AFRICAN AMERICAN                                2                 32
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   25                451
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V8, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     0  16
  16Q GAIN WILD-TYPE  10 311
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0   16
  16Q GAIN WILD-TYPE   10  311
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               16                311
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    17   4
  17P GAIN WILD-TYPE 251 288
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                21                539 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 4                288 
$`17P GAIN MUTATED`
TCGA-04-1341 TCGA-09-0369 TCGA-09-2051 TCGA-13-0800 TCGA-13-0897 TCGA-13-0920 
        1.08        35.57        63.09         8.12        57.47        13.81 
TCGA-13-1412 TCGA-13-2057 TCGA-13-2060 TCGA-20-1683 TCGA-23-1114 TCGA-24-1845 
        5.33        14.24         8.61        25.38        68.68         3.81 
TCGA-29-1763 TCGA-29-2429 TCGA-36-1569 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 
       66.81        13.84        29.10        27.85        24.23        24.69 
TCGA-36-2552 TCGA-61-1900 TCGA-61-1904 
       11.47         5.79         9.07 

$`17P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       43.92        41.00         1.81        49.15         2.01        46.62 
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-04-1364 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-09-0364 TCGA-09-0365 TCGA-09-0366 
       31.86        47.70        45.37        29.16         9.47        57.76 
TCGA-09-0367 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       17.98         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-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       12.46        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-13-0762 TCGA-13-0764 
       11.18        11.38        11.54        34.06        32.25        31.04 
TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 
       21.40         8.45        38.93        36.72        28.70        30.35 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 
       19.59         8.71         7.79         8.28         8.19        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        91.40 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 
       74.27        66.67        70.39        61.84        67.99        69.01 
TCGA-13-0893 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 
       43.36        56.15        57.07        19.36        47.38        48.33 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       47.84        44.94        44.84        37.08        27.72        34.06 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       29.98        21.17        14.89         4.64         6.41         6.08 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
       10.88         6.61         7.36         6.05         5.92         6.84 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
        4.70         4.21        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 
       98.04        20.68        22.39        70.82        82.88        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
       73.55        38.20        49.25         4.24        54.31        37.61 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       38.40        13.97        32.84        16.57         4.21         4.41 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 
        4.77         4.18         2.56         3.91         3.09        12.23 
TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
       10.78         8.75         6.28        54.77         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         4.57 
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-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        7.63        19.66        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-24-1430 TCGA-24-1431 
        5.95         5.36         4.83        17.39        28.37        19.17 
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-24-1545 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-24-1850 TCGA-24-1920 
        3.72         4.37        11.28         5.79         5.52         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-24-2020 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-24-2035 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-25-1316 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-25-2392 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-29-1764 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-29-1774 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-29-2431 TCGA-29-2432 TCGA-29-2434 
       65.00        62.47        45.11        42.25        21.47        11.47 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 
        9.76        35.77        38.07        51.91        36.26         2.47 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 
       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-36-1570 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-36-2529 TCGA-36-2530 TCGA-36-2532 
        8.55        30.08        25.74        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-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
       13.81        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-59-A5PD TCGA-5X-AA5U TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 
       44.81        20.52        11.87        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-61-1737 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-61-1901 TCGA-61-1903 TCGA-61-1906 TCGA-61-1907 
        1.45         8.42        11.41        13.02        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-61-2016 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-61-2097 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 
        8.61        39.68        18.94         0.79         9.99 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              1.08               0.26 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             68.68             180.20 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             14.24              29.03 
[1] "1.1 - 68.7 (14.2)"  "0.3 - 180.2 (29.0)"
[1] "hr=" "2"  
D30V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  17P GAIN MUTATED         0    21                0
  17P GAIN WILD-TYPE       3   537                2
D30V3, multiclass
                  clus
vv                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  OMENTUM                         0                  3
  OVARY                          21                537
  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, continuous
D30V5, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0  22
  17P GAIN WILD-TYPE   3 548
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   22
  17P GAIN WILD-TYPE    3  548
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 0                  3
  YES               22                548
[1] 2 2
[1] FALSE
                    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-04-1516         TCGA-04-1644         TCGA-13-0807 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-13-0911         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-3P-A9WA         TCGA-42-2582         TCGA-42-2587 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-42-2588         TCGA-42-2589         TCGA-42-2590 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-42-2593         TCGA-57-1993         TCGA-59-2363 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-59-2372         TCGA-5X-AA5U         TCGA-61-2612 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-61-2613         TCGA-61-2614         TCGA-OY-A56P 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-OY-A56Q         TCGA-VG-A8LO 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P GAIN MUTATED                                  0     1
  17P GAIN WILD-TYPE                                3    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  17P GAIN MUTATED                           2
  17P GAIN WILD-TYPE                        32
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17P GAIN MUTATED                                           0    16
  17P GAIN WILD-TYPE                                         1   460
D30V7, multiclass
                                           clus
vv                                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    1                 18
  BLACK OR AFRICAN AMERICAN                                2                 32
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   16                460
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0  12
  17P GAIN WILD-TYPE  10 315
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   12
  17P GAIN WILD-TYPE   10  315
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               12                315
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    25  22
  17Q GAIN WILD-TYPE 243 270
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                47                513 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                22                270 
$`17Q GAIN MUTATED`
TCGA-04-1337 TCGA-04-1341 TCGA-04-1362 TCGA-04-1530 TCGA-09-0369 TCGA-09-2051 
        2.01         1.08        44.32       119.08        35.57        63.09 
TCGA-10-0936 TCGA-13-0730 TCGA-13-0760 TCGA-13-0768 TCGA-13-0800 TCGA-13-0897 
       36.92        17.82        11.54         8.45         8.12        57.47 
TCGA-13-0920 TCGA-13-1408 TCGA-13-1412 TCGA-13-1477 TCGA-13-1483 TCGA-13-1489 
       13.81         5.92         5.33        54.64        29.42        82.88 
TCGA-13-2057 TCGA-13-2060 TCGA-23-1109 TCGA-23-1114 TCGA-24-1464 TCGA-24-1844 
       14.24         8.61        51.35        68.68        12.46         3.72 
TCGA-24-1845 TCGA-24-1850 TCGA-24-2020 TCGA-24-2298 TCGA-25-1319 TCGA-25-2392 
        3.81         5.52       152.02        53.26        65.00         1.02 
TCGA-29-1699 TCGA-30-1862 TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 TCGA-36-1578 
       36.36         6.12        29.10        21.53        22.55        27.85 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2552 TCGA-42-2588 TCGA-42-2593 TCGA-61-1737 
       24.23        24.69        11.47        28.93         1.48        44.84 
TCGA-61-1900 TCGA-61-1913 TCGA-61-1914 TCGA-61-2098 TCGA-61-2612 
        5.79        48.92        56.61        65.52         6.35 

$`17Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1342 
       43.92        41.00         1.81        49.15        46.62        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 
       11.87        65.52        63.09        48.76        21.57        63.98 
TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 
       65.46         0.53        49.28        32.52        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-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
       38.37        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-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-1659 TCGA-09-1661 
       29.16         9.47        57.76        17.98         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-09-2050 
        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-10-0925 TCGA-10-0926 
       39.75        20.94        26.93        12.46        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-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
       35.44        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-13-0751 
       39.58         2.73        12.39        31.20        15.19        55.17 
TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 
        2.50        11.18        11.38        34.06        32.25        31.04 
TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 
       21.40        38.93        36.72        28.70        30.35        19.59 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 
        8.71         7.79         8.28         8.19        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        91.40        74.27 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
       66.67        70.39        61.84        67.99        69.01        43.36 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       56.15        57.07        19.36        47.38        48.33        47.84 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
       44.94        44.84        37.08        27.72        34.06        29.98 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 
       21.17        14.89         4.64         6.41         6.08        10.88 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
        6.61         7.36         6.05         6.84         4.70         4.21 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 
       87.06        61.71        98.04        20.68        22.39        70.82 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 
       52.44        73.55        38.20        49.25         4.24        54.31 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 
       37.61        38.40        13.97        32.84        16.57         4.21 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
        4.41         4.77         4.18         2.56         3.91         3.09 
TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU 
       12.23        10.78         8.75         6.28        54.77         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-23-1024 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-23-1110 TCGA-23-1111 TCGA-23-1113 
       29.13        18.90         2.76        54.51         3.22        31.20 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 
        4.57        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-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        4.50         7.63        19.66        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 
       19.17        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-24-1846 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-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 
       16.44        11.05        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-24-2260 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-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-25-1320 
       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-25-1632 
       17.03        12.95        20.61        38.20         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-25-2042 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-25-2400 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-29-1701 TCGA-29-1702 
       40.41        33.93        31.20        68.32        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-29-1763 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-29-1778 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-30-1855 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-30-1866 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-36-1571 TCGA-36-1575 TCGA-36-1576 
       44.12         2.20        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-36-2540 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-3P-A9WA TCGA-42-2582 
       20.52        14.17         6.05        16.18        13.81        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-59-A5PD TCGA-5X-AA5U TCGA-61-1721 
        2.14         5.42        44.81        20.52        11.87        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-61-1738 TCGA-61-1740 TCGA-61-1741 
       31.79        28.47        48.79        35.80         2.43        33.67 
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-61-1911 TCGA-61-1915 TCGA-61-1917 
       34.13        31.30        37.05        42.51        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-61-2016 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-61-2097 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       58.39        60.62        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 
       18.94         0.79         9.99 

  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 
             24.23              29.00 
[1] "1.0 - 152.0 (24.2)" "0.3 - 180.2 (29.0)"
[1] "hr=" "1.1"
D31V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  17Q GAIN MUTATED         0    47                0
  17Q GAIN WILD-TYPE       3   511                2
D31V3, multiclass
                  clus
vv                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  OMENTUM                         0                  3
  OVARY                          47                511
  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, continuous
D31V5, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     0  47
  17Q GAIN WILD-TYPE   3 523
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0   47
  17Q GAIN WILD-TYPE    3  523
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 0                  3
  YES               47                523
[1] 2 2
[1] FALSE
                    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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q GAIN MUTATED                                  1     2
  17Q GAIN WILD-TYPE                                2    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  17Q GAIN MUTATED                           2
  17Q GAIN WILD-TYPE                        32
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17Q GAIN MUTATED                                           0    39
  17Q GAIN WILD-TYPE                                         1   437
D31V7, multiclass
                                           clus
vv                                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  2
  ASIAN                                                    2                 17
  BLACK OR AFRICAN AMERICAN                                2                 32
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   39                437
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V8, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     0  28
  17Q GAIN WILD-TYPE  10 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0   28
  17Q GAIN WILD-TYPE   10  299
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               28                299
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    65  52
  18P GAIN WILD-TYPE 203 240
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               117                443 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                52                240 
$`18P GAIN MUTATED`
TCGA-04-1332 TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 TCGA-04-1361 TCGA-04-1371 
       41.00        65.52        63.09        21.57        32.52        82.39 
TCGA-04-1516 TCGA-04-1525 TCGA-04-1536 TCGA-04-1542 TCGA-04-1644 TCGA-04-1646 
       41.59        38.37        29.10        84.20        48.89        27.88 
TCGA-04-1652 TCGA-09-0369 TCGA-09-1665 TCGA-09-1668 TCGA-09-2055 TCGA-10-0930 
       31.86        35.57        41.62        55.36        26.93        34.19 
TCGA-10-0937 TCGA-13-0762 TCGA-13-0768 TCGA-13-0795 TCGA-13-0802 TCGA-13-0885 
       19.99        32.25         8.45        19.59         8.19        91.40 
TCGA-13-0888 TCGA-13-0890 TCGA-13-0899 TCGA-13-0901 TCGA-13-0904 TCGA-13-0919 
       70.39        67.99        56.15        19.36        48.33        14.89 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1481 TCGA-13-1489 TCGA-13-1497 
        6.05         5.92         4.70        87.06        82.88        54.31 
TCGA-13-1499 TCGA-13-1504 TCGA-13-1507 TCGA-13-1510 TCGA-13-2057 TCGA-13-2059 
       38.40        16.57         4.77         2.56        14.24        12.23 
TCGA-13-2060 TCGA-20-0987 TCGA-20-1686 TCGA-23-1022 TCGA-23-1024 TCGA-23-1032 
        8.61        23.05         2.93        49.68        15.39         2.76 
TCGA-23-1110 TCGA-23-1114 TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 
       54.51        68.68         6.38        33.47        58.13         0.53 
TCGA-23-2077 TCGA-24-0968 TCGA-24-1428 TCGA-24-1430 TCGA-24-1434 TCGA-24-1466 
      115.89        19.66        17.39        28.37        18.67        45.14 
TCGA-24-1558 TCGA-24-1567 TCGA-24-1616 TCGA-24-1844 TCGA-24-1845 TCGA-24-1850 
       19.53        17.23        38.24         3.72         3.81         5.52 
TCGA-24-1924 TCGA-24-2019 TCGA-24-2020 TCGA-24-2026 TCGA-24-2030 TCGA-24-2261 
       30.21         4.87       152.02        34.82        55.92         0.79 
TCGA-24-2289 TCGA-25-1314 TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 TCGA-25-1623 
       67.36        33.01        34.98        65.00        33.96        18.58 
TCGA-25-1628 TCGA-25-1635 TCGA-25-2400 TCGA-29-1695 TCGA-29-1698 TCGA-29-1711 
       20.61        52.04        42.02        40.41        68.32        34.62 
TCGA-29-1778 TCGA-29-1784 TCGA-29-2425 TCGA-29-2432 TCGA-29-2434 TCGA-30-1853 
       14.93         5.36        65.00        21.47        11.47        36.26 
TCGA-30-1866 TCGA-31-1959 TCGA-36-1581 TCGA-36-2537 TCGA-36-2547 TCGA-42-2589 
       36.62         2.20        24.69        25.91        20.52        42.02 
TCGA-57-1583 TCGA-57-1586 TCGA-57-1992 TCGA-57-1994 TCGA-59-2352 TCGA-59-2355 
       11.38        22.32        29.00        25.02         9.40         2.14 
TCGA-5X-AA5U TCGA-61-1722 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1740 
       11.87         8.09        27.88         4.34        31.79         2.43 
TCGA-61-1899 TCGA-61-1907 TCGA-61-1917 TCGA-61-2008 TCGA-61-2018 TCGA-61-2096 
        8.42        31.30        43.43        30.64        45.40        58.39 
TCGA-61-2111 TCGA-61-2614 TCGA-WR-A838 
      125.75         8.61         9.99 

$`18P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 
       43.92         1.81        49.15         2.01        46.62         1.08 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 
       18.51        11.87        48.76        63.98        65.46         0.53 
TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 
       49.28        44.32        33.67        76.57       103.40        56.55 
TCGA-04-1517 TCGA-04-1519 TCGA-04-1530 TCGA-04-1638 TCGA-04-1648 TCGA-04-1649 
       19.99         0.79       119.08        55.43        28.64        64.64 
TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 
       36.23        47.70        45.37        29.16         9.47        57.76 
TCGA-09-0367 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 
       17.98         9.99        38.43        89.33        74.93        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-09-2048 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-09-2056 TCGA-10-0925 
       71.11        63.09        39.75        20.94        12.46        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       25.91        81.86        18.51        32.88        14.66         6.71 
TCGA-10-0935 TCGA-10-0936 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
       35.44        36.92        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-13-0761 
       55.17         2.50        11.18        11.38        11.54        34.06 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 
       31.04        21.40        38.93        36.72        28.70        30.35 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 
        8.71         7.79         8.12         8.28        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        74.27        66.67 
TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0903 
       61.84        69.01        43.36        57.47        57.07        47.38 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       47.84        44.94        44.84        37.08        27.72        34.06 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       29.98        21.17        13.81         4.64         6.41         6.08 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1409 TCGA-13-1411 TCGA-13-1412 
       10.88         6.61         7.36         6.84         4.21         5.33 
TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 
       54.64        61.71        29.42        98.04        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        73.55        38.20        49.25         4.24 
TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 
       37.61        13.97        32.84         4.21         4.41         4.18 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT 
        3.91         3.09        10.78         8.75         6.28        54.77 
TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 
        8.42        25.94        26.20        72.20        27.52        25.38 
TCGA-20-1684 TCGA-20-1685 TCGA-20-1687 TCGA-23-1021 TCGA-23-1023 TCGA-23-1026 
       19.10        16.70         2.66        47.54        40.54        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-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 
        3.22        31.20         4.57        33.30        86.01       129.96 
TCGA-23-1120 TCGA-23-1122 TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
        4.27        39.09        24.95        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-24-1431 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1467 
       19.17        43.53         8.55        72.92        12.46       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-24-1560 TCGA-24-1562 
       58.09        88.50        70.62        39.88        44.09        45.50 
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-24-1842 TCGA-24-1843 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1920 
        8.32         3.48         4.37        11.28         5.79         9.80 
TCGA-24-1923 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2023 TCGA-24-2024 
       22.68        16.44        11.05        81.11        44.84        58.16 
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-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 
       44.61         0.82        36.23        16.64        33.11        55.86 
TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
       53.26         1.02        26.96        52.04        42.05         2.01 
TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1625 TCGA-25-1626 
       37.97         2.99        12.99        15.02        27.62        17.03 
TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
       12.95        38.20         0.30        59.15        62.17        35.87 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 
       14.96        24.99        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-25-2404 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-29-1699 
       48.33       101.79        39.02        33.93        31.20        36.36 
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-29-1761 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-29-1781 TCGA-29-1783 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 
       12.30         8.38         7.23        36.30        86.17        62.47 
TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 
       45.11        13.84        42.25         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-30-1867 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-36-1570 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-36-1577 TCGA-36-1578 TCGA-36-1580 
       22.55         8.55        30.08        25.74        27.85        24.23 
TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2538 TCGA-36-2540 
       35.05        33.01        29.49        29.82        25.08        23.80 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2548 TCGA-36-2549 
       21.60         2.24        20.98        18.31        14.17         6.05 
TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
       16.18        11.47        13.81        47.57        23.74        28.93 
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-57-1993 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2354 
       25.08       180.20        80.12        22.32       116.12        34.39 
TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 
        5.42        44.81        20.52        11.11        20.94        31.43 
TCGA-61-1727 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1741 
       18.54        28.47        48.79        44.84        35.80        33.67 
TCGA-61-1743 TCGA-61-1895 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 
       43.69         1.45         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-61-1918 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-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2087 
        4.01        39.85        30.64         1.18        45.96         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-61-2110 TCGA-61-2113 
       55.50         6.48        76.87        20.68        44.52        22.22 
TCGA-61-2612 TCGA-61-2613 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
        6.35        31.07        39.68        18.94         0.79 

  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 
             29.00              28.64 
[1] "0.5 - 152.0 (29.0)" "0.3 - 180.2 (28.6)"
[1] "hr=" "1.2"
D32V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  18P GAIN MUTATED         0   118                0
  18P GAIN WILD-TYPE       3   440                2
D32V3, multiclass
                  clus
vv                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  OMENTUM                         0                  3
  OVARY                         118                440
  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, continuous
D32V5, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     0 120
  18P GAIN WILD-TYPE   3 450
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0  120
  18P GAIN WILD-TYPE    3  450
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 0                  3
  YES              120                450
[1] 2 2
[1] FALSE
                    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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P GAIN MUTATED                                  0     3
  18P GAIN WILD-TYPE                                3    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  18P GAIN MUTATED                           7
  18P GAIN WILD-TYPE                        27
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18P GAIN MUTATED                                           0   103
  18P GAIN WILD-TYPE                                         1   373
D32V7, multiclass
                                           clus
vv                                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    3                 16
  BLACK OR AFRICAN AMERICAN                                7                 27
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                  103                373
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V8, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     2  66
  18P GAIN WILD-TYPE   8 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2   66
  18P GAIN WILD-TYPE    8  261
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO               66                261
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    38  32
  18Q GAIN WILD-TYPE 230 260
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                70                490 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                32                260 
$`18Q GAIN MUTATED`
TCGA-04-1346 TCGA-04-1349 TCGA-04-1516 TCGA-04-1536 TCGA-04-1542 TCGA-04-1644 
       65.52        21.57        41.59        29.10        84.20        48.89 
TCGA-04-1646 TCGA-04-1652 TCGA-09-0369 TCGA-09-1661 TCGA-09-1665 TCGA-09-1668 
       27.88        31.86        35.57        38.43        41.62        55.36 
TCGA-09-2055 TCGA-13-0717 TCGA-13-0762 TCGA-13-0795 TCGA-13-0802 TCGA-13-0890 
       26.93        24.59        32.25        19.59         8.19        67.99 
TCGA-13-0901 TCGA-13-0904 TCGA-13-0919 TCGA-13-1410 TCGA-13-1489 TCGA-13-1497 
       19.36        48.33        14.89         4.70        82.88        54.31 
TCGA-13-1504 TCGA-13-1507 TCGA-13-1510 TCGA-13-2057 TCGA-13-2060 TCGA-23-1024 
       16.57         4.77         2.56        14.24         8.61        15.39 
TCGA-23-1114 TCGA-23-1123 TCGA-23-1809 TCGA-23-2077 TCGA-24-0968 TCGA-24-1430 
       68.68        33.47         0.53       115.89        19.66        28.37 
TCGA-24-1434 TCGA-24-1466 TCGA-24-1604 TCGA-24-1845 TCGA-24-1924 TCGA-24-2019 
       18.67        45.14        88.37         3.81        30.21         4.87 
TCGA-24-2026 TCGA-24-2030 TCGA-25-1314 TCGA-25-1318 TCGA-25-1319 TCGA-25-1635 
       34.82        55.92        33.01        34.98        65.00        52.04 
TCGA-29-1695 TCGA-29-1698 TCGA-29-1705 TCGA-29-1778 TCGA-29-1784 TCGA-29-2432 
       40.41        68.32        18.25        14.93         5.36        21.47 
TCGA-30-1853 TCGA-36-1581 TCGA-36-2537 TCGA-61-1722 TCGA-61-1728 TCGA-61-1733 
       36.26        24.69        25.91         8.09        27.88        31.79 
TCGA-61-1740 TCGA-61-1899 TCGA-61-1907 TCGA-61-1917 TCGA-61-1998 TCGA-61-2008 
        2.43         8.42        31.30        43.43         5.52        30.64 
TCGA-61-2096 TCGA-61-2101 TCGA-61-2111 TCGA-61-2614 
       58.39        55.50       125.75         8.61 

$`18Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       43.92        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1347 TCGA-04-1348 TCGA-04-1350 
        1.08        18.51        11.87        63.09        48.76        63.98 
TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 
       65.46         0.53        49.28        32.52        44.32        33.67 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 TCGA-04-1519 
       76.57       103.40        82.39        56.55        19.99         0.79 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1638 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 
       38.37       119.08        55.43        28.64        64.64        36.23 
TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 
       47.70        45.37        29.16         9.47        57.76        17.98 
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-10-0925 TCGA-10-0926 TCGA-10-0927 
       39.75        20.94        12.46        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-10-0938 TCGA-13-0714 TCGA-13-0720 TCGA-13-0723 
       36.92        19.99        20.91         6.21        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        34.06        31.04 
TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 
       21.40         8.45        38.93        36.72        28.70        30.35 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 
        8.71         7.79         8.12         8.28        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        91.40        74.27 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 
       66.67        70.39        61.84        69.01        43.36        57.47 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 
       56.15        57.07        47.38        47.84        44.94        44.84 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 
       37.08        27.72        34.06        29.98        21.17        13.81 
TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
        4.64         6.41         6.08        10.88         6.61         7.36 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 
        6.05         5.92         6.84         4.21         5.33        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        98.04        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        73.55        38.20        49.25         4.24 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 
       37.61        38.40        13.97        32.84         4.21         4.41 
TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 
        4.18         3.91         3.09        12.23        10.78         8.75 
TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
        6.28        54.77         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         4.57        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        19.17        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-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 
      152.02        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-24-2261 
       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-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1320 
        1.02        26.96        52.04        42.05         2.01        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-25-1632 
       17.03        12.95        20.61        38.20         0.30        59.15 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 
       62.17        35.87        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-29-1696 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-29-1707 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-29-1774 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-29-2425 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-30-1855 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-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-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2538 
       24.23        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-36-2547 
       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-3P-A9WA TCGA-42-2582 
       14.17         6.05        16.18        11.47        13.81        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-59-A5PD 
        9.40        34.39         2.14         5.42        44.81        20.52 
TCGA-5X-AA5U TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1730 
       11.87        11.11        20.94        31.43        18.54         4.34 
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-61-1900 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 
       39.68        18.94         0.79         9.99 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.53               0.26 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            125.75             180.20 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            30.425             28.325 
[1] "0.5 - 125.8 (30.4)" "0.3 - 180.2 (28.3)"
[1] "hr=" "1.2"
D33V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  18Q GAIN MUTATED         0    71                0
  18Q GAIN WILD-TYPE       3   487                2
D33V3, multiclass
                  clus
vv                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  OMENTUM                         0                  3
  OVARY                          71                487
  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, continuous
D33V5, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     0  72
  18Q GAIN WILD-TYPE   3 498
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0   72
  18Q GAIN WILD-TYPE    3  498
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 0                  3
  YES               72                498
[1] 2 2
[1] FALSE
                    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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q GAIN MUTATED                                  0     3
  18Q GAIN WILD-TYPE                                3    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  18Q GAIN MUTATED                           2
  18Q GAIN WILD-TYPE                        32
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18Q GAIN MUTATED                                           0    64
  18Q GAIN WILD-TYPE                                         1   412
D33V7, multiclass
                                           clus
vv                                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    3                 16
  BLACK OR AFRICAN AMERICAN                                2                 32
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   64                412
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V8, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     0  40
  18Q GAIN WILD-TYPE  10 287
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0   40
  18Q GAIN WILD-TYPE   10  287
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               40                287
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    85  80
  19P GAIN WILD-TYPE 183 212
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               165                395 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                80                212 
$`19P GAIN MUTATED`
TCGA-04-1335 TCGA-04-1338 TCGA-04-1346 TCGA-04-1514 TCGA-04-1519 TCGA-04-1525 
        1.81        46.62        65.52        56.55         0.79        38.37 
TCGA-04-1542 TCGA-04-1648 TCGA-04-1649 TCGA-04-1652 TCGA-09-0367 TCGA-09-0369 
       84.20        28.64        64.64        31.86        17.98        35.57 
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-10-0926 TCGA-10-0933 TCGA-10-0938 TCGA-13-0727 
        6.18        20.94        25.91        14.66        20.91        15.19 
TCGA-13-0751 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 TCGA-13-0791 
       55.17        11.38        11.54        34.06        31.04        38.93 
TCGA-13-0802 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0887 TCGA-13-0888 
        8.19        13.61        68.94       107.18        66.67        70.39 
TCGA-13-0905 TCGA-13-0920 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1481 
       47.84        13.81         6.05         5.92         4.70        87.06 
TCGA-13-1482 TCGA-13-1484 TCGA-13-1491 TCGA-13-1495 TCGA-13-1501 TCGA-13-1506 
       61.71        98.04        52.44        49.25        32.84         4.41 
TCGA-13-1510 TCGA-13-2057 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 
        2.56        14.24        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         4.57        33.30        86.01         6.38 
TCGA-23-1809 TCGA-23-2645 TCGA-24-1105 TCGA-24-1417 TCGA-24-1426 TCGA-24-1428 
        0.53         4.50        47.41         7.82         5.36        17.39 
TCGA-24-1436 TCGA-24-1469 TCGA-24-1471 TCGA-24-1545 TCGA-24-1548 TCGA-24-1551 
        8.55         9.11         1.18        57.40        16.21        51.91 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1614 TCGA-24-1616 TCGA-24-1843 TCGA-24-1844 
       39.88        19.53        48.33        38.24         3.48         3.72 
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-25-1319 TCGA-25-1320 
       33.11         1.02        33.01        34.98        65.00        37.97 
TCGA-25-1321 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-2398 TCGA-29-1695 
       33.96        12.99        15.02        18.58        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-29-2432 TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1855 
       36.30        21.47        11.47        35.77        38.07         2.47 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1867 TCGA-30-1892 
        0.26        48.10        44.91         6.12         1.22        48.79 
TCGA-31-1944 TCGA-31-1950 TCGA-36-1578 TCGA-36-2529 TCGA-36-2534 TCGA-36-2543 
       45.57        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-5X-AA5U 
       11.38        22.32       180.20       116.12         2.14        11.87 
TCGA-61-1725 TCGA-61-1728 TCGA-61-1730 TCGA-61-1741 TCGA-61-1899 TCGA-61-1904 
       31.43        27.88         4.34        33.67         8.42         9.07 
TCGA-61-1906 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1918 TCGA-61-2000 
       34.13        42.51        48.92        56.61        15.75        14.50 
TCGA-61-2009 TCGA-61-2012 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2104 
       39.85        30.64        58.39        60.62        65.52        76.87 
TCGA-61-2111 TCGA-61-2113 TCGA-WR-A838 
      125.75        22.22         9.99 

$`19P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1341 TCGA-04-1342 
       43.92        41.00        49.15         2.01         1.08        18.51 
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-04-1356 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-04-1517 TCGA-04-1530 TCGA-04-1536 
      103.40        82.39        41.59        19.99       119.08        29.10 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 
       55.43        48.89        27.88        36.23        47.70        45.37 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       29.16         9.47        57.76         9.99        38.43        89.33 
TCGA-09-1664 TCGA-09-1666 TCGA-09-1668 TCGA-09-1672 TCGA-09-1673 TCGA-09-2044 
       74.93        57.60        55.36         5.85         3.02         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-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       26.93        12.46        54.31        81.86        18.51        34.19 
TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-13-0714 
       32.88         6.71        35.44        36.92        19.99         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-13-0730 TCGA-13-0755 TCGA-13-0757 TCGA-13-0762 TCGA-13-0766 TCGA-13-0768 
       17.82         2.50        11.18        32.25        21.40         8.45 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 
       36.72        28.70        30.35        19.59         8.71         7.79 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0885 
        8.12         8.28        43.86        35.28        35.31        91.40 
TCGA-13-0886 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 
       74.27        61.84        67.99        69.01        43.36        57.47 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 
       56.15        57.07        19.36        47.38        48.33        44.94 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       44.84        37.08        27.72        34.06        29.98        21.17 
TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 
       14.89         4.64         6.41         6.08        10.88         6.61 
TCGA-13-1405 TCGA-13-1409 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1483 
        7.36         6.84         4.21         5.33        54.64        29.42 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1492 TCGA-13-1494 
       20.68        22.39        70.82        82.88        73.55        38.20 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 
        4.24        54.31        37.61        38.40        13.97        16.57 
TCGA-13-1505 TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 
        4.21         4.77         4.18         3.91         3.09        12.23 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU 
        8.61        10.78         8.75         6.28        54.77         8.42 
TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-23-1023 TCGA-23-1027 
       72.20        25.38        19.10        16.70        40.54        32.09 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 
       49.41         8.81        29.13        18.90         2.76        54.51 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 
       31.20        68.68       129.96         4.27        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-24-0966 TCGA-24-0968 TCGA-24-0970 
       49.84         2.76         4.70         7.63        19.66        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-24-1413 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        19.17        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-24-1550 TCGA-24-1552 
       22.22        26.96        64.27        56.58        41.06        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       58.09        88.50        70.62        44.09        45.50        47.70 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1842 
       25.87        10.26        17.23        90.15        88.37         8.32 
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-25-1322 
       53.26        26.96        52.04        42.05         2.01         2.99 
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-25-2392 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-29-2429 TCGA-29-2431 TCGA-29-2436 
       65.00        62.47        45.11        13.84        42.25         9.76 
TCGA-30-1718 TCGA-30-1853 TCGA-30-1856 TCGA-30-1861 TCGA-30-1866 TCGA-30-1880 
       51.91        36.26        15.68        34.78        36.62        57.57 
TCGA-30-1887 TCGA-30-1891 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 
       24.26        30.05        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-3P-A9WA TCGA-42-2587 
       18.31        14.17         6.05        16.18        13.81        23.74 
TCGA-42-2588 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1584 TCGA-57-1585 
       28.93        10.42        40.77         1.48        21.14         1.74 
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-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 
       34.39         5.42        44.81        20.52        11.11         8.09 
TCGA-61-1724 TCGA-61-1727 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       20.94        18.54        31.79        28.47        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-61-1907 TCGA-61-1910 TCGA-61-1915 TCGA-61-1917 TCGA-61-1919 
       13.02        31.30        37.05        67.76        43.43        38.17 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2016 
        2.01         5.52        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-61-2101 TCGA-61-2102 TCGA-61-2109 TCGA-61-2110 TCGA-61-2612 
       61.64        55.50         6.48        20.68        44.52         6.35 
TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
       31.07         8.61        39.68        18.94         0.79 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.26               0.30 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            180.20             129.96 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             27.52              29.00 
[1] "0.3 - 180.2 (27.5)" "0.3 - 130.0 (29.0)"
[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, continuous
D34V5, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     2 167
  19P GAIN WILD-TYPE   1 403
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      2  167
  19P GAIN WILD-TYPE    1  403
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 2                  1
  YES              167                403
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  19P GAIN MUTATED    6  7  0  0
  19P GAIN WILD-TYPE  9 19  5  3
D34V6, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0                6                  9
  R1                7                 19
  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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P GAIN MUTATED                                  0     4
  19P GAIN WILD-TYPE                                3    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  19P GAIN MUTATED                           8
  19P GAIN WILD-TYPE                        26
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19P GAIN MUTATED                                           1   142
  19P GAIN WILD-TYPE                                         0   334
D34V7, multiclass
                                           clus
vv                                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    4                 15
  BLACK OR AFRICAN AMERICAN                                8                 26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  142                334
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V8, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     2  96
  19P GAIN WILD-TYPE   8 231
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      2   96
  19P GAIN WILD-TYPE    8  231
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO               96                231
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    75  81
  19Q GAIN WILD-TYPE 193 211
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               156                404 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                81                211 
$`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-09-0364 TCGA-09-0365 TCGA-09-0367 TCGA-09-0369 TCGA-09-1669 TCGA-09-1670 
       29.16         9.47        17.98        35.57        30.51        17.98 
TCGA-09-1674 TCGA-09-2043 TCGA-10-0926 TCGA-10-0933 TCGA-13-0717 TCGA-13-0727 
        8.55         6.18        25.91        14.66        24.59        15.19 
TCGA-13-0751 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0791 TCGA-13-0794 
       55.17        11.38        11.54        34.06        38.93        30.35 
TCGA-13-0802 TCGA-13-0883 TCGA-13-0885 TCGA-13-0888 TCGA-13-0905 TCGA-13-0920 
        8.19        68.94        91.40        70.39        47.84        13.81 
TCGA-13-1408 TCGA-13-1410 TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 TCGA-13-1491 
        5.92         4.70        87.06        61.71        98.04        52.44 
TCGA-13-1492 TCGA-13-1495 TCGA-13-1501 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 
       73.55        49.25        32.84        16.57         4.41         4.77 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1687 TCGA-23-1022 
       23.05        25.94        26.20        27.52         2.66        49.68 
TCGA-23-1026 TCGA-23-1111 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1121 
       26.83         3.22         4.57        33.30        86.01         6.38 
TCGA-23-1809 TCGA-23-2645 TCGA-24-1105 TCGA-24-1417 TCGA-24-1426 TCGA-24-1428 
        0.53         4.50        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-24-1557 TCGA-24-1558 TCGA-24-1614 TCGA-24-1616 
       51.91        41.39        39.88        19.53        48.33        38.24 
TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 TCGA-24-1850 TCGA-24-1923 
        3.48         3.72         3.81        11.28         5.52        22.68 
TCGA-24-2020 TCGA-24-2030 TCGA-24-2033 TCGA-24-2261 TCGA-24-2267 TCGA-24-2280 
      152.02        55.92        18.48         0.79        47.54        70.45 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2295 TCGA-25-1312 TCGA-25-1314 TCGA-25-1317 
       44.61         0.82        33.11         1.02        33.01         2.01 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1323 TCGA-25-1329 
       34.98        65.00        37.97        33.96        12.99        15.02 
TCGA-25-1623 TCGA-25-2398 TCGA-29-1691 TCGA-29-1695 TCGA-29-1698 TCGA-29-1701 
       18.58        45.01        48.33        40.41        68.32        16.93 
TCGA-29-1766 TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1785 TCGA-29-2432 
       39.42        24.36        17.33        12.36        36.30        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-31-1944 TCGA-31-1959 
       48.10        44.91         1.22        48.79        45.57         2.20 
TCGA-36-1578 TCGA-36-2529 TCGA-36-2534 TCGA-36-2543 TCGA-36-2544 TCGA-36-2552 
       27.85        35.05        29.82         2.24        20.98        11.47 
TCGA-42-2582 TCGA-42-2589 TCGA-57-1582 TCGA-57-1586 TCGA-59-2348 TCGA-59-2351 
       47.57        42.02        24.03        22.32       180.20       116.12 
TCGA-59-2355 TCGA-61-1722 TCGA-61-1728 TCGA-61-1730 TCGA-61-1741 TCGA-61-1904 
        2.14         8.09        27.88         4.34        33.67         9.07 
TCGA-61-1906 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1918 TCGA-61-2009 
       34.13        42.51        48.92        56.61        15.75        39.85 
TCGA-61-2012 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2113 TCGA-WR-A838 
       30.64        58.39        60.62        65.52        22.22         9.99 

$`19Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1341 TCGA-04-1342 
       43.92         1.81        49.15         2.01         1.08        18.51 
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-04-1530 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
       82.39        56.55       119.08        55.43        48.89        27.88 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 TCGA-09-0366 TCGA-09-1659 
       64.64        36.23        47.70        45.37        57.76         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-09-1672 TCGA-09-1673 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 
       55.36         5.85         3.02        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-10-0925 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       26.93        12.46        54.31        81.86        18.51        34.19 
TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 
       32.88         6.71        35.44        36.92        19.99        20.91 
TCGA-13-0714 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 
        6.21        44.55        39.58         2.73        12.39        31.20 
TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 
       17.82         2.50        11.18        32.25        31.04        21.40 
TCGA-13-0768 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 
        8.45        36.72        28.70        19.59         8.71         7.79 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
        8.12         8.28        43.86        35.28        35.31        13.61 
TCGA-13-0884 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 
      107.18        74.27        66.67        61.84        67.99        69.01 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       43.36        57.47        56.15        57.07        19.36        47.38 
TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       48.33        44.94        44.84        37.08        27.72        34.06 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       29.98        21.17        14.89         4.64         6.41         6.08 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1409 TCGA-13-1411 
       10.88         6.61         7.36         6.05         6.84         4.21 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 
        5.33        54.64        29.42        20.68        22.39        70.82 
TCGA-13-1489 TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 
       82.88        38.20         4.24        54.31        37.61        38.40 
TCGA-13-1500 TCGA-13-1505 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
       13.97         4.21         4.18         2.56         3.91         3.09 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 
       14.24        12.23         8.61        10.78         8.75         6.28 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 
       54.77         8.42        72.20        25.38        19.10        16.70 
TCGA-20-1686 TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 TCGA-23-1027 TCGA-23-1028 
        2.93        47.54        40.54        15.39        32.09        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 
        8.81        29.13        18.90         2.76        51.35        54.51 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 
       31.20        68.68       129.96         4.27        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-24-0966 TCGA-24-0968 TCGA-24-0970 
       49.84         2.76         4.70         7.63        19.66        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-24-1413 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        19.17        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-24-1553 TCGA-24-1555 
       22.22        26.96        64.27        56.58        58.09        88.50 
TCGA-24-1556 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 
       70.62        44.09        45.50        47.70        25.87        10.26 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1842 TCGA-24-1846 TCGA-24-1849 
       17.23        90.15        88.37         8.32         4.37         5.79 
TCGA-24-1920 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 
        9.80        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-24-2035 
       44.84        58.16        34.82       109.71        14.43        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 TCGA-24-2271 
       64.01        44.52        57.07        36.16         0.36        31.63 
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-25-1315 TCGA-25-1316 TCGA-25-1322 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 
       52.04        42.05         2.99        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-25-2399 
       49.05         1.02        38.04         3.02        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-29-1696 TCGA-29-1697 TCGA-29-1699 
       47.61       101.79        39.02        33.93        31.20        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-29-1768 TCGA-29-1769 
       17.36        86.60        66.81        62.93        31.30        22.98 
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-29-1784 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 
        5.36        86.17        65.00        62.47        45.11        13.84 
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-31-1946 TCGA-31-1950 
       36.62        57.57        24.26        30.05        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-36-1577 
       21.53        22.85        22.55         8.55        30.08        25.74 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 TCGA-36-2537 TCGA-36-2538 
       24.23        24.69        33.01        29.49        25.91        25.08 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 
       23.80        21.60        18.31        20.52        14.17         6.05 
TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 TCGA-42-2591 
       16.18        13.81        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-59-A5PD TCGA-5X-AA5U TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 
       44.81        20.52        11.87        11.11        20.94        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-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 
        2.43        43.69         1.45         8.42         5.79        11.41 
TCGA-61-1903 TCGA-61-1907 TCGA-61-1910 TCGA-61-1915 TCGA-61-1917 TCGA-61-1919 
       13.02        31.30        37.05        67.76        43.43        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-61-2016 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-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       71.74        61.64        55.50         6.48        76.87        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P 
       44.52       125.75         6.35        31.07         8.61        39.68 
TCGA-OY-A56Q TCGA-VG-A8LO 
       18.94         0.79 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.26               0.30 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            180.20             129.96 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            28.260             28.735 
[1] "0.3 - 180.2 (28.3)" "0.3 - 130.0 (28.7)"
[1] "hr=" "1.1"
D35V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  19Q GAIN MUTATED         1   155                2
  19Q GAIN WILD-TYPE       2   403                0
D35V3, multiclass
                  clus
vv                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  OMENTUM                         1                  2
  OVARY                         155                403
  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, continuous
D35V5, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     2 158
  19Q GAIN WILD-TYPE   1 412
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2  158
  19Q GAIN WILD-TYPE    1  412
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 2                  1
  YES              158                412
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  19Q GAIN MUTATED    5  6  0  0
  19Q GAIN WILD-TYPE 10 20  5  3
D35V6, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0                5                 10
  R1                6                 20
  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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  0     4
  19Q GAIN WILD-TYPE                                3    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  19Q GAIN MUTATED                           4
  19Q GAIN WILD-TYPE                        30
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19Q GAIN MUTATED                                           1   139
  19Q GAIN WILD-TYPE                                         0   337
D35V7, multiclass
                                           clus
vv                                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    4                 15
  BLACK OR AFRICAN AMERICAN                                4                 30
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  139                337
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V8, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     2  89
  19Q GAIN WILD-TYPE   8 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2   89
  19Q GAIN WILD-TYPE    8  238
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO               89                238
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   118 163
  20P GAIN WILD-TYPE 150 129
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               281                279 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               163                129 
$`20P GAIN MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1337 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 
       43.92        41.00         2.01         1.08        18.51        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 
       65.52        63.09        21.57        63.98        65.46        49.28 
TCGA-04-1364 TCGA-04-1514 TCGA-04-1517 TCGA-04-1542 TCGA-04-1646 TCGA-04-1649 
       33.67        56.55        19.99        84.20        27.88        64.64 
TCGA-04-1655 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 
       45.37        57.76        17.98        35.57         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-10-0933 TCGA-10-0935 TCGA-10-0936 TCGA-10-0938 TCGA-13-0717 
       39.75        14.66        35.44        36.92        20.91        24.59 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0727 TCGA-13-0751 TCGA-13-0757 
       39.58         2.73        12.39        15.19        55.17        11.18 
TCGA-13-0758 TCGA-13-0760 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0794 
       11.38        11.54        32.25        31.04        21.40        30.35 
TCGA-13-0800 TCGA-13-0802 TCGA-13-0803 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 
        8.12         8.19        43.86       107.18        91.40        66.67 
TCGA-13-0888 TCGA-13-0890 TCGA-13-0899 TCGA-13-0904 TCGA-13-0913 TCGA-13-0919 
       70.39        67.99        56.15        48.33        29.98        14.89 
TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
       13.81         6.41         6.08         6.05         5.92         6.84 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 
       87.06        61.71        98.04        20.68        22.39        70.82 
TCGA-13-1492 TCGA-13-1497 TCGA-13-1499 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       73.55        54.31        38.40        16.57         4.21         4.41 
TCGA-13-1507 TCGA-13-2057 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FU TCGA-20-0990 
        4.77        14.24        10.78         8.75         8.42        25.94 
TCGA-20-0991 TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 TCGA-23-1024 TCGA-23-1031 
       26.20        16.70         2.93        47.54        15.39        18.90 
TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 TCGA-23-1121 
        2.76        51.35        54.51         3.22        68.68         6.38 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2084 
       39.09        33.47        58.13         0.53       115.89        49.84 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0975 TCGA-24-0982 TCGA-24-1105 
        4.70         4.50         7.63        21.80        22.32        47.41 
TCGA-24-1413 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1427 TCGA-24-1430 
        6.31         0.76         6.25         6.02         4.83        28.37 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 
       19.17        18.67         8.55        12.46        45.14         9.11 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1553 
       22.22        26.96        57.40        64.27        16.21        58.09 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1564 TCGA-24-1604 TCGA-24-1842 TCGA-24-1843 
       70.62        39.88        25.87        88.37         8.32         3.48 
TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 TCGA-24-1850 TCGA-24-1923 TCGA-24-1928 
        3.72         3.81        11.28         5.52        22.68        11.05 
TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2026 TCGA-24-2027 TCGA-24-2030 
       81.11         4.87       152.02        34.82       109.71        55.92 
TCGA-24-2033 TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 
       18.48        36.16         0.79        47.54        70.45        44.61 
TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-25-1312 
        0.82        67.36        36.23        16.64        33.11         1.02 
TCGA-25-1313 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 
       26.96        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-25-1626 
       33.96         2.99        12.99        15.02        18.58        17.03 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
       12.95        20.61         0.30        59.15        62.17        35.87 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2393 
       52.04        14.96        24.99        24.00        85.05        38.04 
TCGA-25-2396 TCGA-25-2398 TCGA-25-2400 TCGA-25-2404 TCGA-25-2408 TCGA-29-1688 
        3.02        45.01        42.02        29.03        31.00        78.90 
TCGA-29-1691 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 
       48.33        40.41        31.20        68.32        36.36        16.93 
TCGA-29-1703 TCGA-29-1707 TCGA-29-1710 TCGA-29-1761 TCGA-29-1763 TCGA-29-1764 
       59.67        41.98        31.27        17.36        66.81        62.93 
TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 TCGA-29-1775 TCGA-29-1778 TCGA-29-1783 
       39.42        22.98        24.36        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-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-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1892 
       48.10        34.78         6.12        36.62         1.22        48.79 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1955 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 
       18.77        22.49        42.51         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-59-A5PD TCGA-5X-AA5U TCGA-61-1722 TCGA-61-1727 
        5.42        44.81        20.52        11.87         8.09        18.54 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1743 TCGA-61-1899 TCGA-61-1900 TCGA-61-1903 
        4.34        31.79        43.69         8.42         5.79        13.02 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1911 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 
        9.07        34.13        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 
        6.35         8.61        39.68        18.94         0.79 

$`20P GAIN WILD-TYPE`
TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1348 TCGA-04-1353 TCGA-04-1361 
        1.81        49.15        46.62        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-09-0364 TCGA-09-0365 TCGA-09-1662 
       36.23        31.86        47.70        29.16         9.47        89.33 
TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 TCGA-09-1672 TCGA-09-1673 
       74.93        57.60        61.87        30.51         5.85         3.02 
TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 
       97.55         6.12        35.15         4.54       112.41        71.11 
TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 
       20.94        26.93        12.46        54.31        25.91        81.86 
TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 TCGA-10-0937 TCGA-13-0714 
       18.51        34.19        32.88         6.71        19.99         6.21 
TCGA-13-0720 TCGA-13-0726 TCGA-13-0730 TCGA-13-0755 TCGA-13-0761 TCGA-13-0768 
       44.55        31.20        17.82         2.50        34.06         8.45 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 
       38.93        36.72        28.70        19.59         8.71         7.79 
TCGA-13-0801 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0886 
        8.28        35.28        35.31        13.61        68.94        74.27 
TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 
       61.84        69.01        43.36        57.47        57.07        19.36 
TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       47.38        47.84        44.94        44.84        37.08        27.72 
TCGA-13-0912 TCGA-13-0916 TCGA-13-0921 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
       34.06        21.17         4.64        10.88         6.61         7.36 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1483 TCGA-13-1489 
        4.70         4.21         5.33        54.64        29.42        82.88 
TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1500 
       52.44        38.20        49.25         4.24        37.61        13.97 
TCGA-13-1501 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 
       32.84         4.18         2.56         3.91         3.09        12.23 
TCGA-13-2060 TCGA-13-2071 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0996 TCGA-20-1682 
        8.61         6.28        54.77        23.05        72.20        27.52 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1687 TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 
       25.38        19.10         2.66        49.68        40.54        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1113 TCGA-23-1116 
       32.09        49.41         8.81        29.13        31.20         4.57 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-2072 TCGA-23-2078 
       33.30        86.01       129.96         4.27        24.95        87.48 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2641 TCGA-24-0968 TCGA-24-0970 TCGA-24-0979 
       91.66        77.00         2.76        19.66        11.64        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-24-1419 TCGA-24-1425 TCGA-24-1426 TCGA-24-1428 TCGA-24-1435 TCGA-24-1463 
        7.86         5.95         5.36        17.39        43.53        72.92 
TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 
      105.99         3.45         1.18        56.58        41.06        51.91 
TCGA-24-1552 TCGA-24-1555 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       41.39        88.50        19.53        44.09        45.50        47.70 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1614 TCGA-24-1616 TCGA-24-1846 
       10.26        17.23        90.15        48.33        38.24         4.37 
TCGA-24-1849 TCGA-24-1920 TCGA-24-1924 TCGA-24-1927 TCGA-24-2023 TCGA-24-2024 
        5.79         9.80        30.21        16.44        44.84        58.16 
TCGA-24-2029 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2262 
       14.43        28.18        64.01        44.52        57.07         0.36 
TCGA-24-2271 TCGA-24-2297 TCGA-24-2298 TCGA-25-1314 TCGA-25-1315 TCGA-25-1625 
       31.63        55.86        53.26        33.01        52.04        27.62 
TCGA-25-1630 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2397 TCGA-25-2399 
       38.20        13.02        49.05         1.02        12.00        19.99 
TCGA-25-2401 TCGA-25-2409 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 
        2.96        26.99        47.61       101.79        39.02        33.93 
TCGA-29-1702 TCGA-29-1705 TCGA-29-1711 TCGA-29-1762 TCGA-29-1768 TCGA-29-1771 
       23.93        18.25        34.62        86.60        31.30        22.55 
TCGA-29-1774 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1785 TCGA-29-2427 
       17.33        11.84        12.30         8.38        36.30        62.47 
TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-30-1857 TCGA-30-1860 TCGA-30-1880 
       21.47        11.47         9.76         0.26        44.91        57.57 
TCGA-30-1887 TCGA-30-1891 TCGA-31-1944 TCGA-31-1946 TCGA-31-1953 TCGA-31-1956 
       24.26        30.05        45.57        30.18         6.71        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-3P-A9WA TCGA-42-2582 
        2.24        20.98        18.31         6.05        13.81        47.57 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2591 TCGA-57-1582 TCGA-57-1584 TCGA-57-1992 
       28.93        42.02        40.77        24.03        21.14        29.00 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2354 
       25.08        25.02       180.20        80.12        22.32        34.39 
TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1728 TCGA-61-1734 TCGA-61-1736 
       11.11        20.94        31.43        27.88        28.47        48.79 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 TCGA-61-1901 
       44.84        35.80         2.43        33.67         1.45        11.41 
TCGA-61-1907 TCGA-61-1910 TCGA-61-1913 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       31.30        37.05        48.92         2.01         5.52        14.50 
TCGA-61-2002 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
       17.98         1.18        45.96        45.40         4.80         4.77 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2109 TCGA-61-2110 
       51.72        71.74        61.64        58.39        20.68        44.52 
TCGA-61-2111 TCGA-61-2613 TCGA-WR-A838 
      125.75        31.07         9.99 

  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 
             24.99              29.49 
[1] "0.3 - 152.0 (25.0)" "0.3 - 180.2 (29.5)"
[1] "hr=" "1.4"
D36V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  20P GAIN MUTATED         3   279                1
  20P GAIN WILD-TYPE       0   279                1
D36V3, multiclass
                  clus
vv                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  OMENTUM                         3                  0
  OVARY                         279                279
  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, continuous
D36V5, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     2 285
  20P GAIN WILD-TYPE   1 285
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      2  285
  20P GAIN WILD-TYPE    1  285
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 2                  1
  YES              285                285
[1] 2 2
[1] FALSE
                    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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P GAIN MUTATED                                  2     5
  20P GAIN WILD-TYPE                                1    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  20P GAIN MUTATED                          19
  20P GAIN WILD-TYPE                        15
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20P GAIN MUTATED                                           1   243
  20P GAIN WILD-TYPE                                         0   233
D36V7, multiclass
                                           clus
vv                                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  1
  ASIAN                                                    5                 14
  BLACK OR AFRICAN AMERICAN                               19                 15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  243                233
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V8, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     4 159
  20P GAIN WILD-TYPE   6 168
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      4  159
  20P GAIN WILD-TYPE    6  168
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  6
  NOT HISPANIC OR LATINO              159                168
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   145 174
  20Q GAIN WILD-TYPE 123 118
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               319                241 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               174                118 
$`20Q GAIN MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1337 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 
       43.92        41.00         2.01         1.08        18.51        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 
       65.52        63.09        21.57        63.98        65.46         0.53 
TCGA-04-1356 TCGA-04-1364 TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 TCGA-04-1525 
       49.28        33.67        82.39        56.55        19.99        38.37 
TCGA-04-1542 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1652 TCGA-04-1655 
       84.20        27.88        28.64        64.64        31.86        45.37 
TCGA-09-0364 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 
       29.16        57.76        17.98        35.57         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-10-0933 TCGA-10-0935 TCGA-10-0936 TCGA-10-0938 TCGA-13-0717 
       39.75        14.66        35.44        36.92        20.91        24.59 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
       39.58         2.73        12.39        15.19        17.82        55.17 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0762 TCGA-13-0766 TCGA-13-0794 
       11.18        11.38        11.54        32.25        21.40        30.35 
TCGA-13-0795 TCGA-13-0800 TCGA-13-0802 TCGA-13-0803 TCGA-13-0884 TCGA-13-0885 
       19.59         8.12         8.19        43.86       107.18        91.40 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 TCGA-13-0893 TCGA-13-0899 
       74.27        66.67        70.39        67.99        43.36        56.15 
TCGA-13-0901 TCGA-13-0905 TCGA-13-0906 TCGA-13-0911 TCGA-13-0913 TCGA-13-0919 
       19.36        47.84        44.94        27.72        29.98        14.89 
TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1407 TCGA-13-1408 
       13.81         6.41         6.08        10.88         6.05         5.92 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1412 TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 
        6.84         4.70         5.33        87.06        61.71        98.04 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1492 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 
       20.68        22.39        73.55        38.40        32.84        16.57 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 
        4.21         4.41         4.77        14.24         8.61        10.78 
TCGA-13-2065 TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1685 
        8.75         8.42        25.94        26.20        27.52        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-23-1116 TCGA-23-1117 
       51.35        54.51         3.22        68.68         4.57        33.30 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 
        6.38        39.09        33.47        58.13         0.53       115.89 
TCGA-23-2079 TCGA-23-2084 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 
       91.66        49.84         4.70         4.50         7.63        19.66 
TCGA-24-0975 TCGA-24-0982 TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 TCGA-24-1417 
       21.80        22.32        54.12        47.41         6.31         7.82 
TCGA-24-1418 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1426 TCGA-24-1427 
        7.99         0.76         6.25         6.02         5.36         4.83 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 
       19.17        18.67         8.55        12.46        45.14         9.11 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1553 
       22.22        26.96        57.40        64.27        16.21        58.09 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1604 TCGA-24-1842 TCGA-24-1843 
       70.62        39.88        19.53        88.37         8.32         3.48 
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-24-1924 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-24-2026 TCGA-24-2027 TCGA-24-2033 TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 
       34.82       109.71        18.48        36.16         0.79        47.54 
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-25-1314 TCGA-25-1316 TCGA-25-1317 
       33.11         1.02        26.96        33.01        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-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 
       15.02        18.58        17.03        12.95        20.61         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-25-2393 TCGA-25-2396 TCGA-25-2398 TCGA-25-2400 
       24.00        85.05        38.04         3.02        45.01        42.02 
TCGA-25-2404 TCGA-25-2408 TCGA-29-1688 TCGA-29-1691 TCGA-29-1693 TCGA-29-1697 
       29.03        31.00        78.90        48.33       101.79        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-29-1710 TCGA-29-1761 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1769 
       31.27        17.36        66.81        62.93        39.42        22.98 
TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1778 TCGA-29-1783 TCGA-29-1784 
       24.36        17.33        12.36        14.93         7.23         5.36 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2436 
       86.17        65.00        45.11        13.84        42.25         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-30-1859 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-31-1955 TCGA-31-1959 
       48.79        45.57        18.77        22.49        42.51         2.20 
TCGA-36-1569 TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1580 TCGA-36-1581 
       29.10        22.85         8.55        30.08        24.23        24.69 
TCGA-36-2534 TCGA-36-2547 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA 
       29.82        20.52        14.17        16.18        11.47        13.81 
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-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2351 TCGA-59-2352 
       22.32        29.00        25.08        25.02       116.12         9.40 
TCGA-59-2355 TCGA-59-2372 TCGA-59-A5PD TCGA-5X-AA5U TCGA-61-1722 TCGA-61-1727 
        2.14        44.81        20.52        11.87         8.09        18.54 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1737 TCGA-61-1741 TCGA-61-1743 
       27.88         4.34        31.79        44.84        33.67        43.69 
TCGA-61-1899 TCGA-61-1900 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1911 
        8.42         5.79        13.02         9.07        34.13        42.51 
TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-2003 
       56.61        67.76        43.43        15.75        38.17         4.01 
TCGA-61-2009 TCGA-61-2012 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 
       39.85        30.64        60.62        65.52        55.50         6.48 
TCGA-61-2104 TCGA-61-2113 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
       76.87        22.22         6.35         8.61        39.68        18.94 
TCGA-VG-A8LO 
        0.79 

$`20Q GAIN WILD-TYPE`
TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1348 TCGA-04-1361 TCGA-04-1362 
        1.81        49.15        46.62        48.76        32.52        44.32 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1516 TCGA-04-1519 TCGA-04-1530 TCGA-04-1536 
       76.57       103.40        41.59         0.79       119.08        29.10 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1651 TCGA-04-1654 TCGA-09-0365 TCGA-09-1662 
       55.43        48.89        36.23        47.70         9.47        89.33 
TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 
       74.93        57.60        61.87         5.85         3.02        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-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 
       20.94        26.93        12.46        54.31        25.91        81.86 
TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 TCGA-10-0937 TCGA-13-0714 
       18.51        34.19        32.88         6.71        19.99         6.21 
TCGA-13-0720 TCGA-13-0726 TCGA-13-0755 TCGA-13-0761 TCGA-13-0764 TCGA-13-0768 
       44.55        31.20         2.50        34.06        31.04         8.45 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 
       38.93        36.72        28.70         8.71         7.79         8.28 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0889 TCGA-13-0891 
       35.28        35.31        13.61        68.94        61.84        69.01 
TCGA-13-0897 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0908 TCGA-13-0910 
       57.47        57.07        47.38        48.33        44.84        37.08 
TCGA-13-0912 TCGA-13-0916 TCGA-13-0921 TCGA-13-1404 TCGA-13-1405 TCGA-13-1411 
       34.06        21.17         4.64         6.61         7.36         4.21 
TCGA-13-1477 TCGA-13-1483 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 
       54.64        29.42        70.82        82.88        52.44        38.20 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 TCGA-13-1509 
       49.25         4.24        54.31        37.61        13.97         4.18 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2071 TCGA-13-A5FT 
        2.56         3.91         3.09        12.23         6.28        54.77 
TCGA-20-0987 TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 TCGA-20-1687 TCGA-23-1023 
       23.05        72.20        25.38        19.10         2.66        40.54 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1113 
       26.83        32.09        49.41         8.81        29.13        31.20 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-2072 TCGA-23-2078 TCGA-23-2081 
       86.01       129.96         4.27        24.95        87.48        77.00 
TCGA-23-2641 TCGA-24-0970 TCGA-24-0979 TCGA-24-0980 TCGA-24-1104 TCGA-24-1416 
        2.76        11.64        41.56         7.66        63.55         6.38 
TCGA-24-1419 TCGA-24-1425 TCGA-24-1428 TCGA-24-1430 TCGA-24-1435 TCGA-24-1463 
        7.86         5.95        17.39        28.37        43.53        72.92 
TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 
      105.99         3.45         1.18        56.58        41.06        51.91 
TCGA-24-1552 TCGA-24-1555 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
       41.39        88.50        44.09        45.50        47.70        25.87 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1614 TCGA-24-1616 TCGA-24-1846 
       10.26        17.23        90.15        48.33        38.24         4.37 
TCGA-24-1927 TCGA-24-2023 TCGA-24-2024 TCGA-24-2029 TCGA-24-2030 TCGA-24-2035 
       16.44        44.84        58.16        14.43        55.92        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2262 TCGA-24-2271 TCGA-24-2297 
       64.01        44.52        57.07         0.36        31.63        55.86 
TCGA-24-2298 TCGA-25-1315 TCGA-25-1625 TCGA-25-1630 TCGA-25-2042 TCGA-25-2391 
       53.26        52.04        27.62        38.20        13.02        49.05 
TCGA-25-2392 TCGA-25-2397 TCGA-25-2399 TCGA-25-2401 TCGA-25-2409 TCGA-29-1690 
        1.02        12.00        19.99         2.96        26.99        47.61 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1702 TCGA-29-1711 TCGA-29-1762 
       39.02        40.41        33.93        23.93        34.62        86.60 
TCGA-29-1768 TCGA-29-1771 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1785 
       31.30        22.55        11.84        12.30         8.38        36.30 
TCGA-29-2427 TCGA-29-2432 TCGA-29-2434 TCGA-30-1857 TCGA-30-1860 TCGA-30-1880 
       62.47        21.47        11.47         0.26        44.91        57.57 
TCGA-30-1891 TCGA-31-1946 TCGA-31-1953 TCGA-31-1956 TCGA-36-1568 TCGA-36-1570 
       30.05        30.18         6.71        44.12        28.77        21.53 
TCGA-36-1574 TCGA-36-1577 TCGA-36-1578 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 
       22.55        25.74        27.85        35.05        33.01        29.49 
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-36-2549 TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
       18.31         6.05        47.57        28.93        42.02        10.42 
TCGA-57-1584 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2354 TCGA-59-2363 
       21.14       180.20        80.12        22.32        34.39         5.42 
TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1734 TCGA-61-1736 TCGA-61-1738 
       11.11        20.94        31.43        28.47        48.79        35.80 
TCGA-61-1740 TCGA-61-1895 TCGA-61-1901 TCGA-61-1907 TCGA-61-1910 TCGA-61-1913 
        2.43         1.45        11.41        31.30        37.05        48.92 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2008 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-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2613 
       61.64        58.39        20.68        44.52       125.75        31.07 
TCGA-WR-A838 
        9.99 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.30               0.26 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            152.02             180.20 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             24.69              31.20 
[1] "0.3 - 152.0 (24.7)" "0.3 - 180.2 (31.2)"
[1] "hr=" "1.3"
D37V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  20Q GAIN MUTATED         3   317                1
  20Q GAIN WILD-TYPE       0   241                1
D37V3, multiclass
                  clus
vv                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  OMENTUM                         3                  0
  OVARY                         317                241
  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, continuous
D37V5, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     2 324
  20Q GAIN WILD-TYPE   1 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      2  324
  20Q GAIN WILD-TYPE    1  246
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 2                  1
  YES              324                246
[1] 2 2
[1] FALSE
                    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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q GAIN MUTATED                                  2     5
  20Q GAIN WILD-TYPE                                1    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  20Q GAIN MUTATED                          22
  20Q GAIN WILD-TYPE                        12
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20Q GAIN MUTATED                                           1   278
  20Q GAIN WILD-TYPE                                         0   198
D37V7, multiclass
                                           clus
vv                                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  1
  ASIAN                                                    5                 14
  BLACK OR AFRICAN AMERICAN                               22                 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  278                198
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V8, 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    53  51
  21Q GAIN WILD-TYPE 215 241
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               104                456 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                51                241 
$`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-09-0365 
       82.39        56.55        41.59        19.99        29.10         9.47 
TCGA-09-0366 TCGA-09-1670 TCGA-09-2043 TCGA-10-0928 TCGA-10-0936 TCGA-13-0724 
       57.76        17.98         6.18        18.51        36.92         2.73 
TCGA-13-0726 TCGA-13-0762 TCGA-13-0768 TCGA-13-0795 TCGA-13-0888 TCGA-13-0890 
       31.20        32.25         8.45        19.59        70.39        67.99 
TCGA-13-0904 TCGA-13-0911 TCGA-13-1408 TCGA-13-1410 TCGA-13-1496 TCGA-13-1499 
       48.33        27.72         5.92         4.70         4.24        38.40 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-2059 TCGA-20-0990 TCGA-20-0991 
       16.57         4.21         4.41        12.23        25.94        26.20 
TCGA-20-1683 TCGA-23-1021 TCGA-23-1110 TCGA-23-1116 TCGA-23-1119 TCGA-23-1121 
       25.38        47.54        54.51         4.57       129.96         6.38 
TCGA-23-2078 TCGA-23-2643 TCGA-24-0979 TCGA-24-1104 TCGA-24-1424 TCGA-24-1427 
       87.48         4.70        41.56        63.55         6.02         4.83 
TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 TCGA-24-1474 TCGA-24-1552 TCGA-24-1558 
        8.55        12.46        45.14        22.22        41.39        19.53 
TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1847 TCGA-24-1923 TCGA-24-1928 
        8.32         3.48         3.72        11.28        22.68        11.05 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2260 TCGA-24-2280 TCGA-24-2295 TCGA-25-1312 
        4.87       152.02        36.16        70.45        33.11         1.02 
TCGA-25-1319 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1628 
       65.00        12.99        15.02        18.58        17.03        20.61 
TCGA-25-1877 TCGA-25-2393 TCGA-25-2401 TCGA-29-1698 TCGA-29-1701 TCGA-29-1707 
       24.00        38.04         2.96        68.32        16.93        41.98 
TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 TCGA-29-1778 TCGA-29-2428 TCGA-30-1861 
       86.60        62.93        39.42        14.93        45.11        34.78 
TCGA-30-1862 TCGA-30-1867 TCGA-31-1959 TCGA-36-1571 TCGA-36-1578 TCGA-36-2529 
        6.12         1.22         2.20        22.85        27.85        35.05 
TCGA-36-2542 TCGA-36-2551 TCGA-57-1585 TCGA-61-1722 TCGA-61-1743 TCGA-61-1906 
       21.60        16.18         1.74         8.09        43.69        34.13 
TCGA-61-1907 TCGA-61-1914 TCGA-61-1915 TCGA-61-2003 TCGA-61-2101 TCGA-61-2102 
       31.30        56.61        67.76         4.01        55.50         6.48 
TCGA-61-2111 TCGA-61-2614 
      125.75         8.61 

$`21Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 
       43.92         1.81        49.15         2.01        46.62         1.08 
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-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1519 TCGA-04-1525 
       44.32        33.67        76.57       103.40         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-09-0364 
       64.64        36.23        31.86        47.70        45.37        29.16 
TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       17.98        35.57         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-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 
       12.46        54.31        25.91        81.86        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-13-0727 TCGA-13-0730 
       24.59        44.55        39.58        12.39        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        34.06 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 
       31.04        21.40        38.93        36.72        28.70        30.35 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 
        8.71         7.79         8.12         8.28         8.19        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        91.40 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 
       74.27        66.67        61.84        69.01        43.36        57.47 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 
       56.15        57.07        19.36        47.38        47.84        44.94 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
       44.84        37.08        34.06        29.98        21.17        14.89 
TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 
       13.81         4.64         6.41         6.08        10.88         6.61 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1409 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 
        7.36         6.05         6.84         4.21         5.33        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        98.04        20.68        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       70.82        82.88        52.44        73.55        38.20        49.25 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1507 TCGA-13-1509 
       54.31        37.61        13.97        32.84         4.77         4.18 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 
        2.56         3.91         3.09        14.24         8.61        10.78 
TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0996 
        8.75         6.28        54.77         8.42        23.05        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-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 
       29.13        18.90         2.76        51.35         3.22        31.20 
TCGA-23-1114 TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 
       68.68        33.30        86.01         4.27        39.09        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-23-2084 TCGA-23-2641 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 
       49.84         2.76         4.50         7.63        19.66        11.64 
TCGA-24-0975 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 
       21.80         7.66        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-24-1430 TCGA-24-1431 TCGA-24-1434 
        5.95         5.36        17.39        28.37        19.17        18.67 
TCGA-24-1435 TCGA-24-1463 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 
       43.53        72.92       105.99         9.11         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-24-1553 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-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1845 TCGA-24-1846 TCGA-24-1849 
       88.37        48.33        38.24         3.81         4.37         5.79 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 TCGA-24-2023 
        5.52         9.80        30.21        16.44        81.11        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-24-2261 TCGA-24-2262 
       28.18        64.01        44.52        57.07         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-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 
       16.64        55.86        53.26        26.96        33.01        52.04 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 
       42.05         2.01        34.98        37.97        33.96         2.99 
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-25-1878 TCGA-25-2042 
       35.87        52.04        14.96        24.99        85.05        13.02 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 
       49.05         1.02         3.02        12.00        45.01        19.99 
TCGA-25-2400 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 
       42.02        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-29-1699 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 
       36.36        23.93        59.67        18.25        31.27        34.62 
TCGA-29-1761 TCGA-29-1763 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 
       17.36        66.81        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-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2429 
        5.36        36.30        86.17        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-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 
       51.91        36.26         2.47        15.68         0.26        48.10 
TCGA-30-1860 TCGA-30-1866 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 
       44.91        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-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 TCGA-36-1575 
       44.12        28.77        29.10        21.53        22.55         8.55 
TCGA-36-1576 TCGA-36-1577 TCGA-36-1580 TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 
       30.08        25.74        24.23        24.69        33.01        29.49 
TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2543 TCGA-36-2544 
       29.82        25.91        25.08        23.80         2.24        20.98 
TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2552 TCGA-3P-A9WA 
       18.31        20.52        14.17         6.05        11.47        13.81 
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-57-1586 TCGA-57-1992 
        1.48        24.03        11.38        21.14        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-59-A5PD 
        9.40        34.39         2.14         5.42        44.81        20.52 
TCGA-5X-AA5U TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 
       11.87        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 

  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 
             22.45              29.29 
[1] "1.0 - 152.0 (22.4)" "0.3 - 180.2 (29.3)"
[1] "hr=" "1"  
D38V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  21Q GAIN MUTATED         0   104                2
  21Q GAIN WILD-TYPE       3   454                0
D38V3, multiclass
                  clus
vv                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  OMENTUM                         0                  3
  OVARY                         104                454
  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, continuous
D38V5, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     0 109
  21Q GAIN WILD-TYPE   3 461
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0  109
  21Q GAIN WILD-TYPE    3  461
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 0                  3
  YES              109                461
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  21Q GAIN MUTATED    1  6  0  0
  21Q GAIN WILD-TYPE 14 20  5  3
D38V6, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0                1                 14
  R1                6                 20
  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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q GAIN MUTATED                                  0     2
  21Q GAIN WILD-TYPE                                3    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  21Q GAIN MUTATED                           4
  21Q GAIN WILD-TYPE                        30
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  21Q GAIN MUTATED                                           0    93
  21Q GAIN WILD-TYPE                                         1   383
D38V7, multiclass
                                           clus
vv                                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    2                 17
  BLACK OR AFRICAN AMERICAN                                4                 30
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   93                383
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V8, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     2  56
  21Q GAIN WILD-TYPE   8 271
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      2   56
  21Q GAIN WILD-TYPE    8  271
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO               56                271
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    13  10
  22Q GAIN WILD-TYPE 255 282
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                23                537 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                10                282 
$`22Q GAIN MUTATED`
TCGA-13-0760 TCGA-13-0762 TCGA-13-1405 TCGA-13-1488 TCGA-23-1119 TCGA-23-2077 
       11.54        32.25         7.36        70.82       129.96       115.89 
TCGA-24-1463 TCGA-24-1469 TCGA-24-1556 TCGA-24-1928 TCGA-24-2290 TCGA-25-1627 
       72.92         9.11        70.62        11.05        36.23        12.95 
TCGA-29-1699 TCGA-29-1764 TCGA-29-1770 TCGA-29-1777 TCGA-29-2425 TCGA-29-2427 
       36.36        62.93        24.36        12.30        65.00        62.47 
TCGA-30-1861 TCGA-31-1950 TCGA-36-2547 TCGA-57-1585 TCGA-61-1904 
       34.78        18.77        20.52         1.74         9.07 

$`22Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       43.92        41.00         1.81        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-04-1356 TCGA-04-1361 
       21.57        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-04-1514 
       44.32        33.67        76.57       103.40        82.39        56.55 
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-09-0364 TCGA-09-0365 
       36.23        31.86        47.70        45.37        29.16         9.47 
TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       57.76        17.98        35.57         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-09-2049 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-10-0925 TCGA-10-0926 
       39.75        20.94        26.93        12.46        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-13-0723 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        34.06 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       31.04        21.40         8.45        38.93        36.72        28.70 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
       30.35        19.59         8.71         7.79         8.12         8.28 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
        8.19        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        91.40        74.27        66.67        70.39        61.84 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       67.99        69.01        43.36        57.47        56.15        57.07 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 
       19.36        47.38        48.33        47.84        44.94        44.84 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
       37.08        27.72        34.06        29.98        21.17        14.89 
TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 
       13.81         4.64         6.41         6.08        10.88         6.61 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
        6.05         5.92         6.84         4.70         4.21         5.33 
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        98.04        20.68 
TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       22.39        82.88        52.44        73.55        38.20        49.25 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 
        4.24        54.31        37.61        38.40        13.97        32.84 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 
       16.57         4.21         4.41         4.77         4.18         2.56 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 
        3.91         3.09        14.24        12.23         8.61        10.78 
TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
        8.75         6.28        54.77         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-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-23-1114 
        2.76        51.35        54.51         3.22        31.20        68.68 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 
        4.57        33.30        86.01         4.27         6.38        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 
       33.47        58.13         0.53        24.95        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-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
       19.66        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        19.17        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 
       43.53         8.55        12.46        45.14       105.99         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-24-1557 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-24-1930 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-24-2030 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-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 
       44.52        57.07        36.16         0.79         0.36        47.54 
TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2293 
       31.63        70.45        44.61         0.82        67.36        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-29-1701 TCGA-29-1702 
       40.41        33.93        31.20        68.32        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-29-1763 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 
       86.60        66.81        39.42        31.30        22.98        22.55 
TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 
       17.33        12.36        11.84        14.93         8.38         7.23 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 
        5.36        36.30        86.17        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-30-1862 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-36-1568 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-36-2529 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-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 
       14.17         6.05        16.18        11.47        13.81        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-57-1586 TCGA-57-1992 TCGA-57-1993 
       24.03        11.38        21.14        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-59-A5PD TCGA-5X-AA5U 
       34.39         2.14         5.42        44.81        20.52        11.87 
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 
       18.94         0.79         9.99 

  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 
             32.25              28.64 
[1] "1.7 - 130.0 (32.2)" "0.3 - 180.2 (28.6)"
[1] "hr=" "1.6"
D39V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  22Q GAIN MUTATED         1    23                0
  22Q GAIN WILD-TYPE       2   535                2
D39V3, multiclass
                  clus
vv                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  OMENTUM                         1                  2
  OVARY                          23                535
  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, continuous
D39V5, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     0  24
  22Q GAIN WILD-TYPE   3 546
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0   24
  22Q GAIN WILD-TYPE    3  546
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 0                  3
  YES               24                546
[1] 2 2
[1] FALSE
                    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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q GAIN MUTATED                                  0     0
  22Q GAIN WILD-TYPE                                3    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  22Q GAIN MUTATED                           0
  22Q GAIN WILD-TYPE                        34
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  22Q GAIN MUTATED                                           0    22
  22Q GAIN WILD-TYPE                                         1   454
D39V7, multiclass
                                           clus
vv                                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    0                 19
  BLACK OR AFRICAN AMERICAN                                0                 34
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   22                454
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V8, 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    35  42
  XP GAIN WILD-TYPE 233 250
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               77               483 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               42               250 
$`XP GAIN MUTATED`
TCGA-04-1332 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1351 TCGA-09-1674 
       41.00         1.08        18.51        11.87        65.46         8.55 
TCGA-09-2043 TCGA-09-2045 TCGA-09-2048 TCGA-10-0933 TCGA-10-0936 TCGA-13-0723 
        6.18        35.15         4.54        14.66        36.92        39.58 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0751 TCGA-13-0768 TCGA-13-0800 TCGA-13-0884 
       31.20        15.19        55.17         8.45         8.12       107.18 
TCGA-13-0890 TCGA-13-0897 TCGA-13-0901 TCGA-13-0916 TCGA-13-0921 TCGA-13-0923 
       67.99        57.47        19.36        21.17         4.64         6.41 
TCGA-13-1409 TCGA-13-1485 TCGA-13-1488 TCGA-13-1497 TCGA-13-1507 TCGA-13-2057 
        6.84        20.68        70.82        54.31         4.77        14.24 
TCGA-13-2060 TCGA-13-2065 TCGA-13-2071 TCGA-23-1110 TCGA-23-1114 TCGA-23-1117 
        8.61         8.75         6.28        54.51        68.68        33.30 
TCGA-23-1122 TCGA-23-1124 TCGA-23-1809 TCGA-23-2084 TCGA-24-1425 TCGA-24-1466 
       39.09        58.13         0.53        49.84         5.95        45.14 
TCGA-24-1470 TCGA-24-1474 TCGA-24-1556 TCGA-24-1564 TCGA-24-1604 TCGA-24-1843 
        3.45        22.22        70.62        25.87        88.37         3.48 
TCGA-24-1924 TCGA-24-1927 TCGA-24-2038 TCGA-24-2261 TCGA-24-2281 TCGA-25-1319 
       30.21        16.44        44.52         0.79        44.61        65.00 
TCGA-25-1329 TCGA-25-1633 TCGA-25-1877 TCGA-25-2398 TCGA-29-1691 TCGA-29-1764 
       15.02        62.17        24.00        45.01        48.33        62.93 
TCGA-29-1766 TCGA-29-1776 TCGA-30-1855 TCGA-30-1862 TCGA-30-1867 TCGA-36-2529 
       39.42        11.84         2.47         6.12         1.22        35.05 
TCGA-42-2589 TCGA-57-1993 TCGA-59-2348 TCGA-59-2372 TCGA-5X-AA5U TCGA-61-1722 
       42.02        25.08       180.20        44.81        11.87         8.09 
TCGA-61-1741 TCGA-61-1900 TCGA-61-1911 TCGA-61-2109 TCGA-VG-A8LO 
       33.67         5.79        42.51        20.68         0.79 

$`XP GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1346 
       43.92         1.81        49.15         2.01        46.62        65.52 
TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1353 TCGA-04-1356 
       63.09        48.76        21.57        63.98         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-04-1516 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-04-1648 
       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-09-0364 
       64.64        36.23        31.86        47.70        45.37        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 
        9.47        57.76        17.98        35.57         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-09-1675 TCGA-09-2044 
       30.51        17.98         5.85         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-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       12.46        54.31        25.91        81.86        18.51        34.19 
TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
       32.88         6.71        35.44        19.99        20.91         6.21 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 TCGA-13-0730 TCGA-13-0755 
       24.59        44.55         2.73        12.39        17.82         2.50 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 
       11.18        11.38        11.54        34.06        32.25        31.04 
TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 
       21.40        38.93        36.72        28.70        30.35        19.59 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 
        8.71         7.79         8.28         8.19        43.86        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        91.40        74.27        66.67 
TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 TCGA-13-0900 
       70.39        61.84        69.01        43.36        56.15        57.07 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
       47.38        48.33        47.84        44.94        44.84        37.08 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0919 TCGA-13-0920 TCGA-13-0924 
       27.72        34.06        29.98        14.89        13.81         6.08 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 
       10.88         6.61         7.36         6.05         5.92         4.70 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
        4.21         5.33        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 
       98.04        22.39        82.88        52.44        73.55        38.20 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 
       49.25         4.24        37.61        38.40        13.97        32.84 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
       16.57         4.21         4.41         4.18         2.56         3.91 
TCGA-13-1512 TCGA-13-2059 TCGA-13-2061 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
        3.09        12.23        10.78        54.77         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-23-1030 
       15.39        26.83        32.09        49.41         8.81        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 
       18.90         2.76        51.35         3.22        31.20         4.57 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1123 TCGA-23-2072 
       86.01       129.96         4.27         6.38        33.47        24.95 
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-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        4.50         7.63        19.66        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-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 
        6.02         5.36         4.83        17.39        28.37        19.17 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1467 
       18.67        43.53         8.55        72.92        12.46       105.99 
TCGA-24-1469 TCGA-24-1471 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 
        9.11         1.18        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-24-1565 
       39.88        19.53        44.09        45.50        47.70        10.26 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1844 
       17.23        90.15        48.33        38.24         8.32         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-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 
       22.68        11.05        81.11         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-24-2254 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-25-1320 TCGA-25-1321 
       52.04        42.05         2.01        34.98        37.97        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-25-1628 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-25-1870 TCGA-25-1871 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 
       14.96        24.99        85.05        13.02        49.05         1.02 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 
       38.04         3.02        12.00        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-29-1701 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-29-1763 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-29-1778 
       24.36        22.55        17.33        12.36        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-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 
       62.47        45.11        13.84        42.25        21.47        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-30-1866 TCGA-30-1880 
        0.26        48.10        44.91        34.78        36.62        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-36-1581 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-36-2548 TCGA-36-2549 TCGA-36-2551 
       20.98        18.31        20.52        14.17         6.05        16.18 
TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 
       11.47        13.81        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-57-1994 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 
       22.32        29.00        25.02        80.12        22.32       116.12 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-A5PD TCGA-61-1721 
        9.40        34.39         2.14         5.42        20.52        11.11 
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-61-1743 
       28.47        48.79        44.84        35.80         2.43        43.69 
TCGA-61-1895 TCGA-61-1899 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 
        1.45         8.42        11.41        13.02         9.07        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-61-2009 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-61-2097 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-61-2110 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-WR-A838 
       39.68        18.94         9.99 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.53              0.26 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           180.20            152.02 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            24.00             28.93 
[1] "0.5 - 180.2 (24.0)" "0.3 - 152.0 (28.9)"
[1] "hr=" "1.1"
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, continuous
D40V5, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     0  78
  XP GAIN WILD-TYPE   3 492
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      0   78
  XP GAIN WILD-TYPE    3  492
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO                0                 3
  YES              78               492
[1] 2 2
[1] FALSE
                   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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP GAIN MUTATED                                  0     2
  XP GAIN WILD-TYPE                                3    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  XP GAIN MUTATED                           7
  XP GAIN WILD-TYPE                        27
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XP GAIN MUTATED                                           0    66
  XP GAIN WILD-TYPE                                         1   410
D40V7, multiclass
                                           clus
vv                                          XP GAIN MUTATED XP GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   2                17
  BLACK OR AFRICAN AMERICAN                               7                27
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  66               410
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V8, 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    50  58
  XQ GAIN WILD-TYPE 218 234
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              108               452 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               58               234 
$`XQ GAIN MUTATED`
TCGA-04-1342 TCGA-04-1346 TCGA-04-1351 TCGA-04-1525 TCGA-04-1652 TCGA-04-1655 
       18.51        65.52        65.46        38.37        31.86        45.37 
TCGA-09-1674 TCGA-09-2043 TCGA-09-2045 TCGA-09-2048 TCGA-10-0927 TCGA-10-0933 
        8.55         6.18        35.15         4.54        81.86        14.66 
TCGA-10-0936 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0727 TCGA-13-0751 
       36.92        24.59        44.55        39.58        15.19        55.17 
TCGA-13-0757 TCGA-13-0761 TCGA-13-0768 TCGA-13-0795 TCGA-13-0797 TCGA-13-0800 
       11.18        34.06         8.45        19.59         8.71         8.12 
TCGA-13-0804 TCGA-13-0884 TCGA-13-0890 TCGA-13-0897 TCGA-13-0901 TCGA-13-0916 
       35.28       107.18        67.99        57.47        19.36        21.17 
TCGA-13-0921 TCGA-13-1404 TCGA-13-1409 TCGA-13-1485 TCGA-13-1488 TCGA-13-1504 
        4.64         6.61         6.84        20.68        70.82        16.57 
TCGA-13-1505 TCGA-13-2057 TCGA-13-2060 TCGA-13-2065 TCGA-20-0987 TCGA-20-0991 
        4.21        14.24         8.61         8.75        23.05        26.20 
TCGA-20-1683 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1109 TCGA-23-1110 
       25.38        16.70         2.93         2.66        51.35        54.51 
TCGA-23-1111 TCGA-23-1114 TCGA-23-1809 TCGA-23-2077 TCGA-23-2079 TCGA-23-2084 
        3.22        68.68         0.53       115.89        91.66        49.84 
TCGA-24-1104 TCGA-24-1474 TCGA-24-1555 TCGA-24-1556 TCGA-24-1563 TCGA-24-1564 
       63.55        22.22        88.50        70.62        47.70        25.87 
TCGA-24-1843 TCGA-24-1846 TCGA-24-1924 TCGA-24-2033 TCGA-24-2038 TCGA-24-2261 
        3.48         4.37        30.21        18.48        44.52         0.79 
TCGA-24-2281 TCGA-25-1319 TCGA-25-1320 TCGA-25-1329 TCGA-25-1632 TCGA-25-1871 
       44.61        65.00        37.97        15.02        59.15        24.99 
TCGA-25-1877 TCGA-25-2397 TCGA-25-2398 TCGA-25-2400 TCGA-29-1691 TCGA-29-1699 
       24.00        12.00        45.01        42.02        48.33        36.36 
TCGA-29-1710 TCGA-29-1764 TCGA-29-1766 TCGA-29-1776 TCGA-29-1778 TCGA-29-A5NZ 
       31.27        62.93        39.42        11.84        14.93        35.77 
TCGA-30-1718 TCGA-30-1855 TCGA-30-1862 TCGA-30-1867 TCGA-30-1887 TCGA-31-1951 
       51.91         2.47         6.12         1.22        24.26        22.49 
TCGA-36-2529 TCGA-57-1584 TCGA-57-1586 TCGA-59-2348 TCGA-59-2372 TCGA-5X-AA5U 
       35.05        21.14        22.32       180.20        44.81        11.87 
TCGA-61-1722 TCGA-61-1741 TCGA-61-1899 TCGA-61-1900 TCGA-61-1911 TCGA-61-1915 
        8.09        33.67         8.42         5.79        42.51        67.76 
TCGA-61-2003 TCGA-61-2087 TCGA-61-2109 TCGA-61-2612 TCGA-61-2614 TCGA-VG-A8LO 
        4.01         4.80        20.68         6.35         8.61         0.79 

$`XQ GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       43.92        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1341 TCGA-04-1343 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 
        1.08        11.87        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-04-1530 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-04-1654 TCGA-09-0364 TCGA-09-0365 
       28.64        64.64        36.23        47.70        29.16         9.47 
TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       57.76        17.98        35.57         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-09-1675 TCGA-09-2044 TCGA-09-2049 
       17.98         5.85         3.02        97.55         6.12       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-10-0925 TCGA-10-0926 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 
       54.31        25.91        18.51        34.19        32.88         6.71 
TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0724 TCGA-13-0725 
       35.44        19.99        20.91         6.21         2.73        12.39 
TCGA-13-0726 TCGA-13-0730 TCGA-13-0755 TCGA-13-0758 TCGA-13-0760 TCGA-13-0762 
       31.20        17.82         2.50        11.38        11.54        32.25 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 
       31.04        21.40        38.93        36.72        28.70        30.35 
TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 
        7.79         8.28         8.19        43.86        35.31        13.61 
TCGA-13-0883 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 
       68.94        91.40        74.27        66.67        70.39        61.84 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 
       69.01        43.36        56.15        57.07        47.38        48.33 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       47.84        44.94        44.84        37.08        27.72        34.06 
TCGA-13-0913 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 
       29.98        14.89        13.81         6.41         6.08        10.88 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
        7.36         6.05         5.92         4.70         4.21         5.33 
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        98.04        22.39 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
       82.88        52.44        73.55        38.20        49.25         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1506 
       54.31        37.61        38.40        13.97        32.84         4.41 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 
        4.77         4.18         2.56         3.91         3.09        12.23 
TCGA-13-2061 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-0996 
       10.78         6.28        54.77         8.42        25.94        72.20 
TCGA-20-1682 TCGA-20-1684 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 
       27.52        19.10        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-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 
        2.76        31.20         4.57        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-23-2078 TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 
       87.48        77.00         2.76         4.70         4.50         7.63 
TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
       19.66        11.64        21.80        41.56         7.66        22.32 
TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 
       54.12        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-24-1434 TCGA-24-1435 
        4.83        17.39        28.37        19.17        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-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 
        3.45         1.18        26.96        57.40        64.27        16.21 
TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1557 
       56.58        41.06        51.91        41.39        58.09        39.88 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       19.53        44.09        45.50        10.26        17.23        90.15 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 
       88.37        48.33        38.24         8.32         3.72         3.81 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1927 
       11.28         5.79         5.52         9.80        22.68        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-24-2035 TCGA-24-2036 
       34.82       109.71        14.43        55.92        28.18        64.01 
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-24-2288 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-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1623 
        2.01        34.98        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-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1878 TCGA-25-2042 
       62.17        35.87        52.04        14.96        85.05        13.02 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2399 TCGA-25-2401 
       49.05         1.02        38.04         3.02        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-29-1701 
       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-29-1762 TCGA-29-1763 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 
       86.60        66.81        31.30        22.98        24.36        22.55 
TCGA-29-1774 TCGA-29-1775 TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
       17.33        12.36        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-30-1714 TCGA-30-1853 
       42.25        21.47        11.47         9.76        38.07        36.26 
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-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 
       57.57        30.05        48.79        45.57        30.18        18.77 
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-36-1581 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-36-2543 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-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
       13.81        47.57        23.74        28.93        42.02        10.42 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1585 TCGA-57-1992 
       40.77         1.48        24.03        11.38         1.74        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-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1724 
       34.39         2.14         5.42        20.52        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 
       18.94         9.99 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.53              0.26 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           180.20            152.02 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            24.13             29.10 
[1] "0.5 - 180.2 (24.1)" "0.3 - 152.0 (29.1)"
[1] "hr=" "1.1"
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, continuous
D41V5, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     0 108
  XQ GAIN WILD-TYPE   3 462
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0  108
  XQ GAIN WILD-TYPE    3  462
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                0                 3
  YES             108               462
[1] 2 2
[1] FALSE
                   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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ GAIN MUTATED                                  0     2
  XQ GAIN WILD-TYPE                                3    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  XQ GAIN MUTATED                           9
  XQ GAIN WILD-TYPE                        25
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XQ GAIN MUTATED                                           0    93
  XQ GAIN WILD-TYPE                                         1   383
D41V7, multiclass
                                           clus
vv                                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   2                17
  BLACK OR AFRICAN AMERICAN                               9                25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  93               383
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V8, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     2  70
  XQ GAIN WILD-TYPE   8 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      2   70
  XQ GAIN WILD-TYPE    8  257
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 8
  NOT HISPANIC OR LATINO              70               257
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    30  32
  1P LOSS WILD-TYPE 238 260
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               62               498 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               32               260 
$`1P LOSS MUTATED`
TCGA-04-1341 TCGA-04-1351 TCGA-04-1362 TCGA-04-1514 TCGA-04-1519 TCGA-04-1542 
        1.08        65.46        44.32        56.55         0.79        84.20 
TCGA-04-1638 TCGA-09-1669 TCGA-09-1672 TCGA-09-2056 TCGA-10-0928 TCGA-10-0935 
       55.43        30.51         5.85        12.46        18.51        35.44 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0794 TCGA-13-0905 TCGA-13-1409 TCGA-13-1477 
       34.06        32.25        30.35        47.84         6.84        54.64 
TCGA-13-1484 TCGA-13-1489 TCGA-13-1497 TCGA-13-2065 TCGA-20-1682 TCGA-20-1686 
       98.04        82.88        54.31         8.75        27.52         2.93 
TCGA-20-1687 TCGA-23-1022 TCGA-23-2643 TCGA-23-2645 TCGA-24-0982 TCGA-24-1103 
        2.66        49.68         4.70         4.50        22.32        54.12 
TCGA-24-1105 TCGA-24-1423 TCGA-24-1424 TCGA-24-1850 TCGA-24-2020 TCGA-25-1316 
       47.41         6.25         6.02         5.52       152.02        42.05 
TCGA-25-1877 TCGA-25-2396 TCGA-25-2408 TCGA-29-1690 TCGA-29-1705 TCGA-29-1763 
       24.00         3.02        31.00        47.61        18.25        66.81 
TCGA-29-1768 TCGA-29-2429 TCGA-30-1853 TCGA-30-1859 TCGA-30-1860 TCGA-36-1569 
       31.30        13.84        36.26        48.10        44.91        29.10 
TCGA-36-1576 TCGA-36-1580 TCGA-36-2540 TCGA-36-2543 TCGA-36-2552 TCGA-57-1585 
       30.08        24.23        23.80         2.24        11.47         1.74 
TCGA-59-2352 TCGA-59-A5PD TCGA-61-1727 TCGA-61-1918 TCGA-61-2012 TCGA-61-2101 
        9.40        20.52        18.54        15.75        30.64        55.50 
TCGA-61-2612 TCGA-WR-A838 
        6.35         9.99 

$`1P LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       43.92        41.00         1.81        49.15         2.01        46.62 
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-04-1356 TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 
       63.98         0.53        49.28        32.52        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-04-1536 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 
       29.10        48.89        27.88        28.64        64.64        36.23 
TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 
       31.86        47.70        45.37        29.16         9.47        57.76 
TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       17.98        35.57         9.99        38.43        89.33        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1670 TCGA-09-1673 
       41.62        57.60        61.87        55.36        17.98         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-09-2050 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-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-10-0936 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-13-0727 
       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-13-0760 
       17.82        55.17         2.50        11.18        11.38        11.54 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       31.04        21.40         8.45        38.93        36.72        28.70 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 
       19.59         8.71         7.79         8.12         8.28         8.19 
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 
       91.40        74.27        66.67        70.39        61.84        67.99 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
       69.01        43.36        57.47        56.15        57.07        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       47.38        48.33        44.94        44.84        37.08        27.72 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 
       34.06        29.98        21.17        14.89        13.81         4.64 
TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 
        6.41         6.08        10.88         6.61         7.36         6.05 
TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 TCGA-13-1482 
        5.92         4.70         4.21         5.33        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        73.55 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 
       38.20        49.25         4.24        37.61        38.40        13.97 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       32.84        16.57         4.21         4.41         4.77         4.18 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
        2.56         3.91         3.09        14.24        12.23         8.61 
TCGA-13-2061 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
       10.78         6.28        54.77         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         4.57        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-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        2.76         7.63        19.66        11.64        21.80        41.56 
TCGA-24-0980 TCGA-24-1104 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 
        7.66        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-24-1428 
        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        19.17        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-24-1558 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-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 
        5.79         9.80        22.68        30.21        16.44        11.05 
TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 
       81.11         4.87        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-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 
       52.04         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-25-1878 TCGA-25-2042 
       35.87        52.04        14.96        24.99        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-29-1764 TCGA-29-1766 TCGA-29-1769 
       34.62        17.36        86.60        62.93        39.42        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-29-1778 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-29-2431 TCGA-29-2432 TCGA-29-2434 
       65.00        62.47        45.11        42.25        21.47        11.47 
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-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 
        0.26        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-36-1577 TCGA-36-1578 
       21.53        22.85        22.55         8.55        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-36-2542 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 
       25.08        21.60        20.98        18.31        20.52        14.17 
TCGA-36-2549 TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
        6.05        16.18        13.81        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-5X-AA5U TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
       44.81        11.87        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 

  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 
            28.31             28.67 
[1] "0.8 - 152.0 (28.3)" "0.3 - 180.2 (28.7)"
[1] "hr=" "1"  
D42V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  1P LOSS MUTATED         0    63                0
  1P LOSS WILD-TYPE       3   495                2
D42V3, multiclass
                  clus
vv                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  OMENTUM                        0                 3
  OVARY                         63               495
  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, continuous
D42V5, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     1  63
  1P LOSS WILD-TYPE   2 507
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1   63
  1P LOSS WILD-TYPE    2  507
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                1                 2
  YES              63               507
[1] 2 2
[1] FALSE
                   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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P LOSS MUTATED                                  0     1
  1P LOSS WILD-TYPE                                3    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  1P LOSS MUTATED                           6
  1P LOSS WILD-TYPE                        28
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1P LOSS MUTATED                                           0    50
  1P LOSS WILD-TYPE                                         1   426
D42V7, multiclass
                                           clus
vv                                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   1                18
  BLACK OR AFRICAN AMERICAN                               6                28
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  50               426
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V8, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     2  36
  1P LOSS WILD-TYPE   8 291
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2   36
  1P LOSS WILD-TYPE    8  291
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 8
  NOT HISPANIC OR LATINO              36               291
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    18  23
  1Q LOSS WILD-TYPE 250 269
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               41               519 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               23               269 
$`1Q LOSS MUTATED`
TCGA-04-1341 TCGA-04-1351 TCGA-04-1362 TCGA-04-1519 TCGA-10-0928 TCGA-13-0761 
        1.08        65.46        44.32         0.79        18.51        34.06 
TCGA-13-0794 TCGA-13-0905 TCGA-13-1407 TCGA-13-1477 TCGA-13-1489 TCGA-13-1497 
       30.35        47.84         6.05        54.64        82.88        54.31 
TCGA-13-2065 TCGA-20-1682 TCGA-23-1022 TCGA-23-1109 TCGA-23-2643 TCGA-23-2645 
        8.75        27.52        49.68        51.35         4.70         4.50 
TCGA-24-1103 TCGA-24-1105 TCGA-24-1424 TCGA-24-1850 TCGA-24-2020 TCGA-25-1877 
       54.12        47.41         6.02         5.52       152.02        24.00 
TCGA-25-2408 TCGA-29-1705 TCGA-29-1763 TCGA-29-1768 TCGA-29-2429 TCGA-30-1853 
       31.00        18.25        66.81        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-59-A5PD TCGA-61-1727 TCGA-61-2012 TCGA-61-2612 TCGA-WR-A838 
       20.52        18.54        30.64         6.35         9.99 

$`1Q LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       43.92        41.00         1.81        49.15         2.01        46.62 
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-04-1356 TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 
       63.98         0.53        49.28        32.52        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-04-1542 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-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 
       29.16         9.47        57.76        17.98        35.57         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-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        32.25        31.04        21.40         8.45        38.93 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 
       36.72        28.70        19.59         8.71         7.79         8.12 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
        8.28         8.19        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        91.40        74.27        66.67        70.39 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 
       61.84        67.99        69.01        43.36        57.47        56.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 
       57.07        19.36        47.38        48.33        44.94        44.84 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
       37.08        27.72        34.06        29.98        21.17        14.89 
TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 
       13.81         4.64         6.41         6.08        10.88         6.61 
TCGA-13-1405 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
        7.36         5.92         6.84         4.70         4.21         5.33 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 
       87.06        61.71        29.42        98.04        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        73.55        38.20        49.25         4.24 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 
       37.61        38.40        13.97        32.84        16.57         4.21 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
        4.41         4.77         4.18         2.56         3.91         3.09 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2071 TCGA-13-A5FT 
       14.24        12.23         8.61        10.78         6.28        54.77 
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-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1023 
       19.10        16.70         2.93         2.66        47.54        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-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 
       18.90         2.76        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 
        4.57        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-24-0966 
       87.48        91.66        77.00        49.84         2.76         7.63 
TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
       19.66        11.64        21.80        41.56         7.66        22.32 
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-24-1427 TCGA-24-1428 
        0.76         6.25         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        19.17        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-24-1558 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-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 
        5.79         9.80        22.68        30.21        16.44        11.05 
TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 
       81.11         4.87        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-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 
       17.03        12.95        20.61        38.20         0.30        59.15 
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-25-2397 
       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-25-2409 
       45.01        19.99        42.02         2.96        29.03        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-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 
       59.67        41.98        31.27        34.62        17.36        86.60 
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-3P-A9WA TCGA-42-2582 TCGA-42-2587 
        6.05        16.18        11.47        13.81        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-5X-AA5U TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 
        5.42        44.81        11.87        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-61-1741 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-61-1995 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-61-2016 TCGA-61-2017 
       17.98         4.01        30.64        39.85         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-61-2613 TCGA-61-2614 
       20.68        44.52       125.75        22.22        31.07         8.61 
TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
       39.68        18.94         0.79 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.79              0.26 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           152.02            180.20 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            27.52             28.70 
[1] "0.8 - 152.0 (27.5)" "0.3 - 180.2 (28.7)"
[1] "hr=" "1.1"
D43V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  1Q LOSS MUTATED         0    42                0
  1Q LOSS WILD-TYPE       3   516                2
D43V3, multiclass
                  clus
vv                 1Q LOSS MUTATED 1Q LOSS 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"
D43V4, continuous
D43V5, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     1  42
  1Q LOSS WILD-TYPE   2 528
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1   42
  1Q LOSS WILD-TYPE    2  528
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                1                 2
  YES              42               528
[1] 2 2
[1] FALSE
                   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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q LOSS MUTATED                                  0     1
  1Q LOSS WILD-TYPE                                3    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  1Q LOSS MUTATED                           5
  1Q LOSS WILD-TYPE                        29
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1Q LOSS MUTATED                                           0    32
  1Q LOSS WILD-TYPE                                         1   444
D43V7, multiclass
                                           clus
vv                                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   1                18
  BLACK OR AFRICAN AMERICAN                               5                29
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  32               444
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V8, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     1  24
  1Q LOSS WILD-TYPE   9 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1   24
  1Q LOSS WILD-TYPE    9  303
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              24               303
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    22  30
  2P LOSS WILD-TYPE 246 262
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               52               508 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               30               262 
$`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-13-0723 TCGA-13-0751 TCGA-13-0762 TCGA-13-0883 TCGA-13-0890 
        3.02        39.58        55.17        32.25        68.94        67.99 
TCGA-13-0891 TCGA-13-0904 TCGA-13-0916 TCGA-13-0924 TCGA-13-1411 TCGA-13-1484 
       69.01        48.33        21.17         6.08         4.21        98.04 
TCGA-13-1494 TCGA-13-1507 TCGA-20-0991 TCGA-20-1682 TCGA-23-1116 TCGA-24-1413 
       38.20         4.77        26.20        27.52         4.57         6.31 
TCGA-24-1464 TCGA-24-1563 TCGA-24-1614 TCGA-24-1847 TCGA-24-1923 TCGA-24-1930 
       12.46        47.70        48.33        11.28        22.68        81.11 
TCGA-24-2020 TCGA-24-2260 TCGA-24-2280 TCGA-25-1313 TCGA-25-1318 TCGA-25-1321 
      152.02        36.16        70.45        26.96        34.98        33.96 
TCGA-25-1627 TCGA-25-1878 TCGA-25-2392 TCGA-29-1688 TCGA-29-1693 TCGA-29-1699 
       12.95        85.05         1.02        78.90       101.79        36.36 
TCGA-29-1761 TCGA-29-1770 TCGA-30-1853 TCGA-36-2543 TCGA-36-2545 TCGA-61-1743 
       17.36        24.36        36.26         2.24        18.31        43.69 
TCGA-61-2016 TCGA-61-2087 TCGA-61-2092 TCGA-61-2109 
        1.18         4.80        51.72        20.68 

$`2P LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       43.92        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1341 TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1350 
        1.08        18.51        65.52        63.09        48.76        63.98 
TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 
       65.46         0.53        49.28        32.52        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-04-1542 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-09-0364 TCGA-09-0365 
       36.23        31.86        47.70        45.37        29.16         9.47 
TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       57.76        17.98        35.57         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-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 
       17.98         5.85         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-10-0925 TCGA-10-0926 TCGA-10-0927 
       20.94        26.93        12.46        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-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
       36.92        19.99        20.91         6.21        24.59        44.55 
TCGA-13-0724 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-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 
       11.18        11.38        11.54        34.06        31.04        21.40 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 
        8.45        38.93        36.72        28.70        30.35        19.59 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 
        8.71         7.79         8.12         8.28         8.19        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        91.40        74.27 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 
       66.67        70.39        61.84        43.36        57.47        56.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 
       57.07        19.36        47.38        47.84        44.94        44.84 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0919 TCGA-13-0920 
       37.08        27.72        34.06        29.98        14.89        13.81 
TCGA-13-0921 TCGA-13-0923 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 
        4.64         6.41        10.88         6.61         7.36         6.05 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
        5.92         6.84         4.70         5.33        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        82.88 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
       52.44        73.55        49.25         4.24        54.31        37.61 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       38.40        13.97        32.84        16.57         4.21         4.41 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 
        4.18         2.56         3.91         3.09        14.24        12.23 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU 
        8.61        10.78         8.75         6.28        54.77         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-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 
        2.76        51.35        54.51         3.22        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-23-2079 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-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        7.63        19.66        11.64        21.80        41.56         7.66 
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-24-1424 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        19.17        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 
       43.53         8.55        72.92        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-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 
       25.87        10.26        17.23        90.15        88.37        38.24 
TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1849 
        8.32         3.48         3.72         3.81         4.37         5.79 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 
        5.52         9.80        30.21        16.44        11.05         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-24-2261 
       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-25-1322 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-25-1628 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-25-2042 TCGA-25-2391 
       52.04        14.96        24.99        24.00        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-29-1690 TCGA-29-1691 
        2.96        29.03        31.00        26.99        47.61        48.33 
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-29-1762 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-29-1771 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-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 
       62.47        45.11        13.84        42.25        21.47        11.47 
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-30-1866 
        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-36-1575 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-36-2547 TCGA-36-2548 TCGA-36-2549 
       23.80        21.60        20.98        20.52        14.17         6.05 
TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
       16.18        11.47        13.81        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-59-A5PD TCGA-5X-AA5U TCGA-61-1721 
        2.14         5.42        44.81        20.52        11.87        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-61-2094 TCGA-61-2095 
       30.64        45.96        45.40         4.77        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-61-2110 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 
       39.68        18.94         0.79         9.99 

  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 
           30.675            28.555 
[1] "1.0 - 152.0 (30.7)" "0.3 - 180.2 (28.6)"
[1] "hr=" "1.1"
D44V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  2P LOSS MUTATED         0    53                0
  2P LOSS WILD-TYPE       3   505                2
D44V3, multiclass
                  clus
vv                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  OMENTUM                        0                 3
  OVARY                         53               505
  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, continuous
D44V5, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0  53
  2P LOSS WILD-TYPE   3 517
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   53
  2P LOSS WILD-TYPE    3  517
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                0                 3
  YES              53               517
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  2P LOSS MUTATED    1  1  0  0
  2P LOSS WILD-TYPE 14 25  5  3
D44V6, multiclass
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2                47 
       TCGA-04-1516        TCGA-04-1644        TCGA-13-0807        TCGA-13-0911 
"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-36-2544        TCGA-36-2547        TCGA-36-2548        TCGA-36-2549 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-36-2551        TCGA-36-2552        TCGA-3P-A9WA        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-5X-AA5U        TCGA-61-2612        TCGA-61-2613        TCGA-61-2614 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-OY-A56P        TCGA-OY-A56Q        TCGA-VG-A8LO 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P LOSS MUTATED                                  0     1
  2P LOSS WILD-TYPE                                3    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  2P LOSS MUTATED                           2
  2P LOSS WILD-TYPE                        32
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2P LOSS MUTATED                                           0    47
  2P LOSS WILD-TYPE                                         1   429
D44V7, multiclass
                                           clus
vv                                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   1                18
  BLACK OR AFRICAN AMERICAN                               2                32
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  47               429
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0  31
  2P LOSS WILD-TYPE  10 296
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   31
  2P LOSS WILD-TYPE   10  296
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                10
  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    27  30
  2Q LOSS WILD-TYPE 241 262
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               57               503 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               30               262 
$`2Q LOSS MUTATED`
TCGA-04-1336 TCGA-04-1342 TCGA-04-1349 TCGA-04-1517 TCGA-09-1673 TCGA-13-0723 
       49.15        18.51        21.57        19.99         3.02        39.58 
TCGA-13-0751 TCGA-13-0762 TCGA-13-0890 TCGA-13-0891 TCGA-13-0904 TCGA-13-0916 
       55.17        32.25        67.99        69.01        48.33        21.17 
TCGA-13-0924 TCGA-13-1411 TCGA-13-1484 TCGA-13-1494 TCGA-13-1507 TCGA-13-A5FU 
        6.08         4.21        98.04        38.20         4.77         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         4.57         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-30-1887 TCGA-36-1575 TCGA-36-2529 TCGA-36-2543 TCGA-36-2545 TCGA-61-2016 
       24.26         8.55        35.05         2.24        18.31         1.18 
TCGA-61-2087 TCGA-61-2092 TCGA-61-2109 
        4.80        51.72        20.68 

$`2Q LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 
       43.92        41.00         1.81         2.01        46.62         1.08 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 
       11.87        65.52        63.09        48.76        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-04-1519 TCGA-04-1525 
      103.40        82.39        56.55        41.59         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-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 
       29.16         9.47        57.76        17.98        35.57         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-09-1674 TCGA-09-1675 
       55.36        30.51        17.98         5.85         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-10-0925 
       63.09        39.75        20.94        26.93        12.46        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-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 
       24.59        44.55         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        34.06 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       31.04        21.40         8.45        38.93        36.72        28.70 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
       30.35        19.59         8.71         7.79         8.12         8.28 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
        8.19        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        91.40        74.27        66.67        70.39        61.84 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       43.36        57.47        56.15        57.07        19.36        47.38 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       47.84        44.94        44.84        37.08        27.72        34.06 
TCGA-13-0913 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-1403 
       29.98        14.89        13.81         4.64         6.41        10.88 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
        6.61         7.36         6.05         5.92         6.84         4.70 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 
        5.33        54.64        87.06        61.71        29.42        20.68 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1495 
       22.39        70.82        82.88        52.44        73.55        49.25 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 
        4.24        54.31        37.61        38.40        13.97        32.84 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
       16.57         4.21         4.41         4.18         2.56         3.91 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 
        3.09        14.24        12.23         8.61        10.78         8.75 
TCGA-13-2071 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 TCGA-20-0996 TCGA-20-1683 
        6.28        54.77        23.05        25.94        72.20        25.38 
TCGA-20-1684 TCGA-20-1685 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 
       19.10        16.70         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-23-1111 TCGA-23-1113 
       18.90         2.76        51.35        54.51         3.22        31.20 
TCGA-23-1114 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 
       68.68        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-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        4.50         7.63        19.66        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        19.17 
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-30-1860 
       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-30-1891 
       34.78         6.12        36.62         1.22        57.57        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-36-1576 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-36-2544 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 
       23.80        21.60        20.98        20.52        14.17         6.05 
TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
       16.18        11.47        13.81        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-59-A5PD TCGA-5X-AA5U TCGA-61-1721 
        2.14         5.42        44.81        20.52        11.87        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-61-1900 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-61-2002 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-61-2017 TCGA-61-2018 TCGA-61-2088 TCGA-61-2094 
       39.85        30.64        45.96        45.40         4.77        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 
        8.61        39.68        18.94         0.79         9.99 

  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 
            24.26             29.10 
[1] "1.0 - 152.0 (24.3)" "0.3 - 180.2 (29.1)"
[1] "hr=" "1"  
D45V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  2Q LOSS MUTATED         0    57                1
  2Q LOSS WILD-TYPE       3   501                1
D45V3, multiclass
                  clus
vv                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  OMENTUM                        0                 3
  OVARY                         57               501
  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, continuous
D45V5, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0  59
  2Q LOSS WILD-TYPE   3 511
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   59
  2Q LOSS WILD-TYPE    3  511
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                0                 3
  YES              59               511
[1] 2 2
[1] FALSE
                   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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q LOSS MUTATED                                  0     1
  2Q LOSS WILD-TYPE                                3    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  2Q LOSS MUTATED                           2
  2Q LOSS WILD-TYPE                        32
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2Q LOSS MUTATED                                           0    50
  2Q LOSS WILD-TYPE                                         1   426
D45V7, multiclass
                                           clus
vv                                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   1                18
  BLACK OR AFRICAN AMERICAN                               2                32
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  50               426
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0  30
  2Q LOSS WILD-TYPE  10 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   30
  2Q LOSS WILD-TYPE   10  297
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              30               297
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    45  48
  3P LOSS WILD-TYPE 223 244
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               93               467 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               48               244 
$`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-04-1652 TCGA-09-0369 
       56.55        38.37       119.08        84.20        31.86        35.57 
TCGA-09-1667 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-10-0938 TCGA-13-0730 
       61.87        71.11        63.09        39.75        20.91        17.82 
TCGA-13-0757 TCGA-13-0792 TCGA-13-0794 TCGA-13-0890 TCGA-13-0920 TCGA-13-1407 
       11.18        36.72        30.35        67.99        13.81         6.05 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1411 TCGA-13-1487 TCGA-13-1492 TCGA-13-1499 
        5.92         6.84         4.21        22.39        73.55        38.40 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2060 TCGA-20-0990 TCGA-23-1024 TCGA-23-1031 
        3.09        14.24         8.61        25.94        15.39        18.90 
TCGA-23-1032 TCGA-23-1114 TCGA-24-0968 TCGA-24-0970 TCGA-24-1417 TCGA-24-1418 
        2.76        68.68        19.66        11.64         7.82         7.99 
TCGA-24-1464 TCGA-24-1469 TCGA-24-1545 TCGA-24-1548 TCGA-24-1550 TCGA-24-1846 
       12.46         9.11        57.40        16.21        41.06         4.37 
TCGA-24-1930 TCGA-24-2026 TCGA-24-2027 TCGA-24-2262 TCGA-24-2288 TCGA-24-2293 
       81.11        34.82       109.71         0.36         0.82        16.64 
TCGA-25-1312 TCGA-25-1317 TCGA-25-1320 TCGA-25-1323 TCGA-25-1627 TCGA-25-1633 
        1.02         2.01        37.97        12.99        12.95        62.17 
TCGA-25-1870 TCGA-25-2392 TCGA-25-2397 TCGA-29-1691 TCGA-29-1693 TCGA-29-1699 
       14.96         1.02        12.00        48.33       101.79        36.36 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1777 TCGA-30-1855 TCGA-30-1887 TCGA-31-1959 
       66.81        62.93        12.30         2.47        24.26         2.20 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1580 TCGA-36-2530 TCGA-36-2552 TCGA-42-2589 
        8.55        30.08        24.23        33.01        11.47        42.02 
TCGA-42-2593 TCGA-57-1992 TCGA-59-2363 TCGA-61-1722 TCGA-61-1730 TCGA-61-1733 
        1.48        29.00         5.42         8.09         4.34        31.79 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1914 TCGA-61-1917 TCGA-61-1919 TCGA-61-2012 
       33.67        43.69        56.61        43.43        38.17        30.64 
TCGA-61-2016 TCGA-61-2104 TCGA-61-2113 
        1.18        76.87        22.22 

$`3P LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       43.92        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 
        1.08        18.51        11.87        48.76        21.57        63.98 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1367 TCGA-04-1371 TCGA-04-1516 
       32.52        44.32        33.67       103.40        82.39        41.59 
TCGA-04-1517 TCGA-04-1519 TCGA-04-1536 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
       19.99         0.79        29.10        55.43        48.89        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 
       28.64        64.64        36.23        47.70        45.37        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
        9.47        57.76        17.98         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-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-13-0714 
       14.66         6.71        35.44        36.92        19.99         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-13-0751 TCGA-13-0755 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 
       15.19        55.17         2.50        11.38        11.54        34.06 
TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0793 
       32.25        31.04        21.40         8.45        38.93        28.70 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 
       19.59         8.71         7.79         8.12         8.28         8.19 
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 
       91.40        74.27        66.67        70.39        61.84        69.01 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       43.36        57.47        56.15        57.07        19.36        47.38 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       48.33        47.84        44.94        44.84        37.08        27.72 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 
       34.06        29.98        21.17        14.89         4.64         6.41 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1410 TCGA-13-1412 
        6.08        10.88         6.61         7.36         4.70         5.33 
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        98.04        20.68 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
       70.82        82.88        52.44        38.20        49.25         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 
       54.31        37.61        13.97        32.84        16.57         4.21 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-2059 
        4.41         4.77         4.18         2.56         3.91        12.23 
TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
       10.78         8.75         6.28        54.77         8.42        23.05 
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-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 
        2.93         2.66        47.54        49.68        40.54        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1109 TCGA-23-1110 
       32.09        49.41         8.81        29.13        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         4.57        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-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0975 TCGA-24-0979 
        2.76         4.70         4.50         7.63        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-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 
        6.38         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        19.17        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 
       43.53         8.55        72.92        45.14       105.99         3.45 
TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1546 TCGA-24-1549 TCGA-24-1551 
        1.18        22.22        26.96        64.27        56.58        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-24-1845 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-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 TCGA-24-2020 
       22.68        30.21        16.44        11.05         4.87       152.02 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 
       44.84        58.16        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-25-1313 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-25-1322 TCGA-25-1329 TCGA-25-1623 
       34.98        65.00        33.96         2.99        15.02        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 
       27.62        17.03        20.61        38.20         0.30        59.15 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 
       35.87        52.04        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-29-1694 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-29-1766 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-29-1776 TCGA-29-1778 TCGA-29-1781 
       22.55        17.33        12.36        11.84        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-29-2432 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-30-1862 TCGA-30-1866 TCGA-30-1867 
       48.10        44.91        34.78         6.12        36.62         1.22 
TCGA-30-1880 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 
       57.57        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-36-1577 TCGA-36-1578 TCGA-36-1581 
       21.53        22.85        22.55        25.74        27.85        24.69 
TCGA-36-2529 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       35.05        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-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
        6.05        16.18        13.81        47.57        23.74        28.93 
TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 
       10.42        40.77        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-59-2372 TCGA-59-A5PD 
      116.12         9.40        34.39         2.14        44.81        20.52 
TCGA-5X-AA5U TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 
       11.87        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 
        8.61        39.68        18.94         0.79         9.99 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.36              0.26 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           119.08            180.20 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            24.26             28.77 
[1] "0.4 - 119.1 (24.3)" "0.3 - 180.2 (28.8)"
[1] "hr=" "1"  
D46V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  3P LOSS MUTATED         1    93                0
  3P LOSS WILD-TYPE       2   465                2
D46V3, multiclass
                  clus
vv                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  OMENTUM                        1                 2
  OVARY                         93               465
  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, continuous
D46V5, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     1  93
  3P LOSS WILD-TYPE   2 477
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1   93
  3P LOSS WILD-TYPE    2  477
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                1                 2
  YES              93               477
[1] 2 2
[1] FALSE
                   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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  1     3
  3P LOSS WILD-TYPE                                2    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  3P LOSS MUTATED                           2
  3P LOSS WILD-TYPE                        32
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3P LOSS MUTATED                                           0    80
  3P LOSS WILD-TYPE                                         1   396
D46V7, multiclass
                                           clus
vv                                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 2
  ASIAN                                                   3                16
  BLACK OR AFRICAN AMERICAN                               2                32
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  80               396
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V8, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     1  56
  3P LOSS WILD-TYPE   9 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1   56
  3P LOSS WILD-TYPE    9  271
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              56               271
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    20  22
  3Q LOSS WILD-TYPE 248 270
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               42               518 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               22               270 
$`3Q LOSS MUTATED`
TCGA-04-1351 TCGA-04-1356 TCGA-04-1514 TCGA-04-1652 TCGA-09-2050 TCGA-10-0938 
       65.46        49.28        56.55        31.86        71.11        20.91 
TCGA-13-0730 TCGA-13-0762 TCGA-13-0794 TCGA-13-0890 TCGA-13-1407 TCGA-13-1408 
       17.82        32.25        30.35        67.99         6.05         5.92 
TCGA-13-1492 TCGA-13-1499 TCGA-13-1512 TCGA-23-1024 TCGA-23-1032 TCGA-24-0968 
       73.55        38.40         3.09        15.39         2.76        19.66 
TCGA-24-1418 TCGA-24-1469 TCGA-24-1545 TCGA-24-1550 TCGA-24-2262 TCGA-24-2288 
        7.99         9.11        57.40        41.06         0.36         0.82 
TCGA-24-2293 TCGA-25-1320 TCGA-25-2392 TCGA-25-2397 TCGA-29-1691 TCGA-29-1699 
       16.64        37.97         1.02        12.00        48.33        36.36 
TCGA-29-1763 TCGA-29-1777 TCGA-30-1855 TCGA-31-1959 TCGA-36-1575 TCGA-36-1580 
       66.81        12.30         2.47         2.20         8.55        24.23 
TCGA-42-2589 TCGA-57-1992 TCGA-61-1730 TCGA-61-1741 TCGA-61-1743 TCGA-61-2012 
       42.02        29.00         4.34        33.67        43.69        30.64 

$`3Q LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       43.92        41.00         1.81        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-04-1353 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 
       21.57        63.98         0.53        32.52        44.32        33.67 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 
       76.57       103.40        82.39        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-04-1654 TCGA-04-1655 
       27.88        28.64        64.64        36.23        47.70        45.37 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 
       29.16         9.47        57.76        17.98        35.57         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-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 
       63.09        39.75        20.94        26.93        12.46        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        34.06 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       31.04        21.40         8.45        38.93        36.72        28.70 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 
       19.59         8.71         7.79         8.12         8.28         8.19 
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 
       91.40        74.27        66.67        70.39        61.84        69.01 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       43.36        57.47        56.15        57.07        19.36        47.38 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       48.33        47.84        44.94        44.84        37.08        27.72 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 
       34.06        29.98        21.17        14.89        13.81         4.64 
TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1409 
        6.41         6.08        10.88         6.61         7.36         6.84 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 
        4.70         4.21         5.33        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        98.04        20.68        22.39        70.82        82.88 
TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
       52.44        38.20        49.25         4.24        54.31        37.61 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
       13.97        32.84        16.57         4.21         4.41         4.77 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
        4.18         2.56         3.91        14.24        12.23         8.61 
TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
       10.78         8.75         6.28        54.77         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-23-1030 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-23-1114 TCGA-23-1116 
       51.35        54.51         3.22        31.20        68.68         4.57 
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-24-1419 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-24-1434 TCGA-24-1435 
        4.83        17.39        28.37        19.17        18.67        43.53 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 
        8.55        72.92        12.46        45.14       105.99         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-24-1551 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-24-1850 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-24-2030 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-24-2260 TCGA-24-2261 TCGA-24-2267 TCGA-24-2271 
       44.52        57.07        36.16         0.79        47.54        31.63 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2289 TCGA-24-2290 TCGA-24-2295 TCGA-24-2297 
       70.45        44.61        67.36        36.23        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-25-1321 TCGA-25-1322 TCGA-25-1323 
        2.01        34.98        65.00        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-25-1635 
       38.20         0.30        59.15        62.17        35.87        52.04 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 
       14.96        24.99        24.00        85.05        13.02        49.05 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 
       38.04         3.02        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-29-1701 
       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-29-1764 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-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1778 
       24.36        22.55        17.33        12.36        11.84        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-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 
       62.47        45.11        13.84        42.25        21.47        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-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1576 
       28.77        29.10        21.53        22.85        22.55        30.08 
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-36-2540 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-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 
       11.47        13.81        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-59-A5PD TCGA-5X-AA5U TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
       20.52        11.87        11.11         8.09        20.94        31.43 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       18.54        27.88        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-61-1915 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-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
       39.85         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-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
       22.22         6.35        31.07         8.61        39.68        18.94 
TCGA-VG-A8LO TCGA-WR-A838 
        0.79         9.99 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.36              0.26 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            73.55            180.20 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           26.615            28.670 
[1] "0.4 - 73.5 (26.6)"  "0.3 - 180.2 (28.7)"
[1] "hr=" "1.2"
D47V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  3Q LOSS MUTATED         1    42                0
  3Q LOSS WILD-TYPE       2   516                2
D47V3, multiclass
                  clus
vv                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  OMENTUM                        1                 2
  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"
D47V4, continuous
D47V5, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     1  42
  3Q LOSS WILD-TYPE   2 528
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1   42
  3Q LOSS WILD-TYPE    2  528
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                1                 2
  YES              42               528
[1] 2 2
[1] FALSE
                   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-04-1516        TCGA-04-1644        TCGA-13-0807        TCGA-13-0911 
"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-3P-A9WA        TCGA-42-2582        TCGA-42-2587        TCGA-42-2588 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-42-2590        TCGA-42-2593        TCGA-57-1993        TCGA-59-2363 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-59-2372        TCGA-5X-AA5U        TCGA-61-2612        TCGA-61-2613 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-61-2614        TCGA-OY-A56P        TCGA-OY-A56Q        TCGA-VG-A8LO 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  0     0
  3Q LOSS WILD-TYPE                                3    19
                   vv
clus                BLACK OR AFRICAN AMERICAN
  3Q LOSS MUTATED                           2
  3Q LOSS WILD-TYPE                        32
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3Q LOSS MUTATED                                           0    37
  3Q LOSS WILD-TYPE                                         1   439
D47V7, multiclass
                                           clus
vv                                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   0                19
  BLACK OR AFRICAN AMERICAN                               2                32
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  37               439
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     1  24
  3Q LOSS WILD-TYPE   9 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1   24
  3Q LOSS WILD-TYPE    9  303
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              24               303
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED   142 159
  4P LOSS WILD-TYPE 126 133
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              301               259 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              159               133 
$`4P LOSS MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1338 TCGA-04-1341 TCGA-04-1343 TCGA-04-1348 
       43.92        41.00        46.62         1.08        11.87        48.76 
TCGA-04-1350 TCGA-04-1353 TCGA-04-1361 TCGA-04-1362 TCGA-04-1371 TCGA-04-1514 
       63.98         0.53        32.52        44.32        82.39        56.55 
TCGA-04-1516 TCGA-04-1517 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 
       41.59        19.99        29.10        84.20        55.43        48.89 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0365 
       64.64        36.23        31.86        47.70        45.37         9.47 
TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1667 
       17.98        35.57         9.99        38.43        89.33        61.87 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 TCGA-09-2043 TCGA-09-2044 TCGA-09-2049 
       30.51        17.98         3.02         6.18         6.12       112.41 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-10-0927 TCGA-10-0928 
       71.11        63.09        39.75        20.94        81.86        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0935 TCGA-13-0717 TCGA-13-0725 
       34.19        32.88        14.66        35.44        24.59        12.39 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0760 
       15.19        17.82        55.17         2.50        11.18        11.54 
TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0793 TCGA-13-0795 TCGA-13-0801 
       32.25        31.04        21.40        28.70        19.59         8.28 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 
       43.86        35.28        35.31       107.18        91.40        66.67 
TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 
       70.39        61.84        67.99        56.15        57.07        47.38 
TCGA-13-0904 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0919 TCGA-13-0921 
       48.33        37.08        27.72        34.06        14.89         4.64 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
        6.08        10.88         6.05         5.92         6.84         4.70 
TCGA-13-1411 TCGA-13-1481 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 
        4.21        87.06        98.04        22.39        70.82        82.88 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1495 TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 
       52.44        73.55        49.25        54.31        37.61        13.97 
TCGA-13-1504 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2061 
       16.57         4.18         3.91         3.09        12.23        10.78 
TCGA-13-2065 TCGA-13-A5FT TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 
        8.75        54.77        25.94        26.20        27.52        25.38 
TCGA-20-1684 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1028 
       19.10         2.93         2.66        47.54        49.68        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-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1122 TCGA-23-1123 
        4.57        33.30        86.01       129.96        39.09        33.47 
TCGA-23-2072 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-24-0968 TCGA-24-0970 
       24.95        49.84         2.76         4.70        19.66        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-24-1422 TCGA-24-1425 TCGA-24-1426 
        6.38         7.82         7.99         0.76         5.95         5.36 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 TCGA-24-1469 TCGA-24-1470 
       19.17        18.67         8.55        72.92         9.11         3.45 
TCGA-24-1471 TCGA-24-1474 TCGA-24-1548 TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 
        1.18        22.22        16.21        51.91        41.39        88.50 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 
       44.09        45.50        17.23        90.15        88.37        38.24 
TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1850 
        8.32         3.72         3.81         4.37        11.28         5.52 
TCGA-24-1923 TCGA-24-1924 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 
       22.68        30.21        81.11         4.87       152.02        44.84 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2254 TCGA-24-2261 TCGA-24-2267 
      109.71        14.43        55.92        57.07         0.79        47.54 
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-25-1314 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
       55.86        53.26        33.01        42.05         2.01        34.98 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1623 TCGA-25-1626 
       37.97        33.96         2.99        12.99        18.58        17.03 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 
       12.95        20.61         0.30        62.17        35.87        14.96 
TCGA-25-1871 TCGA-25-2400 TCGA-25-2404 TCGA-29-1688 TCGA-29-1695 TCGA-29-1697 
       24.99        42.02        29.03        78.90        40.41        31.20 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1705 TCGA-29-1762 TCGA-29-1764 
       68.32        36.36        16.93        18.25        86.60        62.93 
TCGA-29-1768 TCGA-29-1771 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 
       31.30        22.55        12.30        14.93         8.38         7.23 
TCGA-29-1784 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2431 TCGA-29-2434 
        5.36        86.17        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-59-A5PD TCGA-61-1730 
       34.39         2.14         5.42        44.81        20.52         4.34 
TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 
       28.47        48.79        44.84        33.67         1.45         8.42 
TCGA-61-1900 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1913 TCGA-61-1914 
        5.79        13.02         9.07        34.13        48.92        56.61 
TCGA-61-1917 TCGA-61-1919 TCGA-61-1995 TCGA-61-2003 TCGA-61-2016 TCGA-61-2018 
       43.43        38.17         2.01         4.01         1.18        45.40 
TCGA-61-2087 TCGA-61-2092 TCGA-61-2094 TCGA-61-2101 TCGA-61-2102 TCGA-61-2109 
        4.80        51.72        71.74        55.50         6.48        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-OY-A56P 
       44.52       125.75        22.22         6.35        31.07        39.68 
TCGA-OY-A56Q 
       18.94 

$`4P LOSS WILD-TYPE`
TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 
        1.81        49.15         2.01        18.51        65.52        63.09 
TCGA-04-1349 TCGA-04-1351 TCGA-04-1356 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       21.57        65.46        49.28        33.67        76.57       103.40 
TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1646 TCGA-04-1648 TCGA-09-0364 
        0.79        38.37       119.08        27.88        28.64        29.16 
TCGA-09-0366 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1668 TCGA-09-1672 
       57.76        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-10-0925 TCGA-10-0926 TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 
       54.31        25.91         6.71        36.92        19.99        20.91 
TCGA-13-0714 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 TCGA-13-0758 
        6.21        44.55        39.58         2.73        31.20        11.38 
TCGA-13-0761 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0794 TCGA-13-0797 
       34.06         8.45        38.93        36.72        30.35         8.71 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0802 TCGA-13-0807 TCGA-13-0883 TCGA-13-0886 
        7.79         8.12         8.19        13.61        68.94        74.27 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0901 TCGA-13-0905 TCGA-13-0906 
       69.01        43.36        57.47        19.36        47.84        44.94 
TCGA-13-0908 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0923 TCGA-13-1404 
       44.84        29.98        21.17        13.81         6.41         6.61 
TCGA-13-1405 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 
        7.36         5.33        54.64        61.71        29.42        20.68 
TCGA-13-1494 TCGA-13-1496 TCGA-13-1499 TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 
       38.20         4.24        38.40        32.84         4.21         4.41 
TCGA-13-1507 TCGA-13-1510 TCGA-13-2057 TCGA-13-2060 TCGA-13-2071 TCGA-13-A5FU 
        4.77         2.56        14.24         8.61         6.28         8.42 
TCGA-20-0987 TCGA-20-0996 TCGA-20-1685 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
       23.05        72.20        16.70        40.54        15.39        26.83 
TCGA-23-1027 TCGA-23-1109 TCGA-23-1110 TCGA-23-1114 TCGA-23-1120 TCGA-23-1121 
       32.09        51.35        54.51        68.68         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-24-1419 TCGA-24-1423 
        4.50         7.63         7.66        63.55         7.86         6.25 
TCGA-24-1424 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1435 TCGA-24-1464 
        6.02         4.83        17.39        28.37        43.53        12.46 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1549 
       45.14       105.99        26.96        57.40        64.27        56.58 
TCGA-24-1550 TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1563 
       41.06        58.09        70.62        39.88        19.53        47.70 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1614 TCGA-24-1843 TCGA-24-1849 TCGA-24-1920 
       25.87        10.26        48.33         3.48         5.79         9.80 
TCGA-24-1927 TCGA-24-1928 TCGA-24-2024 TCGA-24-2026 TCGA-24-2033 TCGA-24-2035 
       16.44        11.05        58.16        34.82        18.48        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2260 TCGA-24-2262 TCGA-24-2281 TCGA-24-2289 
       64.01        44.52        36.16         0.36        44.61        67.36 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1315 TCGA-25-1319 TCGA-25-1329 TCGA-25-1625 
        1.02        26.96        52.04        65.00        15.02        27.62 
TCGA-25-1630 TCGA-25-1632 TCGA-25-1635 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 
       38.20        59.15        52.04        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-25-2401 TCGA-25-2408 TCGA-25-2409 TCGA-29-1690 TCGA-29-1691 
       19.99         2.96        31.00        26.99        47.61        48.33 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 
      101.79        39.02        33.93        23.93        59.67        41.98 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1763 TCGA-29-1766 TCGA-29-1769 
       31.27        34.62        17.36        66.81        39.42        22.98 
TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1785 TCGA-29-2427 
       24.36        17.33        12.36        11.84        36.30        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-3P-A9WA TCGA-42-2582 TCGA-42-2589 TCGA-42-2590 TCGA-42-2593 TCGA-57-1583 
       13.81        47.57        42.02        10.42         1.48        11.38 
TCGA-57-1586 TCGA-59-2348 TCGA-59-2349 TCGA-59-2351 TCGA-5X-AA5U TCGA-61-1721 
       22.32       180.20        80.12       116.12        11.87        11.11 
TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 
        8.09        20.94        31.43        18.54        27.88        31.79 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1743 TCGA-61-1901 TCGA-61-1907 TCGA-61-1910 
       35.80         2.43        43.69        11.41        31.30        37.05 
TCGA-61-1911 TCGA-61-1915 TCGA-61-1918 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       42.51        67.76        15.75         5.52        14.50        17.98 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2017 TCGA-61-2088 TCGA-61-2095 
       30.64        39.85        30.64        45.96         4.77        61.64 
TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2104 TCGA-61-2614 TCGA-VG-A8LO 
       58.39        60.62        65.52        76.87         8.61         0.79 
TCGA-WR-A838 
        9.99 

  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 
            28.70             28.64 
[1] "0.3 - 152.0 (28.7)" "0.3 - 180.2 (28.6)"
[1] "hr=" "1.1"
D48V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  4P LOSS MUTATED         2   302                0
  4P LOSS WILD-TYPE       1   256                2
D48V3, multiclass
                  clus
vv                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  OMENTUM                        2                 1
  OVARY                        302               256
  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, continuous
D48V5, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     2 311
  4P LOSS WILD-TYPE   1 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      2  311
  4P LOSS WILD-TYPE    1  259
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO                2                 1
  YES             311               259
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  4P LOSS MUTATED    9 13  2  2
  4P LOSS WILD-TYPE  6 13  3  1
D48V6, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0               9                 6
  R1              13                13
  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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P LOSS MUTATED                                  1     9
  4P LOSS WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN
  4P LOSS MUTATED                          15
  4P LOSS WILD-TYPE                        19
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4P LOSS MUTATED                                           1   261
  4P LOSS WILD-TYPE                                         0   215
D48V7, multiclass
                                           clus
vv                                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 2
  ASIAN                                                   9                10
  BLACK OR AFRICAN AMERICAN                              15                19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 261               215
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V8, 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   165 182
  4Q LOSS WILD-TYPE 103 110
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              347               213 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              182               110 
$`4Q LOSS MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1338 TCGA-04-1341 TCGA-04-1343 
       43.92        41.00        49.15        46.62         1.08        11.87 
TCGA-04-1348 TCGA-04-1350 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1367 
       48.76        63.98        32.52        44.32        33.67       103.40 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1536 TCGA-04-1542 
       82.39        56.55        41.59        19.99        29.10        84.20 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1649 TCGA-04-1652 TCGA-04-1654 
       55.43        48.89        27.88        64.64        31.86        47.70 
TCGA-04-1655 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       45.37        17.98        35.57         9.99        38.43        89.33 
TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 
       74.93        57.60        61.87        30.51        17.98         3.02 
TCGA-09-1674 TCGA-09-2043 TCGA-09-2044 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
        8.55         6.18         6.12       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 
       39.75        20.94        26.93        12.46        25.91        81.86 
TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0935 TCGA-10-0937 
       18.51        34.19        32.88        14.66        35.44        19.99 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 
       24.59        44.55         2.73        12.39        15.19        17.82 
TCGA-13-0751 TCGA-13-0757 TCGA-13-0760 TCGA-13-0762 TCGA-13-0766 TCGA-13-0793 
       55.17        11.18        11.54        32.25        21.40        28.70 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 
       19.59         8.71         8.28        43.86        35.28        35.31 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 
      107.18        91.40        66.67        70.39        61.84        67.99 
TCGA-13-0899 TCGA-13-0903 TCGA-13-0904 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       56.15        47.38        48.33        37.08        27.72        34.06 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 
       21.17        14.89         4.64         6.08        10.88         6.61 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1481 TCGA-13-1483 
        6.05         5.92         6.84         4.70        87.06        29.42 
TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
       98.04        22.39        70.82        82.88        52.44        73.55 
TCGA-13-1495 TCGA-13-1497 TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 TCGA-13-1505 
       49.25        54.31        38.40        13.97        16.57         4.21 
TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 
        4.18         3.91         3.09        12.23        10.78         8.75 
TCGA-13-A5FT TCGA-20-0990 TCGA-20-1683 TCGA-20-1684 TCGA-20-1686 TCGA-20-1687 
       54.77        25.94        25.38        19.10         2.93         2.66 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 
       47.54        49.68        49.41         8.81        29.13        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         4.57 
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-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 
       49.84         2.76         4.70        19.66        11.64        21.80 
TCGA-24-0979 TCGA-24-0982 TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
       41.56        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-24-1425 
        7.82         7.99         7.86         0.76         6.25         5.95 
TCGA-24-1426 TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 
        5.36        17.39        19.17        18.67         8.55        72.92 
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-24-1548 TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 TCGA-24-1560 TCGA-24-1562 
       16.21        51.91        41.39        88.50        44.09        45.50 
TCGA-24-1563 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 
       47.70        17.23        90.15        88.37        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-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 
        9.80        22.68        11.05        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-24-2281 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-25-1314 
       16.64        33.11        55.86        53.26         1.02        33.01 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 
       52.04        42.05         2.01        34.98        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-25-1633 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-25-2042 TCGA-25-2391 TCGA-25-2392 
       52.04        14.96        24.99        13.02        49.05         1.02 
TCGA-25-2398 TCGA-25-2400 TCGA-25-2404 TCGA-25-2408 TCGA-29-1688 TCGA-29-1695 
       45.01        42.02        29.03        31.00        78.90        40.41 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1705 TCGA-29-1762 TCGA-29-1764 
       31.20        68.32        36.36        18.25        86.60        62.93 
TCGA-29-1769 TCGA-29-1771 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 
       22.98        22.55        11.84        12.30         8.38         7.23 
TCGA-29-1784 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2431 TCGA-29-2434 
        5.36        86.17        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-31-1946 TCGA-31-1950 TCGA-31-1953 TCGA-31-1955 
       57.57        30.05        30.18        18.77         6.71        42.51 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 TCGA-36-1576 TCGA-36-1577 
        2.20        28.77        21.53        22.85        30.08        25.74 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2538 
       24.23        24.69        35.05        33.01        29.49        25.08 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2545 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 
       21.60         2.24        18.31        14.17        16.18        11.47 
TCGA-3P-A9WA TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
       13.81        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-59-A5PD TCGA-5X-AA5U TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 
       20.52        11.87         4.34        31.79        28.47        48.79 
TCGA-61-1737 TCGA-61-1741 TCGA-61-1899 TCGA-61-1900 TCGA-61-1903 TCGA-61-1904 
       44.84        33.67         8.42         5.79        13.02         9.07 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 
       34.13        31.30        56.61        43.43        15.75        38.17 
TCGA-61-1995 TCGA-61-2003 TCGA-61-2009 TCGA-61-2016 TCGA-61-2018 TCGA-61-2087 
        2.01         4.01        39.85         1.18        45.40         4.80 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 
       51.72        71.74        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 
       31.07         8.61        39.68        18.94         0.79 

$`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-09-0364 TCGA-09-0365 TCGA-09-0366 
      119.08        28.64        36.23        29.16         9.47        57.76 
TCGA-09-1665 TCGA-09-1668 TCGA-09-1672 TCGA-09-1675 TCGA-09-2045 TCGA-09-2048 
       41.62        55.36         5.85        97.55        35.15         4.54 
TCGA-10-0925 TCGA-10-0934 TCGA-10-0936 TCGA-10-0938 TCGA-13-0714 TCGA-13-0723 
       54.31         6.71        36.92        20.91         6.21        39.58 
TCGA-13-0726 TCGA-13-0755 TCGA-13-0758 TCGA-13-0761 TCGA-13-0764 TCGA-13-0768 
       31.20         2.50        11.38        34.06        31.04         8.45 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0794 TCGA-13-0799 TCGA-13-0800 TCGA-13-0802 
       38.93        36.72        30.35         7.79         8.12         8.19 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0886 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 
       13.61        68.94        74.27        69.01        43.36        57.47 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0913 
       57.07        19.36        47.84        44.94        44.84        29.98 
TCGA-13-0920 TCGA-13-0923 TCGA-13-1405 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 
       13.81         6.41         7.36         4.21         5.33        54.64 
TCGA-13-1482 TCGA-13-1485 TCGA-13-1494 TCGA-13-1496 TCGA-13-1498 TCGA-13-1501 
       61.71        20.68        38.20         4.24        37.61        32.84 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1510 TCGA-13-2057 TCGA-13-2060 TCGA-13-2071 
        4.41         4.77         2.56        14.24         8.61         6.28 
TCGA-13-A5FU TCGA-20-0987 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1685 
        8.42        23.05        26.20        72.20        27.52        16.70 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1109 TCGA-23-1120 
       40.54        15.39        26.83        32.09        51.35         4.27 
TCGA-23-1121 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 
        6.38        58.13         0.53       115.89        87.48        91.66 
TCGA-23-2081 TCGA-23-2645 TCGA-24-0966 TCGA-24-0980 TCGA-24-1104 TCGA-24-1424 
       77.00         4.50         7.63         7.66        63.55         6.02 
TCGA-24-1427 TCGA-24-1430 TCGA-24-1435 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 
        4.83        28.37        43.53        12.46        45.14       105.99 
TCGA-24-1546 TCGA-24-1549 TCGA-24-1550 TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 
       64.27        56.58        41.06        58.09        70.62        39.88 
TCGA-24-1558 TCGA-24-1564 TCGA-24-1565 TCGA-24-1614 TCGA-24-1843 TCGA-24-1924 
       19.53        25.87        10.26        48.33         3.48        30.21 
TCGA-24-1927 TCGA-24-2024 TCGA-24-2026 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 
       16.44        58.16        34.82        18.48        28.18        64.01 
TCGA-24-2038 TCGA-24-2260 TCGA-24-2262 TCGA-24-2289 TCGA-25-1313 TCGA-25-1319 
       44.52        36.16         0.36        67.36        26.96        65.00 
TCGA-25-1632 TCGA-25-1877 TCGA-25-1878 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 
       59.15        24.00        85.05        38.04         3.02        12.00 
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-29-1696 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 
       39.02        33.93        16.93        23.93        59.67        41.98 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1763 TCGA-29-1766 TCGA-29-1768 
       31.27        34.62        17.36        66.81        39.42        31.30 
TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1778 TCGA-29-1785 TCGA-29-2427 
       24.36        17.33        12.36        14.93        36.30        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-31-1951 TCGA-31-1956 TCGA-36-1569 TCGA-36-1574 TCGA-36-1575 
       45.57        22.49        44.12        29.10        22.55         8.55 
TCGA-36-1578 TCGA-36-2534 TCGA-36-2537 TCGA-36-2540 TCGA-36-2544 TCGA-36-2547 
       27.85        29.82        25.91        23.80        20.98        20.52 
TCGA-36-2549 TCGA-42-2582 TCGA-57-1583 TCGA-57-1586 TCGA-59-2348 TCGA-59-2349 
        6.05        47.57        11.38        22.32       180.20        80.12 
TCGA-59-2351 TCGA-59-2354 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
      116.12        34.39        11.11         8.09        20.94        31.43 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1738 TCGA-61-1740 TCGA-61-1743 TCGA-61-1895 
       18.54        27.88        35.80         2.43        43.69         1.45 
TCGA-61-1901 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1915 TCGA-61-1998 
       11.41        37.05        42.51        48.92        67.76         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2008 TCGA-61-2012 TCGA-61-2017 TCGA-61-2088 
       14.50        17.98        30.64        30.64        45.96         4.77 
TCGA-61-2095 TCGA-61-2096 TCGA-WR-A838 
       61.64        58.39         9.99 

  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 
            27.88             29.16 
[1] "0.3 - 152.0 (27.9)" "0.3 - 180.2 (29.2)"
[1] "hr=" "1.1"
D49V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  4Q LOSS MUTATED         2   347                1
  4Q LOSS WILD-TYPE       1   211                1
D49V3, multiclass
                  clus
vv                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  OMENTUM                        2                 1
  OVARY                        347               211
  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, continuous
D49V5, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     2 357
  4Q LOSS WILD-TYPE   1 213
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      2  357
  4Q LOSS WILD-TYPE    1  213
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO                2                 1
  YES             357               213
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  4Q LOSS MUTATED   11 17  4  3
  4Q LOSS WILD-TYPE  4  9  1  0
D49V6, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0              11                 4
  R1              17                 9
  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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q LOSS MUTATED                                  3     9
  4Q LOSS WILD-TYPE                                0    10
                   vv
clus                BLACK OR AFRICAN AMERICAN
  4Q LOSS MUTATED                          21
  4Q LOSS WILD-TYPE                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4Q LOSS MUTATED                                           1   297
  4Q LOSS WILD-TYPE                                         0   179
D49V7, multiclass
                                           clus
vv                                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        3                 0
  ASIAN                                                   9                10
  BLACK OR AFRICAN AMERICAN                              21                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 297               179
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V8, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     8 196
  4Q LOSS WILD-TYPE   2 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      8  196
  4Q LOSS WILD-TYPE    2  131
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   8                 2
  NOT HISPANIC OR LATINO             196               131
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    59  70
  5P LOSS WILD-TYPE 209 222
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              129               431 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               70               222 
$`5P LOSS MUTATED`
TCGA-04-1332 TCGA-04-1336 TCGA-04-1338 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 
       41.00        49.15        46.62        65.46        49.28        32.52 
TCGA-04-1371 TCGA-04-1517 TCGA-04-1519 TCGA-04-1648 TCGA-09-0364 TCGA-09-0365 
       82.39        19.99         0.79        28.64        29.16         9.47 
TCGA-09-1669 TCGA-09-2044 TCGA-09-2049 TCGA-10-0938 TCGA-13-0714 TCGA-13-0724 
       30.51         6.12       112.41        20.91         6.21         2.73 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0791 TCGA-13-0795 TCGA-13-0800 TCGA-13-0803 
       34.06        32.25        38.93        19.59         8.12        43.86 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 
       35.28        35.31       107.18        91.40        66.67        70.39 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0919 TCGA-13-0920 TCGA-13-1405 
       67.99        69.01        43.36        14.89        13.81         7.36 
TCGA-13-1412 TCGA-13-1491 TCGA-13-1496 TCGA-13-1497 TCGA-13-2057 TCGA-13-2059 
        5.33        52.44         4.24        54.31        14.24        12.23 
TCGA-13-2060 TCGA-20-1682 TCGA-20-1683 TCGA-23-1021 TCGA-23-1022 TCGA-23-1028 
        8.61        27.52        25.38        47.54        49.68        49.41 
TCGA-23-1109 TCGA-23-1114 TCGA-23-1118 TCGA-23-1122 TCGA-23-1123 TCGA-23-2072 
       51.35        68.68        86.01        39.09        33.47        24.95 
TCGA-24-0970 TCGA-24-1419 TCGA-24-1424 TCGA-24-1430 TCGA-24-1431 TCGA-24-1464 
       11.64         7.86         6.02        28.37        19.17        12.46 
TCGA-24-1466 TCGA-24-1548 TCGA-24-1558 TCGA-24-1567 TCGA-24-1614 TCGA-24-1842 
       45.14        16.21        19.53        17.23        48.33         8.32 
TCGA-24-1843 TCGA-24-1920 TCGA-24-2019 TCGA-24-2035 TCGA-24-2254 TCGA-24-2261 
        3.48         9.80         4.87        28.18        57.07         0.79 
TCGA-24-2271 TCGA-24-2293 TCGA-25-1312 TCGA-25-1313 TCGA-25-1317 TCGA-25-1320 
       31.63        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-3P-A9WA 
        2.20         8.55        25.08        20.52        11.47        13.81 
TCGA-57-1583 TCGA-57-1994 TCGA-59-2348 TCGA-59-2351 TCGA-59-2352 TCGA-59-2363 
       11.38        25.02       180.20       116.12         9.40         5.42 
TCGA-61-1724 TCGA-61-1728 TCGA-61-1730 TCGA-61-1741 TCGA-61-1743 TCGA-61-1906 
       20.94        27.88         4.34        33.67        43.69        34.13 
TCGA-61-1907 TCGA-61-1917 TCGA-61-1998 TCGA-61-2094 TCGA-61-2097 TCGA-61-2102 
       31.30        43.43         5.52        71.74        60.62         6.48 
TCGA-61-2104 TCGA-OY-A56Q TCGA-WR-A838 
       76.87        18.94         9.99 

$`5P LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1337 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 
       43.92         1.81         2.01         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-04-1362 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-04-1525 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-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 
       27.88        64.64        36.23        31.86        47.70        45.37 
TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       57.76        17.98        35.57         9.99        38.43        89.33 
TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1670 
       74.93        41.62        57.60        61.87        55.36        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2045 
        5.85         3.02         8.55        97.55         6.18        35.15 
TCGA-09-2048 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 
        4.54        71.11        63.09        39.75        20.94        26.93 
TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       12.46        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 
       31.04        21.40         8.45        36.72        28.70        30.35 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0807 TCGA-13-0883 
        8.71         7.79         8.28         8.19        13.61        68.94 
TCGA-13-0886 TCGA-13-0889 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
       74.27        61.84        57.47        56.15        57.07        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
       47.38        48.33        47.84        44.94        44.84        37.08 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0921 TCGA-13-0923 
       27.72        34.06        29.98        21.17         4.64         6.41 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
        6.08        10.88         6.61         6.05         5.92         6.84 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
        4.70         4.21        54.64        87.06        61.71        29.42 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1492 
       98.04        20.68        22.39        70.82        82.88        73.55 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 
       38.20        49.25        37.61        38.40        13.97        32.84 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 
       16.57         4.21         4.41         4.77         4.18         2.56 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT 
        3.91         3.09        10.78         8.75         6.28        54.77 
TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1684 
        8.42        23.05        25.94        26.20        72.20        19.10 
TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
       16.70         2.93         2.66        40.54        15.39        26.83 
TCGA-23-1027 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 
       32.09         8.81        29.13        18.90         2.76        54.51 
TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1119 TCGA-23-1120 
        3.22        31.20         4.57        33.30       129.96         4.27 
TCGA-23-1121 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 
        6.38        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-24-0968 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 
       19.66        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-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        0.76         6.25         5.95         5.36         4.83        17.39 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1467 TCGA-24-1469 
       18.67        43.53         8.55        72.92       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-24-1549 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-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
       70.62        39.88        44.09        45.50        47.70        25.87 
TCGA-24-1565 TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-1844 TCGA-24-1845 
       10.26        90.15        88.37        38.24         3.72         3.81 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1923 TCGA-24-1924 
        4.37        11.28         5.79         5.52        22.68        30.21 
TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 
       16.44        11.05        81.11       152.02        44.84        58.16 
TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2036 
       34.82       109.71        14.43        55.92        18.48        64.01 
TCGA-24-2038 TCGA-24-2260 TCGA-24-2262 TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 
       44.52        36.16         0.36        47.54        70.45        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-59-2349 TCGA-59-2350 TCGA-59-2354 
       22.32        29.00        25.08        80.12        22.32        34.39 
TCGA-59-2355 TCGA-59-2372 TCGA-59-A5PD TCGA-5X-AA5U TCGA-61-1721 TCGA-61-1722 
        2.14        44.81        20.52        11.87        11.11         8.09 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       31.43        18.54        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-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 
       13.02         9.07        37.05        42.51        48.92        56.61 
TCGA-61-1915 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-2000 TCGA-61-2002 
       67.76        15.75        38.17         2.01        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-61-2095 TCGA-61-2096 
       45.40         4.80         4.77        51.72        61.64        58.39 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
       65.52        55.50        20.68        44.52       125.75        22.22 
TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-VG-A8LO 
        6.35        31.07         8.61        39.68         0.79 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.79              0.26 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           180.20            152.02 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            27.88             29.00 
[1] "0.8 - 180.2 (27.9)" "0.3 - 152.0 (29.0)"
[1] "hr=" "1.1"
D50V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  5P LOSS MUTATED         1   129                0
  5P LOSS WILD-TYPE       2   429                2
D50V3, multiclass
                  clus
vv                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  OMENTUM                        1                 2
  OVARY                        129               429
  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, continuous
D50V5, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     0 131
  5P LOSS WILD-TYPE   3 439
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0  131
  5P LOSS WILD-TYPE    3  439
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                0                 3
  YES             131               439
[1] 2 2
[1] FALSE
                   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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P LOSS MUTATED                                  0     5
  5P LOSS WILD-TYPE                                3    14
                   vv
clus                BLACK OR AFRICAN AMERICAN
  5P LOSS MUTATED                           6
  5P LOSS WILD-TYPE                        28
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5P LOSS MUTATED                                           0   112
  5P LOSS WILD-TYPE                                         1   364
D50V7, multiclass
                                           clus
vv                                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   5                14
  BLACK OR AFRICAN AMERICAN                               6                28
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 112               364
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V8, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     3  76
  5P LOSS WILD-TYPE   7 251
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      3   76
  5P LOSS WILD-TYPE    7  251
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 7
  NOT HISPANIC OR LATINO              76               251
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED   106 109
  5Q LOSS WILD-TYPE 162 183
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              215               345 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              109               183 
$`5Q LOSS MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1338 TCGA-04-1341 TCGA-04-1350 
       43.92        41.00        49.15        46.62         1.08        63.98 
TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1371 TCGA-04-1517 TCGA-04-1519 
       65.46        49.28        32.52        82.39        19.99         0.79 
TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 
       27.88        28.64        64.64        29.16         9.47        57.76 
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-10-0927 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 
       81.86        20.91         6.21        24.59        39.58         2.73 
TCGA-13-0730 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 
       17.82        11.54        34.06        32.25        31.04        21.40 
TCGA-13-0791 TCGA-13-0793 TCGA-13-0794 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 
       38.93        28.70        30.35         8.12         8.28         8.19 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 
       43.86        35.28       107.18        91.40        66.67        70.39 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 TCGA-13-0901 TCGA-13-0904 
       67.99        69.01        43.36        56.15        19.36        48.33 
TCGA-13-0906 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-1405 TCGA-13-1407 
       44.94        21.17        14.89        13.81         7.36         6.05 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1484 TCGA-13-1491 TCGA-13-1496 TCGA-13-1497 
        4.21         5.33        98.04        52.44         4.24        54.31 
TCGA-13-1499 TCGA-13-1505 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-20-0990 
       38.40         4.21        14.24        12.23         8.61        25.94 
TCGA-20-0991 TCGA-20-1682 TCGA-20-1684 TCGA-20-1686 TCGA-23-1021 TCGA-23-1022 
       26.20        27.52        19.10         2.93        47.54        49.68 
TCGA-23-1026 TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 
       26.83        49.41        29.13        18.90         2.76        51.35 
TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 TCGA-23-1118 TCGA-23-1119 TCGA-23-1122 
       54.51        31.20        68.68        86.01       129.96        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2643 TCGA-24-0970 
       33.47        58.13        24.95       115.89         4.70        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        19.17        12.46        45.14 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1548 TCGA-24-1549 TCGA-24-1558 TCGA-24-1564 
      105.99         9.11        16.21        56.58        19.53        25.87 
TCGA-24-1567 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1924 
       17.23        48.33        38.24         8.32         3.48        30.21 
TCGA-24-1928 TCGA-24-2019 TCGA-24-2020 TCGA-24-2026 TCGA-24-2030 TCGA-24-2035 
       11.05         4.87       152.02        34.82        55.92        28.18 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 
       57.07        36.16         0.79        31.63        70.45        44.61 
TCGA-24-2293 TCGA-24-2295 TCGA-25-1312 TCGA-25-1313 TCGA-25-1315 TCGA-25-1317 
       16.64        33.11         1.02        26.96        52.04         2.01 
TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1626 
       34.98        37.97        33.96         2.99        12.99        17.03 
TCGA-25-1630 TCGA-25-1633 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
       38.20        62.17        52.04        14.96        24.99        24.00 
TCGA-25-2396 TCGA-25-2398 TCGA-25-2400 TCGA-25-2404 TCGA-29-1691 TCGA-29-1695 
        3.02        45.01        42.02        29.03        48.33        40.41 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 TCGA-29-1711 TCGA-29-1762 
       31.20        68.32        16.93        23.93        34.62        86.60 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1775 TCGA-29-1778 TCGA-29-1783 TCGA-29-1784 
       62.93        39.42        12.36        14.93         7.23         5.36 
TCGA-29-2425 TCGA-29-2428 TCGA-30-1718 TCGA-30-1855 TCGA-30-1859 TCGA-30-1861 
       65.00        45.11        51.91         2.47        48.10        34.78 
TCGA-30-1866 TCGA-30-1867 TCGA-30-1887 TCGA-30-1891 TCGA-31-1953 TCGA-31-1955 
       36.62         1.22        24.26        30.05         6.71        42.51 
TCGA-31-1959 TCGA-36-1575 TCGA-36-1576 TCGA-36-1581 TCGA-36-2537 TCGA-36-2538 
        2.20         8.55        30.08        24.69        25.91        25.08 
TCGA-36-2547 TCGA-36-2552 TCGA-3P-A9WA TCGA-57-1582 TCGA-57-1583 TCGA-57-1992 
       20.52        11.47        13.81        24.03        11.38        29.00 
TCGA-57-1994 TCGA-59-2348 TCGA-59-2351 TCGA-59-2352 TCGA-59-2363 TCGA-59-A5PD 
       25.02       180.20       116.12         9.40         5.42        20.52 
TCGA-61-1722 TCGA-61-1724 TCGA-61-1728 TCGA-61-1730 TCGA-61-1734 TCGA-61-1743 
        8.09        20.94        27.88         4.34        28.47        43.69 
TCGA-61-1895 TCGA-61-1899 TCGA-61-1906 TCGA-61-1907 TCGA-61-1917 TCGA-61-1919 
        1.45         8.42        34.13        31.30        43.43        38.17 
TCGA-61-1998 TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 TCGA-61-2088 TCGA-61-2094 
        5.52         4.01        30.64        30.64         4.77        71.74 
TCGA-61-2097 TCGA-61-2102 TCGA-61-2104 TCGA-OY-A56Q TCGA-WR-A838 
       60.62         6.48        76.87        18.94         9.99 

$`5Q LOSS WILD-TYPE`
TCGA-04-1335 TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 
        1.81         2.01        18.51        11.87        65.52        63.09 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1353 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
       48.76        21.57         0.53        44.32        33.67        76.57 
TCGA-04-1367 TCGA-04-1514 TCGA-04-1516 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 
      103.40        56.55        41.59        38.37       119.08        29.10 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 
       84.20        55.43        48.89        36.23        31.86        47.70 
TCGA-04-1655 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       45.37        17.98        35.57         9.99        38.43        89.33 
TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1670 
       74.93        41.62        57.60        61.87        55.36        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 
        5.85         3.02        97.55        35.15         4.54        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 
       63.09        39.75        26.93        12.46        54.31        25.91 
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-13-0720 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 
       36.92        19.99        44.55        12.39        31.20        15.19 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0768 TCGA-13-0792 
       55.17         2.50        11.18        11.38         8.45        36.72 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
       19.59         8.71         7.79        35.31        13.61        68.94 
TCGA-13-0886 TCGA-13-0889 TCGA-13-0897 TCGA-13-0900 TCGA-13-0903 TCGA-13-0905 
       74.27        61.84        57.47        57.07        47.38        47.84 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0921 
       44.84        37.08        27.72        34.06        29.98         4.64 
TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1408 TCGA-13-1409 
        6.41         6.08        10.88         6.61         5.92         6.84 
TCGA-13-1410 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 
        4.70        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        82.88        73.55        38.20        49.25 
TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 
       37.61        13.97        32.84        16.57         4.41         4.77 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2061 TCGA-13-2065 
        4.18         2.56         3.91         3.09        10.78         8.75 
TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0996 TCGA-20-1683 
        6.28        54.77         8.42        23.05        72.20        25.38 
TCGA-20-1685 TCGA-20-1687 TCGA-23-1023 TCGA-23-1024 TCGA-23-1027 TCGA-23-1029 
       16.70         2.66        40.54        15.39        32.09         8.81 
TCGA-23-1111 TCGA-23-1116 TCGA-23-1117 TCGA-23-1120 TCGA-23-1121 TCGA-23-1809 
        3.22         4.57        33.30         4.27         6.38         0.53 
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-24-0968 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
        7.63        19.66        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-24-1470 
       17.39        18.67        43.53         8.55        72.92         3.45 
TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1550 
        1.18        22.22        26.96        57.40        64.27        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-24-1565 TCGA-24-1603 TCGA-24-1604 
       44.09        45.50        47.70        10.26        90.15        88.37 
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-24-1927 TCGA-24-1930 TCGA-24-2023 TCGA-24-2024 
        9.80        22.68        16.44        81.11        44.84        58.16 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 TCGA-24-2036 TCGA-24-2038 TCGA-24-2262 
      109.71        14.43        18.48        64.01        44.52         0.36 
TCGA-24-2267 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2297 TCGA-24-2298 
       47.54         0.82        67.36        36.23        55.86        53.26 
TCGA-25-1314 TCGA-25-1316 TCGA-25-1319 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       33.01        42.05        65.00        15.02        18.58        27.62 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1634 TCGA-25-1878 
       12.95        20.61         0.30        59.15        35.87        85.05 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2397 TCGA-25-2399 
       13.02        49.05         1.02        38.04        12.00        19.99 
TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 
        2.96        31.00        26.99        78.90        47.61       101.79 
TCGA-29-1694 TCGA-29-1696 TCGA-29-1699 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
       39.02        33.93        36.36        59.67        18.25        41.98 
TCGA-29-1710 TCGA-29-1761 TCGA-29-1763 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 
       31.27        17.36        66.81        31.30        22.98        24.36 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1785 
       22.55        17.33        11.84        12.30         8.38        36.30 
TCGA-29-2414 TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 
       86.17        62.47        13.84        42.25        21.47        11.47 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 
        9.76        35.77        38.07        36.26        15.68         0.26 
TCGA-30-1860 TCGA-30-1862 TCGA-30-1880 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 
       44.91         6.12        57.57        48.79        45.57        30.18 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
       18.77        22.49        44.12        28.77        29.10        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-2529 
       22.85        22.55        25.74        27.85        24.23        35.05 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 
       33.01        29.49        29.82        23.80        21.60         2.24 
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-42-2587 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-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1993 TCGA-59-2349 TCGA-59-2350 
       21.14         1.74        22.32        25.08        80.12        22.32 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2372 TCGA-5X-AA5U TCGA-61-1721 TCGA-61-1725 
       34.39         2.14        44.81        11.87        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-61-1903 TCGA-61-1904 TCGA-61-1910 
       33.67         5.79        11.41        13.02         9.07        37.05 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 TCGA-61-1995 
       42.51        48.92        56.61        67.76        15.75         2.01 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
       14.50        17.98        39.85         1.18        45.96        45.40 
TCGA-61-2087 TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 TCGA-61-2101 
        4.80        51.72        61.64        58.39        65.52        55.50 
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-VG-A8LO 
        8.61        39.68         0.79 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.79              0.26 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           180.20            125.75 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            28.64             28.77 
[1] "0.8 - 180.2 (28.6)" "0.3 - 125.8 (28.8)"
[1] "hr=" "1.1"
D51V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  5Q LOSS MUTATED         1   214                1
  5Q LOSS WILD-TYPE       2   344                1
D51V3, multiclass
                  clus
vv                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  OMENTUM                        1                 2
  OVARY                        214               344
  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, continuous
D51V5, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     1 220
  5Q LOSS WILD-TYPE   2 350
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1  220
  5Q LOSS WILD-TYPE    2  350
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                1                 2
  YES             220               350
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  5Q LOSS MUTATED    3  4  0  2
  5Q LOSS WILD-TYPE 12 22  5  1
D51V6, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0               3                12
  R1               4                22
  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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q LOSS MUTATED                                  1     8
  5Q LOSS WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN
  5Q LOSS MUTATED                          11
  5Q LOSS WILD-TYPE                        23
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5Q LOSS MUTATED                                           0   185
  5Q LOSS WILD-TYPE                                         1   291
D51V7, multiclass
                                           clus
vv                                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 2
  ASIAN                                                   8                11
  BLACK OR AFRICAN AMERICAN                              11                23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 185               291
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V8, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     5 129
  5Q LOSS WILD-TYPE   5 198
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      5  129
  5Q LOSS WILD-TYPE    5  198
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 5
  NOT HISPANIC OR LATINO             129               198
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    79  80
  6P LOSS WILD-TYPE 189 212
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              159               401 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               80               212 
$`6P LOSS MUTATED`
TCGA-04-1331 TCGA-04-1348 TCGA-04-1351 TCGA-04-1367 TCGA-04-1519 TCGA-04-1646 
       43.92        48.76        65.46       103.40         0.79        27.88 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1655 TCGA-09-0365 TCGA-09-1659 TCGA-09-1670 
       64.64        36.23        45.37         9.47         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-10-0925 TCGA-10-0926 TCGA-13-0720 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 
       54.31        25.91        44.55        17.82        55.17        11.18 
TCGA-13-0758 TCGA-13-0762 TCGA-13-0766 TCGA-13-0801 TCGA-13-0803 TCGA-13-0883 
       11.38        32.25        21.40         8.28        43.86        68.94 
TCGA-13-0884 TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 TCGA-13-0891 TCGA-13-0897 
      107.18        66.67        70.39        67.99        69.01        57.47 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0905 TCGA-13-0910 TCGA-13-0911 TCGA-13-0919 
       56.15        57.07        47.84        37.08        27.72        14.89 
TCGA-13-0921 TCGA-13-1405 TCGA-13-1410 TCGA-13-1483 TCGA-13-1484 TCGA-13-1491 
        4.64         7.36         4.70        29.42        98.04        52.44 
TCGA-13-1495 TCGA-13-1497 TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 TCGA-13-1512 
       49.25        54.31        32.84         4.21         4.41         3.09 
TCGA-13-2059 TCGA-13-A5FU TCGA-20-1683 TCGA-23-1021 TCGA-23-1030 TCGA-23-1113 
       12.23         8.42        25.38        47.54        29.13        31.20 
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-23-2078 TCGA-23-2641 TCGA-23-2643 TCGA-24-0966 TCGA-24-0970 TCGA-24-1416 
       87.48         2.76         4.70         7.63        11.64         6.38 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
        5.36         4.83        17.39        18.67        43.53         8.55 
TCGA-24-1467 TCGA-24-1471 TCGA-24-1546 TCGA-24-1552 TCGA-24-1553 TCGA-24-1560 
      105.99         1.18        64.27        41.39        58.09        44.09 
TCGA-24-1842 TCGA-24-1845 TCGA-24-1849 TCGA-24-1923 TCGA-24-1927 TCGA-24-1928 
        8.32         3.81         5.79        22.68        16.44        11.05 
TCGA-24-2019 TCGA-24-2023 TCGA-24-2027 TCGA-24-2029 TCGA-24-2271 TCGA-24-2280 
        4.87        44.84       109.71        14.43        31.63        70.45 
TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 
       16.64        55.86        53.26        26.96        52.04        42.05 
TCGA-25-1320 TCGA-25-1322 TCGA-25-1329 TCGA-25-1627 TCGA-25-1628 TCGA-25-1635 
       37.97         2.99        15.02        12.95        20.61        52.04 
TCGA-25-2396 TCGA-25-2399 TCGA-29-1688 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 
        3.02        19.99        78.90       101.79        39.02        33.93 
TCGA-29-1697 TCGA-29-1707 TCGA-29-1763 TCGA-29-1769 TCGA-29-1775 TCGA-29-1781 
       31.20        41.98        66.81        22.98        12.36         8.38 
TCGA-29-1784 TCGA-29-2428 TCGA-30-1714 TCGA-30-1853 TCGA-30-1855 TCGA-30-1857 
        5.36        45.11        38.07        36.26         2.47         0.26 
TCGA-30-1866 TCGA-30-1880 TCGA-31-1951 TCGA-36-1569 TCGA-36-2543 TCGA-36-2548 
       36.62        57.57        22.49        29.10         2.24        14.17 
TCGA-42-2588 TCGA-42-2591 TCGA-59-2350 TCGA-59-2351 TCGA-59-2355 TCGA-59-2372 
       28.93        40.77        22.32       116.12         2.14        44.81 
TCGA-59-A5PD TCGA-61-1724 TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 TCGA-61-1734 
       20.52        20.94        18.54        27.88        31.79        28.47 
TCGA-61-1736 TCGA-61-1738 TCGA-61-1740 TCGA-61-1895 TCGA-61-1899 TCGA-61-1904 
       48.79        35.80         2.43         1.45         8.42         9.07 
TCGA-61-1906 TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 TCGA-61-1995 TCGA-61-2008 
       34.13        37.05        48.92        56.61         2.01        30.64 
TCGA-61-2096 TCGA-61-2110 TCGA-61-2613 
       58.39        44.52        31.07 

$`6P LOSS WILD-TYPE`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 
       41.00         1.81        49.15         2.01        46.62         1.08 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 
       18.51        11.87        65.52        63.09        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-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 
       82.39        56.55        41.59        19.99        38.37       119.08 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1652 
       29.10        84.20        55.43        48.89        28.64        31.86 
TCGA-04-1654 TCGA-09-0364 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1661 
       47.70        29.16        57.76        17.98        35.57        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-09-1673 TCGA-09-1674 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 
       30.51         3.02         8.55        35.15         4.54       112.41 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2054 TCGA-09-2055 TCGA-10-0927 TCGA-10-0928 
       71.11        63.09        20.94        26.93        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-13-0723 TCGA-13-0724 
       19.99        20.91         6.21        24.59        39.58         2.73 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 
       12.39        31.20        15.19         2.50        11.54        34.06 
TCGA-13-0764 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 
       31.04         8.45        38.93        36.72        28.70        30.35 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0802 TCGA-13-0804 
       19.59         8.71         7.79         8.12         8.19        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0885 TCGA-13-0886 TCGA-13-0889 TCGA-13-0893 
       35.31        13.61        91.40        74.27        61.84        43.36 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 TCGA-13-0912 
       19.36        47.38        48.33        44.94        44.84        34.06 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 
       29.98        21.17        13.81         6.41         6.08        10.88 
TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1411 TCGA-13-1412 
        6.61         6.05         5.92         6.84         4.21         5.33 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 
       54.64        87.06        61.71        20.68        22.39        70.82 
TCGA-13-1489 TCGA-13-1492 TCGA-13-1494 TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 
       82.88        73.55        38.20         4.24        37.61        38.40 
TCGA-13-1500 TCGA-13-1504 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
       13.97        16.57         4.77         4.18         2.56         3.91 
TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT 
       14.24         8.61        10.78         8.75         6.28        54.77 
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-20-1686 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-23-1031 TCGA-23-1032 
       26.83        32.09        49.41         8.81        18.90         2.76 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 TCGA-23-1120 
       51.35        54.51         3.22        68.68         4.57         4.27 
TCGA-23-1121 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 
        6.38        58.13         0.53       115.89        91.66        77.00 
TCGA-23-2084 TCGA-23-2645 TCGA-24-0968 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
       49.84         4.50        19.66        21.80        41.56         7.66 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1417 
       22.32        54.12        63.55        47.41         6.31         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-24-1430 TCGA-24-1431 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 
       28.37        19.17        72.92        12.46        45.14         9.11 
TCGA-24-1470 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 
        3.45        22.22        26.96        57.40        16.21        56.58 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 
       41.06        51.91        88.50        70.62        39.88        19.53 
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-24-1844 TCGA-24-1846 
       88.37        48.33        38.24         3.48         3.72         4.37 
TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-1930 TCGA-24-2020 
       11.28         5.52         9.80        30.21        81.11       152.02 
TCGA-24-2024 TCGA-24-2026 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 
       58.16        34.82        55.92        18.48        28.18        64.01 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 
       44.52        57.07        36.16         0.79         0.36        47.54 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2295 TCGA-25-1312 
       44.61         0.82        67.36        36.23        33.11         1.02 
TCGA-25-1314 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 TCGA-25-1323 
       33.01         2.01        34.98        65.00        33.96        12.99 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 
       18.58        27.62        17.03        38.20         0.30        59.15 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 
       62.17        35.87        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-25-2400 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-29-1695 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 
       48.33        40.41        68.32        36.36        16.93        23.93 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 
       59.67        18.25        31.27        34.62        17.36        86.60 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
       62.93        39.42        31.30        24.36        22.55        17.33 
TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1783 TCGA-29-1785 TCGA-29-2414 
       11.84        12.30        14.93         7.23        36.30        86.17 
TCGA-29-2425 TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 
       65.00        62.47        13.84        42.25        21.47        11.47 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1856 TCGA-30-1859 TCGA-30-1860 
        9.76        35.77        51.91        15.68        48.10        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-31-1956 
       45.57        30.18        18.77         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-36-1578 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-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 TCGA-36-2551 
       21.60        20.98        18.31        20.52         6.05        16.18 
TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2589 TCGA-42-2590 
       11.47        13.81        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-5X-AA5U TCGA-61-1721 TCGA-61-1722 TCGA-61-1725 
       34.39         5.42        11.87        11.11         8.09        31.43 
TCGA-61-1730 TCGA-61-1737 TCGA-61-1741 TCGA-61-1743 TCGA-61-1900 TCGA-61-1901 
        4.34        44.84        33.67        43.69         5.79        11.41 
TCGA-61-1903 TCGA-61-1907 TCGA-61-1911 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 
       13.02        31.30        42.51        67.76        43.43        15.75 
TCGA-61-1919 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2009 
       38.17         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-61-2097 TCGA-61-2098 TCGA-61-2101 
       51.72        71.74        61.64        60.62        65.52        55.50 
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-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
        8.61        39.68        18.94         0.79         9.99 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.26              0.30 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           129.96            180.20 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            30.64             27.62 
[1] "0.3 - 130.0 (30.6)" "0.3 - 180.2 (27.6)"
[1] "hr=" "1.2"
D52V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  6P LOSS MUTATED         1   159                0
  6P LOSS WILD-TYPE       2   399                2
D52V3, multiclass
                  clus
vv                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  OMENTUM                        1                 2
  OVARY                        159               399
  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, continuous
D52V5, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     1 162
  6P LOSS WILD-TYPE   2 408
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1  162
  6P LOSS WILD-TYPE    2  408
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                1                 2
  YES             162               408
[1] 2 2
[1] FALSE
                   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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P LOSS MUTATED                                  0     4
  6P LOSS WILD-TYPE                                3    15
                   vv
clus                BLACK OR AFRICAN AMERICAN
  6P LOSS MUTATED                           6
  6P LOSS WILD-TYPE                        28
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6P LOSS MUTATED                                           0   142
  6P LOSS WILD-TYPE                                         1   334
D52V7, multiclass
                                           clus
vv                                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   4                15
  BLACK OR AFRICAN AMERICAN                               6                28
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 142               334
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V8, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     2  96
  6P LOSS WILD-TYPE   8 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      2   96
  6P LOSS WILD-TYPE    8  231
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 8
  NOT HISPANIC OR LATINO              96               231
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED   107 126
  6Q LOSS WILD-TYPE 161 166
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              233               327 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              126               166 
$`6Q LOSS MUTATED`
TCGA-04-1331 TCGA-04-1337 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 
       43.92         2.01        48.76        21.57        63.98        65.46 
TCGA-04-1367 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1646 TCGA-04-1649 
      103.40        19.99         0.79        38.37        27.88        64.64 
TCGA-04-1651 TCGA-04-1655 TCGA-09-0365 TCGA-09-0367 TCGA-09-1659 TCGA-09-1661 
       36.23        45.37         9.47        17.98         9.99        38.43 
TCGA-09-1662 TCGA-09-1670 TCGA-09-1672 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 
       89.33        17.98         5.85        97.55         6.18         6.12 
TCGA-09-2045 TCGA-09-2053 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 
       35.15        39.75        26.93        12.46        54.31        25.91 
TCGA-10-0927 TCGA-10-0935 TCGA-10-0938 TCGA-13-0717 TCGA-13-0726 TCGA-13-0751 
       81.86        35.44        20.91        24.59        31.20        55.17 
TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0762 TCGA-13-0766 TCGA-13-0793 
        2.50        11.18        11.38        32.25        21.40        28.70 
TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0883 TCGA-13-0884 
        7.79         8.28         8.19        43.86        68.94       107.18 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 TCGA-13-0891 TCGA-13-0897 TCGA-13-0899 
       66.67        70.39        67.99        69.01        57.47        56.15 
TCGA-13-0900 TCGA-13-0905 TCGA-13-0910 TCGA-13-0911 TCGA-13-0919 TCGA-13-0921 
       57.07        47.84        37.08        27.72        14.89         4.64 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 
        6.61         7.36         6.05         4.70         4.21        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1491 TCGA-13-1495 TCGA-13-1497 
       61.71        29.42        98.04        52.44        49.25        54.31 
TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 TCGA-13-1512 TCGA-13-2059 TCGA-13-A5FU 
       32.84         4.21         4.41         3.09        12.23         8.42 
TCGA-20-1683 TCGA-20-1686 TCGA-23-1021 TCGA-23-1027 TCGA-23-1029 TCGA-23-1030 
       25.38         2.93        47.54        32.09         8.81        29.13 
TCGA-23-1109 TCGA-23-1113 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1122 
       51.35        31.20        33.30        86.01       129.96        39.09 
TCGA-23-1123 TCGA-23-2072 TCGA-23-2078 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 
       33.47        24.95        87.48        49.84         2.76         4.70 
TCGA-24-0966 TCGA-24-0970 TCGA-24-0980 TCGA-24-0982 TCGA-24-1105 TCGA-24-1416 
        7.63        11.64         7.66        22.32        47.41         6.38 
TCGA-24-1417 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1434 TCGA-24-1435 
        7.82         5.36         4.83        17.39        18.67        43.53 
TCGA-24-1436 TCGA-24-1467 TCGA-24-1471 TCGA-24-1546 TCGA-24-1552 TCGA-24-1553 
        8.55       105.99         1.18        64.27        41.39        58.09 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1564 TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 
       44.09        45.50        25.87         8.32         3.72         3.81 
TCGA-24-1849 TCGA-24-1923 TCGA-24-1927 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 
        5.79        22.68        16.44         4.87       152.02        44.84 
TCGA-24-2029 TCGA-24-2261 TCGA-24-2262 TCGA-24-2271 TCGA-24-2280 TCGA-24-2290 
       14.43         0.79         0.36        31.63        70.45        36.23 
TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 
       16.64        33.11        55.86        53.26        26.96        52.04 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 
       42.05         2.01        34.98        37.97        33.96         2.99 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1627 TCGA-25-1628 TCGA-25-1634 TCGA-25-1878 
       12.99        15.02        12.95        20.61        35.87        85.05 
TCGA-25-2042 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2409 
       13.02         3.02        12.00        45.01        19.99        26.99 
TCGA-29-1688 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1707 
       78.90       101.79        39.02        33.93        31.20        41.98 
TCGA-29-1762 TCGA-29-1763 TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 TCGA-29-1775 
       86.60        66.81        31.30        22.98        22.55        12.36 
TCGA-29-1781 TCGA-29-1784 TCGA-29-2428 TCGA-29-2432 TCGA-30-1714 TCGA-30-1718 
        8.38         5.36        45.11        21.47        38.07        51.91 
TCGA-30-1853 TCGA-30-1855 TCGA-30-1857 TCGA-30-1866 TCGA-30-1880 TCGA-31-1951 
       36.26         2.47         0.26        36.62        57.57        22.49 
TCGA-31-1953 TCGA-31-1956 TCGA-31-1959 TCGA-36-1569 TCGA-36-1571 TCGA-36-1574 
        6.71        44.12         2.20        29.10        22.85        22.55 
TCGA-36-1580 TCGA-36-2542 TCGA-36-2543 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 
       24.23        21.60         2.24        18.31        20.52        14.17 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2591 TCGA-57-1583 TCGA-57-1584 TCGA-59-2350 
       28.93        42.02        40.77        11.38        21.14        22.32 
TCGA-59-2351 TCGA-59-2355 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1724 TCGA-61-1727 
      116.12         2.14        44.81        20.52        20.94        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-61-1903 TCGA-61-1904 
       35.80         2.43         1.45         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 
       76.87        44.52        31.07         8.61        39.68 

$`6Q LOSS WILD-TYPE`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 
       41.00         1.81        49.15        46.62         1.08        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 
       11.87        65.52        63.09         0.53        49.28        32.52 
TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 
       44.32        33.67        76.57        82.39        56.55        41.59 
TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 
      119.08        29.10        84.20        55.43        48.89        28.64 
TCGA-04-1652 TCGA-04-1654 TCGA-09-0364 TCGA-09-0366 TCGA-09-0369 TCGA-09-1664 
       31.86        47.70        29.16        57.76        35.57        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-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2054 
        8.55         4.54       112.41        71.11        63.09        20.94 
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-10-0937 TCGA-13-0714 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 
       19.99         6.21        44.55        39.58         2.73        12.39 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 TCGA-13-0768 
       15.19        17.82        11.54        34.06        31.04         8.45 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0800 
       38.93        36.72        30.35        19.59         8.71         8.12 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0885 TCGA-13-0886 TCGA-13-0889 
       35.28        35.31        13.61        91.40        74.27        61.84 
TCGA-13-0893 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 
       43.36        19.36        47.38        48.33        44.94        44.84 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 
       34.06        29.98        21.17        13.81         6.41         6.08 
TCGA-13-1403 TCGA-13-1408 TCGA-13-1409 TCGA-13-1412 TCGA-13-1477 TCGA-13-1485 
       10.88         5.92         6.84         5.33        54.64        20.68 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1492 TCGA-13-1494 TCGA-13-1496 
       22.39        70.82        82.88        73.55        38.20         4.24 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 TCGA-13-1507 TCGA-13-1509 
       37.61        38.40        13.97        16.57         4.77         4.18 
TCGA-13-1510 TCGA-13-1511 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 
        2.56         3.91        14.24         8.61        10.78         8.75 
TCGA-13-2071 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 
        6.28        54.77        23.05        25.94        26.20        72.20 
TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 TCGA-20-1687 TCGA-23-1022 TCGA-23-1023 
       27.52        19.10        16.70         2.66        49.68        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1028 TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 
       15.39        26.83        49.41        18.90         2.76        54.51 
TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 TCGA-23-1120 TCGA-23-1121 TCGA-23-1124 
        3.22        68.68         4.57         4.27         6.38        58.13 
TCGA-23-1809 TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-23-2645 TCGA-24-0968 
        0.53       115.89        91.66        77.00         4.50        19.66 
TCGA-24-0975 TCGA-24-0979 TCGA-24-1103 TCGA-24-1104 TCGA-24-1413 TCGA-24-1418 
       21.80        41.56        54.12        63.55         6.31         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1430 
        7.86         0.76         6.25         6.02         5.95        28.37 
TCGA-24-1431 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 
       19.17        72.92        12.46        45.14         9.11         3.45 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 
       22.22        26.96        57.40        16.21        56.58        41.06 
TCGA-24-1551 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1563 
       51.91        88.50        70.62        39.88        19.53        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-24-1843 TCGA-24-1846 TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 
        3.48         4.37        11.28         5.52         9.80        30.21 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2030 
       11.05        81.11        58.16        34.82       109.71        55.92 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 
       18.48        28.18        64.01        44.52        57.07        36.16 
TCGA-24-2267 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-25-1312 TCGA-25-1314 
       47.54        44.61         0.82        67.36         1.02        33.01 
TCGA-25-1319 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1630 TCGA-25-1631 
       65.00        18.58        27.62        17.03        38.20         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
       59.15        62.17        52.04        14.96        24.99        24.00 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 
       49.05         1.02        38.04        42.02         2.96        29.03 
TCGA-25-2408 TCGA-29-1690 TCGA-29-1691 TCGA-29-1695 TCGA-29-1698 TCGA-29-1699 
       31.00        47.61        48.33        40.41        68.32        36.36 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 
       16.93        23.93        59.67        18.25        31.27        34.62 
TCGA-29-1761 TCGA-29-1764 TCGA-29-1766 TCGA-29-1770 TCGA-29-1774 TCGA-29-1776 
       17.36        62.93        39.42        24.36        17.33        11.84 
TCGA-29-1777 TCGA-29-1778 TCGA-29-1783 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 
       12.30        14.93         7.23        36.30        86.17        65.00 
TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ 
       62.47        13.84        42.25        11.47         9.76        35.77 
TCGA-30-1856 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1867 
       15.68        48.10        44.91        34.78         6.12         1.22 
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-31-1955 TCGA-36-1568 TCGA-36-1570 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 
       42.51        28.77        21.53         8.55        30.08        25.74 
TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       27.85        24.69        35.05        33.01        29.49        29.82 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2544 TCGA-36-2549 TCGA-36-2551 
       25.91        25.08        23.80        20.98         6.05        16.18 
TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2590 TCGA-42-2593 
       11.47        13.81        47.57        23.74        10.42         1.48 
TCGA-57-1582 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 
       24.03         1.74        22.32        29.00        25.08        25.02 
TCGA-59-2348 TCGA-59-2349 TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 TCGA-5X-AA5U 
      180.20        80.12         9.40        34.39         5.42        11.87 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1725 TCGA-61-1741 TCGA-61-1743 TCGA-61-1900 
       11.11         8.09        31.43        33.67        43.69         5.79 
TCGA-61-1901 TCGA-61-1907 TCGA-61-1911 TCGA-61-1915 TCGA-61-1917 TCGA-61-1919 
       11.41        31.30        42.51        67.76        43.43        38.17 
TCGA-61-2000 TCGA-61-2003 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 
       14.50         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-61-2098 TCGA-61-2102 TCGA-61-2109 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 
       65.52         6.48        20.68       125.75        22.22         6.35 
TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       18.94         0.79         9.99 

  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 
            27.88             29.00 
[1] "0.3 - 152.0 (27.9)" "0.3 - 180.2 (29.0)"
[1] "hr=" "1.1"
D53V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  6Q LOSS MUTATED         2   232                0
  6Q LOSS WILD-TYPE       1   326                2
D53V3, multiclass
                  clus
vv                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  OMENTUM                        2                 1
  OVARY                        232               326
  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, continuous
D53V5, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     1 237
  6Q LOSS WILD-TYPE   2 333
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      1  237
  6Q LOSS WILD-TYPE    2  333
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO                1                 2
  YES             237               333
[1] 2 2
[1] FALSE
                   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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q LOSS MUTATED                                  1    10
  6Q LOSS WILD-TYPE                                2     9
                   vv
clus                BLACK OR AFRICAN AMERICAN
  6Q LOSS MUTATED                           8
  6Q LOSS WILD-TYPE                        26
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6Q LOSS MUTATED                                           1   202
  6Q LOSS WILD-TYPE                                         0   274
D53V7, multiclass
                                           clus
vv                                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 2
  ASIAN                                                  10                 9
  BLACK OR AFRICAN AMERICAN                               8                26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 202               274
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V8, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     3 142
  6Q LOSS WILD-TYPE   7 185
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      3  142
  6Q LOSS WILD-TYPE    7  185
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 7
  NOT HISPANIC OR LATINO             142               185
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    55  63
  7P LOSS WILD-TYPE 213 229
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
              118               442 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               63               229 
$`7P LOSS MUTATED`
TCGA-04-1338 TCGA-04-1341 TCGA-04-1347 TCGA-04-1349 TCGA-04-1362 TCGA-04-1638 
       46.62         1.08        63.09        21.57        44.32        55.43 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 TCGA-10-0928 
       35.57         9.99        57.60        55.36        30.51        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0935 TCGA-10-0938 TCGA-13-0724 TCGA-13-0751 
       34.19        32.88        35.44        20.91         2.73        55.17 
TCGA-13-0792 TCGA-13-0800 TCGA-13-0885 TCGA-13-0887 TCGA-13-0890 TCGA-13-0897 
       36.72         8.12        91.40        66.67        67.99        57.47 
TCGA-13-0919 TCGA-13-1409 TCGA-13-1487 TCGA-13-1497 TCGA-13-1499 TCGA-13-1505 
       14.89         6.84        22.39        54.31        38.40         4.21 
TCGA-13-1510 TCGA-13-2061 TCGA-20-1685 TCGA-23-1029 TCGA-23-1109 TCGA-23-1114 
        2.56        10.78        16.70         8.81        51.35        68.68 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1122 TCGA-23-2078 TCGA-23-2084 TCGA-23-2641 
       86.01       129.96        39.09        87.48        49.84         2.76 
TCGA-24-0982 TCGA-24-1104 TCGA-24-1105 TCGA-24-1417 TCGA-24-1425 TCGA-24-1426 
       22.32        63.55        47.41         7.82         5.95         5.36 
TCGA-24-1427 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 
        4.83        18.67        43.53         8.55        72.92        12.46 
TCGA-24-1469 TCGA-24-1546 TCGA-24-1548 TCGA-24-1562 TCGA-24-1567 TCGA-24-1842 
        9.11        64.27        16.21        45.50        17.23         8.32 
TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 TCGA-24-1930 TCGA-24-2254 
        3.48         3.72         4.37        11.28        81.11        57.07 
TCGA-24-2260 TCGA-24-2262 TCGA-24-2298 TCGA-25-1317 TCGA-25-1321 TCGA-25-1630 
       36.16         0.36        53.26         2.01        33.96        38.20 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 
       59.15        62.17        52.04        13.02        49.05         1.02 
TCGA-25-2396 TCGA-25-2399 TCGA-29-1691 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 
        3.02        19.99        48.33        16.93        23.93        59.67 
TCGA-29-1711 TCGA-29-1761 TCGA-29-1766 TCGA-29-1776 TCGA-29-1781 TCGA-29-2414 
       34.62        17.36        39.42        11.84         8.38        86.17 
TCGA-29-2425 TCGA-29-2431 TCGA-30-1718 TCGA-30-1855 TCGA-30-1887 TCGA-36-1569 
       65.00        42.25        51.91         2.47        24.26        29.10 
TCGA-36-1570 TCGA-36-1574 TCGA-36-1578 TCGA-36-2552 TCGA-42-2589 TCGA-57-1992 
       21.53        22.55        27.85        11.47        42.02        29.00 
TCGA-57-1994 TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 TCGA-61-1722 TCGA-61-1724 
       25.02         9.40        34.39         5.42         8.09        20.94 
TCGA-61-1740 TCGA-61-1906 TCGA-61-1913 TCGA-61-1995 TCGA-61-2008 TCGA-61-2009 
        2.43        34.13        48.92         2.01        30.64        39.85 
TCGA-61-2096 TCGA-61-2612 TCGA-OY-A56P TCGA-WR-A838 
       58.39         6.35        39.68         9.99 

$`7P LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 
       43.92        41.00         1.81        49.15         2.01        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 
       11.87        65.52        48.76        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-04-1525 TCGA-04-1530 
       56.55        41.59        19.99         0.79        38.37       119.08 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 
       29.10        84.20        48.89        27.88        28.64        64.64 
TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 
       36.23        31.86        47.70        45.37        29.16         9.47 
TCGA-09-0366 TCGA-09-0367 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       57.76        17.98        38.43        89.33        74.93        41.62 
TCGA-09-1667 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 
       61.87        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-10-0925 
       63.09        39.75        20.94        26.93        12.46        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0933 TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 
       25.91        81.86        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-13-0760 
       15.19        17.82         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 
       34.06        32.25        31.04        21.40         8.45        38.93 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 
       28.70        30.35        19.59         8.71         7.79         8.28 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
        8.19        43.86        35.28        35.31        13.61        68.94 
TCGA-13-0884 TCGA-13-0886 TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 
      107.18        74.27        70.39        61.84        69.01        43.36 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       56.15        57.07        19.36        47.38        48.33        47.84 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
       44.94        44.84        37.08        27.72        34.06        29.98 
TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 
       21.17        13.81         4.64         6.41         6.08        10.88 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 
        6.61         7.36         6.05         5.92         4.70         4.21 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
        5.33        54.64        87.06        61.71        29.42        98.04 
TCGA-13-1485 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       20.68        70.82        82.88        52.44        73.55        38.20 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 
       49.25         4.24        37.61        13.97        32.84        16.57 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 
        4.41         4.77         4.18         3.91         3.09        14.24 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU 
       12.23         8.61         8.75         6.28        54.77         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-20-1686 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-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 
        2.76        54.51         3.22        31.20         4.57        33.30 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 
        4.27         6.38        33.47        58.13         0.53        24.95 
TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 
      115.89        91.66        77.00         4.70         4.50         7.63 
TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 
       19.66        11.64        21.80        41.56         7.66        54.12 
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-24-1466 TCGA-24-1467 
        6.02        17.39        28.37        19.17        45.14       105.99 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1549 
        3.45         1.18        22.22        26.96        57.40        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-24-1563 TCGA-24-1564 TCGA-24-1565 
       39.88        19.53        44.09        47.70        25.87        10.26 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1845 TCGA-24-1849 
       90.15        88.37        48.33        38.24         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-24-2261 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-24-2289 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-25-1318 TCGA-25-1319 
       26.96        33.01        52.04        42.05        34.98        65.00 
TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       37.97         2.99        12.99        15.02        18.58        27.62 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1634 TCGA-25-1870 
       17.03        12.95        20.61         0.30        35.87        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2393 TCGA-25-2397 TCGA-25-2398 
       24.99        24.00        85.05        38.04        12.00        45.01 
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-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1762 
       68.32        36.36        18.25        41.98        31.27        86.60 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 
       66.81        62.93        31.30        22.98        24.36        22.55 
TCGA-29-1774 TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 TCGA-29-1783 TCGA-29-1784 
       17.33        12.36        12.30        14.93         7.23         5.36 
TCGA-29-1785 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2432 TCGA-29-2434 
       36.30        62.47        45.11        13.84        21.47        11.47 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 
        9.76        35.77        38.07        36.26        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-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 
       57.57        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-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1580 TCGA-36-1581 
       22.85         8.55        30.08        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-36-2551 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 
       14.17         6.05        16.18        13.81        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-59-A5PD TCGA-5X-AA5U 
       22.32       116.12         2.14        44.81        20.52        11.87 
TCGA-61-1721 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 
       11.11        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-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 
       31.30        37.05        42.51        56.61        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-61-2012 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-61-2101 
       51.72        71.74        61.64        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-61-2613 TCGA-61-2614 TCGA-OY-A56Q TCGA-VG-A8LO 
       31.07         8.61        18.94         0.79 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.36              0.26 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           129.96            180.20 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           29.050            28.555 
[1] "0.4 - 130.0 (29.1)" "0.3 - 180.2 (28.6)"
[1] "hr=" "1"  
D54V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  7P LOSS MUTATED         0   117                1
  7P LOSS WILD-TYPE       3   441                1
D54V3, multiclass
                  clus
vv                 7P LOSS MUTATED 7P LOSS WILD-TYPE
  OMENTUM                        0                 3
  OVARY                        117               441
  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, continuous
D54V5, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0 120
  7P LOSS WILD-TYPE   3 450
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0  120
  7P LOSS WILD-TYPE    3  450
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                0                 3
  YES             120               450
[1] 2 2
[1] FALSE
                   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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P LOSS MUTATED                                  1     5
  7P LOSS WILD-TYPE                                2    14
                   vv
clus                BLACK OR AFRICAN AMERICAN
  7P LOSS MUTATED                           6
  7P LOSS WILD-TYPE                        28
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7P LOSS MUTATED                                           0   102
  7P LOSS WILD-TYPE                                         1   374
D54V7, multiclass
                                           clus
vv                                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 2
  ASIAN                                                   5                14
  BLACK OR AFRICAN AMERICAN                               6                28
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 102               374
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V8, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     1  64
  7P LOSS WILD-TYPE   9 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1   64
  7P LOSS WILD-TYPE    9  263
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              64               263
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED    38  43
  7Q LOSS WILD-TYPE 230 249
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               81               479 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               43               249 
$`7Q LOSS MUTATED`
TCGA-04-1349 TCGA-04-1638 TCGA-09-0369 TCGA-09-1659 TCGA-09-1668 TCGA-10-0930 
       21.57        55.43        35.57         9.99        55.36        34.19 
TCGA-10-0931 TCGA-13-0751 TCGA-13-0792 TCGA-13-0800 TCGA-13-0887 TCGA-13-0890 
       32.88        55.17        36.72         8.12        66.67        67.99 
TCGA-13-0897 TCGA-13-0919 TCGA-13-1487 TCGA-13-1499 TCGA-13-1505 TCGA-13-1510 
       57.47        14.89        22.39        38.40         4.21         2.56 
TCGA-13-2061 TCGA-20-1683 TCGA-20-1685 TCGA-23-1029 TCGA-23-1114 TCGA-23-2078 
       10.78        25.38        16.70         8.81        68.68        87.48 
TCGA-23-2084 TCGA-24-0982 TCGA-24-1417 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
       49.84        22.32         7.82         5.95         5.36         4.83 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1463 TCGA-24-1469 TCGA-24-1564 TCGA-24-1567 
       18.67        43.53        72.92         9.11        25.87        17.23 
TCGA-24-1842 TCGA-24-1846 TCGA-24-1847 TCGA-24-1930 TCGA-24-2260 TCGA-24-2298 
        8.32         4.37        11.28        81.11        36.16        53.26 
TCGA-25-1317 TCGA-25-1321 TCGA-25-1630 TCGA-25-1632 TCGA-25-1633 TCGA-25-1877 
        2.01        33.96        38.20        59.15        62.17        24.00 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2396 TCGA-29-1691 TCGA-29-1701 
       13.02        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-61-2008 TCGA-61-2096 TCGA-61-2612 
       30.64        58.39         6.35 

$`7Q LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       43.92        41.00         1.81        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-04-1350 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-04-1516 
       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-04-1644 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-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 
       47.70        45.37        29.16         9.47        57.76        17.98 
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-10-0925 
       63.09        39.75        20.94        26.93        12.46        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 
       25.91        81.86        18.51        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-13-0727 TCGA-13-0730 
       39.58         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-13-0762 
        2.50        11.18        11.38        11.54        34.06        32.25 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0793 TCGA-13-0794 
       31.04        21.40         8.45        38.93        28.70        30.35 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 
       19.59         8.71         7.79         8.28         8.19        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        91.40 
TCGA-13-0886 TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 
       74.27        70.39        61.84        69.01        43.36        56.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
       57.07        19.36        47.38        48.33        47.84        44.94 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       44.84        37.08        27.72        34.06        29.98        21.17 
TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 
       13.81         4.64         6.41         6.08        10.88         6.61 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
        7.36         6.05         5.92         6.84         4.70         4.21 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
        5.33        54.64        87.06        61.71        29.42        98.04 
TCGA-13-1485 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       20.68        70.82        82.88        52.44        73.55        38.20 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 
       49.25         4.24        54.31        37.61        13.97        32.84 
TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 
       16.57         4.41         4.77         4.18         3.91         3.09 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT 
       14.24        12.23         8.61         8.75         6.28        54.77 
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         4.57 
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-24-0968 
       77.00         2.76         4.70         4.50         7.63        19.66 
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-24-1418 TCGA-24-1419 TCGA-24-1422 
       47.41         6.31         6.38         7.99         7.86         0.76 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1436 
        6.25         6.02        17.39        28.37        19.17         8.55 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 
       12.46        45.14       105.99         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-24-1565 TCGA-24-1603 
       19.53        44.09        45.50        47.70        10.26        90.15 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 
       88.37        48.33        38.24         3.48         3.72         3.81 
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-24-2019 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-24-2254 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-24-2280 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-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 
       42.05        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-25-1631 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 
        0.30        35.87        52.04        14.96        24.99        85.05 
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-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 
       16.18        13.81        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-57-1585 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-59-2355 TCGA-59-2372 TCGA-59-A5PD TCGA-5X-AA5U 
       22.32       116.12         2.14        44.81        20.52        11.87 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 
       11.11         8.09        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-61-1900 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-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2009 TCGA-61-2012 
        5.52        14.50        17.98         4.01        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-61-2097 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-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
        8.61        39.68        18.94         0.79         9.99 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             1.02              0.26 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            87.48            180.20 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            24.69             29.10 
[1] "1.0 - 87.5 (24.7)"  "0.3 - 180.2 (29.1)"
[1] "hr=" "1.2"
D55V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  7Q LOSS MUTATED         0    80                1
  7Q LOSS WILD-TYPE       3   478                1
D55V3, multiclass
                  clus
vv                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  OMENTUM                        0                 3
  OVARY                         80               478
  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, continuous
D55V5, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1  80
  7Q LOSS WILD-TYPE   2 490
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   80
  7Q LOSS WILD-TYPE    2  490
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                1                 2
  YES              80               490
[1] 2 2
[1] FALSE
                   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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q LOSS MUTATED                                  1     5
  7Q LOSS WILD-TYPE                                2    14
                   vv
clus                BLACK OR AFRICAN AMERICAN
  7Q LOSS MUTATED                           4
  7Q LOSS WILD-TYPE                        30
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7Q LOSS MUTATED                                           0    68
  7Q LOSS WILD-TYPE                                         1   408
D55V7, multiclass
                                           clus
vv                                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 2
  ASIAN                                                   5                14
  BLACK OR AFRICAN AMERICAN                               4                30
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  68               408
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V8, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0  44
  7Q LOSS WILD-TYPE  10 283
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0   44
  7Q LOSS WILD-TYPE   10  283
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              44               283
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED   121 145
  8P LOSS WILD-TYPE 147 147
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              266               294 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              145               147 
$`8P LOSS MUTATED`
TCGA-04-1332 TCGA-04-1338 TCGA-04-1346 TCGA-04-1348 TCGA-04-1356 TCGA-04-1361 
       41.00        46.62        65.52        48.76        49.28        32.52 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 TCGA-04-1530 
       76.57       103.40        82.39        56.55        19.99       119.08 
TCGA-04-1536 TCGA-04-1638 TCGA-04-1646 TCGA-04-1652 TCGA-04-1655 TCGA-09-0366 
       29.10        55.43        27.88        31.86        45.37        57.76 
TCGA-09-0367 TCGA-09-1661 TCGA-09-1664 TCGA-09-1668 TCGA-09-1670 TCGA-09-1674 
       17.98        38.43        74.93        55.36        17.98         8.55 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2054 TCGA-09-2056 TCGA-10-0925 TCGA-10-0927 
       71.11        63.09        20.94        12.46        54.31        81.86 
TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0936 TCGA-13-0723 TCGA-13-0725 
       18.51        34.19        32.88        36.92        39.58        12.39 
TCGA-13-0730 TCGA-13-0757 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0792 
       17.82        11.18        11.54        34.06        32.25        36.72 
TCGA-13-0793 TCGA-13-0795 TCGA-13-0802 TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 
       28.70        19.59         8.19        43.86        35.31        13.61 
TCGA-13-0883 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 TCGA-13-0899 
       68.94        91.40        66.67        70.39        67.99        56.15 
TCGA-13-0901 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       19.36        34.06        29.98        21.17        14.89        13.81 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1407 TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 
        6.08        10.88         6.05         4.70         4.21        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1494 TCGA-13-1495 
       61.71        29.42        98.04        22.39        38.20        49.25 
TCGA-13-1496 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 
        4.24        38.40        13.97        32.84        16.57         4.21 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 
        4.77         4.18         2.56        12.23        10.78         8.75 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-1684 TCGA-20-1686 
       54.77         8.42        25.94        26.20        19.10         2.93 
TCGA-23-1021 TCGA-23-1024 TCGA-23-1031 TCGA-23-1114 TCGA-23-1116 TCGA-23-1120 
       47.54        15.39        18.90        68.68         4.57         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-23-2643 TCGA-23-2645 TCGA-24-0975 TCGA-24-0980 TCGA-24-0982 
      115.89         4.70         4.50        21.80         7.66        22.32 
TCGA-24-1104 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 TCGA-24-1422 
       63.55         6.31         6.38         7.82         7.86         0.76 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 
        6.25         6.02         4.83        17.39        19.17        18.67 
TCGA-24-1436 TCGA-24-1464 TCGA-24-1467 TCGA-24-1470 TCGA-24-1544 TCGA-24-1546 
        8.55        12.46       105.99         3.45        26.96        64.27 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1552 TCGA-24-1558 TCGA-24-1604 
       16.21        56.58        41.06        41.39        19.53        88.37 
TCGA-24-1614 TCGA-24-1842 TCGA-24-1844 TCGA-24-1846 TCGA-24-1850 TCGA-24-1924 
       48.33         8.32         3.72         4.37         5.52        30.21 
TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2024 TCGA-24-2027 TCGA-24-2030 
       16.44        11.05        81.11        58.16       109.71        55.92 
TCGA-24-2035 TCGA-24-2254 TCGA-24-2261 TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 
       28.18        57.07         0.79        47.54        70.45        44.61 
TCGA-24-2288 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-25-1313 TCGA-25-1314 
        0.82        36.23        16.64        33.11        26.96        33.01 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1626 
       34.98        65.00        33.96         2.99        12.99        17.03 
TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 TCGA-25-1633 TCGA-25-1635 TCGA-25-1871 
       12.95        38.20         0.30        62.17        52.04        24.99 
TCGA-25-1878 TCGA-25-2393 TCGA-25-2396 TCGA-25-2399 TCGA-25-2400 TCGA-25-2404 
       85.05        38.04         3.02        19.99        42.02        29.03 
TCGA-25-2409 TCGA-29-1691 TCGA-29-1694 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 
       26.99        48.33        39.02        40.41        31.20        68.32 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 TCGA-29-1710 TCGA-29-1761 
       36.36        16.93        59.67        18.25        31.27        17.36 
TCGA-29-1762 TCGA-29-1768 TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1783 
       86.60        31.30        24.36        17.33        12.36         7.23 
TCGA-29-1784 TCGA-29-2428 TCGA-29-2429 TCGA-29-2432 TCGA-29-2434 TCGA-30-1855 
        5.36        45.11        13.84        21.47        11.47         2.47 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1862 TCGA-30-1866 TCGA-30-1887 TCGA-31-1944 
       15.68         0.26         6.12        36.62        24.26        45.57 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1955 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 
       18.77        22.49        42.51        29.10        21.53        22.85 
TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 TCGA-36-1580 TCGA-36-2534 TCGA-36-2537 
       22.55         8.55        25.74        24.23        29.82        25.91 
TCGA-36-2538 TCGA-36-2542 TCGA-36-2543 TCGA-36-2547 TCGA-36-2552 TCGA-3P-A9WA 
       25.08        21.60         2.24        20.52        11.47        13.81 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2593 TCGA-57-1583 
       23.74        28.93        42.02        10.42         1.48        11.38 
TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 
        1.74        22.32        29.00        25.08        25.02       180.20 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-A5PD TCGA-61-1727 TCGA-61-1728 
       22.32       116.12         9.40        20.52        18.54        27.88 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1737 TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 
        4.34        31.79        44.84         2.43        33.67         1.45 
TCGA-61-1904 TCGA-61-1914 TCGA-61-1915 TCGA-61-1919 TCGA-61-1998 TCGA-61-2000 
        9.07        56.61        67.76        38.17         5.52        14.50 
TCGA-61-2008 TCGA-61-2016 TCGA-61-2018 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 
       30.64         1.18        45.40        60.62        65.52        55.50 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2113 TCGA-61-2613 
        6.48        76.87        20.68        44.52        22.22        31.07 
TCGA-VG-A8LO TCGA-WR-A838 
        0.79         9.99 

$`8P LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1341 TCGA-04-1342 
       43.92         1.81        49.15         2.01         1.08        18.51 
TCGA-04-1343 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 
       11.87        63.09        21.57        63.98        65.46         0.53 
TCGA-04-1362 TCGA-04-1364 TCGA-04-1516 TCGA-04-1519 TCGA-04-1525 TCGA-04-1542 
       44.32        33.67        41.59         0.79        38.37        84.20 
TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-09-0364 
       48.89        28.64        64.64        36.23        47.70        29.16 
TCGA-09-0365 TCGA-09-0369 TCGA-09-1659 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 
        9.47        35.57         9.99        89.33        41.62        57.60 
TCGA-09-1667 TCGA-09-1669 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 
       61.87        30.51         5.85         3.02        97.55         6.18 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2053 TCGA-09-2055 
        6.12        35.15         4.54       112.41        39.75        26.93 
TCGA-10-0926 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 
       25.91        14.66         6.71        35.44        19.99        20.91 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 
        6.21        24.59        44.55         2.73        31.20        15.19 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0758 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 
       55.17         2.50        11.38        31.04        21.40         8.45 
TCGA-13-0791 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
       38.93        30.35         8.71         7.79         8.12         8.28 
TCGA-13-0804 TCGA-13-0884 TCGA-13-0886 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 
       35.28       107.18        74.27        61.84        69.01        43.36 
TCGA-13-0897 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
       57.47        57.07        47.38        48.33        47.84        44.94 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0921 TCGA-13-0923 TCGA-13-1404 
       44.84        37.08        27.72         4.64         6.41         6.61 
TCGA-13-1405 TCGA-13-1408 TCGA-13-1409 TCGA-13-1412 TCGA-13-1477 TCGA-13-1485 
        7.36         5.92         6.84         5.33        54.64        20.68 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1497 TCGA-13-1498 
       70.82        82.88        52.44        73.55        54.31        37.61 
TCGA-13-1506 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2060 TCGA-13-2071 
        4.41         3.91         3.09        14.24         8.61         6.28 
TCGA-20-0987 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1685 TCGA-20-1687 
       23.05        72.20        27.52        25.38        16.70         2.66 
TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 
       49.68        40.54        26.83        32.09        49.41         8.81 
TCGA-23-1030 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 
       29.13         2.76        51.35        54.51         3.22        31.20 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
       33.30        86.01       129.96        87.48        91.66        77.00 
TCGA-23-2084 TCGA-23-2641 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0979 
       49.84         2.76         7.63        19.66        11.64        41.56 
TCGA-24-1103 TCGA-24-1105 TCGA-24-1418 TCGA-24-1425 TCGA-24-1426 TCGA-24-1430 
       54.12        47.41         7.99         5.95         5.36        28.37 
TCGA-24-1435 TCGA-24-1463 TCGA-24-1466 TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 
       43.53        72.92        45.14         9.11         1.18        22.22 
TCGA-24-1545 TCGA-24-1551 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       57.40        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-24-1616 TCGA-24-1843 TCGA-24-1845 TCGA-24-1847 TCGA-24-1849 
       90.15        38.24         3.48         3.81        11.28         5.79 
TCGA-24-1920 TCGA-24-1923 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2026 
        9.80        22.68         4.87       152.02        44.84        34.82 
TCGA-24-2029 TCGA-24-2033 TCGA-24-2036 TCGA-24-2038 TCGA-24-2260 TCGA-24-2262 
       14.43        18.48        64.01        44.52        36.16         0.36 
TCGA-24-2271 TCGA-24-2289 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1315 
       31.63        67.36        55.86        53.26         1.02        52.04 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1320 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       42.05         2.01        37.97        15.02        18.58        27.62 
TCGA-25-1628 TCGA-25-1632 TCGA-25-1634 TCGA-25-1870 TCGA-25-1877 TCGA-25-2042 
       20.61        59.15        35.87        14.96        24.00        13.02 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2397 TCGA-25-2398 TCGA-25-2401 TCGA-25-2408 
       49.05         1.02        12.00        45.01         2.96        31.00 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1696 TCGA-29-1702 TCGA-29-1707 
       78.90        47.61       101.79        33.93        23.93        41.98 
TCGA-29-1711 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1769 TCGA-29-1771 
       34.62        66.81        62.93        39.42        22.98        22.55 
TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1785 TCGA-29-2414 
       11.84        12.30        14.93         8.38        36.30        86.17 
TCGA-29-2425 TCGA-29-2427 TCGA-29-2431 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 
       65.00        62.47        42.25         9.76        35.77        38.07 
TCGA-30-1718 TCGA-30-1853 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1867 
       51.91        36.26        48.10        44.91        34.78         1.22 
TCGA-30-1880 TCGA-30-1891 TCGA-30-1892 TCGA-31-1946 TCGA-31-1953 TCGA-31-1956 
       57.57        30.05        48.79        30.18         6.71        44.12 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1576 TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 
        2.20        28.77        30.08        27.85        24.69        35.05 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2540 TCGA-36-2544 TCGA-36-2545 TCGA-36-2548 
       33.01        29.49        23.80        20.98        18.31        14.17 
TCGA-36-2549 TCGA-36-2551 TCGA-42-2582 TCGA-42-2591 TCGA-57-1582 TCGA-57-1584 
        6.05        16.18        47.57        40.77        24.03        21.14 
TCGA-59-2349 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-5X-AA5U 
       80.12        34.39         2.14         5.42        44.81        11.87 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1734 TCGA-61-1736 
       11.11         8.09        20.94        31.43        28.47        48.79 
TCGA-61-1738 TCGA-61-1743 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 
       35.80        43.69         8.42         5.79        11.41        13.02 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1917 
       34.13        31.30        37.05        42.51        48.92        43.43 
TCGA-61-1918 TCGA-61-1995 TCGA-61-2002 TCGA-61-2003 TCGA-61-2009 TCGA-61-2012 
       15.75         2.01        17.98         4.01        39.85        30.64 
TCGA-61-2017 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       45.96         4.80         4.77        51.72        71.74        61.64 
TCGA-61-2096 TCGA-61-2111 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
       58.39       125.75         6.35         8.61        39.68        18.94 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.26              0.36 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           180.20            152.02 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            25.05             31.12 
[1] "0.3 - 180.2 (25.0)" "0.4 - 152.0 (31.1)"
[1] "hr=" "1.2"
D56V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  8P LOSS MUTATED         2   266                0
  8P LOSS WILD-TYPE       1   292                2
D56V3, multiclass
                  clus
vv                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  OMENTUM                        2                 1
  OVARY                        266               292
  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, continuous
D56V5, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     1 272
  8P LOSS WILD-TYPE   2 298
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1  272
  8P LOSS WILD-TYPE    2  298
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                1                 2
  YES             272               298
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  8P LOSS MUTATED    5 12  4  2
  8P LOSS WILD-TYPE 10 14  1  1
D56V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0               5                10
  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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P LOSS MUTATED                                  2     8
  8P LOSS WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN
  8P LOSS MUTATED                          17
  8P LOSS WILD-TYPE                        17
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8P LOSS MUTATED                                           1   224
  8P LOSS WILD-TYPE                                         0   252
D56V7, multiclass
                                           clus
vv                                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        2                 1
  ASIAN                                                   8                11
  BLACK OR AFRICAN AMERICAN                              17                17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 224               252
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V8, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     6 148
  8P LOSS WILD-TYPE   4 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      6  148
  8P LOSS WILD-TYPE    4  179
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                 4
  NOT HISPANIC OR LATINO             148               179
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    37  49
  8Q LOSS WILD-TYPE 231 243
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               86               474 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               49               243 
$`8Q LOSS MUTATED`
TCGA-04-1332 TCGA-04-1346 TCGA-04-1356 TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 
       41.00        65.52        49.28        82.39        56.55        19.99 
TCGA-04-1655 TCGA-09-0366 TCGA-09-2051 TCGA-09-2054 TCGA-10-0928 TCGA-13-0725 
       45.37        57.76        63.09        20.94        18.51        12.39 
TCGA-13-0730 TCGA-13-0757 TCGA-13-0760 TCGA-13-0762 TCGA-13-0803 TCGA-13-0885 
       17.82        11.18        11.54        32.25        43.86        91.40 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0901 TCGA-13-0913 TCGA-13-0920 TCGA-13-1407 
       66.67        70.39        19.36        29.98        13.81         6.05 
TCGA-13-1483 TCGA-13-1510 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-20-1684 
       29.42         2.56        10.78         8.75        54.77        19.10 
TCGA-23-1032 TCGA-23-1114 TCGA-23-1122 TCGA-23-1809 TCGA-24-0980 TCGA-24-0982 
        2.76        68.68        39.09         0.53         7.66        22.32 
TCGA-24-1416 TCGA-24-1424 TCGA-24-1427 TCGA-24-1431 TCGA-24-1544 TCGA-24-1548 
        6.38         6.02         4.83        19.17        26.96        16.21 
TCGA-24-1842 TCGA-24-1850 TCGA-24-1928 TCGA-24-2030 TCGA-24-2254 TCGA-24-2261 
        8.32         5.52        11.05        55.92        57.07         0.79 
TCGA-24-2267 TCGA-24-2280 TCGA-25-1318 TCGA-25-1319 TCGA-25-1322 TCGA-25-1626 
       47.54        70.45        34.98        65.00         2.99        17.03 
TCGA-25-1630 TCGA-25-1634 TCGA-25-1635 TCGA-25-1871 TCGA-25-2393 TCGA-25-2400 
       38.20        35.87        52.04        24.99        38.04        42.02 
TCGA-25-2409 TCGA-29-1691 TCGA-29-1770 TCGA-29-1775 TCGA-29-2428 TCGA-30-1855 
       26.99        48.33        24.36        12.36        45.11         2.47 
TCGA-31-1955 TCGA-36-1571 TCGA-36-1575 TCGA-36-2537 TCGA-36-2547 TCGA-36-2552 
       42.51        22.85         8.55        25.91        20.52        11.47 
TCGA-42-2587 TCGA-42-2589 TCGA-57-1994 TCGA-59-2352 TCGA-61-1727 TCGA-61-1730 
       23.74        42.02        25.02         9.40        18.54         4.34 
TCGA-61-1733 TCGA-61-1904 TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 TCGA-61-2110 
       31.79         9.07        60.62        55.50         6.48        44.52 
TCGA-61-2113 TCGA-WR-A838 
       22.22         9.99 

$`8Q LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 
       43.92         1.81        49.15         2.01        46.62         1.08 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 
       18.51        11.87        63.09        48.76        21.57        63.98 
TCGA-04-1351 TCGA-04-1353 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
       65.46         0.53        32.52        44.32        33.67        76.57 
TCGA-04-1367 TCGA-04-1516 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 
      103.40        41.59         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-09-0364 TCGA-09-0365 TCGA-09-0367 
       36.23        31.86        47.70        29.16         9.47        17.98 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       35.57         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-09-2055 TCGA-09-2056 
        4.54       112.41        71.11        39.75        26.93        12.46 
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-13-0726 TCGA-13-0727 
       24.59        44.55        39.58         2.73        31.20        15.19 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0758 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 
       55.17         2.50        11.38        34.06        31.04        21.40 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 
        8.45        38.93        36.72        28.70        30.35        19.59 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 
        8.71         7.79         8.12         8.28         8.19        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        74.27        61.84 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       67.99        69.01        43.36        57.47        56.15        57.07 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
       47.38        48.33        47.84        44.94        44.84        37.08 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 
       27.72        34.06        21.17        14.89         4.64         6.41 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1409 
        6.08        10.88         6.61         7.36         5.92         6.84 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 
        4.70         4.21         5.33        54.64        87.06        61.71 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
       98.04        20.68        22.39        70.82        82.88        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
       73.55        38.20        49.25         4.24        54.31        37.61 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       38.40        13.97        32.84        16.57         4.21         4.41 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 
        4.77         4.18         3.91         3.09        14.24        12.23 
TCGA-13-2060 TCGA-13-2071 TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
        8.61         6.28         8.42        23.05        25.94        26.20 
TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 
       72.20        27.52        25.38        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-23-1109 TCGA-23-1110 
       49.41         8.81        29.13        18.90        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         4.57        33.30        86.01       129.96 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 
        4.27         6.38        33.47        58.13        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-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        4.50         7.63        19.66        11.64        21.80        41.56 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1417 TCGA-24-1418 
       54.12        63.55        47.41         6.31         7.82         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 TCGA-24-1428 
        7.86         0.76         6.25         5.95         5.36        17.39 
TCGA-24-1430 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 
       28.37        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-24-1545 TCGA-24-1546 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
       57.40        64.27        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-24-1843 TCGA-24-1844 TCGA-24-1845 
       88.37        48.33        38.24         3.48         3.72         3.81 
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-24-1927 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-24-2033 TCGA-24-2035 TCGA-24-2036 
       34.82       109.71        14.43        18.48        28.18        64.01 
TCGA-24-2038 TCGA-24-2260 TCGA-24-2262 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 
       44.52        36.16         0.36        31.63        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-25-1313 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-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       37.97        33.96        12.99        15.02        18.58        27.62 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1870 
       12.95        20.61         0.30        59.15        62.17        14.96 
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-25-2398 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-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-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 
       66.81        62.93        39.42        31.30        22.98        22.55 
TCGA-29-1774 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 
       17.33        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-29-2429 
        5.36        36.30        86.17        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-30-1859 TCGA-30-1860 
       51.91        36.26        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-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
        6.71        44.12         2.20        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-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2538 TCGA-36-2540 
       35.05        33.01        29.49        29.82        25.08        23.80 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2548 TCGA-36-2549 
       21.60         2.24        20.98        18.31        14.17         6.05 
TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2588 TCGA-42-2590 TCGA-42-2591 
       16.18        13.81        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-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-5X-AA5U 
       34.39         2.14         5.42        44.81        20.52        11.87 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1728 TCGA-61-1734 
       11.11         8.09        20.94        31.43        27.88        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-61-1906 
        1.45         8.42         5.79        11.41        13.02        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-61-1995 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-61-2098 TCGA-61-2104 TCGA-61-2109 TCGA-61-2111 
       61.64        58.39        65.52        76.87        20.68       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 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.53              0.26 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             91.4             180.2 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            24.05             29.10 
[1] "0.5 - 91.4 (24.0)"  "0.3 - 180.2 (29.1)"
[1] "hr=" "1.3"
D57V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  8Q LOSS MUTATED         0    86                0
  8Q LOSS WILD-TYPE       3   472                2
D57V3, multiclass
                  clus
vv                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  OMENTUM                        0                 3
  OVARY                         86               472
  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, continuous
D57V5, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0  89
  8Q LOSS WILD-TYPE   3 481
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   89
  8Q LOSS WILD-TYPE    3  481
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                0                 3
  YES              89               481
[1] 2 2
[1] FALSE
                   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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  0     1
  8Q LOSS WILD-TYPE                                3    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  8Q LOSS MUTATED                           6
  8Q LOSS WILD-TYPE                        28
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8Q LOSS MUTATED                                           0    74
  8Q LOSS WILD-TYPE                                         1   402
D57V7, multiclass
                                           clus
vv                                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   1                18
  BLACK OR AFRICAN AMERICAN                               6                28
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  74               402
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     2  47
  8Q LOSS WILD-TYPE   8 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      2   47
  8Q LOSS WILD-TYPE    8  280
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 8
  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   117 137
  9P LOSS WILD-TYPE 151 155
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              254               306 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              137               155 
$`9P LOSS MUTATED`
TCGA-04-1332 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1343 TCGA-04-1346 
       41.00         2.01        46.62         1.08        11.87        65.52 
TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 
       63.09        21.57        63.98        65.46        49.28        32.52 
TCGA-04-1364 TCGA-04-1371 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1536 
       33.67        82.39        19.99         0.79        38.37        29.10 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1646 TCGA-04-1649 TCGA-04-1652 TCGA-09-0364 
       84.20        55.43        27.88        64.64        31.86        29.16 
TCGA-09-0365 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
        9.47        17.98        35.57         9.99        38.43        89.33 
TCGA-09-1665 TCGA-09-1667 TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 TCGA-09-1675 
       41.62        61.87        30.51        17.98         3.02        97.55 
TCGA-09-2044 TCGA-09-2049 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 
        6.12       112.41        39.75        20.94        26.93        12.46 
TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
       81.86        34.19        32.88        20.91         6.21        24.59 
TCGA-13-0724 TCGA-13-0760 TCGA-13-0762 TCGA-13-0764 TCGA-13-0795 TCGA-13-0800 
        2.73        11.54        32.25        31.04        19.59         8.12 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0883 TCGA-13-0885 TCGA-13-0886 TCGA-13-0888 
       35.28        35.31        68.94        91.40        74.27        70.39 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0900 TCGA-13-0904 TCGA-13-0908 TCGA-13-0921 
       61.84        67.99        57.07        48.33        44.84         4.64 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
        6.08        10.88         6.05         5.92         6.84         4.70 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 
        4.21         5.33        87.06        29.42        98.04        20.68 
TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1500 
       22.39        82.88        52.44        38.20        49.25        13.97 
TCGA-13-1509 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT 
        4.18        14.24         8.61        10.78         8.75        54.77 
TCGA-13-A5FU TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 TCGA-23-1021 TCGA-23-1022 
        8.42        27.52        19.10        16.70        47.54        49.68 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 TCGA-23-1114 TCGA-23-1116 
       32.09        49.41        29.13        18.90        68.68         4.57 
TCGA-23-1118 TCGA-23-1119 TCGA-23-2072 TCGA-23-2081 TCGA-23-2643 TCGA-23-2645 
       86.01       129.96        24.95        77.00         4.70         4.50 
TCGA-24-0982 TCGA-24-1105 TCGA-24-1413 TCGA-24-1419 TCGA-24-1422 TCGA-24-1426 
       22.32        47.41         6.31         7.86         0.76         5.36 
TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 TCGA-24-1463 TCGA-24-1464 TCGA-24-1545 
        4.83        28.37        19.17        72.92        12.46        57.40 
TCGA-24-1546 TCGA-24-1549 TCGA-24-1550 TCGA-24-1560 TCGA-24-1563 TCGA-24-1564 
       64.27        56.58        41.06        44.09        47.70        25.87 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1843 TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 
       90.15        88.37         3.48        81.11         4.87        44.84 
TCGA-24-2024 TCGA-24-2029 TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 TCGA-24-2260 
       58.16        14.43        55.92        28.18        64.01        36.16 
TCGA-24-2261 TCGA-24-2267 TCGA-24-2293 TCGA-24-2295 TCGA-25-1312 TCGA-25-1314 
        0.79        47.54        16.64        33.11         1.02        33.01 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1321 TCGA-25-1323 TCGA-25-1625 
       42.05         2.01        34.98        33.96        12.99        27.62 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 
       17.03        12.95        62.17        35.87        14.96        24.99 
TCGA-25-1877 TCGA-25-2392 TCGA-25-2393 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 
       24.00         1.02        38.04        19.99        42.02         2.96 
TCGA-29-1688 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1698 TCGA-29-1699 
       78.90       101.79        39.02        40.41        68.32        36.36 
TCGA-29-1702 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1766 TCGA-29-1770 
       23.93        18.25        41.98        31.27        39.42        24.36 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1783 TCGA-29-2425 TCGA-29-2434 
       22.55        17.33        12.36         7.23        65.00        11.47 
TCGA-29-2436 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 
        9.76        38.07        51.91        36.26        15.68         0.26 
TCGA-30-1861 TCGA-30-1866 TCGA-30-1880 TCGA-30-1891 TCGA-31-1953 TCGA-31-1955 
       34.78        36.62        57.57        30.05         6.71        42.51 
TCGA-31-1959 TCGA-36-1569 TCGA-36-1571 TCGA-36-1576 TCGA-36-1580 TCGA-36-2529 
        2.20        29.10        22.85        30.08        24.23        35.05 
TCGA-36-2537 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-36-2547 TCGA-36-2548 
       25.91        23.80        21.60        20.98        20.52        14.17 
TCGA-36-2549 TCGA-36-2552 TCGA-42-2589 TCGA-42-2590 TCGA-42-2593 TCGA-57-1582 
        6.05        11.47        42.02        10.42         1.48        24.03 
TCGA-57-1583 TCGA-57-1585 TCGA-57-1992 TCGA-57-1994 TCGA-59-2351 TCGA-59-2352 
       11.38         1.74        29.00        25.02       116.12         9.40 
TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1728 TCGA-61-1730 
        2.14         5.42        44.81        20.52        27.88         4.34 
TCGA-61-1733 TCGA-61-1736 TCGA-61-1899 TCGA-61-1900 TCGA-61-1907 TCGA-61-1910 
       31.79        48.79         8.42         5.79        31.30        37.05 
TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-2000 
       56.61        67.76        15.75        38.17         2.01        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-61-2095 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-61-2113 TCGA-61-2612 TCGA-OY-A56P TCGA-OY-A56Q 
       76.87        20.68        22.22         6.35        39.68        18.94 
TCGA-VG-A8LO TCGA-WR-A838 
        0.79         9.99 

$`9P LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1342 TCGA-04-1348 TCGA-04-1353 
       43.92         1.81        49.15        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-04-1644 TCGA-04-1648 TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 TCGA-09-0366 
       48.89        28.64        36.23        47.70        45.37        57.76 
TCGA-09-1664 TCGA-09-1666 TCGA-09-1668 TCGA-09-1672 TCGA-09-1674 TCGA-09-2043 
       74.93        57.60        55.36         5.85         8.55         6.18 
TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 TCGA-09-2051 TCGA-10-0925 TCGA-10-0926 
       35.15         4.54        71.11        63.09        54.31        25.91 
TCGA-10-0928 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 
       18.51        14.66         6.71        35.44        36.92        19.99 
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-13-0757 TCGA-13-0758 TCGA-13-0761 TCGA-13-0766 
       55.17         2.50        11.18        11.38        34.06        21.40 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 
        8.45        38.93        36.72        28.70        30.35         8.71 
TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0807 TCGA-13-0884 
        7.79         8.28         8.19        43.86        13.61       107.18 
TCGA-13-0887 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0901 
       66.67        69.01        43.36        57.47        56.15        19.36 
TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       47.38        47.84        44.94        37.08        27.72        34.06 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-1404 
       29.98        21.17        14.89        13.81         6.41         6.61 
TCGA-13-1405 TCGA-13-1477 TCGA-13-1482 TCGA-13-1488 TCGA-13-1492 TCGA-13-1496 
        7.36        54.64        61.71        70.82        73.55         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 
       54.31        37.61        38.40        32.84        16.57         4.21 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 
        4.41         4.77         2.56         3.91         3.09        12.23 
TCGA-13-2071 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 
        6.28        23.05        25.94        26.20        72.20        25.38 
TCGA-20-1686 TCGA-20-1687 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1029 
        2.93         2.66        40.54        15.39        26.83         8.81 
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-23-1120 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-23-2084 TCGA-23-2641 TCGA-24-0966 
      115.89        87.48        91.66        49.84         2.76         7.63 
TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 
       19.66        11.64        21.80        41.56         7.66        54.12 
TCGA-24-1104 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1423 TCGA-24-1424 
       63.55         6.38         7.82         7.99         6.25         6.02 
TCGA-24-1425 TCGA-24-1428 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1466 
        5.95        17.39        18.67        43.53         8.55        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-24-1548 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-24-1558 TCGA-24-1562 TCGA-24-1565 TCGA-24-1567 TCGA-24-1614 
       39.88        19.53        45.50        10.26        17.23        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-24-1924 TCGA-24-1927 
        5.79         5.52         9.80        22.68        30.21        16.44 
TCGA-24-1928 TCGA-24-2020 TCGA-24-2026 TCGA-24-2027 TCGA-24-2033 TCGA-24-2038 
       11.05       152.02        34.82       109.71        18.48        44.52 
TCGA-24-2254 TCGA-24-2262 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
       57.07         0.36        31.63        70.45        44.61         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 
       67.36        36.23        55.86        53.26        26.96        52.04 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1628 
       65.00        37.97         2.99        15.02        18.58        20.61 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1635 TCGA-25-1878 TCGA-25-2042 
       38.20         0.30        59.15        52.04        85.05        13.02 
TCGA-25-2391 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2404 TCGA-25-2408 
       49.05         3.02        12.00        45.01        29.03        31.00 
TCGA-25-2409 TCGA-29-1690 TCGA-29-1691 TCGA-29-1696 TCGA-29-1697 TCGA-29-1701 
       26.99        47.61        48.33        33.93        31.20        16.93 
TCGA-29-1703 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 
       59.67        34.62        17.36        86.60        66.81        62.93 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 
       31.30        22.98        11.84        12.30        14.93         8.38 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 
        5.36        36.30        86.17        62.47        45.11        13.84 
TCGA-29-2431 TCGA-29-2432 TCGA-29-A5NZ TCGA-30-1855 TCGA-30-1859 TCGA-30-1860 
       42.25        21.47        35.77         2.47        48.10        44.91 
TCGA-30-1862 TCGA-30-1867 TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 
        6.12         1.22        24.26        48.79        45.57        30.18 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1956 TCGA-36-1568 TCGA-36-1570 TCGA-36-1574 
       18.77        22.49        44.12        28.77        21.53        22.55 
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-36-2538 TCGA-36-2543 TCGA-36-2545 TCGA-36-2551 TCGA-3P-A9WA 
       29.82        25.08         2.24        18.31        16.18        13.81 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2591 TCGA-57-1584 TCGA-57-1586 
       47.57        23.74        28.93        40.77        21.14        22.32 
TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2354 TCGA-5X-AA5U 
       25.08       180.20        80.12        22.32        34.39        11.87 
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 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.26              0.30 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           129.96            180.20 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           28.685            28.670 
[1] "0.3 - 130.0 (28.7)" "0.3 - 180.2 (28.7)"
[1] "hr=" "1"  
D58V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  9P LOSS MUTATED         1   253                2
  9P LOSS WILD-TYPE       2   305                0
D58V3, multiclass
                  clus
vv                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  OMENTUM                        1                 2
  OVARY                        253               305
  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, continuous
D58V5, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     2 260
  9P LOSS WILD-TYPE   1 310
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      2  260
  9P LOSS WILD-TYPE    1  310
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO                2                 1
  YES             260               310
[1] 2 2
[1] FALSE
                   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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P LOSS MUTATED                                  1     7
  9P LOSS WILD-TYPE                                2    12
                   vv
clus                BLACK OR AFRICAN AMERICAN
  9P LOSS MUTATED                          17
  9P LOSS WILD-TYPE                        17
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9P LOSS MUTATED                                           1   213
  9P LOSS WILD-TYPE                                         0   263
D58V7, multiclass
                                           clus
vv                                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 2
  ASIAN                                                   7                12
  BLACK OR AFRICAN AMERICAN                              17                17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 213               263
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V8, 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   129 147
  9Q LOSS WILD-TYPE 139 145
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              276               284 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              147               145 
$`9Q LOSS MUTATED`
TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1343 
       41.00        49.15         2.01        46.62         1.08        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 
       65.52        63.09        21.57        63.98        65.46        49.28 
TCGA-04-1361 TCGA-04-1364 TCGA-04-1371 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 
       32.52        33.67        82.39        19.99         0.79        38.37 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1646 TCGA-04-1649 TCGA-04-1655 TCGA-09-0364 
       84.20        55.43        27.88        64.64        45.37        29.16 
TCGA-09-0365 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1667 
        9.47        17.98        35.57         9.99        38.43        61.87 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 
       30.51        17.98         3.02         8.55        97.55         6.12 
TCGA-09-2049 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-10-0927 TCGA-10-0936 
      112.41        39.75        20.94        26.93        81.86        36.92 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0724 TCGA-13-0751 TCGA-13-0757 
       20.91         6.21        24.59         2.73        55.17        11.18 
TCGA-13-0760 TCGA-13-0762 TCGA-13-0764 TCGA-13-0768 TCGA-13-0793 TCGA-13-0795 
       11.54        32.25        31.04         8.45        28.70        19.59 
TCGA-13-0800 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
        8.12        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-13-0899 
      107.18        91.40        74.27        70.39        61.84        56.15 
TCGA-13-0900 TCGA-13-0904 TCGA-13-0908 TCGA-13-0913 TCGA-13-0921 TCGA-13-0923 
       57.07        48.33        44.84        29.98         4.64         6.41 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
        6.08        10.88         6.05         5.92         6.84         4.70 
TCGA-13-1411 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 
        4.21        29.42        98.04        22.39        82.88        52.44 
TCGA-13-1495 TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 TCGA-13-1507 TCGA-13-1509 
       49.25        38.40        13.97        16.57         4.77         4.18 
TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU 
       14.24         8.61        10.78         8.75        54.77         8.42 
TCGA-20-0990 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 
       25.94        27.52        19.10        16.70         2.93        47.54 
TCGA-23-1022 TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 TCGA-23-1111 TCGA-23-1114 
       49.68        49.41        29.13        18.90         3.22        68.68 
TCGA-23-1116 TCGA-23-1118 TCGA-23-1119 TCGA-23-1123 TCGA-23-2072 TCGA-23-2077 
        4.57        86.01       129.96        33.47        24.95       115.89 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0968 TCGA-24-0975 TCGA-24-0979 TCGA-24-0982 
        4.70         4.50        19.66        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-24-1431 TCGA-24-1464 TCGA-24-1469 TCGA-24-1471 TCGA-24-1544 TCGA-24-1545 
       19.17        12.46         9.11         1.18        26.96        57.40 
TCGA-24-1549 TCGA-24-1550 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       56.58        41.06        19.53        44.09        45.50        47.70 
TCGA-24-1564 TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-1843 TCGA-24-1845 
       25.87        90.15        88.37        38.24         3.48         3.81 
TCGA-24-1924 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 
       30.21        11.05        81.11         4.87        44.84        58.16 
TCGA-24-2026 TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2260 TCGA-24-2261 
       34.82        14.43        18.48        28.18        36.16         0.79 
TCGA-24-2267 TCGA-24-2288 TCGA-24-2293 TCGA-24-2295 TCGA-25-1312 TCGA-25-1314 
       47.54         0.82        16.64        33.11         1.02        33.01 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 TCGA-25-1323 
       42.05         2.01        34.98        37.97        33.96        12.99 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 
       17.03        12.95        38.20         0.30        62.17        35.87 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-2392 TCGA-25-2393 TCGA-25-2398 
       14.96        24.99        24.00         1.02        38.04        45.01 
TCGA-25-2399 TCGA-25-2400 TCGA-29-1688 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 
       19.99        42.02        78.90       101.79        39.02        40.41 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1702 TCGA-29-1705 TCGA-29-1710 TCGA-29-1761 
       68.32        36.36        23.93        18.25        31.27        17.36 
TCGA-29-1763 TCGA-29-1766 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 
       66.81        39.42        24.36        22.55        17.33        12.36 
TCGA-29-1777 TCGA-29-1783 TCGA-29-2425 TCGA-29-2434 TCGA-30-1714 TCGA-30-1853 
       12.30         7.23        65.00        11.47        38.07        36.26 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 
       15.68         0.26        34.78        36.62         1.22        57.57 
TCGA-31-1944 TCGA-31-1950 TCGA-31-1953 TCGA-31-1955 TCGA-36-1569 TCGA-36-1571 
       45.57        18.77         6.71        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-57-1585 TCGA-57-1992 
       42.02        10.42         1.48        24.03         1.74        29.00 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD 
      116.12         9.40         2.14         5.42        44.81        20.52 
TCGA-5X-AA5U TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 TCGA-61-1741 TCGA-61-1743 
       11.87         4.34        31.79        48.79        33.67        43.69 
TCGA-61-1899 TCGA-61-1904 TCGA-61-1906 TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 
        8.42         9.07        34.13        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-61-2094 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 
       30.64         1.18        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-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-WR-A838 
        6.35        31.07         8.61        39.68        18.94         9.99 

$`9Q LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1342 TCGA-04-1348 TCGA-04-1353 TCGA-04-1362 
       43.92         1.81        18.51        48.76         0.53        44.32 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 TCGA-04-1516 TCGA-04-1530 TCGA-04-1536 
       76.57       103.40        56.55        41.59       119.08        29.10 
TCGA-04-1644 TCGA-04-1648 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-09-0366 
       48.89        28.64        36.23        31.86        47.70        57.76 
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-10-0925 TCGA-10-0926 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 
       54.31        25.91        18.51        34.19        32.88        14.66 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 
        6.71        35.44        19.99        44.55        39.58        12.39 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 TCGA-13-0758 TCGA-13-0761 
       31.20        15.19        17.82         2.50        11.38        34.06 
TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 
       21.40        38.93        36.72        30.35         8.71         7.79 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0887 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
        8.28         8.19        66.67        67.99        69.01        43.36 
TCGA-13-0897 TCGA-13-0901 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 
       57.47        19.36        47.38        47.84        44.94        37.08 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-1404 
       27.72        34.06        21.17        14.89        13.81         6.61 
TCGA-13-1405 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1485 
        7.36         5.33        54.64        87.06        61.71        20.68 
TCGA-13-1488 TCGA-13-1492 TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
       70.82        73.55        38.20         4.24        54.31        37.61 
TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
       32.84         4.21         4.41         2.56         3.91         3.09 
TCGA-13-2059 TCGA-13-2071 TCGA-20-0987 TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 
       12.23         6.28        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-24-1430 TCGA-24-1434 TCGA-24-1435 
        5.95         4.83        17.39        28.37        18.67        43.53 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1474 
        8.55        72.92        45.14       105.99         3.45        22.22 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       64.27        16.21        51.91        41.39        58.09        88.50 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1565 TCGA-24-1567 TCGA-24-1614 TCGA-24-1842 
       70.62        39.88        10.26        17.23        48.33         8.32 
TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 
        3.72         4.37        11.28         5.79         5.52         9.80 
TCGA-24-1923 TCGA-24-1927 TCGA-24-2020 TCGA-24-2027 TCGA-24-2030 TCGA-24-2036 
       22.68        16.44       152.02       109.71        55.92        64.01 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2262 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 
       44.52        57.07         0.36        31.63        70.45        44.61 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 
       67.36        36.23        55.86        53.26        26.96        52.04 
TCGA-25-1319 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1628 
       65.00         2.99        15.02        18.58        27.62        20.61 
TCGA-25-1632 TCGA-25-1635 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2396 
       59.15        52.04        85.05        13.02        49.05         3.02 
TCGA-25-2397 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1690 
       12.00         2.96        29.03        31.00        26.99        47.61 
TCGA-29-1691 TCGA-29-1696 TCGA-29-1697 TCGA-29-1701 TCGA-29-1703 TCGA-29-1707 
       48.33        33.93        31.20        16.93        59.67        41.98 
TCGA-29-1711 TCGA-29-1762 TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 TCGA-29-1776 
       34.62        86.60        62.93        31.30        22.98        11.84 
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-29-2436 TCGA-29-A5NZ 
       45.11        13.84        42.25        21.47         9.76        35.77 
TCGA-30-1718 TCGA-30-1855 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1887 
       51.91         2.47        48.10        44.91         6.12        24.26 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1946 TCGA-31-1951 TCGA-31-1956 TCGA-31-1959 
       30.05        48.79        30.18        22.49        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-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2591 
       16.18        13.81        47.57        23.74        28.93        40.77 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 
       11.38        21.14        22.32        25.08        25.02       180.20 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2354 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 
       80.12        22.32        34.39        11.11         8.09        20.94 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1734 TCGA-61-1737 TCGA-61-1738 
       31.43        18.54        27.88        28.47        44.84        35.80 
TCGA-61-1740 TCGA-61-1895 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1907 
        2.43         1.45         5.79        11.41        13.02        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1917 TCGA-61-1998 TCGA-61-2008 
       37.05        42.51        48.92        43.43         5.52        30.64 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2095 
       45.96        45.40         4.80         4.77        51.72        61.64 
TCGA-61-2109 TCGA-VG-A8LO 
       20.68         0.79 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.26              0.36 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           129.96            180.20 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           26.945            29.295 
[1] "0.3 - 130.0 (26.9)" "0.4 - 180.2 (29.3)"
[1] "hr=" "1.1"
D59V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  9Q LOSS MUTATED         1   276                2
  9Q LOSS WILD-TYPE       2   282                0
D59V3, multiclass
                  clus
vv                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  OMENTUM                        1                 2
  OVARY                        276               282
  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, continuous
D59V5, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     2 284
  9Q LOSS WILD-TYPE   1 286
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      2  284
  9Q LOSS WILD-TYPE    1  286
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                2                 1
  YES             284               286
[1] 2 2
[1] FALSE
                   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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q LOSS MUTATED                                  1     6
  9Q LOSS WILD-TYPE                                2    13
                   vv
clus                BLACK OR AFRICAN AMERICAN
  9Q LOSS MUTATED                          17
  9Q LOSS WILD-TYPE                        17
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9Q LOSS MUTATED                                           1   234
  9Q LOSS WILD-TYPE                                         0   242
D59V7, multiclass
                                           clus
vv                                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 2
  ASIAN                                                   6                13
  BLACK OR AFRICAN AMERICAN                              17                17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 234               242
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V8, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     5 160
  9Q LOSS WILD-TYPE   5 167
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      5  160
  9Q LOSS WILD-TYPE    5  167
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 5
  NOT HISPANIC OR LATINO             160               167
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    46  46
  10P LOSS WILD-TYPE 222 246
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                92                468 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                46                246 
$`10P LOSS MUTATED`
TCGA-04-1341 TCGA-04-1364 TCGA-04-1371 TCGA-04-1648 TCGA-09-0364 TCGA-09-0366 
        1.08        33.67        82.39        28.64        29.16        57.76 
TCGA-09-0367 TCGA-09-2043 TCGA-09-2053 TCGA-10-0935 TCGA-10-0938 TCGA-13-0724 
       17.98         6.18        39.75        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        31.04        30.35         8.12        43.86        61.84 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0904 TCGA-13-0921 TCGA-13-1408 TCGA-13-1484 
       69.01        43.36        48.33         4.64         5.92        98.04 
TCGA-13-1489 TCGA-13-1500 TCGA-13-1507 TCGA-13-2057 TCGA-13-2065 TCGA-20-1684 
       82.88        13.97         4.77        14.24         8.75        19.10 
TCGA-23-1114 TCGA-23-2072 TCGA-23-2078 TCGA-24-0979 TCGA-24-1104 TCGA-24-1416 
       68.68        24.95        87.48        41.56        63.55         6.38 
TCGA-24-1425 TCGA-24-1431 TCGA-24-1435 TCGA-24-1466 TCGA-24-1467 TCGA-24-1471 
        5.95        19.17        43.53        45.14       105.99         1.18 
TCGA-24-1474 TCGA-24-1557 TCGA-24-1558 TCGA-24-1614 TCGA-24-1842 TCGA-24-1844 
       22.22        39.88        19.53        48.33         8.32         3.72 
TCGA-24-1923 TCGA-24-2019 TCGA-24-2026 TCGA-24-2030 TCGA-24-2254 TCGA-24-2280 
       22.68         4.87        34.82        55.92        57.07        70.45 
TCGA-24-2288 TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1323 TCGA-25-1625 
        0.82        55.86        53.26        26.96        12.99        27.62 
TCGA-25-1632 TCGA-25-2393 TCGA-25-2398 TCGA-25-2399 TCGA-29-1697 TCGA-29-1698 
       59.15        38.04        45.01        19.99        31.20        68.32 
TCGA-29-1699 TCGA-29-1707 TCGA-29-1761 TCGA-29-1769 TCGA-30-1714 TCGA-30-1855 
       36.36        41.98        17.36        22.98        38.07         2.47 
TCGA-31-1944 TCGA-31-1951 TCGA-31-1959 TCGA-36-2532 TCGA-36-2534 TCGA-36-2538 
       45.57        22.49         2.20        29.49        29.82        25.08 
TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-42-2589 TCGA-59-A5PD 
       21.60        20.98        18.31        20.52        42.02        20.52 
TCGA-61-1734 TCGA-61-1737 TCGA-61-1743 TCGA-61-1913 TCGA-61-1914 TCGA-61-2092 
       28.47        44.84        43.69        48.92        56.61        51.72 
TCGA-61-2094 TCGA-61-2113 
       71.74        22.22 

$`10P LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       43.92        41.00         1.81        49.15         2.01        46.62 
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-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 
       76.57       103.40        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-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 
       27.88        64.64        36.23        31.86        47.70        45.37 
TCGA-09-0365 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
        9.47        35.57         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-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       12.46        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        34.06 
TCGA-13-0762 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       32.25        21.40         8.45        38.93        36.72        28.70 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 
       19.59         8.71         7.79         8.28         8.19        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        91.40        74.27 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       66.67        70.39        67.99        57.47        56.15        57.07 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
       19.36        47.38        47.84        44.94        44.84        37.08 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       27.72        34.06        29.98        21.17        14.89        13.81 
TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 
        6.41         6.08        10.88         6.61         7.36         6.05 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
        6.84         4.70         4.21         5.33        54.64        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-13-1497 TCGA-13-1498 
       73.55        38.20        49.25         4.24        54.31        37.61 
TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 
       38.40        32.84        16.57         4.21         4.41         4.18 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 
        2.56         3.91         3.09        12.23         8.61        10.78 
TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
        6.28        54.77         8.42        23.05        25.94        26.20 
TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 
       72.20        27.52        25.38        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-23-1116 TCGA-23-1117 TCGA-23-1118 
       54.51         3.22        31.20         4.57        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-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
        0.53       115.89        91.66        77.00        49.84         2.76 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 
        4.70         4.50         7.63        19.66        11.64        21.80 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 TCGA-24-1417 
        7.66        22.32        54.12        47.41         6.31         7.82 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1426 
        7.99         7.86         0.76         6.25         6.02         5.36 
TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 
        4.83        17.39        28.37        18.67         8.55        72.92 
TCGA-24-1464 TCGA-24-1469 TCGA-24-1470 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 
       12.46         9.11         3.45        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-24-1560 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-24-1616 TCGA-24-1843 
       10.26        17.23        90.15        88.37        38.24         3.48 
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-24-1924 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-24-2027 TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 
       58.16       109.71        14.43        18.48        28.18        64.01 
TCGA-24-2038 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 
       44.52        36.16         0.79         0.36        47.54        31.63 
TCGA-24-2281 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-25-1312 
       44.61        67.36        36.23        16.64        33.11         1.02 
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-25-1321 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 
       37.97        33.96         2.99        15.02        18.58        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-25-2396 TCGA-25-2397 TCGA-25-2400 TCGA-25-2401 
       49.05         1.02         3.02        12.00        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-29-1695 TCGA-29-1696 TCGA-29-1701 TCGA-29-1702 
      101.79        39.02        40.41        33.93        16.93        23.93 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 TCGA-29-1762 TCGA-29-1763 
       59.67        18.25        31.27        34.62        86.60        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
       62.93        39.42        31.30        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-29-2429 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-30-1853 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-30-1862 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-31-1946 TCGA-31-1950 TCGA-31-1953 TCGA-31-1955 
       30.05        48.79        30.18        18.77         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-36-1575 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-36-2537 TCGA-36-2540 TCGA-36-2543 TCGA-36-2548 
       35.05        33.01        25.91        23.80         2.24        14.17 
TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 
        6.05        16.18        11.47        13.81        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-57-1993 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-5X-AA5U TCGA-61-1721 TCGA-61-1722 
        2.14         5.42        44.81        11.87        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-61-1736 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 
       48.79        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-61-1915 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-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 
        4.77        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-61-2612 
        6.48        76.87        20.68        44.52       125.75         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 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.82               0.26 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            105.99             180.20 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            29.655             28.030 
[1] "0.8 - 106.0 (29.7)" "0.3 - 180.2 (28.0)"
[1] "hr=" "1.1"
D60V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  10P LOSS MUTATED         0    93                0
  10P LOSS WILD-TYPE       3   465                2
D60V3, multiclass
                  clus
vv                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  OMENTUM                         0                  3
  OVARY                          93                465
  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, continuous
D60V5, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     1  95
  10P LOSS WILD-TYPE   2 475
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1   95
  10P LOSS WILD-TYPE    2  475
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 1                  2
  YES               95                475
[1] 2 2
[1] FALSE
                    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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P LOSS MUTATED                                  0     2
  10P LOSS WILD-TYPE                                3    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  10P LOSS MUTATED                           5
  10P LOSS WILD-TYPE                        29
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10P LOSS MUTATED                                           1    78
  10P LOSS WILD-TYPE                                         0   398
D60V7, multiclass
                                           clus
vv                                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    2                 17
  BLACK OR AFRICAN AMERICAN                                5                 29
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   78                398
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V8, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     1  47
  10P LOSS WILD-TYPE   9 280
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1   47
  10P LOSS WILD-TYPE    9  280
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO               47                280
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    59  60
  10Q LOSS WILD-TYPE 209 232
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               119                441 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                60                232 
$`10Q LOSS MUTATED`
TCGA-04-1343 TCGA-04-1364 TCGA-04-1648 TCGA-04-1649 TCGA-09-0364 TCGA-09-0366 
       11.87        33.67        28.64        64.64        29.16        57.76 
TCGA-09-0367 TCGA-09-0369 TCGA-09-1667 TCGA-09-1673 TCGA-09-2043 TCGA-09-2053 
       17.98        35.57        61.87         3.02         6.18        39.75 
TCGA-10-0935 TCGA-10-0938 TCGA-13-0724 TCGA-13-0751 TCGA-13-0760 TCGA-13-0764 
       35.44        20.91         2.73        55.17        11.54        31.04 
TCGA-13-0794 TCGA-13-0800 TCGA-13-0803 TCGA-13-0807 TCGA-13-0889 TCGA-13-0891 
       30.35         8.12        43.86        13.61        61.84        69.01 
TCGA-13-0893 TCGA-13-0899 TCGA-13-0904 TCGA-13-0911 TCGA-13-0916 TCGA-13-0921 
       43.36        56.15        48.33        27.72        21.17         4.64 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1489 TCGA-13-1492 TCGA-13-1496 TCGA-13-1497 
        6.05         5.92        82.88        73.55         4.24        54.31 
TCGA-13-1507 TCGA-13-2057 TCGA-13-2065 TCGA-20-1684 TCGA-20-1686 TCGA-23-1114 
        4.77        14.24         8.75        19.10         2.93        68.68 
TCGA-23-2072 TCGA-24-0979 TCGA-24-1104 TCGA-24-1416 TCGA-24-1418 TCGA-24-1430 
       24.95        41.56        63.55         6.38         7.99        28.37 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1466 TCGA-24-1467 
       19.17        18.67        43.53         8.55        45.14       105.99 
TCGA-24-1471 TCGA-24-1474 TCGA-24-1557 TCGA-24-1614 TCGA-24-1842 TCGA-24-1844 
        1.18        22.22        39.88        48.33         8.32         3.72 
TCGA-24-1850 TCGA-24-1928 TCGA-24-2026 TCGA-24-2030 TCGA-24-2254 TCGA-24-2280 
        5.52        11.05        34.82        55.92        57.07        70.45 
TCGA-24-2288 TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1320 TCGA-25-1323 
        0.82        55.86        53.26        26.96        37.97        12.99 
TCGA-25-1632 TCGA-25-1635 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-29-1697 
       59.15        52.04        45.01        19.99        42.02        31.20 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 TCGA-29-1761 TCGA-29-1766 
       68.32        36.36        16.93        59.67        17.36        39.42 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1778 TCGA-30-1714 TCGA-30-1855 TCGA-30-1856 
       22.98        24.36        14.93        38.07         2.47        15.68 
TCGA-30-1859 TCGA-31-1944 TCGA-31-1951 TCGA-31-1953 TCGA-31-1959 TCGA-36-1577 
       48.10        45.57        22.49         6.71         2.20        25.74 
TCGA-36-1581 TCGA-36-2532 TCGA-36-2534 TCGA-36-2538 TCGA-36-2542 TCGA-36-2543 
       24.69        29.49        29.82        25.08        21.60         2.24 
TCGA-36-2545 TCGA-36-2547 TCGA-42-2589 TCGA-61-1728 TCGA-61-1734 TCGA-61-1737 
       18.31        20.52        42.02        27.88        28.47        44.84 
TCGA-61-1743 TCGA-61-1913 TCGA-61-1914 TCGA-61-1918 TCGA-61-2012 TCGA-61-2088 
       43.69        48.92        56.61        15.75        30.64         4.77 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2102 TCGA-61-2113 TCGA-OY-A56P 
       51.72        71.74         6.48        22.22        39.68 

$`10Q LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       43.92        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1341 TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 
        1.08        18.51        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-04-1638 
        0.79        38.37       119.08        29.10        84.20        55.43 
TCGA-04-1644 TCGA-04-1646 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 
       48.89        27.88        36.23        31.86        47.70        45.37 
TCGA-09-0365 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
        9.47         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-09-1674 
       57.60        55.36        30.51        17.98         5.85         8.55 
TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 
       97.55         6.12        35.15         4.54       112.41        71.11 
TCGA-09-2051 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 
       63.09        20.94        26.93        12.46        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-10-0936 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-13-0761 TCGA-13-0762 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 
       11.38        34.06        32.25        21.40         8.45        38.93 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 
       36.72        28.70        19.59         8.71         7.79         8.28 
TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 
        8.19        35.28        35.31        68.94       107.18        91.40 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 TCGA-13-0897 TCGA-13-0900 
       74.27        66.67        70.39        67.99        57.47        57.07 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
       19.36        47.38        47.84        44.94        44.84        37.08 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 
       34.06        29.98        14.89        13.81         6.41         6.08 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
       10.88         6.61         7.36         6.84         4.70         4.21 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
        5.33        54.64        87.06        61.71        29.42        98.04 
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        38.20        49.25 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 
       37.61        38.40        13.97        32.84        16.57         4.21 
TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 
        4.41         4.18         2.56         3.91         3.09        12.23 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
        8.61        10.78         6.28        54.77         8.42        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1685 
       25.94        26.20        72.20        27.52        25.38        16.70 
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-23-1116 TCGA-23-1117 
       51.35        54.51         3.22        31.20         4.57        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-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
       58.13         0.53       115.89        87.48        91.66        77.00 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 
       49.84         2.76         4.70         4.50         7.63        19.66 
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-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
        6.31         7.82         7.86         0.76         6.25         6.02 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1463 TCGA-24-1464 
        5.95         5.36         4.83        17.39        72.92        12.46 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 
        9.11         3.45        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-24-1558 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-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-1843 
       10.26        17.23        90.15        88.37        38.24         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-24-1924 TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 
       30.21        16.44        81.11         4.87       152.02        44.84 
TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 
       58.16       109.71        14.43        18.48        28.18        64.01 
TCGA-24-2038 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 
       44.52        36.16         0.79         0.36        47.54        31.63 
TCGA-24-2281 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-25-1312 
       44.61        67.36        36.23        16.64        33.11         1.02 
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-25-1321 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-25-1627 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-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 
       14.96        24.99        24.00        85.05        13.02        49.05 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2401 TCGA-25-2404 
        1.02        38.04         3.02        12.00         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-29-1702 TCGA-29-1705 TCGA-29-1707 
       39.02        40.41        33.93        23.93        18.25        41.98 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1768 
       31.27        34.62        86.60        66.81        62.93        31.30 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 
       22.55        17.33        12.36        11.84        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-29-A5NZ TCGA-30-1718 TCGA-30-1853 TCGA-30-1857 TCGA-30-1860 TCGA-30-1861 
       35.77        51.91        36.26         0.26        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-31-1946 TCGA-31-1950 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 
       48.79        30.18        18.77        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-36-1578 TCGA-36-1580 TCGA-36-2529 TCGA-36-2530 TCGA-36-2537 TCGA-36-2540 
       27.85        24.23        35.05        33.01        25.91        23.80 
TCGA-36-2544 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA 
       20.98        14.17         6.05        16.18        11.47        13.81 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 
       47.57        23.74        28.93        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-59-A5PD 
        9.40        34.39         2.14         5.42        44.81        20.52 
TCGA-5X-AA5U TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
       11.87        11.11         8.09        20.94        31.43        18.54 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 
        4.34        31.79        48.79        35.80         2.43        33.67 
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-61-1915 TCGA-61-1917 
       34.13        31.30        37.05        42.51        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-61-2095 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-61-2111 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       20.68        44.52       125.75         6.35        31.07         8.61 
TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       18.94         0.79         9.99 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.82               0.26 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            105.99             180.20 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             28.47              28.77 
[1] "0.8 - 106.0 (28.5)" "0.3 - 180.2 (28.8)"
[1] "hr=" "1"  
D61V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  10Q LOSS MUTATED         0   119                1
  10Q LOSS WILD-TYPE       3   439                1
D61V3, multiclass
                  clus
vv                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  OMENTUM                         0                  3
  OVARY                         119                439
  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, continuous
D61V5, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     3 121
  10Q LOSS WILD-TYPE   0 449
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      3  121
  10Q LOSS WILD-TYPE    0  449
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                 3                  0
  YES              121                449
[1] 2 2
[1] FALSE
                    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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q LOSS MUTATED                                  0     4
  10Q LOSS WILD-TYPE                                3    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  10Q LOSS MUTATED                           6
  10Q LOSS WILD-TYPE                        28
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10Q LOSS MUTATED                                           1   102
  10Q LOSS WILD-TYPE                                         0   374
D61V7, multiclass
                                           clus
vv                                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    4                 15
  BLACK OR AFRICAN AMERICAN                                6                 28
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  102                374
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V8, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     1  65
  10Q LOSS WILD-TYPE   9 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1   65
  10Q LOSS WILD-TYPE    9  262
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO               65                262
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    87 103
  11P LOSS WILD-TYPE 181 189
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               190                370 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               103                189 
$`11P LOSS MUTATED`
TCGA-04-1331 TCGA-04-1338 TCGA-04-1341 TCGA-04-1347 TCGA-04-1351 TCGA-04-1356 
       43.92        46.62         1.08        63.09        65.46        49.28 
TCGA-04-1367 TCGA-04-1517 TCGA-04-1536 TCGA-04-1542 TCGA-04-1644 TCGA-04-1646 
      103.40        19.99        29.10        84.20        48.89        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1655 TCGA-09-0366 TCGA-09-1659 TCGA-09-1661 
       28.64        64.64        45.37        57.76         9.99        38.43 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1670 TCGA-09-1674 TCGA-09-2053 
       57.60        61.87        55.36        17.98         8.55        39.75 
TCGA-10-0926 TCGA-10-0928 TCGA-10-0930 TCGA-10-0937 TCGA-10-0938 TCGA-13-0723 
       25.91        18.51        34.19        19.99        20.91        39.58 
TCGA-13-0751 TCGA-13-0758 TCGA-13-0760 TCGA-13-0762 TCGA-13-0764 TCGA-13-0768 
       55.17        11.38        11.54        32.25        31.04         8.45 
TCGA-13-0802 TCGA-13-0804 TCGA-13-0886 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
        8.19        35.28        74.27        56.15        57.07        19.36 
TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 TCGA-13-0913 TCGA-13-0920 TCGA-13-0921 
       48.33        44.94        44.84        29.98        13.81         4.64 
TCGA-13-1404 TCGA-13-1409 TCGA-13-1411 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 
        6.61         6.84         4.21        54.64        61.71        29.42 
TCGA-13-1484 TCGA-13-1487 TCGA-13-1489 TCGA-13-1494 TCGA-13-1495 TCGA-13-1500 
       98.04        22.39        82.88        38.20        49.25        13.97 
TCGA-13-1505 TCGA-13-1507 TCGA-13-1512 TCGA-13-2060 TCGA-13-2065 TCGA-13-A5FU 
        4.21         4.77         3.09         8.61         8.75         8.42 
TCGA-20-0990 TCGA-20-0991 TCGA-20-1683 TCGA-20-1686 TCGA-20-1687 TCGA-23-1022 
       25.94        26.20        25.38         2.93         2.66        49.68 
TCGA-23-1027 TCGA-23-1031 TCGA-23-1113 TCGA-23-1114 TCGA-23-1118 TCGA-23-1122 
       32.09        18.90        31.20        68.68        86.01        39.09 
TCGA-23-2077 TCGA-23-2643 TCGA-24-0968 TCGA-24-0970 TCGA-24-1105 TCGA-24-1418 
      115.89         4.70        19.66        11.64        47.41         7.99 
TCGA-24-1427 TCGA-24-1428 TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 TCGA-24-1474 
        4.83        17.39         8.55        72.92        45.14        22.22 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1549 TCGA-24-1562 TCGA-24-1563 TCGA-24-1567 
       26.96        57.40        56.58        45.50        47.70        17.23 
TCGA-24-1846 TCGA-24-1923 TCGA-24-1924 TCGA-24-1930 TCGA-24-2019 TCGA-24-2026 
        4.37        22.68        30.21        81.11         4.87        34.82 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 
      109.71        14.43        57.07        36.16         0.79        47.54 
TCGA-24-2280 TCGA-24-2293 TCGA-24-2295 TCGA-24-2298 TCGA-25-1318 TCGA-25-1319 
       70.45        16.64        33.11        53.26        34.98        65.00 
TCGA-25-1320 TCGA-25-1323 TCGA-25-1329 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
       37.97        12.99        15.02        20.61        38.20         0.30 
TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-2392 TCGA-25-2393 TCGA-29-1688 
       35.87        14.96        24.99         1.02        38.04        78.90 
TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1702 TCGA-29-1703 
       40.41        33.93        31.20        68.32        23.93        59.67 
TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1769 
       34.62        17.36        86.60        66.81        62.93        22.98 
TCGA-29-1770 TCGA-29-1777 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2434 
       24.36        12.30        86.17        65.00        45.11        11.47 
TCGA-30-1853 TCGA-30-1861 TCGA-30-1866 TCGA-30-1887 TCGA-31-1950 TCGA-31-1953 
       36.26        34.78        36.62        24.26        18.77         6.71 
TCGA-36-1569 TCGA-36-1577 TCGA-36-1581 TCGA-36-2529 TCGA-36-2538 TCGA-36-2543 
       29.10        25.74        24.69        35.05        25.08         2.24 
TCGA-36-2549 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2589 TCGA-57-1582 TCGA-57-1993 
        6.05        11.47        13.81        42.02        24.03        25.08 
TCGA-59-2352 TCGA-59-2372 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1728 
        9.40        44.81         8.09        20.94        31.43        27.88 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1738 TCGA-61-1741 TCGA-61-1904 TCGA-61-1906 
        4.34        31.79        35.80        33.67         9.07        34.13 
TCGA-61-1910 TCGA-61-1917 TCGA-61-1919 TCGA-61-2002 TCGA-61-2018 TCGA-61-2088 
       37.05        43.43        38.17        17.98        45.40         4.77 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2102 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 
       51.72        71.74         6.48       125.75        22.22         6.35 
TCGA-61-2614 TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
        8.61        18.94         0.79         9.99 

$`11P LOSS WILD-TYPE`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 
       41.00         1.81        49.15         2.01        18.51        11.87 
TCGA-04-1346 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1353 TCGA-04-1361 
       65.52        48.76        21.57        63.98         0.53        32.52 
TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 
       44.32        33.67        76.57        82.39        56.55        41.59 
TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1638 TCGA-04-1651 TCGA-04-1652 
        0.79        38.37       119.08        55.43        36.23        31.86 
TCGA-04-1654 TCGA-09-0364 TCGA-09-0365 TCGA-09-0367 TCGA-09-0369 TCGA-09-1662 
       47.70        29.16         9.47        17.98        35.57        89.33 
TCGA-09-1664 TCGA-09-1665 TCGA-09-1669 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 
       74.93        41.62        30.51         5.85         3.02        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-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0927 
       63.09        20.94        26.93        12.46        54.31        81.86 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-13-0714 
       32.88        14.66         6.71        35.44        36.92         6.21 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 
       24.59        44.55         2.73        12.39        31.20        15.19 
TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 TCGA-13-0761 TCGA-13-0766 TCGA-13-0791 
       17.82         2.50        11.18        34.06        21.40        38.93 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 
       36.72        28.70        30.35        19.59         8.71         7.79 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
        8.12         8.28        43.86        35.31        13.61        68.94 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 
      107.18        91.40        66.67        70.39        61.84        67.99 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0903 TCGA-13-0905 TCGA-13-0910 
       69.01        43.36        57.47        47.38        47.84        37.08 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 TCGA-13-0919 TCGA-13-0923 TCGA-13-0924 
       27.72        34.06        21.17        14.89         6.41         6.08 
TCGA-13-1403 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1412 
       10.88         7.36         6.05         5.92         4.70         5.33 
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        73.55         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1506 
       54.31        37.61        38.40        32.84        16.57         4.41 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-2057 TCGA-13-2059 TCGA-13-2061 
        4.18         2.56         3.91        14.24        12.23        10.78 
TCGA-13-2071 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0996 TCGA-20-1682 TCGA-20-1684 
        6.28        54.77        23.05        72.20        27.52        19.10 
TCGA-20-1685 TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1028 
       16.70        47.54        40.54        15.39        26.83        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
        8.81        29.13         2.76        51.35        54.51         3.22 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1123 
        4.57        33.30       129.96         4.27         6.38        33.47 
TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
       58.13         0.53        24.95        87.48        91.66        77.00 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2645 TCGA-24-0966 TCGA-24-0975 TCGA-24-0979 
       49.84         2.76         4.50         7.63        21.80        41.56 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1413 TCGA-24-1416 
        7.66        22.32        54.12        63.55         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-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1464 
        5.36        28.37        19.17        18.67        43.53        12.46 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1546 TCGA-24-1548 
      105.99         9.11         3.45         1.18        64.27        16.21 
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-24-1564 TCGA-24-1565 TCGA-24-1603 
       39.88        19.53        44.09        25.87        10.26        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-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1927 
        3.81        11.28         5.79         5.52         9.80        16.44 
TCGA-24-1928 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2030 TCGA-24-2033 
       11.05       152.02        44.84        58.16        55.92        18.48 
TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2262 TCGA-24-2271 TCGA-24-2281 
       28.18        64.01        44.52         0.36        31.63        44.61 
TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 
        0.82        67.36        36.23        55.86         1.02        26.96 
TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1321 TCGA-25-1322 
       33.01        52.04        42.05         2.01        33.96         2.99 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1632 TCGA-25-1633 
       18.58        27.62        17.03        12.95        59.15        62.17 
TCGA-25-1635 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2396 
       52.04        24.00        85.05        13.02        49.05         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-29-1699 TCGA-29-1701 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1766 
       36.36        16.93        18.25        41.98        31.27        39.42 
TCGA-29-1768 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1778 
       31.30        22.55        17.33        12.36        11.84        14.93 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2427 TCGA-29-2429 
        8.38         7.23         5.36        36.30        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-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 
        1.22        57.57        30.05        48.79        45.57        30.18 
TCGA-31-1951 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1570 
       22.49        42.51        44.12         2.20        28.77        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1578 TCGA-36-1580 
       22.85        22.55         8.55        30.08        27.85        24.23 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2540 TCGA-36-2542 
       33.01        29.49        29.82        25.91        23.80        21.60 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2551 TCGA-42-2582 
       20.98        18.31        20.52        14.17        16.18        47.57 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1583 
       23.74        28.93        10.42        40.77         1.48        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-59-2354 TCGA-59-2355 TCGA-59-2363 
       80.12        22.32       116.12        34.39         2.14         5.42 
TCGA-59-A5PD TCGA-5X-AA5U TCGA-61-1721 TCGA-61-1727 TCGA-61-1734 TCGA-61-1736 
       20.52        11.87        11.11        18.54        28.47        48.79 
TCGA-61-1737 TCGA-61-1740 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
       44.84         2.43        43.69         1.45         8.42         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1907 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 
       11.41        13.02        31.30        42.51        48.92        56.61 
TCGA-61-1915 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 
       67.76        15.75         2.01         5.52        14.50         4.01 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2087 
       30.64        39.85        30.64         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 
       20.68        44.52        31.07        39.68 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.30               0.26 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            125.75             180.20 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            30.095             27.785 
[1] "0.3 - 125.8 (30.1)" "0.3 - 180.2 (27.8)"
[1] "hr=" "1"  
D62V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  11P LOSS MUTATED         1   190                1
  11P LOSS WILD-TYPE       2   368                1
D62V3, multiclass
                  clus
vv                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  OMENTUM                         1                  2
  OVARY                         190                368
  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"
D62V4, continuous
D62V5, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     1 195
  11P LOSS WILD-TYPE   2 375
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      1  195
  11P LOSS WILD-TYPE    2  375
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 1                  2
  YES              195                375
[1] 2 2
[1] FALSE
                    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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  0     5
  11P LOSS WILD-TYPE                                3    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  11P LOSS MUTATED                          15
  11P LOSS WILD-TYPE                        19
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11P LOSS MUTATED                                           0   163
  11P LOSS WILD-TYPE                                         1   313
D62V7, multiclass
                                           clus
vv                                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    5                 14
  BLACK OR AFRICAN AMERICAN                               15                 19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                  163                313
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V8, 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    65  80
  11Q LOSS WILD-TYPE 203 212
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               145                415 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                80                212 
$`11Q LOSS MUTATED`
TCGA-04-1331 TCGA-04-1338 TCGA-04-1341 TCGA-04-1356 TCGA-04-1367 TCGA-04-1517 
       43.92        46.62         1.08        49.28       103.40        19.99 
TCGA-04-1536 TCGA-04-1648 TCGA-04-1649 TCGA-04-1655 TCGA-09-0366 TCGA-09-1666 
       29.10        28.64        64.64        45.37        57.76        57.60 
TCGA-09-1670 TCGA-09-2051 TCGA-09-2053 TCGA-10-0926 TCGA-10-0928 TCGA-10-0930 
       17.98        63.09        39.75        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        32.25         8.45        19.59 
TCGA-13-0804 TCGA-13-0899 TCGA-13-0900 TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 
       35.28        56.15        57.07        48.33        44.94        44.84 
TCGA-13-0920 TCGA-13-0921 TCGA-13-1404 TCGA-13-1409 TCGA-13-1411 TCGA-13-1477 
       13.81         4.64         6.61         6.84         4.21        54.64 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1487 TCGA-13-1489 TCGA-13-1494 TCGA-13-1495 
       61.71        29.42        22.39        82.88        38.20        49.25 
TCGA-13-1501 TCGA-13-1505 TCGA-13-1512 TCGA-13-2060 TCGA-13-2065 TCGA-13-A5FU 
       32.84         4.21         3.09         8.61         8.75         8.42 
TCGA-20-0991 TCGA-20-1683 TCGA-20-1686 TCGA-23-1113 TCGA-23-1114 TCGA-23-1118 
       26.20        25.38         2.93        31.20        68.68        86.01 
TCGA-23-1122 TCGA-23-2077 TCGA-24-0968 TCGA-24-0970 TCGA-24-0982 TCGA-24-1105 
       39.09       115.89        19.66        11.64        22.32        47.41 
TCGA-24-1428 TCGA-24-1463 TCGA-24-1466 TCGA-24-1544 TCGA-24-1562 TCGA-24-1567 
       17.39        72.92        45.14        26.96        45.50        17.23 
TCGA-24-1923 TCGA-24-1924 TCGA-24-2019 TCGA-24-2026 TCGA-24-2254 TCGA-24-2260 
       22.68        30.21         4.87        34.82        57.07        36.16 
TCGA-24-2261 TCGA-24-2280 TCGA-24-2293 TCGA-24-2295 TCGA-24-2298 TCGA-25-1319 
        0.79        70.45        16.64        33.11        53.26        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-29-1769 TCGA-29-1770 
       68.32        59.67        34.62        17.36        22.98        24.36 
TCGA-29-1775 TCGA-29-1777 TCGA-29-2414 TCGA-29-2428 TCGA-29-2434 TCGA-30-1853 
       12.36        12.30        86.17        45.11        11.47        36.26 
TCGA-30-1861 TCGA-30-1866 TCGA-31-1953 TCGA-36-1571 TCGA-36-1581 TCGA-36-2529 
       34.78        36.62         6.71        22.85        24.69        35.05 
TCGA-36-2538 TCGA-36-2543 TCGA-36-2549 TCGA-36-2552 TCGA-42-2589 TCGA-57-1582 
       25.08         2.24         6.05        11.47        42.02        24.03 
TCGA-57-1993 TCGA-59-2348 TCGA-59-2352 TCGA-61-1724 TCGA-61-1725 TCGA-61-1728 
       25.08       180.20         9.40        20.94        31.43        27.88 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1738 TCGA-61-1741 TCGA-61-1743 TCGA-61-1904 
        4.34        31.79        35.80        33.67        43.69         9.07 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1917 TCGA-61-1919 TCGA-61-2012 TCGA-61-2018 
       37.05        42.51        43.43        38.17        30.64        45.40 
TCGA-61-2092 TCGA-61-2102 TCGA-61-2111 TCGA-61-2113 TCGA-61-2614 TCGA-OY-A56Q 
       51.72         6.48       125.75        22.22         8.61        18.94 
TCGA-WR-A838 
        9.99 

$`11Q LOSS WILD-TYPE`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 
       41.00         1.81        49.15         2.01        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-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1371 
        0.53        32.52        44.32        33.67        76.57        82.39 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 
       56.55        41.59         0.79        38.37       119.08        84.20 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 
       55.43        48.89        27.88        36.23        31.86        47.70 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 
       29.16         9.47        17.98        35.57         9.99        38.43 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 
       89.33        74.93        41.62        61.87        55.36        30.51 
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-09-2054 TCGA-09-2055 
       35.15         4.54       112.41        71.11        20.94        26.93 
TCGA-09-2056 TCGA-10-0925 TCGA-10-0927 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       12.46        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        34.06        31.04        21.40 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 
       38.93        36.72        28.70        30.35         8.71         7.79 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 
        8.12         8.28         8.19        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        91.40        74.27        66.67        70.39 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0901 
       61.84        67.99        69.01        43.36        57.47        19.36 
TCGA-13-0903 TCGA-13-0905 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
       47.38        47.84        37.08        27.72        34.06        29.98 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1405 
       21.17        14.89         6.41         6.08        10.88         7.36 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1412 TCGA-13-1481 TCGA-13-1484 
        6.05         5.92         4.70         5.33        87.06        98.04 
TCGA-13-1485 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 TCGA-13-1496 TCGA-13-1497 
       20.68        70.82        52.44        73.55         4.24        54.31 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 
       37.61        38.40        13.97        16.57         4.41         4.77 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-2057 TCGA-13-2059 TCGA-13-2061 
        4.18         2.56         3.91        14.24        12.23        10.78 
TCGA-13-2071 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 TCGA-20-0996 TCGA-20-1682 
        6.28        54.77        23.05        25.94        72.20        27.52 
TCGA-20-1684 TCGA-20-1685 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 
       19.10        16.70         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-23-1111 TCGA-23-1116 
       18.90         2.76        51.35        54.51         3.22         4.57 
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-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0975 TCGA-24-0979 
        2.76         4.70         4.50         7.63        21.80        41.56 
TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 
        7.66        54.12        63.55         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        19.17        18.67        43.53 
TCGA-24-1436 TCGA-24-1464 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 
        8.55        12.46       105.99         9.11         3.45         1.18 
TCGA-24-1474 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 
       22.22        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-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1603 
       19.53        44.09        47.70        25.87        10.26        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-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 
       16.44        11.05        81.11       152.02        44.84        58.16 
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-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 
       44.52         0.36        47.54        31.63        44.61         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 
       67.36        36.23        55.86         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-29-1766 TCGA-29-1768 TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 TCGA-29-1778 
       39.42        31.30        22.55        17.33        11.84        14.93 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2425 TCGA-29-2427 
        8.38         7.23         5.36        36.30        65.00        62.47 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 
       13.84        42.25        21.47         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-30-1862 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 
        6.12         1.22        57.57        24.26        30.05        48.79 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1955 TCGA-31-1956 
       45.57        30.18        18.77        22.49        42.51        44.12 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 TCGA-36-1575 
        2.20        28.77        29.10        21.53        22.55         8.55 
TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 
       30.08        25.74        27.85        24.23        33.01        29.49 
TCGA-36-2534 TCGA-36-2537 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 
       29.82        25.91        23.80        21.60        20.98        18.31 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 
       20.52        14.17        16.18        13.81        47.57        23.74 
TCGA-42-2588 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 
       28.93        10.42        40.77         1.48        11.38        21.14 
TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1994 TCGA-59-2349 TCGA-59-2350 
        1.74        22.32        29.00        25.02        80.12        22.32 
TCGA-59-2351 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD 
      116.12        34.39         2.14         5.42        44.81        20.52 
TCGA-5X-AA5U TCGA-61-1721 TCGA-61-1722 TCGA-61-1727 TCGA-61-1734 TCGA-61-1736 
       11.87        11.11         8.09        18.54        28.47        48.79 
TCGA-61-1737 TCGA-61-1740 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 
       44.84         2.43         1.45         8.42         5.79        11.41 
TCGA-61-1903 TCGA-61-1906 TCGA-61-1907 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 
       13.02        34.13        31.30        48.92        56.61        67.76 
TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 
       15.75         2.01         5.52        14.50        17.98         4.01 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2087 TCGA-61-2088 
       30.64        39.85         1.18        45.96         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-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2612 TCGA-61-2613 TCGA-OY-A56P 
       76.87        20.68        44.52         6.35        31.07        39.68 
TCGA-VG-A8LO 
        0.79 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.79               0.26 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            180.20             152.02 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             30.64              27.88 
[1] "0.8 - 180.2 (30.6)" "0.3 - 152.0 (27.9)"
[1] "hr=" "1.1"
D63V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  11Q LOSS MUTATED         1   144                1
  11Q LOSS WILD-TYPE       2   414                1
D63V3, multiclass
                  clus
vv                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  OMENTUM                         1                  2
  OVARY                         144                414
  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"
D63V4, continuous
D63V5, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     1 147
  11Q LOSS WILD-TYPE   2 423
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      1  147
  11Q LOSS WILD-TYPE    2  423
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 1                  2
  YES              147                423
[1] 2 2
[1] FALSE
                    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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  0     2
  11Q LOSS WILD-TYPE                                3    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  11Q LOSS MUTATED                          10
  11Q LOSS WILD-TYPE                        24
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11Q LOSS MUTATED                                           0   128
  11Q LOSS WILD-TYPE                                         1   348
D63V7, multiclass
                                           clus
vv                                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    2                 17
  BLACK OR AFRICAN AMERICAN                               10                 24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                  128                348
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V8, 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    37  40
  12P LOSS WILD-TYPE 231 252
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                77                483 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                40                252 
$`12P LOSS MUTATED`
TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1364 TCGA-04-1638 TCGA-09-1667 
        1.81        49.15         2.01        33.67        55.43        61.87 
TCGA-09-1675 TCGA-09-2044 TCGA-10-0936 TCGA-13-0724 TCGA-13-0755 TCGA-13-0758 
       97.55         6.12        36.92         2.73         2.50        11.38 
TCGA-13-0766 TCGA-13-0793 TCGA-13-0803 TCGA-13-0807 TCGA-13-0885 TCGA-13-0891 
       21.40        28.70        43.86        13.61        91.40        69.01 
TCGA-13-0905 TCGA-13-0908 TCGA-13-0919 TCGA-13-1403 TCGA-13-1405 TCGA-13-1483 
       47.84        44.84        14.89        10.88         7.36        29.42 
TCGA-13-1488 TCGA-13-1494 TCGA-13-1497 TCGA-13-1501 TCGA-13-1507 TCGA-13-1512 
       70.82        38.20        54.31        32.84         4.77         3.09 
TCGA-20-0987 TCGA-20-1685 TCGA-23-1120 TCGA-23-1122 TCGA-23-2072 TCGA-23-2078 
       23.05        16.70         4.27        39.09        24.95        87.48 
TCGA-24-0979 TCGA-24-1105 TCGA-24-1425 TCGA-24-1428 TCGA-24-1435 TCGA-24-1471 
       41.56        47.41         5.95        17.39        43.53         1.18 
TCGA-24-1550 TCGA-24-1849 TCGA-24-2026 TCGA-24-2036 TCGA-24-2280 TCGA-24-2297 
       41.06         5.79        34.82        64.01        70.45        55.86 
TCGA-25-1320 TCGA-25-1632 TCGA-25-2397 TCGA-25-2404 TCGA-25-2409 TCGA-29-1688 
       37.97        59.15        12.00        29.03        26.99        78.90 
TCGA-29-1691 TCGA-29-1703 TCGA-29-1711 TCGA-29-1764 TCGA-29-1776 TCGA-29-2432 
       48.33        59.67        34.62        62.93        11.84        21.47 
TCGA-30-1718 TCGA-30-1853 TCGA-30-1857 TCGA-30-1861 TCGA-36-2538 TCGA-36-2549 
       51.91        36.26         0.26        34.78        25.08         6.05 
TCGA-57-1585 TCGA-59-A5PD TCGA-61-1727 TCGA-61-1734 TCGA-61-1738 TCGA-61-1903 
        1.74        20.52        18.54        28.47        35.80        13.02 
TCGA-61-1910 TCGA-61-1913 TCGA-61-1919 TCGA-61-2008 TCGA-61-2102 
       37.05        48.92        38.17        30.64         6.48 

$`12P LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 
       43.92        41.00        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-04-1365 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-04-1525 
       82.39        56.55        41.59        19.99         0.79        38.37 
TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 
      119.08        29.10        84.20        48.89        27.88        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 
       64.64        36.23        31.86        47.70        45.37        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 
        9.47        57.76        17.98        35.57         9.99        38.43 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 
       89.33        74.93        41.62        57.60        55.36        30.51 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-2043 TCGA-09-2045 
       17.98         5.85         3.02         8.55         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-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       26.93        12.46        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-13-0714 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-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0760 
       31.20        15.19        17.82        55.17        11.18        11.54 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 
       34.06        32.25        31.04         8.45        38.93        36.72 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
       30.35        19.59         8.71         7.79         8.12         8.28 
TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 
        8.19        35.28        35.31        68.94       107.18        74.27 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 
       66.67        70.39        61.84        67.99        43.36        57.47 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 
       56.15        57.07        19.36        47.38        48.33        44.94 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 
       37.08        27.72        34.06        29.98        21.17        13.81 
TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 
        4.64         6.41         6.08         6.61         6.05         5.92 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
        6.84         4.70         4.21         5.33        54.64        87.06 
TCGA-13-1482 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 
       61.71        98.04        20.68        22.39        82.88        52.44 
TCGA-13-1492 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 
       73.55        49.25         4.24        37.61        38.40        13.97 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
       16.57         4.21         4.41         4.18         2.56         3.91 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 
       14.24        12.23         8.61        10.78         8.75         6.28 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 
       54.77         8.42        25.94        26.20        72.20        27.52 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 
       25.38        19.10         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-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 
       31.20        68.68         4.57        33.30        86.01       129.96 
TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2079 
        6.38        33.47        58.13         0.53       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-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 
       19.66        11.64        21.80         7.66        22.32        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-24-1424 TCGA-24-1426 TCGA-24-1427 TCGA-24-1430 
        0.76         6.25         6.02         5.36         4.83        28.37 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 
       19.17        18.67         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-24-1548 TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 
       64.27        16.21        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-24-1846 TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 
        4.37        11.28         5.52         9.80        22.68        30.21 
TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 
       16.44        11.05        81.11         4.87       152.02        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-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 
       44.52        57.07        36.16         0.79         0.36        47.54 
TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 
       31.63        44.61         0.82        67.36        36.23        16.64 
TCGA-24-2295 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 
       33.11        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-25-1633 TCGA-25-1634 TCGA-25-1635 
       20.61        38.20         0.30        62.17        35.87        52.04 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 
       14.96        24.99        24.00        85.05        13.02        49.05 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 
        1.02        38.04         3.02        45.01        19.99        42.02 
TCGA-25-2401 TCGA-25-2408 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 
        2.96        31.00        47.61       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-29-1705 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-29-1766 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-29-1777 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-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1855 
       42.25        11.47         9.76        35.77        38.07         2.47 
TCGA-30-1856 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 
       15.68        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-31-1950 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-36-1581 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-36-2540 TCGA-36-2542 
       33.01        29.49        29.82        25.91        23.80        21.60 
TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2551 
        2.24        20.98        18.31        20.52        14.17        16.18 
TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 
       11.47        13.81        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-5X-AA5U TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
       44.81        11.87        11.11         8.09        20.94        31.43 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 TCGA-61-1737 TCGA-61-1740 
       27.88         4.34        31.79        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-61-1907 TCGA-61-1911 TCGA-61-1914 TCGA-61-1915 
        9.07        34.13        31.30        42.51        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-61-2003 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
        4.01        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-61-2104 TCGA-61-2109 TCGA-61-2110 
       60.62        65.52        55.50        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 
       18.94         0.79         9.99 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.26               0.30 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             97.55             180.20 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             32.84              27.88 
[1] "0.3 - 97.5 (32.8)"  "0.3 - 180.2 (27.9)"
[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, continuous
D64V5, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     0  78
  12P LOSS WILD-TYPE   3 492
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   78
  12P LOSS WILD-TYPE    3  492
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 0                  3
  YES               78                492
[1] 2 2
[1] FALSE
                    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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P LOSS MUTATED                                  1     2
  12P LOSS WILD-TYPE                                2    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  12P LOSS MUTATED                           8
  12P LOSS WILD-TYPE                        26
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12P LOSS MUTATED                                           0    63
  12P LOSS WILD-TYPE                                         1   413
D64V7, multiclass
                                           clus
vv                                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  2
  ASIAN                                                    2                 17
  BLACK OR AFRICAN AMERICAN                                8                 26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   63                413
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V8, 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    50  50
  12Q LOSS WILD-TYPE 218 242
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               100                460 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                50                242 
$`12Q LOSS MUTATED`
TCGA-04-1335 TCGA-04-1356 TCGA-04-1371 TCGA-04-1542 TCGA-04-1638 TCGA-09-1659 
        1.81        49.28        82.39        84.20        55.43         9.99 
TCGA-09-1667 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-13-0724 TCGA-13-0751 
       61.87         8.55        97.55         6.12         2.73        55.17 
TCGA-13-0755 TCGA-13-0758 TCGA-13-0760 TCGA-13-0766 TCGA-13-0793 TCGA-13-0803 
        2.50        11.38        11.54        21.40        28.70        43.86 
TCGA-13-0807 TCGA-13-0885 TCGA-13-0891 TCGA-13-0904 TCGA-13-0905 TCGA-13-0908 
       13.61        91.40        69.01        48.33        47.84        44.84 
TCGA-13-0919 TCGA-13-0923 TCGA-13-1405 TCGA-13-1408 TCGA-13-1411 TCGA-13-1483 
       14.89         6.41         7.36         5.92         4.21        29.42 
TCGA-13-1489 TCGA-13-1497 TCGA-13-1501 TCGA-13-1507 TCGA-13-1512 TCGA-13-2059 
       82.88        54.31        32.84         4.77         3.09        12.23 
TCGA-20-0987 TCGA-23-1120 TCGA-23-1122 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 
       23.05         4.27        39.09        24.95       115.89        87.48 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1104 TCGA-24-1105 TCGA-24-1425 TCGA-24-1428 
        7.66        22.32        63.55        47.41         5.95        17.39 
TCGA-24-1431 TCGA-24-1471 TCGA-24-1550 TCGA-24-1604 TCGA-24-1614 TCGA-24-1842 
       19.17         1.18        41.06        88.37        48.33         8.32 
TCGA-24-1849 TCGA-24-1920 TCGA-24-1927 TCGA-24-2023 TCGA-24-2026 TCGA-24-2036 
        5.79         9.80        16.44        44.84        34.82        64.01 
TCGA-24-2254 TCGA-24-2280 TCGA-24-2297 TCGA-25-1314 TCGA-25-1320 TCGA-25-1632 
       57.07        70.45        55.86        33.01        37.97        59.15 
TCGA-25-1877 TCGA-25-2397 TCGA-25-2409 TCGA-29-1688 TCGA-29-1691 TCGA-29-1703 
       24.00        12.00        26.99        78.90        48.33        59.67 
TCGA-29-1711 TCGA-29-1776 TCGA-29-2427 TCGA-29-2432 TCGA-30-1718 TCGA-30-1853 
       34.62        11.84        62.47        21.47        51.91        36.26 
TCGA-30-1857 TCGA-30-1861 TCGA-30-1891 TCGA-31-1956 TCGA-36-2538 TCGA-36-2549 
        0.26        34.78        30.05        44.12        25.08         6.05 
TCGA-3P-A9WA TCGA-57-1585 TCGA-59-2363 TCGA-59-A5PD TCGA-61-1727 TCGA-61-1734 
       13.81         1.74         5.42        20.52        18.54        28.47 
TCGA-61-1738 TCGA-61-1895 TCGA-61-1903 TCGA-61-1904 TCGA-61-1913 TCGA-61-1917 
       35.80         1.45        13.02         9.07        48.92        43.43 
TCGA-61-1919 TCGA-61-2008 TCGA-61-2087 TCGA-61-2104 
       38.17        30.64         4.80        76.87 

$`12Q LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 
       43.92        41.00        49.15         2.01        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-04-1361 TCGA-04-1362 TCGA-04-1364 
       63.98        65.46         0.53        32.52        44.32        33.67 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 
       76.57       103.40        56.55        41.59        19.99         0.79 
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-09-0364 
       64.64        36.23        31.86        47.70        45.37        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1661 TCGA-09-1662 
        9.47        57.76        17.98        35.57        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-09-2043 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 
        5.85         3.02         6.18        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-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-13-0725 TCGA-13-0726 
        6.21        24.59        44.55        39.58        12.39        31.20 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0757 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 
       15.19        17.82        11.18        34.06        32.25        31.04 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 
        8.45        38.93        36.72        30.35        19.59         8.71 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 
        7.79         8.12         8.28         8.19        35.28        35.31 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 
       68.94       107.18        74.27        66.67        70.39        61.84 
TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
       67.99        43.36        57.47        56.15        57.07        19.36 
TCGA-13-0903 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
       47.38        44.94        37.08        27.72        34.06        29.98 
TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 
       21.17        13.81         4.64         6.08        10.88         6.61 
TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
        6.05         6.84         4.70         5.33        54.64        87.06 
TCGA-13-1482 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1491 
       61.71        98.04        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 
       73.55        38.20        49.25         4.24        37.61        38.40 
TCGA-13-1500 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 
       13.97        16.57         4.21         4.41         4.18         2.56 
TCGA-13-1511 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 
        3.91        14.24         8.61        10.78         8.75         6.28 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 
       54.77         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-23-1028 
       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         4.57        33.30        86.01 
TCGA-23-1119 TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2079 
      129.96         6.38        33.47        58.13         0.53        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-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-1103 TCGA-24-1413 
       19.66        11.64        21.80        41.56        54.12         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-24-1426 TCGA-24-1427 TCGA-24-1430 TCGA-24-1434 TCGA-24-1435 
        6.02         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-24-1474 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-24-1551 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-24-1616 TCGA-24-1843 TCGA-24-1844 
       10.26        17.23        90.15        38.24         3.48         3.72 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1850 TCGA-24-1923 TCGA-24-1924 
        3.81         4.37        11.28         5.52        22.68        30.21 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2024 TCGA-24-2027 
       11.05        81.11         4.87       152.02        58.16       109.71 
TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2038 TCGA-24-2260 
       14.43        55.92        18.48        28.18        44.52        36.16 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 
        0.79         0.36        47.54        31.63        44.61         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2298 TCGA-25-1312 
       67.36        36.23        16.64        33.11        53.26         1.02 
TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 
       26.96        52.04        42.05         2.01        34.98        65.00 
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-25-1878 TCGA-25-2042 
       35.87        52.04        14.96        24.99        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-25-2404 TCGA-25-2408 TCGA-29-1690 TCGA-29-1693 
       42.02         2.96        29.03        31.00        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-29-1701 TCGA-29-1702 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1761 
       16.93        23.93        18.25        41.98        31.27        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-29-1777 TCGA-29-1778 
       24.36        22.55        17.33        12.36        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-29-2428 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-30-1855 TCGA-30-1856 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 
       38.07         2.47        15.68        48.10        44.91         6.12 
TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 
       36.62         1.22        57.57        24.26        48.79        45.57 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 
       30.18        18.77        22.49         6.71        42.51         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-36-2529 
       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-36-2540 TCGA-36-2542 
       33.01        29.49        29.82        25.91        23.80        21.60 
TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2551 
        2.24        20.98        18.31        20.52        14.17        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-59-2372 TCGA-5X-AA5U 
      116.12         9.40        34.39         2.14        44.81        11.87 
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-61-2612 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 
       39.68        18.94         0.79         9.99 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.26               0.30 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            115.89             180.20 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            29.060             28.505 
[1] "0.3 - 115.9 (29.1)" "0.3 - 180.2 (28.5)"
[1] "hr=" "1.1"
D65V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  12Q LOSS MUTATED         0   101                0
  12Q LOSS WILD-TYPE       3   457                2
D65V3, multiclass
                  clus
vv                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  OMENTUM                         0                  3
  OVARY                         101                457
  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, continuous
D65V5, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     0 103
  12Q LOSS WILD-TYPE   3 467
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0  103
  12Q LOSS WILD-TYPE    3  467
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 0                  3
  YES              103                467
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  12Q LOSS MUTATED    2  4  0  1
  12Q LOSS WILD-TYPE 13 22  5  2
D65V6, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0                2                 13
  R1                4                 22
  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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q LOSS MUTATED                                  0     3
  12Q LOSS WILD-TYPE                                3    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  12Q LOSS MUTATED                           8
  12Q LOSS WILD-TYPE                        26
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12Q LOSS MUTATED                                           0    86
  12Q LOSS WILD-TYPE                                         1   390
D65V7, multiclass
                                           clus
vv                                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    3                 16
  BLACK OR AFRICAN AMERICAN                                8                 26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   86                390
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V8, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     2  62
  12Q LOSS WILD-TYPE   8 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2   62
  12Q LOSS WILD-TYPE    8  265
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO               62                265
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED   148 148
  13Q LOSS WILD-TYPE 120 144
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               296                264 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               148                144 
$`13Q LOSS MUTATED`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1347 
       41.00         1.81         1.08        18.51        11.87        63.09 
TCGA-04-1349 TCGA-04-1353 TCGA-04-1361 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 
       21.57         0.53        32.52        76.57       103.40        56.55 
TCGA-04-1516 TCGA-04-1525 TCGA-04-1530 TCGA-04-1638 TCGA-04-1646 TCGA-04-1648 
       41.59        38.37       119.08        55.43        27.88        28.64 
TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0366 TCGA-09-0367 
       36.23        31.86        47.70        45.37        57.76        17.98 
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-10-0925 TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 
       20.94        26.93        54.31        81.86        34.19        32.88 
TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0717 TCGA-13-0720 TCGA-13-0724 
       36.92        19.99        20.91        24.59        44.55         2.73 
TCGA-13-0726 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0764 TCGA-13-0766 
       31.20        17.82        55.17         2.50        31.04        21.40 
TCGA-13-0768 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 
        8.45        36.72        28.70        19.59         8.71         7.79 
TCGA-13-0800 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0883 TCGA-13-0884 
        8.12         8.19        35.28        35.31        68.94       107.18 
TCGA-13-0885 TCGA-13-0888 TCGA-13-0890 TCGA-13-0891 TCGA-13-0897 TCGA-13-0900 
       91.40        70.39        67.99        69.01        57.47        57.07 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 TCGA-13-0910 TCGA-13-0916 
       19.36        47.38        48.33        44.94        37.08        21.17 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1409 
       14.89        13.81         6.08        10.88         6.61         6.84 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1492 
       61.71        29.42        22.39        70.82        82.88        73.55 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1497 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 
       38.20        49.25        54.31        38.40        13.97        32.84 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1509 TCGA-13-1511 TCGA-13-2061 TCGA-13-2065 
       16.57         4.21         4.18         3.91        10.78         8.75 
TCGA-13-2071 TCGA-13-A5FU TCGA-20-0991 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 
        6.28         8.42        26.20        27.52        19.10        16.70 
TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 
       47.54        40.54        15.39        32.09        49.41         8.81 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1114 TCGA-23-1116 TCGA-23-1118 TCGA-23-1119 
       18.90         2.76        68.68         4.57        86.01       129.96 
TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2081 
        6.38        33.47        58.13         0.53       115.89        77.00 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0968 TCGA-24-0975 
       49.84         2.76         4.70         4.50        19.66        21.80 
TCGA-24-0980 TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 TCGA-24-1417 TCGA-24-1419 
        7.66        54.12        47.41         6.31         7.82         7.86 
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-24-1464 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-24-1548 TCGA-24-1549 TCGA-24-1552 TCGA-24-1555 TCGA-24-1558 TCGA-24-1560 
       16.21        56.58        41.39        88.50        19.53        44.09 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1603 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 
       47.70        25.87        90.15        48.33        38.24         8.32 
TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1850 
        3.48         3.72         3.81         4.37        11.28         5.52 
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-24-2030 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 
       58.16        34.82        55.92        57.07        36.16         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2290 TCGA-25-1313 TCGA-25-1315 TCGA-25-1318 
        0.36        47.54        36.23        26.96        52.04        34.98 
TCGA-25-1319 TCGA-25-1321 TCGA-25-1329 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 
       65.00        33.96        15.02        12.95        20.61         0.30 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1878 TCGA-25-2391 TCGA-25-2392 
       62.17        35.87        52.04        85.05        49.05         1.02 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 
       38.04         3.02        12.00        19.99        42.02         2.96 
TCGA-25-2404 TCGA-25-2409 TCGA-29-1693 TCGA-29-1694 TCGA-29-1697 TCGA-29-1698 
       29.03        26.99       101.79        39.02        31.20        68.32 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 TCGA-29-1763 
       36.36        16.93        23.93        59.67        41.98        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 
       62.93        39.42        31.30        22.55        12.36        11.84 
TCGA-29-1777 TCGA-29-1778 TCGA-29-1784 TCGA-29-2427 TCGA-29-2431 TCGA-29-2432 
       12.30        14.93         5.36        62.47        42.25        21.47 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1866 TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 
       44.91        34.78        36.62        30.05        18.77         6.71 
TCGA-31-1955 TCGA-31-1959 TCGA-36-1569 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 
       42.51         2.20        29.10        22.85        22.55         8.55 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2534 TCGA-36-2542 TCGA-36-2543 
       24.23        24.69        35.05        29.82        21.60         2.24 
TCGA-36-2545 TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2587 TCGA-42-2590 TCGA-57-1584 
       18.31        16.18        13.81        23.74        10.42        21.14 
TCGA-57-1992 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2372 
       29.00        22.32       116.12         9.40        34.39        44.81 
TCGA-59-A5PD TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1730 
       20.52         8.09        20.94        31.43        18.54         4.34 
TCGA-61-1733 TCGA-61-1734 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1743 
       31.79        28.47        44.84        35.80         2.43        43.69 
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-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 
       48.92        56.61        67.76        15.75        38.17         2.01 
TCGA-61-2002 TCGA-61-2012 TCGA-61-2016 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
       17.98        30.64         1.18        45.40         4.80         4.77 
TCGA-61-2094 TCGA-61-2097 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 
       71.74        60.62        44.52       125.75        22.22         6.35 
TCGA-OY-A56P TCGA-OY-A56Q 
       39.68        18.94 

$`13Q LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1346 TCGA-04-1348 
       43.92        49.15         2.01        46.62        65.52        48.76 
TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 TCGA-04-1371 
       63.98        65.46        49.28        44.32        33.67        82.39 
TCGA-04-1517 TCGA-04-1519 TCGA-04-1536 TCGA-04-1542 TCGA-04-1644 TCGA-04-1649 
       19.99         0.79        29.10        84.20        48.89        64.64 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0369 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       29.16         9.47        35.57        89.33        74.93        41.62 
TCGA-09-1669 TCGA-09-1675 TCGA-09-2043 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 
       30.51        97.55         6.18        35.15         4.54       112.41 
TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0928 TCGA-10-0933 TCGA-10-0934 
       39.75        12.46        25.91        18.51        14.66         6.71 
TCGA-10-0935 TCGA-13-0714 TCGA-13-0723 TCGA-13-0725 TCGA-13-0727 TCGA-13-0757 
       35.44         6.21        39.58        12.39        15.19        11.18 
TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0791 TCGA-13-0794 
       11.38        11.54        34.06        32.25        38.93        30.35 
TCGA-13-0801 TCGA-13-0803 TCGA-13-0807 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 
        8.28        43.86        13.61        74.27        66.67        61.84 
TCGA-13-0893 TCGA-13-0899 TCGA-13-0905 TCGA-13-0908 TCGA-13-0911 TCGA-13-0912 
       43.36        56.15        47.84        44.84        27.72        34.06 
TCGA-13-0913 TCGA-13-0921 TCGA-13-0923 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 
       29.98         4.64         6.41         7.36         6.05         5.92 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1484 
        4.70         4.21         5.33        54.64        87.06        98.04 
TCGA-13-1485 TCGA-13-1491 TCGA-13-1496 TCGA-13-1498 TCGA-13-1506 TCGA-13-1507 
       20.68        52.44         4.24        37.61         4.41         4.77 
TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-A5FT 
        2.56         3.09        14.24        12.23         8.61        54.77 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0996 TCGA-20-1683 TCGA-20-1686 TCGA-20-1687 
       23.05        25.94        72.20        25.38         2.93         2.66 
TCGA-23-1022 TCGA-23-1026 TCGA-23-1030 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
       49.68        26.83        29.13        51.35        54.51         3.22 
TCGA-23-1113 TCGA-23-1117 TCGA-23-1120 TCGA-23-1122 TCGA-23-2072 TCGA-23-2078 
       31.20        33.30         4.27        39.09        24.95        87.48 
TCGA-23-2079 TCGA-24-0966 TCGA-24-0970 TCGA-24-0979 TCGA-24-0982 TCGA-24-1104 
       91.66         7.63        11.64        41.56        22.32        63.55 
TCGA-24-1416 TCGA-24-1418 TCGA-24-1422 TCGA-24-1423 TCGA-24-1427 TCGA-24-1431 
        6.38         7.99         0.76         6.25         4.83        19.17 
TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 
       18.67         8.55        72.92       105.99         3.45         1.18 
TCGA-24-1546 TCGA-24-1550 TCGA-24-1551 TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 
       64.27        41.06        51.91        58.09        70.62        39.88 
TCGA-24-1562 TCGA-24-1565 TCGA-24-1567 TCGA-24-1604 TCGA-24-1849 TCGA-24-1920 
       45.50        10.26        17.23        88.37         5.79         9.80 
TCGA-24-1923 TCGA-24-1930 TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 
       22.68        81.11       109.71        14.43        18.48        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
       64.01        44.52        31.63        70.45        44.61         0.82 
TCGA-24-2289 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 
       67.36        16.64        33.11        55.86        53.26         1.02 
TCGA-25-1314 TCGA-25-1316 TCGA-25-1317 TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 
       33.01        42.05         2.01        37.97         2.99        12.99 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1630 TCGA-25-1632 TCGA-25-1870 
       18.58        27.62        17.03        38.20        59.15        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-2042 TCGA-25-2398 TCGA-25-2408 TCGA-29-1688 
       24.99        24.00        13.02        45.01        31.00        78.90 
TCGA-29-1690 TCGA-29-1691 TCGA-29-1695 TCGA-29-1696 TCGA-29-1705 TCGA-29-1710 
       47.61        48.33        40.41        33.93        18.25        31.27 
TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1769 TCGA-29-1770 TCGA-29-1774 
       34.62        17.36        86.60        22.98        24.36        17.33 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 
        8.38         7.23        36.30        86.17        65.00        45.11 
TCGA-29-2429 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 
       13.84        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-30-1862 
       36.26         2.47        15.68         0.26        48.10         6.12 
TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 
        1.22        57.57        24.26        48.79        45.57        30.18 
TCGA-31-1951 TCGA-31-1956 TCGA-36-1568 TCGA-36-1570 TCGA-36-1576 TCGA-36-1577 
       22.49        44.12        28.77        21.53        30.08        25.74 
TCGA-36-1578 TCGA-36-2530 TCGA-36-2532 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       27.85        33.01        29.49        25.91        25.08        23.80 
TCGA-36-2544 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2552 TCGA-42-2582 
       20.98        20.52        14.17         6.05        11.47        47.57 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 
       28.93        42.02        40.77         1.48        24.03        11.38 
TCGA-57-1585 TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 
        1.74        22.32        25.08        25.02       180.20        80.12 
TCGA-59-2355 TCGA-59-2363 TCGA-5X-AA5U TCGA-61-1721 TCGA-61-1728 TCGA-61-1736 
        2.14         5.42        11.87        11.11        27.88        48.79 
TCGA-61-1741 TCGA-61-1895 TCGA-61-1900 TCGA-61-1910 TCGA-61-1911 TCGA-61-1917 
       33.67         1.45         5.79        37.05        42.51        43.43 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2017 
        5.52        14.50         4.01        30.64        39.85        45.96 
TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 
       51.72        61.64        58.39        65.52        55.50         6.48 
TCGA-61-2104 TCGA-61-2109 TCGA-61-2613 TCGA-61-2614 TCGA-VG-A8LO TCGA-WR-A838 
       76.87        20.68        31.07         8.61         0.79         9.99 

  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 
            28.420             29.015 
[1] "0.3 - 152.0 (28.4)" "0.3 - 180.2 (29.0)"
[1] "hr=" "1.1"
D66V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  13Q LOSS MUTATED         1   296                2
  13Q LOSS WILD-TYPE       2   262                0
D66V3, multiclass
                  clus
vv                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  OMENTUM                         1                  2
  OVARY                         296                262
  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, continuous
D66V5, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     1 305
  13Q LOSS WILD-TYPE   2 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      1  305
  13Q LOSS WILD-TYPE    2  265
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 1                  2
  YES              305                265
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  13Q LOSS MUTATED    4 10  2  2
  13Q LOSS WILD-TYPE 11 16  3  1
D66V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0                4                 11
  R1               10                 16
  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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  1    10
  13Q LOSS WILD-TYPE                                2     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  13Q LOSS MUTATED                          21
  13Q LOSS WILD-TYPE                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  13Q LOSS MUTATED                                           1   252
  13Q LOSS WILD-TYPE                                         0   224
D66V7, multiclass
                                           clus
vv                                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  2
  ASIAN                                                   10                  9
  BLACK OR AFRICAN AMERICAN                               21                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  252                224
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V8, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     4 178
  13Q LOSS WILD-TYPE   6 149
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4  178
  13Q LOSS WILD-TYPE    6  149
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  6
  NOT HISPANIC OR LATINO              178                149
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    93 116
  14Q LOSS WILD-TYPE 175 176
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               209                351 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               116                176 
$`14Q LOSS MUTATED`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1341 TCGA-04-1343 TCGA-04-1346 
       41.00         1.81         2.01         1.08        11.87        65.52 
TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 
       65.46         0.53        49.28        32.52        44.32        33.67 
TCGA-04-1365 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1648 
       76.57        38.37       119.08        84.20        55.43        28.64 
TCGA-04-1649 TCGA-04-1655 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1670 
       64.64        45.37        35.57         9.99        38.43        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-2048 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 
        5.85         3.02         4.54        63.09        39.75        12.46 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0928 TCGA-10-0938 TCGA-13-0717 TCGA-13-0723 
       54.31        25.91        18.51        20.91        24.59        39.58 
TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 
        2.73        31.20        15.19        17.82        55.17        11.18 
TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0766 TCGA-13-0792 TCGA-13-0794 
       11.38        11.54        34.06        21.40        36.72        30.35 
TCGA-13-0803 TCGA-13-0884 TCGA-13-0885 TCGA-13-0888 TCGA-13-0891 TCGA-13-0906 
       43.86       107.18        91.40        70.39        69.01        44.94 
TCGA-13-0913 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-1405 TCGA-13-1407 
       29.98        14.89        13.81         4.64         7.36         6.05 
TCGA-13-1411 TCGA-13-1481 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
        4.21        87.06        22.39        70.82        82.88        52.44 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1499 TCGA-13-1504 TCGA-13-1507 TCGA-13-1510 
        4.24        54.31        38.40        16.57         4.77         2.56 
TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FU TCGA-20-1683 TCGA-20-1684 
       10.78         8.75         6.28         8.42        25.38        19.10 
TCGA-20-1687 TCGA-23-1024 TCGA-23-1027 TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 
        2.66        15.39        32.09        49.41        29.13        18.90 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 TCGA-23-1117 TCGA-23-1118 
       51.35        54.51         3.22        68.68        33.30        86.01 
TCGA-23-1119 TCGA-23-1122 TCGA-23-1123 TCGA-23-2072 TCGA-23-2077 TCGA-23-2081 
      129.96        39.09        33.47        24.95       115.89        77.00 
TCGA-23-2643 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0982 
        4.70        19.66        11.64        21.80        41.56        22.32 
TCGA-24-1105 TCGA-24-1424 TCGA-24-1427 TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 
       47.41         6.02         4.83        18.67         8.55        72.92 
TCGA-24-1466 TCGA-24-1469 TCGA-24-1471 TCGA-24-1544 TCGA-24-1546 TCGA-24-1548 
       45.14         9.11         1.18        26.96        64.27        16.21 
TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 TCGA-24-1565 TCGA-24-1604 TCGA-24-1843 
       56.58        51.91        41.39        10.26        88.37         3.48 
TCGA-24-1846 TCGA-24-1924 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 
        4.37        30.21         4.87       152.02        44.84        58.16 
TCGA-24-2026 TCGA-24-2029 TCGA-24-2260 TCGA-24-2267 TCGA-24-2280 TCGA-24-2288 
       34.82        14.43        36.16        47.54        70.45         0.82 
TCGA-24-2295 TCGA-25-1320 TCGA-25-1323 TCGA-25-1626 TCGA-25-1631 TCGA-25-1632 
       33.11        37.97        12.99        17.03         0.30        59.15 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-2391 
       35.87        52.04        14.96        24.99        24.00        49.05 
TCGA-25-2393 TCGA-25-2400 TCGA-25-2404 TCGA-29-1693 TCGA-29-1695 TCGA-29-1697 
       38.04        42.02        29.03       101.79        40.41        31.20 
TCGA-29-1698 TCGA-29-1707 TCGA-29-1710 TCGA-29-1761 TCGA-29-1763 TCGA-29-1766 
       68.32        41.98        31.27        17.36        66.81        39.42 
TCGA-29-1769 TCGA-29-1771 TCGA-29-1775 TCGA-29-1777 TCGA-29-2425 TCGA-29-2427 
       22.98        22.55        12.36        12.30        65.00        62.47 
TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1855 TCGA-30-1859 TCGA-30-1861 
       11.47        35.77        51.91         2.47        48.10        34.78 
TCGA-30-1887 TCGA-31-1944 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-36-1571 
       24.26        45.57        18.77        22.49         6.71        22.85 
TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-2534 TCGA-36-2543 TCGA-36-2551 
       22.55         8.55        30.08        29.82         2.24        16.18 
TCGA-36-2552 TCGA-42-2587 TCGA-42-2589 TCGA-42-2591 TCGA-42-2593 TCGA-57-1992 
       11.47        23.74        42.02        40.77         1.48        29.00 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2372 TCGA-59-A5PD TCGA-5X-AA5U TCGA-61-1722 
       25.08        25.02        44.81        20.52        11.87         8.09 
TCGA-61-1733 TCGA-61-1736 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1901 
       31.79        48.79         2.43        33.67        43.69        11.41 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1917 TCGA-61-2000 TCGA-61-2009 TCGA-61-2088 
        9.07        34.13        43.43        14.50        39.85         4.77 
TCGA-61-2102 TCGA-61-2109 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
        6.48        20.68         8.61        39.68        18.94 

$`14Q LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1336 TCGA-04-1338 TCGA-04-1342 TCGA-04-1347 TCGA-04-1348 
       43.92        49.15        46.62        18.51        63.09        48.76 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 
       21.57        63.98       103.40        82.39        56.55        41.59 
TCGA-04-1517 TCGA-04-1519 TCGA-04-1536 TCGA-04-1644 TCGA-04-1646 TCGA-04-1651 
       19.99         0.79        29.10        48.89        27.88        36.23 
TCGA-04-1652 TCGA-04-1654 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 
       31.86        47.70        29.16         9.47        57.76        17.98 
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-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 
       30.51         8.55        97.55         6.18         6.12        35.15 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2054 TCGA-09-2055 TCGA-10-0927 TCGA-10-0930 
      112.41        71.11        20.94        26.93        81.86        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-13-0714 TCGA-13-0720 TCGA-13-0725 TCGA-13-0755 TCGA-13-0762 TCGA-13-0764 
        6.21        44.55        12.39         2.50        32.25        31.04 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 
        8.45        38.93        28.70        19.59         8.71         7.79 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
        8.12         8.28         8.19        35.28        35.31        13.61 
TCGA-13-0883 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0893 
       68.94        74.27        66.67        61.84        67.99        43.36 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 
       57.47        56.15        57.07        19.36        47.38        48.33 
TCGA-13-0905 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 
       47.84        44.84        37.08        27.72        34.06        21.17 
TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1408 TCGA-13-1409 
        6.41         6.08        10.88         6.61         5.92         6.84 
TCGA-13-1410 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
        4.70         5.33        54.64        61.71        29.42        98.04 
TCGA-13-1485 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1498 TCGA-13-1500 
       20.68        73.55        38.20        49.25        37.61        13.97 
TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 
       32.84         4.21         4.41         4.18         3.91         3.09 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 
       14.24        12.23         8.61        54.77        23.05        25.94 
TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 
       26.20        72.20        27.52        16.70         2.93        47.54 
TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 TCGA-23-1029 TCGA-23-1032 TCGA-23-1113 
       49.68        40.54        26.83         8.81         2.76        31.20 
TCGA-23-1116 TCGA-23-1120 TCGA-23-1121 TCGA-23-1124 TCGA-23-1809 TCGA-23-2078 
        4.57         4.27         6.38        58.13         0.53        87.48 
TCGA-23-2079 TCGA-23-2084 TCGA-23-2641 TCGA-23-2645 TCGA-24-0966 TCGA-24-0980 
       91.66        49.84         2.76         4.50         7.63         7.66 
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-24-1425 TCGA-24-1426 TCGA-24-1428 
        7.86         0.76         6.25         5.95         5.36        17.39 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 TCGA-24-1464 TCGA-24-1467 TCGA-24-1470 
       28.37        19.17        43.53        12.46       105.99         3.45 
TCGA-24-1474 TCGA-24-1545 TCGA-24-1550 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 
       22.22        57.40        41.06        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-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1844 
       17.23        90.15        48.33        38.24         8.32         3.72 
TCGA-24-1845 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 
        3.81        11.28         5.79         5.52         9.80        22.68 
TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2027 TCGA-24-2030 TCGA-24-2033 
       16.44        11.05        81.11       109.71        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-24-2271 TCGA-24-2281 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 
       31.63        44.61        67.36        36.23        16.64        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-25-1321 TCGA-25-1322 TCGA-25-1329 
        2.01        34.98        65.00        33.96         2.99        15.02 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1633 
       18.58        27.62        12.95        20.61        38.20        62.17 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2392 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 
       85.05        13.02         1.02         3.02        12.00        45.01 
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-29-1694 TCGA-29-1696 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 
       48.33        39.02        33.93        36.36        16.93        23.93 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1711 TCGA-29-1762 TCGA-29-1764 TCGA-29-1768 
       59.67        18.25        34.62        86.60        62.93        31.30 
TCGA-29-1770 TCGA-29-1774 TCGA-29-1776 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 
       24.36        17.33        11.84        14.93         8.38         7.23 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 
        5.36        36.30        86.17        45.11        13.84        42.25 
TCGA-29-2432 TCGA-29-2436 TCGA-30-1714 TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 
       21.47         9.76        38.07        36.26        15.68         0.26 
TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1891 
       44.91         6.12        36.62         1.22        57.57        30.05 
TCGA-30-1892 TCGA-31-1946 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 
       48.79        30.18        42.51        44.12         2.20        28.77 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 
       29.10        21.53        25.74        27.85        24.23        24.69 
TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       35.05        33.01        29.49        25.91        25.08        23.80 
TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 
       21.60        20.98        18.31        20.52        14.17         6.05 
TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2588 TCGA-42-2590 TCGA-57-1582 TCGA-57-1583 
       13.81        47.57        28.93        10.42        24.03        11.38 
TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 
       21.14         1.74        22.32       180.20        80.12        22.32 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-61-1721 
      116.12         9.40        34.39         2.14         5.42        11.11 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1734 
       20.94        31.43        18.54        27.88         4.34        28.47 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1903 
       44.84        35.80         1.45         8.42         5.79        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-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2002 TCGA-61-2003 
       15.75        38.17         2.01         5.52        17.98         4.01 
TCGA-61-2008 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
       30.64        30.64         1.18        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-61-2104 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 
       55.50        76.87        44.52       125.75        22.22         6.35 
TCGA-61-2613 TCGA-VG-A8LO TCGA-WR-A838 
       31.07         0.79         9.99 

  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 
             29.03              28.37 
[1] "0.3 - 152.0 (29.0)" "0.3 - 180.2 (28.4)"
[1] "hr=" "1.1"
D67V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  14Q LOSS MUTATED         1   208                1
  14Q LOSS WILD-TYPE       2   350                1
D67V3, multiclass
                  clus
vv                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  OMENTUM                         1                  2
  OVARY                         208                350
  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, continuous
D67V5, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     0 214
  14Q LOSS WILD-TYPE   3 356
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      0  214
  14Q LOSS WILD-TYPE    3  356
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                 0                  3
  YES              214                356
[1] 2 2
[1] FALSE
                    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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q LOSS MUTATED                                  2     5
  14Q LOSS WILD-TYPE                                1    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  14Q LOSS MUTATED                          13
  14Q LOSS WILD-TYPE                        21
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  14Q LOSS MUTATED                                           0   182
  14Q LOSS WILD-TYPE                                         1   294
D67V7, multiclass
                                           clus
vv                                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  1
  ASIAN                                                    5                 14
  BLACK OR AFRICAN AMERICAN                               13                 21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                  182                294
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V8, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     6 122
  14Q LOSS WILD-TYPE   4 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      6  122
  14Q LOSS WILD-TYPE    4  205
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                  4
  NOT HISPANIC OR LATINO              122                205
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED   118 152
  15Q LOSS WILD-TYPE 150 140
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               270                290 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               152                140 
$`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-09-0364 TCGA-09-0365 TCGA-09-1659 TCGA-09-1661 TCGA-09-1667 
       45.37        29.16         9.47         9.99        38.43        61.87 
TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1674 TCGA-09-2050 TCGA-09-2051 
       55.36        30.51        17.98         8.55        71.11        63.09 
TCGA-09-2054 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0936 TCGA-13-0717 
       20.94        54.31        25.91        81.86        36.92        24.59 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0758 
       39.58         2.73        17.82        55.17        11.18        11.38 
TCGA-13-0760 TCGA-13-0762 TCGA-13-0793 TCGA-13-0794 TCGA-13-0802 TCGA-13-0803 
       11.54        32.25        28.70        30.35         8.19        43.86 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 
       13.61        68.94       107.18        91.40        66.67        70.39 
TCGA-13-0889 TCGA-13-0891 TCGA-13-0899 TCGA-13-0910 TCGA-13-0911 TCGA-13-0921 
       61.84        69.01        56.15        37.08        27.72         4.64 
TCGA-13-0923 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
        6.41         7.36         6.05         5.92         6.84         4.70 
TCGA-13-1411 TCGA-13-1482 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 
        4.21        61.71        98.04        22.39        70.82        82.88 
TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1504 TCGA-13-1505 
       52.44        38.20        49.25         4.24        16.57         4.21 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1510 TCGA-13-2057 TCGA-13-2061 TCGA-13-A5FU 
        4.41         4.77         2.56        14.24        10.78         8.42 
TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1686 
       25.94        26.20        27.52        25.38        19.10         2.93 
TCGA-23-1022 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 
       49.68        29.13        18.90         2.76        51.35        54.51 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1123 TCGA-23-2077 TCGA-23-2084 
       31.20        68.68         4.57        33.47       115.89        49.84 
TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0968 TCGA-24-0979 TCGA-24-0982 
        2.76         4.70         4.50        19.66        41.56        22.32 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1417 TCGA-24-1418 TCGA-24-1422 TCGA-24-1424 
       63.55        47.41         7.82         7.99         0.76         6.02 
TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 
        5.36        17.39        28.37        19.17        18.67         8.55 
TCGA-24-1463 TCGA-24-1466 TCGA-24-1469 TCGA-24-1471 TCGA-24-1544 TCGA-24-1548 
       72.92        45.14         9.11         1.18        26.96        16.21 
TCGA-24-1549 TCGA-24-1550 TCGA-24-1552 TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 
       56.58        41.06        41.39        58.09        70.62        39.88 
TCGA-24-1564 TCGA-24-1603 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 
       25.87        90.15        48.33        38.24         8.32         3.48 
TCGA-24-1844 TCGA-24-1845 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-1927 
        3.72         3.81         5.52         9.80        30.21        16.44 
TCGA-24-1928 TCGA-24-2019 TCGA-24-2020 TCGA-24-2026 TCGA-24-2030 TCGA-24-2036 
       11.05         4.87       152.02        34.82        55.92        64.01 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2280 TCGA-24-2288 TCGA-24-2293 
       57.07        36.16         0.79        70.45         0.82        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-25-1316 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 
       42.05        34.98        65.00        37.97        33.96         2.99 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 
       12.99        15.02        18.58        20.61         0.30        59.15 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1871 TCGA-25-1877 TCGA-25-2396 TCGA-25-2397 
       62.17        35.87        24.99        24.00         3.02        12.00 
TCGA-25-2404 TCGA-29-1693 TCGA-29-1695 TCGA-29-1698 TCGA-29-1699 TCGA-29-1702 
       29.03       101.79        40.41        68.32        36.36        23.93 
TCGA-29-1703 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 
       59.67        41.98        31.27        34.62        17.36        86.60 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 TCGA-29-1774 
       66.81        62.93        39.42        22.98        24.36        17.33 
TCGA-29-1777 TCGA-29-1783 TCGA-29-1784 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 
       12.30         7.23         5.36        86.17        65.00        45.11 
TCGA-29-2429 TCGA-29-2432 TCGA-29-2434 TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 
       13.84        21.47        11.47        38.07        51.91         2.47 
TCGA-30-1856 TCGA-30-1859 TCGA-30-1860 TCGA-30-1866 TCGA-30-1867 TCGA-30-1887 
       15.68        48.10        44.91        36.62         1.22        24.26 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1950 TCGA-31-1953 TCGA-36-1581 TCGA-36-2529 
       30.05        48.79        18.77         6.71        24.69        35.05 
TCGA-36-2543 TCGA-36-2545 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2589 
        2.24        18.31        14.17        16.18        11.47        42.02 
TCGA-42-2593 TCGA-57-1583 TCGA-57-1586 TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 
        1.48        11.38        22.32        25.08       180.20        22.32 
TCGA-59-2351 TCGA-61-1724 TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 TCGA-61-1734 
      116.12        20.94        18.54        27.88        31.79        28.47 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1901 
       44.84        35.80         2.43        33.67        43.69        11.41 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 
        9.07        34.13        56.61        43.43        15.75        38.17 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 TCGA-61-2016 TCGA-61-2092 TCGA-61-2094 
        4.01        30.64        30.64         1.18        51.72        71.74 
TCGA-61-2096 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2110 
       58.39        65.52        55.50         6.48        76.87        44.52 
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 

$`15Q LOSS WILD-TYPE`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1343 TCGA-04-1346 
       41.00         1.81        49.15         2.01        11.87        65.52 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1351 TCGA-04-1353 TCGA-04-1361 TCGA-04-1362 
       48.76        21.57        65.46         0.53        32.52        44.32 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1516 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 
       33.67        76.57        41.59       119.08        84.20        55.43 
TCGA-04-1644 TCGA-04-1651 TCGA-04-1654 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 
       48.89        36.23        47.70        57.76        17.98        35.57 
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-10-0928 TCGA-10-0930 TCGA-10-0931 
       39.75        26.93        12.46        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-13-0720 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0755 TCGA-13-0761 
       44.55        12.39        31.20        15.19         2.50        34.06 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0795 
       31.04        21.40         8.45        38.93        36.72        19.59 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0804 TCGA-13-0805 
        8.71         7.79         8.12         8.28        35.28        35.31 
TCGA-13-0886 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 
       74.27        67.99        43.36        57.47        57.07        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0912 
       47.38        48.33        47.84        44.94        44.84        34.06 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0924 TCGA-13-1403 
       29.98        21.17        14.89        13.81         6.08        10.88 
TCGA-13-1404 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1483 TCGA-13-1485 
        6.61         5.33        54.64        87.06        29.42        20.68 
TCGA-13-1492 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 
       73.55        54.31        37.61        38.40        13.97        32.84 
TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2060 TCGA-13-2065 
        4.18         3.91         3.09        12.23         8.61         8.75 
TCGA-13-2071 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0996 TCGA-20-1685 TCGA-20-1687 
        6.28        54.77        23.05        72.20        16.70         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-23-1111 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 
        8.81         3.22        33.30        86.01       129.96         4.27 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2078 
        6.38        39.09        58.13         0.53        24.95        87.48 
TCGA-23-2079 TCGA-23-2081 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 
       91.66        77.00         7.63        11.64        21.80         7.66 
TCGA-24-1103 TCGA-24-1413 TCGA-24-1416 TCGA-24-1419 TCGA-24-1423 TCGA-24-1425 
       54.12         6.31         6.38         7.86         6.25         5.95 
TCGA-24-1427 TCGA-24-1435 TCGA-24-1464 TCGA-24-1467 TCGA-24-1470 TCGA-24-1474 
        4.83        43.53        12.46       105.99         3.45        22.22 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1551 TCGA-24-1555 TCGA-24-1558 TCGA-24-1560 
       57.40        64.27        51.91        88.50        19.53        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1565 TCGA-24-1567 TCGA-24-1604 TCGA-24-1846 
       45.50        47.70        10.26        17.23        88.37         4.37 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1923 TCGA-24-1930 TCGA-24-2023 TCGA-24-2024 
       11.28         5.79        22.68        81.11        44.84        58.16 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2038 TCGA-24-2262 
      109.71        14.43        18.48        28.18        44.52         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 TCGA-24-2289 TCGA-24-2290 TCGA-25-1315 
       47.54        31.63        44.61        67.36        36.23        52.04 
TCGA-25-1317 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1630 TCGA-25-1635 
        2.01        27.62        17.03        12.95        38.20        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-25-2398 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-29-1694 TCGA-29-1696 TCGA-29-1697 
       78.90        47.61        48.33        39.02        33.93        31.20 
TCGA-29-1701 TCGA-29-1705 TCGA-29-1768 TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 
       16.93        18.25        31.30        22.55        12.36        11.84 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1785 TCGA-29-2427 TCGA-29-2431 TCGA-29-2436 
       14.93         8.38        36.30        62.47        42.25         9.76 
TCGA-29-A5NZ TCGA-30-1853 TCGA-30-1857 TCGA-30-1861 TCGA-30-1862 TCGA-30-1880 
       35.77        36.26         0.26        34.78         6.12        57.57 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 
       45.57        30.18        22.49        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-36-2530 TCGA-36-2532 
       30.08        25.74        27.85        24.23        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-36-2547 TCGA-36-2549 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
       20.52         6.05        13.81        47.57        23.74        28.93 
TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 
       10.42        40.77        24.03        21.14         1.74        29.00 
TCGA-57-1994 TCGA-59-2349 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       25.02        80.12         9.40        34.39         2.14         5.42 
TCGA-59-2372 TCGA-59-A5PD TCGA-5X-AA5U TCGA-61-1721 TCGA-61-1722 TCGA-61-1725 
       44.81        20.52        11.87        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-61-2097 TCGA-61-2109 TCGA-61-2613 
        4.80         4.77        61.64        60.62        20.68        31.07 
TCGA-VG-A8LO TCGA-WR-A838 
        0.79         9.99 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.30               0.26 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            180.20             129.96 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            28.670             28.475 
[1] "0.3 - 180.2 (28.7)" "0.3 - 130.0 (28.5)"
[1] "hr=" "1.1"
D68V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  15Q LOSS MUTATED         1   268                2
  15Q LOSS WILD-TYPE       2   290                0
D68V3, multiclass
                  clus
vv                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  OMENTUM                         1                  2
  OVARY                         268                290
  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, continuous
D68V5, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     2 274
  15Q LOSS WILD-TYPE   1 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2  274
  15Q LOSS WILD-TYPE    1  296
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 2                  1
  YES              274                296
[1] 2 2
[1] FALSE
                    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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q LOSS MUTATED                                  2     6
  15Q LOSS WILD-TYPE                                1    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  15Q LOSS MUTATED                          15
  15Q LOSS WILD-TYPE                        19
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  15Q LOSS MUTATED                                           0   237
  15Q LOSS WILD-TYPE                                         1   239
D68V7, multiclass
                                           clus
vv                                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  1
  ASIAN                                                    6                 13
  BLACK OR AFRICAN AMERICAN                               15                 19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                  237                239
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V8, 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   151 172
  16P LOSS WILD-TYPE 117 120
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               323                237 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               172                120 
$`16P LOSS MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1343 
       43.92        41.00         2.01        46.62         1.08        11.87 
TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 
       63.09        21.57        63.98        49.28        44.32        33.67 
TCGA-04-1367 TCGA-04-1516 TCGA-04-1517 TCGA-04-1530 TCGA-04-1638 TCGA-04-1644 
      103.40        41.59        19.99       119.08        55.43        48.89 
TCGA-04-1649 TCGA-04-1652 TCGA-09-0367 TCGA-09-1659 TCGA-09-1665 TCGA-09-1666 
       64.64        31.86        17.98         9.99        41.62        57.60 
TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 TCGA-09-1675 
       61.87        55.36        30.51        17.98         3.02        97.55 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2049 TCGA-09-2053 TCGA-09-2054 TCGA-10-0925 
        6.18         6.12       112.41        39.75        20.94        54.31 
TCGA-10-0926 TCGA-10-0928 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
       25.91        18.51        35.44        19.99        20.91         6.21 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
       24.59        44.55        39.58        15.19        17.82        55.17 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 
       11.18        11.38        11.54        34.06        32.25        31.04 
TCGA-13-0766 TCGA-13-0791 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0801 
       21.40        38.93        28.70        30.35        19.59         8.28 
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        91.40        74.27 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 TCGA-13-0903 
       66.67        70.39        69.01        43.36        56.15        47.38 
TCGA-13-0904 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 
       48.33        44.94        37.08        27.72        34.06        21.17 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 
       14.89        13.81         6.41         6.08        10.88         6.61 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 
        7.36         6.05         5.92         4.70         4.21        87.06 
TCGA-13-1484 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       98.04        70.82        82.88        52.44        73.55        38.20 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1499 TCGA-13-1500 TCGA-13-1505 
       49.25         4.24        54.31        38.40        13.97         4.21 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 
        4.41         4.77         4.18         3.91         3.09        14.24 
TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-20-0990 TCGA-20-1683 TCGA-20-1687 
       10.78         8.75        54.77        25.94        25.38         2.66 
TCGA-23-1022 TCGA-23-1024 TCGA-23-1027 TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 
       49.68        15.39        32.09        49.41        29.13        18.90 
TCGA-23-1032 TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 
        2.76        51.35         3.22        31.20        68.68         4.57 
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-23-2072 TCGA-23-2078 TCGA-23-2645 TCGA-24-0970 TCGA-24-0975 
       33.47        24.95        87.48         4.50        11.64        21.80 
TCGA-24-0979 TCGA-24-1104 TCGA-24-1105 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 
       41.56        63.55        47.41         6.38         7.82         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1426 TCGA-24-1428 TCGA-24-1431 TCGA-24-1436 
        7.86         0.76         5.36        17.39        19.17         8.55 
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-24-1548 TCGA-24-1552 TCGA-24-1555 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 
       16.21        41.39        88.50        19.53        44.09        45.50 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1567 TCGA-24-1603 TCGA-24-1843 TCGA-24-1844 
       47.70        25.87        17.23        90.15         3.48         3.72 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1850 TCGA-24-1923 TCGA-24-1924 TCGA-24-1928 
        4.37        11.28         5.52        22.68        30.21        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-24-2035 TCGA-24-2036 TCGA-24-2260 TCGA-24-2262 
      109.71        14.43        28.18        64.01        36.16         0.36 
TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2290 TCGA-24-2293 
       47.54        70.45        44.61         0.82        36.23        16.64 
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-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 
       42.05         2.01        34.98        65.00        37.97         2.99 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 
       12.99        15.02        17.03        12.95        20.61         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 TCGA-25-1870 TCGA-25-2042 TCGA-25-2391 
       59.15        62.17        52.04        14.96        13.02        49.05 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2400 
        1.02        38.04         3.02        12.00        45.01        42.02 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2409 TCGA-29-1688 TCGA-29-1693 TCGA-29-1697 
        2.96        29.03        26.99        78.90       101.79        31.20 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 TCGA-29-1761 TCGA-29-1762 
       36.36        16.93        59.67        18.25        17.36        86.60 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1775 
       62.93        39.42        22.98        24.36        22.55        12.36 
TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 TCGA-29-1785 TCGA-29-2425 TCGA-29-2428 
       12.30         8.38         7.23        36.30        65.00        45.11 
TCGA-29-2431 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 
       42.25        38.07        51.91        36.26         2.47        15.68 
TCGA-30-1857 TCGA-30-1860 TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-30-1887 
        0.26        44.91        34.78        36.62         1.22        24.26 
TCGA-31-1944 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 
       45.57        18.77        22.49         6.71        42.51         2.20 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 
       28.77        29.10        21.53        22.85         8.55        30.08 
TCGA-36-1577 TCGA-36-1578 TCGA-36-2532 TCGA-36-2534 TCGA-36-2543 TCGA-36-2548 
       25.74        27.85        29.49        29.82         2.24        14.17 
TCGA-36-2551 TCGA-42-2589 TCGA-42-2590 TCGA-42-2593 TCGA-57-1582 TCGA-57-1584 
       16.18        42.02        10.42         1.48        24.03        21.14 
TCGA-57-1992 TCGA-57-1993 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 
       29.00        25.08        22.32       116.12         9.40         2.14 
TCGA-59-2363 TCGA-59-A5PD TCGA-5X-AA5U TCGA-61-1722 TCGA-61-1725 TCGA-61-1730 
        5.42        20.52        11.87         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-61-2003 TCGA-61-2008 TCGA-61-2012 TCGA-61-2088 TCGA-61-2094 
        5.52         4.01        30.64        30.64         4.77        71.74 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2102 TCGA-61-2109 TCGA-61-2113 TCGA-61-2612 
       60.62        65.52         6.48        20.68        22.22         6.35 
TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-VG-A8LO TCGA-WR-A838 
       31.07         8.61        39.68         0.79         9.99 

$`16P LOSS WILD-TYPE`
TCGA-04-1335 TCGA-04-1336 TCGA-04-1342 TCGA-04-1346 TCGA-04-1348 TCGA-04-1351 
        1.81        49.15        18.51        65.52        48.76        65.46 
TCGA-04-1353 TCGA-04-1361 TCGA-04-1365 TCGA-04-1371 TCGA-04-1514 TCGA-04-1519 
        0.53        32.52        76.57        82.39        56.55         0.79 
TCGA-04-1525 TCGA-04-1536 TCGA-04-1542 TCGA-04-1646 TCGA-04-1648 TCGA-04-1651 
       38.37        29.10        84.20        27.88        28.64        36.23 
TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0369 
       47.70        45.37        29.16         9.47        57.76        35.57 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1672 TCGA-09-1674 TCGA-09-2045 
       38.43        89.33        74.93         5.85         8.55        35.15 
TCGA-09-2048 TCGA-09-2050 TCGA-09-2051 TCGA-09-2055 TCGA-09-2056 TCGA-10-0927 
        4.54        71.11        63.09        26.93        12.46        81.86 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0936 TCGA-13-0724 
       34.19        32.88        14.66         6.71        36.92         2.73 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0755 TCGA-13-0768 TCGA-13-0792 TCGA-13-0797 
       12.39        31.20         2.50         8.45        36.72         8.71 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0889 
        7.79         8.12         8.19        43.86        35.28        61.84 
TCGA-13-0890 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 TCGA-13-0905 TCGA-13-0908 
       67.99        57.47        57.07        19.36        47.84        44.84 
TCGA-13-0913 TCGA-13-0921 TCGA-13-1409 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 
       29.98         4.64         6.84         5.33        54.64        61.71 
TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 TCGA-13-1498 TCGA-13-1501 TCGA-13-1504 
       29.42        20.68        22.39        37.61        32.84        16.57 
TCGA-13-1510 TCGA-13-2059 TCGA-13-2060 TCGA-13-2071 TCGA-13-A5FU TCGA-20-0987 
        2.56        12.23         8.61         6.28         8.42        23.05 
TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 
       26.20        72.20        27.52        19.10        16.70         2.93 
TCGA-23-1021 TCGA-23-1023 TCGA-23-1026 TCGA-23-1029 TCGA-23-1110 TCGA-23-1124 
       47.54        40.54        26.83         8.81        54.51        58.13 
TCGA-23-1809 TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
        0.53       115.89        91.66        77.00        49.84         2.76 
TCGA-23-2643 TCGA-24-0966 TCGA-24-0968 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 
        4.70         7.63        19.66         7.66        22.32        54.12 
TCGA-24-1413 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1427 TCGA-24-1430 
        6.31         6.25         6.02         5.95         4.83        28.37 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1464 TCGA-24-1467 TCGA-24-1470 TCGA-24-1544 
       18.67        43.53        12.46       105.99         3.45        26.96 
TCGA-24-1546 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1553 TCGA-24-1556 
       64.27        56.58        41.06        51.91        58.09        70.62 
TCGA-24-1557 TCGA-24-1565 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 
       39.88        10.26        88.37        48.33        38.24         8.32 
TCGA-24-1845 TCGA-24-1849 TCGA-24-1920 TCGA-24-1927 TCGA-24-2030 TCGA-24-2033 
        3.81         5.79         9.80        16.44        55.92        18.48 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2261 TCGA-24-2271 TCGA-24-2289 TCGA-25-1312 
       44.52        57.07         0.79        31.63        67.36         1.02 
TCGA-25-1321 TCGA-25-1623 TCGA-25-1625 TCGA-25-1630 TCGA-25-1634 TCGA-25-1871 
       33.96        18.58        27.62        38.20        35.87        24.99 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2399 TCGA-25-2408 TCGA-29-1690 TCGA-29-1691 
       24.00        85.05        19.99        31.00        47.61        48.33 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1698 TCGA-29-1702 TCGA-29-1707 
       39.02        40.41        33.93        68.32        23.93        41.98 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1763 TCGA-29-1768 TCGA-29-1774 TCGA-29-1776 
       31.27        34.62        66.81        31.30        17.33        11.84 
TCGA-29-1778 TCGA-29-1784 TCGA-29-2414 TCGA-29-2427 TCGA-29-2429 TCGA-29-2432 
       14.93         5.36        86.17        62.47        13.84        21.47 
TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1859 TCGA-30-1862 TCGA-30-1880 
       11.47         9.76        35.77        48.10         6.12        57.57 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1946 TCGA-31-1956 TCGA-36-1574 TCGA-36-1580 
       30.05        48.79        30.18        44.12        22.55        24.23 
TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       24.69        35.05        33.01        25.91        25.08        23.80 
TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 TCGA-36-2552 
       21.60        20.98        18.31        20.52         6.05        11.47 
TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2591 TCGA-57-1583 
       13.81        47.57        23.74        28.93        40.77        11.38 
TCGA-57-1585 TCGA-57-1586 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2354 
        1.74        22.32        25.02       180.20        80.12        34.39 
TCGA-59-2372 TCGA-61-1721 TCGA-61-1724 TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 
       44.81        11.11        20.94        18.54        27.88        31.79 
TCGA-61-1734 TCGA-61-1738 TCGA-61-1740 TCGA-61-1743 TCGA-61-1900 TCGA-61-1901 
       28.47        35.80         2.43        43.69         5.79        11.41 
TCGA-61-1903 TCGA-61-1911 TCGA-61-1913 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 
       13.02        42.51        48.92        67.76        43.43        15.75 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
       14.50        17.98        39.85         1.18        45.96        45.40 
TCGA-61-2087 TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 TCGA-61-2101 TCGA-61-2104 
        4.80        51.72        61.64        58.39        55.50        76.87 
TCGA-61-2110 TCGA-61-2111 TCGA-OY-A56Q 
       44.52       125.75        18.94 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.26               0.53 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            152.02             180.20 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             27.72              29.16 
[1] "0.3 - 152.0 (27.7)" "0.5 - 180.2 (29.2)"
[1] "hr=" "1.1"
D69V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  16P LOSS MUTATED         2   321                1
  16P LOSS WILD-TYPE       1   237                1
D69V3, multiclass
                  clus
vv                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  OMENTUM                         2                  1
  OVARY                         321                237
  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, continuous
D69V5, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     3 328
  16P LOSS WILD-TYPE   0 242
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3  328
  16P LOSS WILD-TYPE    0  242
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 3                  0
  YES              328                242
[1] 2 2
[1] FALSE
                    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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P LOSS MUTATED                                  3    10
  16P LOSS WILD-TYPE                                0     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  16P LOSS MUTATED                          17
  16P LOSS WILD-TYPE                        17
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16P LOSS MUTATED                                           1   279
  16P LOSS WILD-TYPE                                         0   197
D69V7, multiclass
                                           clus
vv                                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         3                  0
  ASIAN                                                   10                  9
  BLACK OR AFRICAN AMERICAN                               17                 17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  279                197
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V8, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     3 196
  16P LOSS WILD-TYPE   7 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3  196
  16P LOSS WILD-TYPE    7  131
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  7
  NOT HISPANIC OR LATINO              196                131
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED   184 215
  16Q LOSS WILD-TYPE  84  77
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               399                161 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               215                 77 
$`16Q LOSS MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 
       43.92        41.00        49.15         2.01        46.62         1.08 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 
       18.51        11.87        65.52        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-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1638 TCGA-04-1644 
       41.59        19.99        38.37       119.08        55.43        48.89 
TCGA-04-1649 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0366 TCGA-09-0367 
       64.64        31.86        47.70        45.37        57.76        17.98 
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-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0935 
       54.31        25.91        81.86        18.51        32.88        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-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
       39.58         2.73        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        34.06        32.25 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 
       31.04        21.40        38.93        28.70        30.35        19.59 
TCGA-13-0797 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
        8.71         8.28         8.19        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        91.40        74.27        66.67        70.39 
TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 TCGA-13-0903 TCGA-13-0906 
       61.84        69.01        43.36        56.15        47.38        44.94 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 TCGA-13-0919 
       44.84        37.08        27.72        34.06        21.17        14.89 
TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
       13.81         6.41         6.08        10.88         6.61         7.36 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 TCGA-13-1483 
        6.05         5.92         4.70         4.21        87.06        29.42 
TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
       98.04        22.39        70.82        82.88        52.44        73.55 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 
       38.20        49.25         4.24        54.31        37.61        38.40 
TCGA-13-1500 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 
       13.97         4.21         4.41         4.77         4.18         3.91 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT 
        3.09        14.24         8.61        10.78         8.75        54.77 
TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 
        8.42        23.05        25.94        26.20        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-23-1027 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         4.57        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-23-2072 TCGA-23-2078 TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 
       24.95        87.48        77.00         2.76         4.70         4.50 
TCGA-24-0966 TCGA-24-0970 TCGA-24-0979 TCGA-24-0982 TCGA-24-1104 TCGA-24-1105 
        7.63        11.64        41.56        22.32        63.55        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-24-1425 TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 
        5.95         5.36        17.39        28.37        19.17        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 TCGA-24-1469 TCGA-24-1471 
       43.53         8.55        72.92        45.14         9.11         1.18 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 TCGA-24-1550 TCGA-24-1551 
       22.22        26.96        57.40        16.21        41.06        51.91 
TCGA-24-1552 TCGA-24-1555 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       41.39        88.50        19.53        44.09        45.50        47.70 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1842 TCGA-24-1843 
       25.87        10.26        17.23        90.15         8.32         3.48 
TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 TCGA-24-1850 TCGA-24-1923 TCGA-24-1924 
        3.72         4.37        11.28         5.52        22.68        30.21 
TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 
       16.44        11.05        81.11         4.87       152.02        44.84 
TCGA-24-2024 TCGA-24-2026 TCGA-24-2029 TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 
       58.16        34.82        14.43        55.92        28.18        64.01 
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-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 
       44.61         0.82        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-25-1322 TCGA-25-1323 TCGA-25-1329 
       34.98        65.00        37.97         2.99        12.99        15.02 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
       17.03        12.95        20.61         0.30        59.15        62.17 
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-29-1691 
       19.99        42.02         2.96        29.03        26.99        48.33 
TCGA-29-1693 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 
      101.79        33.93        31.20        68.32        36.36        16.93 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 
       23.93        59.67        18.25        17.36        86.60        62.93 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1775 
       39.42        31.30        22.98        24.36        22.55        12.36 
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-29-2425 TCGA-29-2428 TCGA-29-2431 TCGA-29-2432 TCGA-29-A5NZ TCGA-30-1714 
       65.00        45.11        42.25        21.47        35.77        38.07 
TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1860 
       51.91        36.26         2.47        15.68         0.26        44.91 
TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 
       34.78        36.62         1.22        24.26        48.79        45.57 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 
       18.77        22.49         6.71         2.20        28.77        29.10 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 
       21.53        22.85         8.55        30.08        25.74        27.85 
TCGA-36-1580 TCGA-36-2529 TCGA-36-2532 TCGA-36-2534 TCGA-36-2542 TCGA-36-2543 
       24.23        35.05        29.49        29.82        21.60         2.24 
TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2589 TCGA-42-2590 TCGA-42-2593 
       14.17        16.18        11.47        42.02        10.42         1.48 
TCGA-57-1582 TCGA-57-1584 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2350 
       24.03        21.14        29.00        25.08        25.02        22.32 
TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 TCGA-59-A5PD TCGA-5X-AA5U TCGA-61-1722 
        9.40         2.14         5.42        20.52        11.87         8.09 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 TCGA-61-1737 
       31.43        18.54         4.34        31.79        48.79        44.84 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1904 
       33.67        43.69         1.45         8.42         5.79         9.07 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 TCGA-61-1919 
       34.13        31.30        37.05        48.92        56.61        38.17 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 TCGA-61-2087 
        2.01         5.52         4.01        30.64        30.64         4.80 
TCGA-61-2088 TCGA-61-2094 TCGA-61-2097 TCGA-61-2098 TCGA-61-2102 TCGA-61-2104 
        4.77        71.74        60.62        65.52         6.48        76.87 
TCGA-61-2109 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       20.68       125.75        22.22         6.35        31.07         8.61 
TCGA-OY-A56P TCGA-VG-A8LO TCGA-WR-A838 
       39.68         0.79         9.99 

$`16Q LOSS WILD-TYPE`
TCGA-04-1335 TCGA-04-1348 TCGA-04-1351 TCGA-04-1353 TCGA-04-1361 TCGA-04-1514 
        1.81        48.76        65.46         0.53        32.52        56.55 
TCGA-04-1519 TCGA-04-1536 TCGA-04-1542 TCGA-04-1646 TCGA-04-1648 TCGA-04-1651 
        0.79        29.10        84.20        27.88        28.64        36.23 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0369 TCGA-09-1664 TCGA-09-1672 TCGA-09-1673 
       29.16         9.47        35.57        74.93         5.85         3.02 
TCGA-09-2045 TCGA-09-2050 TCGA-09-2055 TCGA-09-2056 TCGA-10-0930 TCGA-10-0933 
       35.15        71.11        26.93        12.46        34.19        14.66 
TCGA-10-0934 TCGA-13-0725 TCGA-13-0768 TCGA-13-0792 TCGA-13-0799 TCGA-13-0800 
        6.71        12.39         8.45        36.72         7.79         8.12 
TCGA-13-0803 TCGA-13-0890 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 TCGA-13-0904 
       43.86        67.99        57.47        57.07        19.36        48.33 
TCGA-13-0905 TCGA-13-0913 TCGA-13-0921 TCGA-13-1409 TCGA-13-1412 TCGA-13-1477 
       47.84        29.98         4.64         6.84         5.33        54.64 
TCGA-13-1482 TCGA-13-1485 TCGA-13-1501 TCGA-13-1504 TCGA-13-1510 TCGA-13-2059 
       61.71        20.68        32.84        16.57         2.56        12.23 
TCGA-13-2071 TCGA-20-0996 TCGA-20-1684 TCGA-23-1021 TCGA-23-1026 TCGA-23-1110 
        6.28        72.20        19.10        47.54        26.83        54.51 
TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2079 TCGA-23-2084 TCGA-24-0968 
       58.13         0.53       115.89        91.66        49.84        19.66 
TCGA-24-0975 TCGA-24-0980 TCGA-24-1103 TCGA-24-1423 TCGA-24-1424 TCGA-24-1427 
       21.80         7.66        54.12         6.25         6.02         4.83 
TCGA-24-1464 TCGA-24-1467 TCGA-24-1470 TCGA-24-1546 TCGA-24-1549 TCGA-24-1553 
       12.46       105.99         3.45        64.27        56.58        58.09 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1845 
       70.62        39.88        88.37        48.33        38.24         3.81 
TCGA-24-1849 TCGA-24-1920 TCGA-24-2027 TCGA-24-2033 TCGA-24-2038 TCGA-24-2254 
        5.79         9.80       109.71        18.48        44.52        57.07 
TCGA-24-2289 TCGA-24-2290 TCGA-25-1321 TCGA-25-1623 TCGA-25-1625 TCGA-25-1630 
       67.36        36.23        33.96        18.58        27.62        38.20 
TCGA-25-1634 TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 TCGA-29-1694 TCGA-29-1695 
       35.87        31.00        78.90        47.61        39.02        40.41 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1763 TCGA-29-1774 TCGA-29-1776 
       41.98        31.27        34.62        66.81        17.33        11.84 
TCGA-29-1778 TCGA-29-2427 TCGA-29-2429 TCGA-29-2434 TCGA-29-2436 TCGA-30-1859 
       14.93        62.47        13.84        11.47         9.76        48.10 
TCGA-30-1862 TCGA-30-1880 TCGA-30-1891 TCGA-31-1946 TCGA-31-1955 TCGA-31-1956 
        6.12        57.57        30.05        30.18        42.51        44.12 
TCGA-36-1574 TCGA-36-1581 TCGA-36-2530 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       22.55        24.69        33.01        25.91        25.08        23.80 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 TCGA-3P-A9WA TCGA-42-2582 
       20.98        18.31        20.52         6.05        13.81        47.57 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2591 TCGA-57-1583 TCGA-57-1585 TCGA-57-1586 
       23.74        28.93        40.77        11.38         1.74        22.32 
TCGA-59-2348 TCGA-59-2349 TCGA-59-2351 TCGA-59-2354 TCGA-59-2372 TCGA-61-1721 
      180.20        80.12       116.12        34.39        44.81        11.11 
TCGA-61-1724 TCGA-61-1728 TCGA-61-1734 TCGA-61-1738 TCGA-61-1740 TCGA-61-1901 
       20.94        27.88        28.47        35.80         2.43        11.41 
TCGA-61-1903 TCGA-61-1911 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-2000 
       13.02        42.51        67.76        43.43        15.75        14.50 
TCGA-61-2002 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2092 
       17.98        39.85         1.18        45.96        45.40        51.72 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2101 TCGA-61-2110 TCGA-OY-A56Q 
       61.64        58.39        55.50        44.52        18.94 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.26               0.53 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            152.02             180.20 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             26.99              30.18 
[1] "0.3 - 152.0 (27.0)" "0.5 - 180.2 (30.2)"
[1] "hr=" "1.3"
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, continuous
D70V5, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     3 406
  16Q LOSS WILD-TYPE   0 164
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3  406
  16Q LOSS WILD-TYPE    0  164
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 3                  0
  YES              406                164
[1] 2 2
[1] FALSE
                    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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q LOSS MUTATED                                  3    13
  16Q LOSS WILD-TYPE                                0     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  16Q LOSS MUTATED                          24
  16Q LOSS WILD-TYPE                        10
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16Q LOSS MUTATED                                           1   341
  16Q LOSS WILD-TYPE                                         0   135
D70V7, multiclass
                                           clus
vv                                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         3                  0
  ASIAN                                                   13                  6
  BLACK OR AFRICAN AMERICAN                               24                 10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  341                135
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V8, 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   217 246
  17P LOSS WILD-TYPE  51  46
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               463                 97 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               246                 46 
$`17P LOSS MUTATED`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1343 TCGA-04-1347 
       43.92         1.81        49.15        46.62        11.87        63.09 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1361 
       48.76        21.57        63.98        65.46         0.53        32.52 
TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 
       44.32        33.67        76.57       103.40        82.39        56.55 
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-09-0364 TCGA-09-0365 TCGA-09-0366 
       31.86        47.70        45.37        29.16         9.47        57.76 
TCGA-09-0367 TCGA-09-1659 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 
       17.98         9.99        89.33        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-10-0926 TCGA-10-0927 TCGA-10-0930 TCGA-10-0933 TCGA-10-0936 
       26.93        25.91        81.86        34.19        14.66        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-13-0755 
        2.73        12.39        31.20        15.19        17.82         2.50 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0766 TCGA-13-0768 
       11.18        11.38        11.54        34.06        21.40         8.45 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 
       38.93        36.72        28.70        30.35        19.59         8.71 
TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 
        7.79         8.28         8.19        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        91.40        74.27        66.67 
TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0900 
       70.39        61.84        67.99        69.01        43.36        57.07 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0908 TCGA-13-0910 
       19.36        47.38        48.33        47.84        44.84        37.08 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 
       27.72        34.06        21.17        14.89         4.64         6.41 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 
        6.08        10.88         6.61         7.36         6.05         5.92 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
        6.84         4.70         4.21        87.06        61.71        29.42 
TCGA-13-1484 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       98.04        70.82        82.88        52.44        73.55        38.20 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 
       49.25         4.24        54.31        37.61        38.40        13.97 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 
       32.84        16.57         4.21         4.41         4.18         2.56 
TCGA-13-1511 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU 
        3.91        10.78         8.75         6.28        54.77         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-23-1023 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-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 
       51.35        54.51         3.22        31.20         4.57        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-23-2081 TCGA-23-2084 
       58.13        24.95       115.89        87.48        77.00        49.84 
TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 
        2.76         4.70         4.50         7.63        19.66        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-24-1422 
       47.41         6.31         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        19.17        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-24-1544 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-24-1555 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 
       51.91        41.39        88.50        39.88        19.53        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 
       45.50        47.70        25.87        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-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1927 
       11.28         5.79         5.52         9.80        22.68        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-24-2036 
       34.82       109.71        14.43        55.92        18.48        64.01 
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-25-1313 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-25-1322 TCGA-25-1323 TCGA-25-1329 
       65.00        37.97        33.96         2.99        12.99        15.02 
TCGA-25-1625 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 
       27.62        12.95        20.61        38.20         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-25-2042 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-25-2409 TCGA-29-1688 
       19.99        42.02         2.96        29.03        26.99        78.90 
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-29-1768 TCGA-29-1769 
       34.62        17.36        86.60        62.93        31.30        22.98 
TCGA-29-1770 TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 
       24.36        22.55        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-30-1714 TCGA-30-1718 
       62.47        45.11        42.25        21.47        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-36-1570 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-36-2529 TCGA-36-2530 TCGA-36-2532 
       22.55         8.55        30.08        35.05        33.01        29.49 
TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 
       29.82        25.91        25.08         2.24        20.98        18.31 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2582 
       20.52        14.17         6.05        16.18        13.81        47.57 
TCGA-42-2587 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 
       23.74        42.02        10.42        40.77         1.48        24.03 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 
       11.38        21.14         1.74        25.08       180.20        22.32 
TCGA-59-2351 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD 
      116.12        34.39         2.14         5.42        44.81        20.52 
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 
        9.99 

$`17P LOSS WILD-TYPE`
TCGA-04-1332 TCGA-04-1337 TCGA-04-1341 TCGA-04-1342 TCGA-04-1346 TCGA-04-1356 
       41.00         2.01         1.08        18.51        65.52        49.28 
TCGA-04-1516 TCGA-09-0369 TCGA-09-1661 TCGA-09-1665 TCGA-09-1674 TCGA-09-2043 
       41.59        35.57        38.43        41.62         8.55         6.18 
TCGA-09-2048 TCGA-09-2051 TCGA-09-2056 TCGA-10-0925 TCGA-10-0928 TCGA-10-0931 
        4.54        63.09        12.46        54.31        18.51        32.88 
TCGA-10-0934 TCGA-10-0935 TCGA-13-0751 TCGA-13-0762 TCGA-13-0764 TCGA-13-0800 
        6.71        35.44        55.17        32.25        31.04         8.12 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0906 TCGA-13-0913 TCGA-13-0920 TCGA-13-1412 
       57.47        56.15        44.94        29.98        13.81         5.33 
TCGA-13-1477 TCGA-13-1485 TCGA-13-1487 TCGA-13-1507 TCGA-13-1512 TCGA-13-2057 
       54.64        20.68        22.39         4.77         3.09        14.24 
TCGA-13-2059 TCGA-13-2060 TCGA-20-0996 TCGA-20-1683 TCGA-23-1022 TCGA-23-1114 
       12.23         8.61        72.20        25.38        49.68        68.68 
TCGA-23-1809 TCGA-23-2079 TCGA-24-1419 TCGA-24-1474 TCGA-24-1553 TCGA-24-1556 
        0.53        91.66         7.86        22.22        58.09        70.62 
TCGA-24-1565 TCGA-24-1845 TCGA-24-1924 TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 
       10.26         3.81        30.21        28.18        44.52        57.07 
TCGA-24-2260 TCGA-24-2262 TCGA-24-2289 TCGA-25-1623 TCGA-25-1626 TCGA-25-1878 
       36.16         0.36        67.36        18.58        17.03        85.05 
TCGA-25-2397 TCGA-25-2408 TCGA-29-1690 TCGA-29-1702 TCGA-29-1710 TCGA-29-1763 
       12.00        31.00        47.61        23.93        31.27        66.81 
TCGA-29-1766 TCGA-29-1774 TCGA-29-2429 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ 
       39.42        17.33        13.84        11.47         9.76        35.77 
TCGA-30-1862 TCGA-36-1569 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 
        6.12        29.10        25.74        27.85        24.23        24.69 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2552 TCGA-42-2588 TCGA-57-1586 TCGA-57-1992 
       23.80        21.60        11.47        28.93        22.32        29.00 
TCGA-57-1994 TCGA-59-2349 TCGA-59-2352 TCGA-5X-AA5U TCGA-61-1721 TCGA-61-1722 
       25.02        80.12         9.40        11.87        11.11         8.09 
TCGA-61-1900 TCGA-61-1904 TCGA-61-1911 TCGA-61-2009 TCGA-61-2017 TCGA-61-2018 
        5.79         9.07        42.51        39.85        45.96        45.40 
TCGA-61-2092 
       51.72 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.26               0.36 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            180.20              91.66 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             29.03              25.74 
[1] "0.3 - 180.2 (29.0)" "0.4 - 91.7 (25.7)" 
[1] "hr=" "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, continuous
D71V5, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     2 472
  17P LOSS WILD-TYPE   1  98
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      2  472
  17P LOSS WILD-TYPE    1   98
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 2                  1
  YES              472                 98
[1] 2 2
[1] FALSE
                    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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P LOSS MUTATED                                  3    16
  17P LOSS WILD-TYPE                                0     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  17P LOSS MUTATED                          29
  17P LOSS WILD-TYPE                         5
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17P LOSS MUTATED                                           1   391
  17P LOSS WILD-TYPE                                         0    85
D71V7, multiclass
                                           clus
vv                                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         3                  0
  ASIAN                                                   16                  3
  BLACK OR AFRICAN AMERICAN                               29                  5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  391                 85
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V8, 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   176 193
  17Q LOSS WILD-TYPE  92  99
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               369                191 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               193                 99 
$`17Q LOSS MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1338 TCGA-04-1343 TCGA-04-1347 TCGA-04-1348 
       43.92        41.00        46.62        11.87        63.09        48.76 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1361 TCGA-04-1364 
       21.57        63.98        65.46         0.53        32.52        33.67 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1517 TCGA-04-1519 TCGA-04-1536 
       76.57       103.40        82.39        19.99         0.79        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-09-0364 TCGA-09-0365 
       36.23        31.86        47.70        45.37        29.16         9.47 
TCGA-09-0366 TCGA-09-0367 TCGA-09-1659 TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 
       57.76        17.98         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-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0938 
       26.93        25.91        81.86        18.51        34.19        20.91 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0758 
        6.21        24.59        44.55        39.58         2.73        11.38 
TCGA-13-0762 TCGA-13-0766 TCGA-13-0791 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 
       32.25        21.40        38.93        28.70        19.59         8.71 
TCGA-13-0799 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0883 
        7.79         8.28        43.86        35.28        35.31        68.94 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0890 TCGA-13-0891 
      107.18        91.40        74.27        66.67        67.99        69.01 
TCGA-13-0893 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0908 
       43.36        19.36        47.38        48.33        47.84        44.84 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0924 
       37.08        27.72        21.17        14.89         4.64         6.08 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 
       10.88         6.61         7.36         6.05         6.84         4.70 
TCGA-13-1411 TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 TCGA-13-1488 TCGA-13-1491 
        4.21        87.06        61.71        98.04        70.82        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1497 TCGA-13-1499 TCGA-13-1500 
       73.55        38.20        49.25        54.31        38.40        13.97 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 
       32.84        16.57         4.21         4.41         4.18         2.56 
TCGA-13-1511 TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FU 
        3.91        12.23        10.78         8.75         6.28         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-24-0968 
       77.00        49.84         2.76         4.70         4.50        19.66 
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-24-1422 TCGA-24-1423 TCGA-24-1424 
        6.31         6.38         7.99         0.76         6.25         6.02 
TCGA-24-1425 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 
        5.95         4.83        17.39        28.37        19.17        18.67 
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-24-1544 TCGA-24-1545 TCGA-24-1548 TCGA-24-1550 TCGA-24-1551 
        1.18        26.96        57.40        16.21        41.06        51.91 
TCGA-24-1555 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       88.50        39.88        19.53        44.09        45.50        47.70 
TCGA-24-1564 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 
       25.87        90.15        88.37        48.33        38.24         8.32 
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-31-1950 TCGA-31-1953 TCGA-31-1955 
       57.57        24.26        30.05        18.77         6.71        42.51 
TCGA-31-1956 TCGA-36-1568 TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 
       44.12        28.77        22.85         8.55        30.08        25.74 
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-36-2543 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-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
       13.81        47.57        23.74        42.02        10.42        40.77 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1993 TCGA-59-2348 TCGA-59-2351 
       24.03        11.38        21.14        25.08       180.20       116.12 
TCGA-59-2355 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
        2.14        44.81        20.52        20.94        31.43        18.54 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1740 TCGA-61-1741 
       27.88         4.34        31.79        28.47         2.43        33.67 
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-61-1915 TCGA-61-1917 TCGA-61-1918 
       34.13        31.30        37.05        67.76        43.43        15.75 
TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2003 TCGA-61-2012 TCGA-61-2016 
       38.17         2.01         5.52         4.01        30.64         1.18 
TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2094 TCGA-61-2097 TCGA-61-2101 
       45.40         4.80         4.77        71.74        60.62        55.50 
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-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       18.94         0.79         9.99 

$`17Q LOSS WILD-TYPE`
TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1341 TCGA-04-1342 TCGA-04-1346 
        1.81        49.15         2.01         1.08        18.51        65.52 
TCGA-04-1356 TCGA-04-1362 TCGA-04-1514 TCGA-04-1516 TCGA-04-1525 TCGA-04-1530 
       49.28        44.32        56.55        41.59        38.37       119.08 
TCGA-09-0369 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1674 TCGA-09-2043 
       35.57        38.43        89.33        41.62         8.55         6.18 
TCGA-09-2048 TCGA-09-2051 TCGA-09-2056 TCGA-10-0925 TCGA-10-0931 TCGA-10-0933 
        4.54        63.09        12.46        54.31        32.88        14.66 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-13-0725 TCGA-13-0726 
        6.71        35.44        36.92        19.99        12.39        31.20 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0760 
       15.19        17.82        55.17         2.50        11.18        11.54 
TCGA-13-0761 TCGA-13-0764 TCGA-13-0768 TCGA-13-0792 TCGA-13-0794 TCGA-13-0800 
       34.06        31.04         8.45        36.72        30.35         8.12 
TCGA-13-0802 TCGA-13-0807 TCGA-13-0888 TCGA-13-0889 TCGA-13-0897 TCGA-13-0899 
        8.19        13.61        70.39        61.84        57.47        56.15 
TCGA-13-0900 TCGA-13-0906 TCGA-13-0912 TCGA-13-0913 TCGA-13-0920 TCGA-13-0923 
       57.07        44.94        34.06        29.98        13.81         6.41 
TCGA-13-1408 TCGA-13-1412 TCGA-13-1477 TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 
        5.92         5.33        54.64        29.42        20.68        22.39 
TCGA-13-1489 TCGA-13-1496 TCGA-13-1498 TCGA-13-1507 TCGA-13-1512 TCGA-13-2057 
       82.88         4.24        37.61         4.77         3.09        14.24 
TCGA-13-2060 TCGA-13-A5FT TCGA-20-0996 TCGA-20-1683 TCGA-23-1022 TCGA-23-1023 
        8.61        54.77        72.20        25.38        49.68        40.54 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1109 TCGA-23-1110 TCGA-23-1114 TCGA-23-1116 
       32.09        49.41        51.35        54.51        68.68         4.57 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 TCGA-23-1809 TCGA-23-2078 TCGA-23-2079 
       33.30        86.01         4.27         0.53        87.48        91.66 
TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-1417 TCGA-24-1419 TCGA-24-1426 
        7.63        11.64        21.80         7.82         7.86         5.36 
TCGA-24-1435 TCGA-24-1464 TCGA-24-1474 TCGA-24-1546 TCGA-24-1549 TCGA-24-1552 
       43.53        12.46        22.22        64.27        56.58        41.39 
TCGA-24-1553 TCGA-24-1556 TCGA-24-1565 TCGA-24-1567 TCGA-24-1843 TCGA-24-1844 
       58.09        70.62        10.26        17.23         3.48         3.72 
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-31-1944 
        9.76        35.77         6.12         1.22        48.79        45.57 
TCGA-31-1946 TCGA-31-1951 TCGA-31-1959 TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 
       30.18        22.49         2.20        29.10        21.53        22.55 
TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2540 TCGA-36-2542 TCGA-36-2547 
       27.85        24.23        24.69        23.80        21.60        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-5X-AA5U TCGA-61-1721 TCGA-61-1722 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
       11.87        11.11         8.09        48.79        44.84        35.80 
TCGA-61-1900 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-2000 TCGA-61-2002 
        5.79        42.51        48.92        56.61        14.50        17.98 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2017 TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 
       30.64        39.85        45.96        51.72        61.64        58.39 
TCGA-61-2098 TCGA-61-2102 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P 
       65.52         6.48         6.35         8.61        39.68 

  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 
             28.47              29.00 
[1] "0.3 - 180.2 (28.5)" "0.4 - 152.0 (29.0)"
[1] "hr=" "1"  
D72V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  17Q LOSS MUTATED         2   369                1
  17Q LOSS WILD-TYPE       1   189                1
D72V3, multiclass
                  clus
vv                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  OMENTUM                         2                  1
  OVARY                         369                189
  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, continuous
D72V5, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     3 377
  17Q LOSS WILD-TYPE   0 193
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      3  377
  17Q LOSS WILD-TYPE    0  193
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 3                  0
  YES              377                193
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  17Q LOSS MUTATED    8 19  2  2
  17Q LOSS WILD-TYPE  7  7  3  1
D72V6, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0                8                  7
  R1               19                  7
  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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q LOSS MUTATED                                  1    12
  17Q LOSS WILD-TYPE                                2     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  17Q LOSS MUTATED                          22
  17Q LOSS WILD-TYPE                        12
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17Q LOSS MUTATED                                           1   315
  17Q LOSS WILD-TYPE                                         0   161
D72V7, multiclass
                                           clus
vv                                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  2
  ASIAN                                                   12                  7
  BLACK OR AFRICAN AMERICAN                               22                 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  315                161
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     4 218
  17Q LOSS WILD-TYPE   6 109
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      4  218
  17Q LOSS WILD-TYPE    6  109
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  6
  NOT HISPANIC OR LATINO              218                109
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    98 130
  18P LOSS WILD-TYPE 170 162
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               228                332 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               130                162 
$`18P LOSS MUTATED`
TCGA-04-1338 TCGA-04-1341 TCGA-04-1350 TCGA-04-1351 TCGA-04-1362 TCGA-04-1364 
       46.62         1.08        63.98        65.46        44.32        33.67 
TCGA-04-1514 TCGA-04-1517 TCGA-04-1519 TCGA-04-1530 TCGA-04-1649 TCGA-04-1651 
       56.55        19.99         0.79       119.08        64.64        36.23 
TCGA-04-1655 TCGA-09-0367 TCGA-09-1666 TCGA-09-1667 TCGA-09-1672 TCGA-09-1673 
       45.37        17.98        57.60        61.87         5.85         3.02 
TCGA-09-2044 TCGA-09-2053 TCGA-09-2054 TCGA-10-0926 TCGA-10-0927 TCGA-10-0931 
        6.12        39.75        20.94        25.91        81.86        32.88 
TCGA-13-0714 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 
        6.21        44.55        39.58         2.73        12.39        31.20 
TCGA-13-0727 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 
       15.19        55.17         2.50        11.18        11.38        11.54 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0800 
       31.04        21.40        36.72        28.70        30.35         8.12 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0891 
       43.86        35.28        13.61        68.94       107.18        69.01 
TCGA-13-0903 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0924 TCGA-13-1403 
       47.38        37.08        27.72        34.06         6.08        10.88 
TCGA-13-1405 TCGA-13-1409 TCGA-13-1411 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 
        7.36         6.84         4.21        29.42        98.04        22.39 
TCGA-13-1488 TCGA-13-1495 TCGA-13-1498 TCGA-13-1506 TCGA-13-2061 TCGA-13-2065 
       70.82        49.25        37.61         4.41        10.78         8.75 
TCGA-13-2071 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 
        6.28        25.94        26.20        27.52        25.38        19.10 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1027 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 
        2.66        47.54        32.09         3.22        31.20         4.57 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1122 TCGA-23-2072 TCGA-23-2079 TCGA-23-2084 
       33.30        86.01        39.09        24.95        91.66        49.84 
TCGA-23-2641 TCGA-23-2643 TCGA-24-0966 TCGA-24-0970 TCGA-24-0979 TCGA-24-0982 
        2.76         4.70         7.63        11.64        41.56        22.32 
TCGA-24-1104 TCGA-24-1413 TCGA-24-1416 TCGA-24-1423 TCGA-24-1425 TCGA-24-1427 
       63.55         6.31         6.38         6.25         5.95         4.83 
TCGA-24-1431 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1470 TCGA-24-1471 
       19.17         8.55        72.92        12.46         3.45         1.18 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1551 TCGA-24-1556 
       26.96        57.40        64.27        16.21        51.91        70.62 
TCGA-24-1557 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1603 
       39.88        44.09        45.50        47.70        25.87        90.15 
TCGA-24-1614 TCGA-24-1842 TCGA-24-1843 TCGA-24-1847 TCGA-24-1849 TCGA-24-1920 
       48.33         8.32         3.48        11.28         5.79         9.80 
TCGA-24-1923 TCGA-24-1927 TCGA-24-1928 TCGA-24-2023 TCGA-24-2027 TCGA-24-2260 
       22.68        16.44        11.05        44.84       109.71        36.16 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2288 TCGA-24-2293 TCGA-24-2298 
       47.54        31.63        70.45         0.82        16.64        53.26 
TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1320 TCGA-25-1322 
       26.96        52.04        42.05         2.01        37.97         2.99 
TCGA-25-1329 TCGA-25-1626 TCGA-25-1627 TCGA-25-1630 TCGA-25-1632 TCGA-25-1634 
       15.02        17.03        12.95        38.20        59.15        35.87 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2392 TCGA-25-2393 TCGA-25-2398 
       24.00        85.05        13.02         1.02        38.04        45.01 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2409 TCGA-29-1691 TCGA-29-1694 TCGA-29-1697 
        2.96        29.03        26.99        48.33        39.02        31.20 
TCGA-29-1701 TCGA-29-1703 TCGA-29-1707 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 
       16.93        59.67        41.98        86.60        66.81        62.93 
TCGA-29-1768 TCGA-29-1770 TCGA-29-1775 TCGA-29-1777 TCGA-29-1783 TCGA-29-2414 
       31.30        24.36        12.36        12.30         7.23        86.17 
TCGA-29-2427 TCGA-29-2428 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 
       62.47        45.11        35.77        38.07        51.91         2.47 
TCGA-30-1856 TCGA-30-1860 TCGA-30-1861 TCGA-30-1880 TCGA-30-1891 TCGA-30-1892 
       15.68        44.91        34.78        57.57        30.05        48.79 
TCGA-31-1946 TCGA-36-1568 TCGA-36-1569 TCGA-36-1571 TCGA-36-1575 TCGA-36-1577 
       30.18        28.77        29.10        22.85         8.55        25.74 
TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2542 TCGA-36-2543 
       24.23        33.01        29.49        29.82        21.60         2.24 
TCGA-36-2545 TCGA-36-2548 TCGA-36-2552 TCGA-42-2587 TCGA-42-2591 TCGA-42-2593 
       18.31        14.17        11.47        23.74        40.77         1.48 
TCGA-57-1582 TCGA-57-1585 TCGA-57-1993 TCGA-59-2350 TCGA-59-2351 TCGA-59-2354 
       24.03         1.74        25.08        22.32       116.12        34.39 
TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1727 TCGA-61-1741 TCGA-61-1743 
        5.42        44.81        20.52        18.54        33.67        43.69 
TCGA-61-1895 TCGA-61-1904 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2002 
        1.45         9.07        38.17         2.01         5.52        17.98 
TCGA-61-2009 TCGA-61-2012 TCGA-61-2088 TCGA-61-2094 TCGA-61-2098 TCGA-61-2101 
       39.85        30.64         4.77        71.74        65.52        55.50 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2612 TCGA-61-2613 
        6.48        76.87        20.68        44.52         6.35        31.07 

$`18P LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 
       43.92        41.00         1.81        49.15         2.01        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1353 
       11.87        65.52        63.09        48.76        21.57         0.53 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1516 
       49.28        32.52        76.57       103.40        82.39        41.59 
TCGA-04-1525 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
       38.37        29.10        84.20        55.43        48.89        27.88 
TCGA-04-1648 TCGA-04-1652 TCGA-04-1654 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 
       28.64        31.86        47.70        29.16         9.47        57.76 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       35.57         9.99        38.43        89.33        74.93        41.62 
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-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2055 
       35.15         4.54       112.41        71.11        63.09        26.93 
TCGA-09-2056 TCGA-10-0925 TCGA-10-0928 TCGA-10-0930 TCGA-10-0933 TCGA-10-0934 
       12.46        54.31        18.51        34.19        14.66         6.71 
TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0717 TCGA-13-0730 
       35.44        36.92        19.99        20.91        24.59        17.82 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0768 TCGA-13-0791 TCGA-13-0795 TCGA-13-0797 
       34.06        32.25         8.45        38.93        19.59         8.71 
TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0805 TCGA-13-0885 TCGA-13-0886 
        7.79         8.28         8.19        35.31        91.40        74.27 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 
       66.67        70.39        61.84        67.99        43.36        57.47 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
       56.15        57.07        19.36        48.33        47.84        44.94 
TCGA-13-0908 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 
       44.84        29.98        21.17        14.89        13.81         4.64 
TCGA-13-0923 TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1412 
        6.41         6.61         6.05         5.92         4.70         5.33 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1485 TCGA-13-1489 TCGA-13-1491 
       54.64        87.06        61.71        20.68        82.88        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 TCGA-13-1499 TCGA-13-1500 
       73.55        38.20         4.24        54.31        38.40        13.97 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 
       32.84        16.57         4.21         4.77         4.18         2.56 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-A5FT 
        3.91         3.09        14.24        12.23         8.61        54.77 
TCGA-13-A5FU TCGA-20-0987 TCGA-20-0996 TCGA-20-1685 TCGA-20-1686 TCGA-23-1022 
        8.42        23.05        72.20        16.70         2.93        49.68 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
       40.54        15.39        26.83        49.41         8.81        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1114 TCGA-23-1119 
       18.90         2.76        51.35        54.51        68.68       129.96 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 
        4.27         6.38        33.47        58.13         0.53       115.89 
TCGA-23-2078 TCGA-23-2081 TCGA-23-2645 TCGA-24-0968 TCGA-24-0975 TCGA-24-0980 
       87.48        77.00         4.50        19.66        21.80         7.66 
TCGA-24-1103 TCGA-24-1105 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 
       54.12        47.41         7.82         7.99         7.86         0.76 
TCGA-24-1424 TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 TCGA-24-1434 TCGA-24-1435 
        6.02         5.36        17.39        28.37        18.67        43.53 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1474 TCGA-24-1549 TCGA-24-1550 
       45.14       105.99         9.11        22.22        56.58        41.06 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1558 TCGA-24-1565 TCGA-24-1567 
       41.39        58.09        88.50        19.53        10.26        17.23 
TCGA-24-1604 TCGA-24-1616 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1850 
       88.37        38.24         3.72         3.81         4.37         5.52 
TCGA-24-1924 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2024 TCGA-24-2026 
       30.21        81.11         4.87       152.02        58.16        34.82 
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-24-2281 TCGA-24-2289 TCGA-24-2290 
       57.07         0.79         0.36        44.61        67.36        36.23 
TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 TCGA-25-1314 TCGA-25-1318 TCGA-25-1319 
       33.11        55.86         1.02        33.01        34.98        65.00 
TCGA-25-1321 TCGA-25-1323 TCGA-25-1623 TCGA-25-1625 TCGA-25-1628 TCGA-25-1631 
       33.96        12.99        18.58        27.62        20.61         0.30 
TCGA-25-1633 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-2391 TCGA-25-2396 
       62.17        52.04        14.96        24.99        49.05         3.02 
TCGA-25-2397 TCGA-25-2399 TCGA-25-2400 TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 
       12.00        19.99        42.02        31.00        78.90        47.61 
TCGA-29-1693 TCGA-29-1695 TCGA-29-1696 TCGA-29-1698 TCGA-29-1699 TCGA-29-1702 
      101.79        40.41        33.93        68.32        36.36        23.93 
TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1766 TCGA-29-1769 
       18.25        31.27        34.62        17.36        39.42        22.98 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 TCGA-29-1778 TCGA-29-1781 TCGA-29-1784 
       22.55        17.33        11.84        14.93         8.38         5.36 
TCGA-29-1785 TCGA-29-2425 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 
       36.30        65.00        13.84        42.25        21.47        11.47 
TCGA-29-2436 TCGA-30-1853 TCGA-30-1857 TCGA-30-1859 TCGA-30-1862 TCGA-30-1866 
        9.76        36.26         0.26        48.10         6.12        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-31-1956 TCGA-31-1959 TCGA-36-1570 TCGA-36-1574 TCGA-36-1576 
       42.51        44.12         2.20        21.53        22.55        30.08 
TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       27.85        24.69        35.05        25.91        25.08        23.80 
TCGA-36-2544 TCGA-36-2547 TCGA-36-2549 TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2582 
       20.98        20.52         6.05        16.18        13.81        47.57 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 
       28.93        42.02        10.42        11.38        21.14        22.32 
TCGA-57-1992 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2352 TCGA-59-2355 
       29.00        25.02       180.20        80.12         9.40         2.14 
TCGA-5X-AA5U TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1728 
       11.87        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-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1906 
        2.43         8.42         5.79        11.41        13.02        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-61-2000 TCGA-61-2003 TCGA-61-2008 TCGA-61-2016 
       43.43        15.75        14.50         4.01        30.64         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-61-2097 TCGA-61-2111 TCGA-61-2113 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
       60.62       125.75        22.22         8.61        39.68        18.94 
TCGA-VG-A8LO TCGA-WR-A838 
        0.79         9.99 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.79               0.26 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            119.08             180.20 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            28.735             28.555 
[1] "0.8 - 119.1 (28.7)" "0.3 - 180.2 (28.6)"
[1] "hr=" "1.3"
D73V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  18P LOSS MUTATED         2   226                0
  18P LOSS WILD-TYPE       1   332                2
D73V3, multiclass
                  clus
vv                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  OMENTUM                         2                  1
  OVARY                         226                332
  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, continuous
D73V5, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     3 228
  18P LOSS WILD-TYPE   0 342
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3  228
  18P LOSS WILD-TYPE    0  342
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 3                  0
  YES              228                342
[1] 2 2
[1] FALSE
                    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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P LOSS MUTATED                                  3     6
  18P LOSS WILD-TYPE                                0    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  18P LOSS MUTATED                           9
  18P LOSS WILD-TYPE                        25
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18P LOSS MUTATED                                           1   196
  18P LOSS WILD-TYPE                                         0   280
D73V7, multiclass
                                           clus
vv                                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         3                  0
  ASIAN                                                    6                 13
  BLACK OR AFRICAN AMERICAN                                9                 25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  196                280
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V8, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     4 130
  18P LOSS WILD-TYPE   6 197
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      4  130
  18P LOSS WILD-TYPE    6  197
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  6
  NOT HISPANIC OR LATINO              130                197
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED   130 153
  18Q LOSS WILD-TYPE 138 139
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               283                277 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               153                139 
$`18Q LOSS MUTATED`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1341 TCGA-04-1347 
       41.00         1.81        49.15        46.62         1.08        63.09 
TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 
       63.98        65.46        49.28        32.52        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-09-0367 TCGA-09-1666 TCGA-09-1667 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 
       17.98        57.60        61.87         5.85         3.02        97.55 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2048 TCGA-09-2050 TCGA-09-2053 TCGA-09-2054 
        6.18         6.12         4.54        71.11        39.75        20.94 
TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 TCGA-13-0714 
       12.46        25.91        81.86        34.19        32.88         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-13-0730 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-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0800 
       31.04        21.40        36.72        28.70        30.35         8.12 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 
       43.86        35.28        13.61        68.94       107.18        74.27 
TCGA-13-0899 TCGA-13-0903 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       56.15        47.38        44.94        44.84        37.08        27.72 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0924 TCGA-13-1403 TCGA-13-1405 TCGA-13-1407 
       34.06        29.98         6.08        10.88         7.36         6.05 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1411 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 
        5.92         6.84         4.21        29.42        98.04        22.39 
TCGA-13-1488 TCGA-13-1495 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1505 
       70.82        49.25        37.61        38.40        13.97         4.21 
TCGA-13-1506 TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-20-0987 
        4.41        12.23        10.78         8.75         6.28        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 
       25.94        26.20        27.52        25.38        19.10        16.70 
TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1023 TCGA-23-1027 TCGA-23-1028 
        2.93         2.66        47.54        40.54        32.09        49.41 
TCGA-23-1032 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
        2.76         3.22        31.20         4.57        33.30        86.01 
TCGA-23-1119 TCGA-23-1122 TCGA-23-1124 TCGA-23-2072 TCGA-23-2079 TCGA-23-2081 
      129.96        39.09        58.13        24.95        91.66        77.00 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-24-0966 TCGA-24-0970 TCGA-24-0979 
       49.84         2.76         4.70         7.63        11.64        41.56 
TCGA-24-0982 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 
       22.32        63.55        47.41         6.31         6.38         7.82 
TCGA-24-1418 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1427 TCGA-24-1428 
        7.99         6.25         6.02         5.95         4.83        17.39 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 
        8.55        72.92        12.46         3.45         1.18        22.22 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1552 TCGA-24-1556 
       26.96        57.40        64.27        16.21        41.39        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-24-1603 TCGA-24-1614 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1847 
       90.15        48.33         8.32         3.48         3.72        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-24-2020 TCGA-24-2023 TCGA-24-2027 TCGA-24-2029 TCGA-24-2035 TCGA-24-2260 
      152.02        44.84       109.71        14.43        28.18        36.16 
TCGA-24-2261 TCGA-24-2267 TCGA-24-2271 TCGA-24-2288 TCGA-24-2289 TCGA-24-2293 
        0.79        47.54        31.63         0.82        67.36        16.64 
TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
       53.26         1.02        26.96        52.04        42.05         2.01 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1625 TCGA-25-1626 
       33.96         2.99        12.99        15.02        27.62        17.03 
TCGA-25-1627 TCGA-25-1632 TCGA-25-1634 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 
       12.95        59.15        35.87        24.00        85.05        13.02 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2401 TCGA-25-2404 TCGA-25-2409 TCGA-29-1691 
        1.02        38.04         2.96        29.03        26.99        48.33 
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-59-A5PD TCGA-61-1724 TCGA-61-1730 
        2.14         5.42        44.81        20.52        20.94         4.34 
TCGA-61-1737 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1904 TCGA-61-1906 
       44.84        33.67        43.69         1.45         9.07        34.13 
TCGA-61-1995 TCGA-61-2002 TCGA-61-2012 TCGA-61-2088 TCGA-61-2094 TCGA-61-2097 
        2.01        17.98        30.64         4.77        71.74        60.62 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2612 TCGA-61-2613 
        6.48        76.87        20.68        44.52         6.35        31.07 
TCGA-WR-A838 
        9.99 

$`18Q LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 
       43.92         2.01        18.51        11.87        65.52        48.76 
TCGA-04-1349 TCGA-04-1353 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 
       21.57         0.53        76.57       103.40        82.39        56.55 
TCGA-04-1516 TCGA-04-1525 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 
       41.59        38.37        29.10        84.20        55.43        48.89 
TCGA-04-1646 TCGA-04-1648 TCGA-04-1652 TCGA-04-1654 TCGA-09-0364 TCGA-09-0365 
       27.88        28.64        31.86        47.70        29.16         9.47 
TCGA-09-0366 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       57.76        35.57         9.99        38.43        89.33        74.93 
TCGA-09-1665 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1674 TCGA-09-2045 
       41.62        55.36        30.51        17.98         8.55        35.15 
TCGA-09-2049 TCGA-09-2051 TCGA-09-2055 TCGA-10-0925 TCGA-10-0928 TCGA-10-0933 
      112.41        63.09        26.93        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-13-0761 TCGA-13-0762 TCGA-13-0768 TCGA-13-0791 TCGA-13-0795 TCGA-13-0797 
       34.06        32.25         8.45        38.93        19.59         8.71 
TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0805 TCGA-13-0885 TCGA-13-0887 
        7.79         8.28         8.19        35.31        91.40        66.67 
TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 
       70.39        61.84        67.99        69.01        43.36        57.47 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0904 TCGA-13-0905 TCGA-13-0916 TCGA-13-0919 
       57.07        19.36        48.33        47.84        21.17        14.89 
TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-1404 TCGA-13-1410 TCGA-13-1412 
       13.81         4.64         6.41         6.61         4.70         5.33 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1485 TCGA-13-1489 TCGA-13-1491 
       54.64        87.06        61.71        20.68        82.88        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 TCGA-13-1501 TCGA-13-1504 
       73.55        38.20         4.24        54.31        32.84        16.57 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 
        4.77         4.18         2.56         3.91         3.09        14.24 
TCGA-13-2060 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0996 TCGA-23-1022 TCGA-23-1024 
        8.61        54.77         8.42        72.20        49.68        15.39 
TCGA-23-1026 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1109 TCGA-23-1110 
       26.83         8.81        29.13        18.90        51.35        54.51 
TCGA-23-1114 TCGA-23-1120 TCGA-23-1121 TCGA-23-1123 TCGA-23-1809 TCGA-23-2077 
       68.68         4.27         6.38        33.47         0.53       115.89 
TCGA-23-2078 TCGA-23-2645 TCGA-24-0968 TCGA-24-0975 TCGA-24-0980 TCGA-24-1103 
       87.48         4.50        19.66        21.80         7.66        54.12 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1426 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 
        7.86         0.76         5.36        28.37        19.17        18.67 
TCGA-24-1435 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1549 TCGA-24-1550 
       43.53        45.14       105.99         9.11        56.58        41.06 
TCGA-24-1551 TCGA-24-1553 TCGA-24-1555 TCGA-24-1565 TCGA-24-1567 TCGA-24-1604 
       51.91        58.09        88.50        10.26        17.23        88.37 
TCGA-24-1616 TCGA-24-1845 TCGA-24-1846 TCGA-24-1924 TCGA-24-1930 TCGA-24-2019 
       38.24         3.81         4.37        30.21        81.11         4.87 
TCGA-24-2024 TCGA-24-2026 TCGA-24-2030 TCGA-24-2033 TCGA-24-2036 TCGA-24-2038 
       58.16        34.82        55.92        18.48        64.01        44.52 
TCGA-24-2254 TCGA-24-2262 TCGA-24-2280 TCGA-24-2281 TCGA-24-2290 TCGA-24-2295 
       57.07         0.36        70.45        44.61        36.23        33.11 
TCGA-24-2297 TCGA-25-1314 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1623 
       55.86        33.01        34.98        65.00        37.97        18.58 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1633 TCGA-25-1635 TCGA-25-1870 
       20.61        38.20         0.30        62.17        52.04        14.96 
TCGA-25-1871 TCGA-25-2391 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 
       24.99        49.05         3.02        12.00        45.01        19.99 
TCGA-25-2400 TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1695 
       42.02        31.00        78.90        47.61       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-3P-A9WA TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
       16.18        13.81        47.57        28.93        42.02        10.42 
TCGA-57-1584 TCGA-57-1586 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-5X-AA5U 
       21.14        22.32        25.02       180.20        80.12        11.87 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 
       11.11         8.09        31.43        18.54        27.88        31.79 
TCGA-61-1734 TCGA-61-1736 TCGA-61-1738 TCGA-61-1740 TCGA-61-1899 TCGA-61-1900 
       28.47        48.79        35.80         2.43         8.42         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 
       11.41        13.02        31.30        37.05        42.51        48.92 
TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1998 
       56.61        67.76        43.43        15.75        38.17         5.52 
TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 
       14.50         4.01        30.64        39.85         1.18        45.96 
TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 
       45.40         4.80        51.72        61.64        58.39        65.52 
TCGA-61-2101 TCGA-61-2111 TCGA-61-2113 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
       55.50       125.75        22.22         8.61        39.68        18.94 
TCGA-VG-A8LO 
        0.79 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.79               0.26 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            152.02             180.20 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             25.94              31.27 
[1] "0.8 - 152.0 (25.9)" "0.3 - 180.2 (31.3)"
[1] "hr=" "1.2"
D74V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  18Q LOSS MUTATED         2   281                0
  18Q LOSS WILD-TYPE       1   277                2
D74V3, multiclass
                  clus
vv                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  OMENTUM                         2                  1
  OVARY                         281                277
  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, continuous
D74V5, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     3 286
  18Q LOSS WILD-TYPE   0 284
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3  286
  18Q LOSS WILD-TYPE    0  284
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 3                  0
  YES              286                284
[1] 2 2
[1] FALSE
                    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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q LOSS MUTATED                                  3     6
  18Q LOSS WILD-TYPE                                0    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  18Q LOSS MUTATED                          14
  18Q LOSS WILD-TYPE                        20
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18Q LOSS MUTATED                                           1   243
  18Q LOSS WILD-TYPE                                         0   233
D74V7, multiclass
                                           clus
vv                                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         3                  0
  ASIAN                                                    6                 13
  BLACK OR AFRICAN AMERICAN                               14                 20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  243                233
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V8, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     7 159
  18Q LOSS WILD-TYPE   3 168
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      7  159
  18Q LOSS WILD-TYPE    3  168
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    7                  3
  NOT HISPANIC OR LATINO              159                168
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    87  93
  19P LOSS WILD-TYPE 181 199
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               180                380 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                93                199 
$`19P LOSS MUTATED`
TCGA-04-1332 TCGA-04-1341 TCGA-04-1343 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 
       41.00         1.08        11.87        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-04-1516 TCGA-04-1517 TCGA-04-1530 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
       41.59        19.99       119.08        55.43        48.89        27.88 
TCGA-04-1654 TCGA-04-1655 TCGA-09-0366 TCGA-09-1659 TCGA-09-1661 TCGA-09-1668 
       47.70        45.37        57.76         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-10-0928 TCGA-10-0936 TCGA-10-0937 TCGA-13-0723 TCGA-13-0724 
       12.46        18.51        36.92        19.99        39.58         2.73 
TCGA-13-0730 TCGA-13-0762 TCGA-13-0768 TCGA-13-0800 TCGA-13-0803 TCGA-13-0885 
       17.82        32.25         8.45         8.12        43.86        91.40 
TCGA-13-0886 TCGA-13-0899 TCGA-13-0908 TCGA-13-0911 TCGA-13-0919 TCGA-13-0921 
       74.27        56.15        44.84        27.72        14.89         4.64 
TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1411 
        6.41         6.08        10.88         6.61         7.36         4.21 
TCGA-13-1412 TCGA-13-1483 TCGA-13-1489 TCGA-13-1492 TCGA-13-1496 TCGA-13-1498 
        5.33        29.42        82.88        73.55         4.24        37.61 
TCGA-13-1499 TCGA-13-1504 TCGA-13-1507 TCGA-13-2060 TCGA-13-2061 TCGA-23-1027 
       38.40        16.57         4.77         8.61        10.78        32.09 
TCGA-23-1030 TCGA-23-1032 TCGA-23-1110 TCGA-23-1113 TCGA-23-1119 TCGA-23-1120 
       29.13         2.76        54.51        31.20       129.96         4.27 
TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2643 TCGA-24-0966 TCGA-24-0968 
       33.47        58.13        24.95         4.70         7.63        19.66 
TCGA-24-0979 TCGA-24-1413 TCGA-24-1424 TCGA-24-1434 TCGA-24-1463 TCGA-24-1464 
       41.56         6.31         6.02        18.67        72.92        12.46 
TCGA-24-1470 TCGA-24-1544 TCGA-24-1549 TCGA-24-1560 TCGA-24-1564 TCGA-24-1565 
        3.45        26.96        56.58        44.09        25.87        10.26 
TCGA-24-1846 TCGA-24-2019 TCGA-24-2024 TCGA-24-2026 TCGA-24-2260 TCGA-24-2288 
        4.37         4.87        58.16        34.82        36.16         0.82 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2298 TCGA-25-1313 TCGA-25-1316 TCGA-25-1317 
       36.23        16.64        53.26        26.96        42.05         2.01 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
       12.95        20.61        38.20        59.15        62.17        35.87 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2392 
       52.04        14.96        24.99        24.00        85.05         1.02 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2399 TCGA-25-2400 TCGA-25-2404 TCGA-29-1691 
       38.04         3.02        19.99        42.02        29.03        48.33 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 TCGA-29-1701 TCGA-29-1705 TCGA-29-1707 
       33.93        31.20        36.36        16.93        18.25        41.98 
TCGA-29-1710 TCGA-29-1761 TCGA-29-1763 TCGA-29-1769 TCGA-29-1771 TCGA-29-1774 
       31.27        17.36        66.81        22.98        22.55        17.33 
TCGA-29-1778 TCGA-29-2427 TCGA-29-2428 TCGA-30-1853 TCGA-30-1861 TCGA-30-1866 
       14.93        62.47        45.11        36.26        34.78        36.62 
TCGA-30-1891 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 
       30.05         6.71        42.51        44.12         2.20        28.77 
TCGA-36-1569 TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1581 TCGA-36-2530 
       29.10        22.85         8.55        30.08        24.69        33.01 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2548 TCGA-36-2551 TCGA-3P-A9WA TCGA-57-1584 
       25.91        25.08        14.17        16.18        13.81        21.14 
TCGA-57-1585 TCGA-57-1993 TCGA-57-1994 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1722 
        1.74        25.08        25.02        44.81        20.52         8.09 
TCGA-61-1733 TCGA-61-1738 TCGA-61-1740 TCGA-61-1903 TCGA-61-1907 TCGA-61-1915 
       31.79        35.80         2.43        13.02        31.30        67.76 
TCGA-61-1917 TCGA-61-1919 TCGA-61-2002 TCGA-61-2016 TCGA-61-2017 TCGA-61-2087 
       43.43        38.17        17.98         1.18        45.96         4.80 
TCGA-61-2088 TCGA-61-2102 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
        4.77         6.48         6.35         8.61        39.68        18.94 

$`19P LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       43.92         1.81        49.15         2.01        46.62        18.51 
TCGA-04-1346 TCGA-04-1348 TCGA-04-1351 TCGA-04-1353 TCGA-04-1361 TCGA-04-1514 
       65.52        48.76        65.46         0.53        32.52        56.55 
TCGA-04-1519 TCGA-04-1525 TCGA-04-1536 TCGA-04-1542 TCGA-04-1648 TCGA-04-1649 
        0.79        38.37        29.10        84.20        28.64        64.64 
TCGA-04-1651 TCGA-04-1652 TCGA-09-0364 TCGA-09-0365 TCGA-09-0367 TCGA-09-0369 
       36.23        31.86        29.16         9.47        17.98        35.57 
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-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 
       17.98         8.55        97.55         6.18         6.12        35.15 
TCGA-09-2048 TCGA-09-2050 TCGA-09-2054 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 
        4.54        71.11        20.94        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        34.06 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 
       31.04        21.40        38.93        36.72        28.70        30.35 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 
       19.59         8.71         7.79         8.28         8.19        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        70.39 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 
       61.84        67.99        69.01        43.36        57.47        57.07 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 
       19.36        47.38        48.33        47.84        44.94        37.08 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-1407 TCGA-13-1408 
       34.06        29.98        21.17        13.81         6.05         5.92 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 
        6.84         4.70        54.64        87.06        61.71        98.04 
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        38.20        49.25 
TCGA-13-1497 TCGA-13-1500 TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 
       54.31        13.97        32.84         4.21         4.41         4.18 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2065 
        2.56         3.91         3.09        14.24        12.23         8.75 
TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
        6.28        54.77         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-23-1028 TCGA-23-1029 TCGA-23-1031 TCGA-23-1109 TCGA-23-1111 TCGA-23-1114 
       49.41         8.81        18.90        51.35         3.22        68.68 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1121 TCGA-23-1122 TCGA-23-1809 
        4.57        33.30        86.01         6.38        39.09         0.53 
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-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 
        4.50        11.64        21.80         7.66        22.32        54.12 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       63.55        47.41         6.38         7.82         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        0.76         6.25         5.95         5.36         4.83        17.39 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 TCGA-24-1436 TCGA-24-1466 TCGA-24-1467 
       28.37        19.17        43.53         8.55        45.14       105.99 
TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 
        9.11         1.18        22.22        57.40        64.27        16.21 
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-24-1562 TCGA-24-1563 TCGA-24-1567 TCGA-24-1603 
       39.88        19.53        45.50        47.70        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-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 
        3.81        11.28         5.79         5.52         9.80        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-24-2027 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-24-2280 TCGA-24-2281 TCGA-24-2289 TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 
       70.45        44.61        67.36        33.11        55.86         1.02 
TCGA-25-1314 TCGA-25-1315 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 
       33.01        52.04        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-25-1631 TCGA-25-2042 TCGA-25-2391 TCGA-25-2397 TCGA-25-2398 TCGA-25-2401 
        0.30        13.02        49.05        12.00        45.01         2.96 
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-29-1695 TCGA-29-1698 TCGA-29-1702 TCGA-29-1703 TCGA-29-1711 TCGA-29-1762 
       40.41        68.32        23.93        59.67        34.62        86.60 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1770 TCGA-29-1775 TCGA-29-1776 
       62.93        39.42        31.30        24.36        12.36        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-29-2425 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 
       65.00        13.84        42.25        21.47        11.47         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-30-1887 
       48.10        44.91         6.12         1.22        57.57        24.26 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-36-1570 
       48.79        45.57        30.18        18.77        22.49        21.53 
TCGA-36-1574 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-2529 TCGA-36-2532 
       22.55        25.74        27.85        24.23        35.05        29.49 
TCGA-36-2534 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 
       29.82        23.80        21.60         2.24        20.98        18.31 
TCGA-36-2547 TCGA-36-2549 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
       20.52         6.05        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-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 
       22.32        29.00       180.20        80.12        22.32       116.12 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-5X-AA5U TCGA-61-1721 
        9.40        34.39         2.14         5.42        11.87        11.11 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1734 
       20.94        31.43        18.54        27.88         4.34        28.47 
TCGA-61-1736 TCGA-61-1737 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 
       48.79        44.84        33.67        43.69         1.45         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1904 TCGA-61-1906 TCGA-61-1910 TCGA-61-1911 
        5.79        11.41         9.07        34.13        37.05        42.51 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       48.92        56.61        15.75         2.01         5.52        14.50 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2018 TCGA-61-2092 
        4.01        30.64        39.85        30.64        45.40        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-61-2104 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-VG-A8LO TCGA-WR-A838 
        0.79         9.99 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.82               0.26 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            129.96             180.20 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            27.340             28.965 
[1] "0.8 - 130.0 (27.3)" "0.3 - 180.2 (29.0)"
[1] "hr=" "1.1"
D75V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  19P LOSS MUTATED         2   179                0
  19P LOSS WILD-TYPE       1   379                2
D75V3, multiclass
                  clus
vv                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  OMENTUM                         2                  1
  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, continuous
D75V5, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     0 184
  19P LOSS WILD-TYPE   3 386
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0  184
  19P LOSS WILD-TYPE    3  386
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 0                  3
  YES              184                386
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  19P LOSS MUTATED    3 11  1  2
  19P LOSS WILD-TYPE 12 15  4  1
D75V6, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0                3                 12
  R1               11                 15
  R2                1                  4
  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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P LOSS MUTATED                                  1     3
  19P LOSS WILD-TYPE                                2    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  19P LOSS MUTATED                          12
  19P LOSS WILD-TYPE                        22
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19P LOSS MUTATED                                           0   157
  19P LOSS WILD-TYPE                                         1   319
D75V7, multiclass
                                           clus
vv                                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  2
  ASIAN                                                    3                 16
  BLACK OR AFRICAN AMERICAN                               12                 22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                  157                319
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V8, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     4 107
  19P LOSS WILD-TYPE   6 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      4  107
  19P LOSS WILD-TYPE    6  220
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  6
  NOT HISPANIC OR LATINO              107                220
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    86  86
  19Q LOSS WILD-TYPE 182 206
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               172                388 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                86                206 
$`19Q LOSS MUTATED`
TCGA-04-1341 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 TCGA-04-1362 
        1.08        63.09        21.57        63.98        49.28        44.32 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1530 TCGA-04-1638 
       33.67        76.57       103.40        82.39       119.08        55.43 
TCGA-04-1644 TCGA-04-1646 TCGA-04-1654 TCGA-04-1655 TCGA-09-0366 TCGA-09-1659 
       48.89        27.88        47.70        45.37        57.76         9.99 
TCGA-09-1664 TCGA-09-1667 TCGA-09-1668 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 
       74.93        61.87        55.36         5.85         3.02        97.55 
TCGA-09-2049 TCGA-09-2051 TCGA-09-2053 TCGA-09-2055 TCGA-09-2056 TCGA-10-0928 
      112.41        63.09        39.75        26.93        12.46        18.51 
TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0723 TCGA-13-0724 TCGA-13-0762 
       36.92        19.99        20.91        39.58         2.73        32.25 
TCGA-13-0768 TCGA-13-0800 TCGA-13-0803 TCGA-13-0804 TCGA-13-0807 TCGA-13-0886 
        8.45         8.12        43.86        35.28        13.61        74.27 
TCGA-13-0899 TCGA-13-0908 TCGA-13-0911 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 
       56.15        44.84        27.72        14.89         4.64         6.41 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1411 TCGA-13-1412 
       10.88         6.61         7.36         6.05         4.21         5.33 
TCGA-13-1489 TCGA-13-1494 TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 TCGA-13-1510 
       82.88        38.20         4.24        37.61        38.40         2.56 
TCGA-13-2060 TCGA-13-2061 TCGA-20-1686 TCGA-23-1021 TCGA-23-1024 TCGA-23-1030 
        8.61        10.78         2.93        47.54        15.39        29.13 
TCGA-23-1032 TCGA-23-1110 TCGA-23-1113 TCGA-23-1119 TCGA-23-1120 TCGA-23-1123 
        2.76        54.51        31.20       129.96         4.27        33.47 
TCGA-23-1124 TCGA-23-2072 TCGA-23-2643 TCGA-24-0966 TCGA-24-0968 TCGA-24-0979 
       58.13        24.95         4.70         7.63        19.66        41.56 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1413 TCGA-24-1424 TCGA-24-1434 TCGA-24-1463 
        7.66        22.32         6.31         6.02        18.67        72.92 
TCGA-24-1464 TCGA-24-1467 TCGA-24-1470 TCGA-24-1549 TCGA-24-1560 TCGA-24-1564 
       12.46       105.99         3.45        56.58        44.09        25.87 
TCGA-24-1565 TCGA-24-1846 TCGA-24-2019 TCGA-24-2024 TCGA-24-2026 TCGA-24-2260 
       10.26         4.37         4.87        58.16        34.82        36.16 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2298 TCGA-25-1316 TCGA-25-1627 TCGA-25-1628 
       36.23        16.64        53.26        42.05        12.95        20.61 
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-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2399 
       24.00        85.05         1.02        38.04         3.02        19.99 
TCGA-25-2400 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 TCGA-29-1705 
       42.02        39.02        33.93        31.20        36.36        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-29-1778 TCGA-29-2427 TCGA-29-2428 TCGA-30-1853 TCGA-30-1861 TCGA-30-1866 
       14.93        62.47        45.11        36.26        34.78        36.62 
TCGA-30-1891 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 
       30.05         6.71        42.51        44.12        28.77        29.10 
TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1580 TCGA-36-1581 TCGA-36-2530 
       22.85         8.55        30.08        24.23        24.69        33.01 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2548 TCGA-36-2551 TCGA-3P-A9WA TCGA-57-1584 
       25.91        25.08        14.17        16.18        13.81        21.14 
TCGA-57-1585 TCGA-57-1993 TCGA-57-1994 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1725 
        1.74        25.08        25.02        44.81        20.52        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-OY-A56Q 
        6.48         6.35        39.68        18.94 

$`19Q LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       43.92        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 TCGA-04-1351 TCGA-04-1353 
       18.51        11.87        65.52        48.76        65.46         0.53 
TCGA-04-1361 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 
       32.52        56.55        41.59        19.99         0.79        38.37 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 
       29.10        84.20        28.64        64.64        36.23        31.86 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0367 TCGA-09-0369 TCGA-09-1661 TCGA-09-1662 
       29.16         9.47        17.98        35.57        38.43        89.33 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 TCGA-09-1670 TCGA-09-1674 TCGA-09-2043 
       41.62        57.60        30.51        17.98         8.55         6.18 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 TCGA-09-2054 TCGA-10-0925 
        6.12        35.15         4.54        71.11        20.94        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-10-0935 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0725 TCGA-13-0726 
       35.44         6.21        24.59        44.55        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-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 
       11.54        34.06        31.04        21.40        38.93        36.72 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 
       28.70        30.35        19.59         8.71         7.79         8.28 
TCGA-13-0802 TCGA-13-0805 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 
        8.19        35.31        68.94       107.18        91.40        66.67 
TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 
       70.39        61.84        67.99        69.01        43.36        57.47 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
       57.07        19.36        47.38        48.33        47.84        44.94 
TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0924 
       37.08        34.06        29.98        21.17        13.81         6.08 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 
        5.92         6.84         4.70        54.64        87.06        61.71 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1491 
       29.42        98.04        20.68        22.39        70.82        52.44 
TCGA-13-1492 TCGA-13-1495 TCGA-13-1497 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 
       73.55        49.25        54.31        13.97        32.84        16.57 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 
        4.21         4.41         4.77         4.18         3.91         3.09 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU 
       14.24        12.23         8.75         6.28        54.77         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-20-1687 TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 
       19.10        16.70         2.66        49.68        40.54        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1031 TCGA-23-1109 TCGA-23-1111 
       32.09        49.41         8.81        18.90        51.35         3.22 
TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1121 TCGA-23-1122 
       68.68         4.57        33.30        86.01         6.38        39.09 
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-23-2645 TCGA-24-0970 TCGA-24-0975 TCGA-24-1103 TCGA-24-1104 
        2.76         4.50        11.64        21.80        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-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 
        6.25         5.95         5.36         4.83        17.39        28.37 
TCGA-24-1431 TCGA-24-1435 TCGA-24-1436 TCGA-24-1466 TCGA-24-1469 TCGA-24-1471 
       19.17        43.53         8.55        45.14         9.11         1.18 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1550 
       22.22        26.96        57.40        64.27        16.21        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-24-1562 TCGA-24-1563 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 
       19.53        45.50        47.70        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-24-1930 TCGA-24-2020 TCGA-24-2023 TCGA-24-2027 
       16.44        11.05        81.11       152.02        44.84       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-24-2295 TCGA-24-2297 TCGA-25-1312 
       44.61         0.82        67.36        33.11        55.86         1.02 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 
       26.96        33.01        52.04         2.01        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-25-1625 TCGA-25-1626 TCGA-25-1630 TCGA-25-1631 TCGA-25-2042 TCGA-25-2391 
       27.62        17.03        38.20         0.30        13.02        49.05 
TCGA-25-2397 TCGA-25-2398 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       12.00        45.01         2.96        29.03        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1695 TCGA-29-1698 
       78.90        47.61        48.33       101.79        40.41        68.32 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1711 TCGA-29-1762 TCGA-29-1764 
       16.93        23.93        59.67        34.62        86.60        62.93 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 
       39.42        31.30        24.36        17.33        12.36        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-29-2425 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 
       65.00        13.84        42.25        21.47        11.47         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-30-1887 
       48.10        44.91         6.12         1.22        57.57        24.26 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1959 
       48.79        45.57        30.18        18.77        22.49         2.20 
TCGA-36-1570 TCGA-36-1574 TCGA-36-1577 TCGA-36-1578 TCGA-36-2529 TCGA-36-2532 
       21.53        22.55        25.74        27.85        35.05        29.49 
TCGA-36-2534 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 
       29.82        23.80        21.60         2.24        20.98        18.31 
TCGA-36-2547 TCGA-36-2549 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
       20.52         6.05        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-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 
       22.32        29.00       180.20        80.12        22.32       116.12 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-5X-AA5U TCGA-61-1721 
        9.40        34.39         2.14         5.42        11.87        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-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 
       48.79        44.84         2.43        33.67        43.69         1.45 
TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1904 TCGA-61-1906 TCGA-61-1910 
        8.42         5.79        11.41         9.07        34.13        37.05 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 
       42.51        48.92        56.61        15.75         2.01         5.52 
TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2018 
       14.50         4.01        30.64        39.85        30.64        45.40 
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-61-2613 TCGA-61-2614 TCGA-VG-A8LO TCGA-WR-A838 
       31.07         8.61         0.79         9.99 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              1.02               0.26 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            129.96             180.20 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            28.935             28.555 
[1] "1.0 - 130.0 (28.9)" "0.3 - 180.2 (28.6)"
[1] "hr=" "1"  
D76V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  19Q LOSS MUTATED         2   170                0
  19Q LOSS WILD-TYPE       1   388                2
D76V3, multiclass
                  clus
vv                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  OMENTUM                         2                  1
  OVARY                         170                388
  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, continuous
D76V5, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     0 176
  19Q LOSS WILD-TYPE   3 394
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0  176
  19Q LOSS WILD-TYPE    3  394
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 0                  3
  YES              176                394
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  19Q LOSS MUTATED    2 11  1  2
  19Q LOSS WILD-TYPE 13 15  4  1
D76V6, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0                2                 13
  R1               11                 15
  R2                1                  4
  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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q LOSS MUTATED                                  0     3
  19Q LOSS WILD-TYPE                                3    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  19Q LOSS MUTATED                          11
  19Q LOSS WILD-TYPE                        23
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19Q LOSS MUTATED                                           0   149
  19Q LOSS WILD-TYPE                                         1   327
D76V7, multiclass
                                           clus
vv                                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    3                 16
  BLACK OR AFRICAN AMERICAN                               11                 23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                  149                327
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V8, 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    29  19
  20P LOSS WILD-TYPE 239 273
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                48                512 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                19                273 
$`20P LOSS MUTATED`
TCGA-04-1336 TCGA-04-1536 TCGA-09-0364 TCGA-09-1667 TCGA-09-2048 TCGA-10-0930 
       49.15        29.10        29.16        61.87         4.54        34.19 
TCGA-13-0720 TCGA-13-0804 TCGA-13-0883 TCGA-13-0893 TCGA-13-0921 TCGA-13-1489 
       44.55        35.28        68.94        43.36         4.64        82.88 
TCGA-13-1494 TCGA-13-1495 TCGA-13-2059 TCGA-13-2071 TCGA-20-0987 TCGA-20-1682 
       38.20        49.25        12.23         6.28        23.05        27.52 
TCGA-20-1687 TCGA-23-1022 TCGA-23-1028 TCGA-23-1118 TCGA-23-1119 TCGA-23-2072 
        2.66        49.68        49.41        86.01       129.96        24.95 
TCGA-24-1417 TCGA-24-1426 TCGA-24-1428 TCGA-24-1463 TCGA-24-1471 TCGA-24-1552 
        7.82         5.36        17.39        72.92         1.18        41.39 
TCGA-24-1603 TCGA-24-2298 TCGA-25-2392 TCGA-29-1693 TCGA-29-1702 TCGA-29-1711 
       90.15        53.26         1.02       101.79        23.93        34.62 
TCGA-29-1781 TCGA-29-2434 TCGA-29-2436 TCGA-36-1577 TCGA-36-1578 TCGA-57-1993 
        8.38        11.47         9.76        25.74        27.85        25.08 
TCGA-61-1725 TCGA-61-1734 TCGA-61-1737 TCGA-61-1741 TCGA-61-2088 TCGA-WR-A838 
       31.43        28.47        44.84        33.67         4.77         9.99 

$`20P LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 
       43.92        41.00         1.81         2.01        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-04-1364 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-04-1542 TCGA-04-1638 
       19.99         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-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 
       47.70        45.37         9.47        57.76        17.98        35.57 
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-10-0925 
       63.09        39.75        20.94        26.93        12.46        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       25.91        81.86        18.51        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-13-0723 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-13-0761 
       55.17         2.50        11.18        11.38        11.54        34.06 
TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 
       32.25        31.04        21.40         8.45        38.93        36.72 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 
       28.70        30.35        19.59         8.71         7.79         8.12 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 TCGA-13-0884 
        8.28         8.19        43.86        35.31        13.61       107.18 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 
       91.40        74.27        66.67        70.39        61.84        67.99 
TCGA-13-0891 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       69.01        57.47        56.15        57.07        19.36        47.38 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       48.33        47.84        44.94        44.84        37.08        27.72 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 
       34.06        29.98        21.17        14.89        13.81         6.41 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 
        6.08        10.88         6.61         7.36         6.05         5.92 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
        6.84         4.70         4.21         5.33        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        98.04        20.68        22.39        70.82 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 
       52.44        73.55         4.24        54.31        37.61        38.40 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
       13.97        32.84        16.57         4.21         4.41         4.77 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2060 
        4.18         2.56         3.91         3.09        14.24         8.61 
TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 
       10.78         8.75        54.77         8.42        25.94        26.20 
TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 
       72.20        25.38        19.10        16.70         2.93        47.54 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1029 TCGA-23-1030 
       40.54        15.39        26.83        32.09         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-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 
       68.68         4.57        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-23-2081 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-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
       19.66        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-24-1418 
       54.12        63.55        47.41         6.31         6.38         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1427 
        7.86         0.76         6.25         6.02         5.95         4.83 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1464 
       28.37        19.17        18.67        43.53         8.55        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-24-1550 TCGA-24-1551 
       57.40        64.27        16.21        56.58        41.06        51.91 
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-24-1604 
       45.50        47.70        25.87        10.26        17.23        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-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-25-1635 
       38.20         0.30        59.15        62.17        35.87        52.04 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 
       14.96        24.99        24.00        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-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 
       48.33        39.02        40.41        33.93        31.20        68.32 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 
       36.36        16.93        59.67        18.25        41.98        31.27 
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-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 
       12.30        14.93         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-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-36-1569 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-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 
        8.55        30.08        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-36-2547 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-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
       16.18        11.47        13.81        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-59-A5PD TCGA-5X-AA5U TCGA-61-1721 TCGA-61-1722 
        5.42        44.81        20.52        11.87        11.11         8.09 
TCGA-61-1724 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 
       20.94        18.54        27.88         4.34        31.79        48.79 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
       35.80         2.43        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-61-2012 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-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 
        4.80        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 
       18.94         0.79 

  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 
            29.130             28.505 
[1] "1.0 - 130.0 (29.1)" "0.3 - 180.2 (28.5)"
[1] "hr=" "1.5"
D77V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  20P LOSS MUTATED         0    48                0
  20P LOSS WILD-TYPE       3   510                2
D77V3, multiclass
                  clus
vv                 20P LOSS MUTATED 20P LOSS WILD-TYPE
  OMENTUM                         0                  3
  OVARY                          48                510
  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, continuous
D77V5, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     1  48
  20P LOSS WILD-TYPE   2 522
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1   48
  20P LOSS WILD-TYPE    2  522
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 1                  2
  YES               48                522
[1] 2 2
[1] FALSE
                    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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P LOSS MUTATED                                  0     2
  20P LOSS WILD-TYPE                                3    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  20P LOSS MUTATED                           4
  20P LOSS WILD-TYPE                        30
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20P LOSS MUTATED                                           0    42
  20P LOSS WILD-TYPE                                         1   434
D77V7, multiclass
                                           clus
vv                                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    2                 17
  BLACK OR AFRICAN AMERICAN                                4                 30
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   42                434
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V8, 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    17  14
  20Q LOSS WILD-TYPE 251 278
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                31                529 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                14                278 
$`20Q LOSS MUTATED`
TCGA-04-1336 TCGA-09-1667 TCGA-09-2048 TCGA-13-0720 TCGA-13-0804 TCGA-13-0883 
       49.15        61.87         4.54        44.55        35.28        68.94 
TCGA-13-1489 TCGA-13-1494 TCGA-13-1495 TCGA-13-2059 TCGA-20-0987 TCGA-23-1028 
       82.88        38.20        49.25        12.23        23.05        49.41 
TCGA-23-1118 TCGA-23-1119 TCGA-23-2072 TCGA-24-1428 TCGA-24-1463 TCGA-24-1471 
       86.01       129.96        24.95        17.39        72.92         1.18 
TCGA-24-1552 TCGA-24-2030 TCGA-24-2298 TCGA-25-2392 TCGA-29-1695 TCGA-29-1702 
       41.39        55.92        53.26         1.02        40.41        23.93 
TCGA-29-1711 TCGA-29-1781 TCGA-36-1578 TCGA-61-1734 TCGA-61-2002 TCGA-61-2088 
       34.62         8.38        27.85        28.47        17.98         4.77 
TCGA-WR-A838 
        9.99 

$`20Q LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 
       43.92        41.00         1.81         2.01        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-04-1364 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-09-0364 TCGA-09-0365 TCGA-09-0366 
       31.86        47.70        45.37        29.16         9.47        57.76 
TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       17.98        35.57         9.99        38.43        89.33        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 
       41.62        57.60        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-09-2049 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-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       12.46        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-13-0723 TCGA-13-0724 TCGA-13-0725 
       20.91         6.21        24.59        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        34.06        32.25        31.04        21.40 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 
        8.45        38.93        36.72        28.70        30.35        19.59 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 
        8.71         7.79         8.12         8.28         8.19        43.86 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
       35.31        13.61       107.18        91.40        74.27        66.67 
TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 
       70.39        61.84        67.99        69.01        43.36        57.47 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       56.15        57.07        19.36        47.38        48.33        47.84 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
       44.94        44.84        37.08        27.72        34.06        29.98 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       21.17        14.89        13.81         4.64         6.41         6.08 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
       10.88         6.61         7.36         6.05         5.92         6.84 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 
        4.70         4.21         5.33        54.64        87.06        61.71 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1491 
       29.42        98.04        20.68        22.39        70.82        52.44 
TCGA-13-1492 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 
       73.55         4.24        54.31        37.61        38.40        13.97 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       32.84        16.57         4.21         4.41         4.77         4.18 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 
        2.56         3.91         3.09        14.24         8.61        10.78 
TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 
        8.75         6.28        54.77         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-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 
       32.09         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         4.57        33.30 
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-23-2084 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-24-0968 TCGA-24-0970 TCGA-24-0975 
        4.70         4.50         7.63        19.66        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-24-1417 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-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1430 
        6.25         6.02         5.95         5.36         4.83        28.37 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 
       19.17        18.67        43.53         8.55        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-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1553 
       64.27        16.21        56.58        41.06        51.91        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-24-2033 
       44.84        58.16        34.82       109.71        14.43        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-25-1319 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-25-1635 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-25-2393 
       24.99        24.00        85.05        13.02        49.05        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-29-1698 TCGA-29-1699 
      101.79        39.02        33.93        31.20        68.32        36.36 
TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1761 
       16.93        59.67        18.25        41.98        31.27        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-29-1778 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 
       14.93         7.23         5.36        36.30        86.17        65.00 
TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 
       62.47        45.11        13.84        42.25        21.47        11.47 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 
        9.76        35.77        38.07        51.91        36.26         2.47 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 
       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-36-1577 TCGA-36-1580 TCGA-36-1581 
       22.55         8.55        30.08        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-36-2551 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 
       14.17         6.05        16.18        11.47        13.81        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-59-A5PD 
        9.40        34.39         2.14         5.42        44.81        20.52 
TCGA-5X-AA5U TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
       11.87        11.11         8.09        20.94        31.43        18.54 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
       27.88         4.34        31.79        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-61-2003 TCGA-61-2008 
       38.17         2.01         5.52        14.50         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-61-2092 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-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
       22.22         6.35        31.07         8.61        39.68        18.94 
TCGA-VG-A8LO 
        0.79 

  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 
             35.28              28.37 
[1] "1.0 - 130.0 (35.3)" "0.3 - 180.2 (28.4)"
[1] "hr=" "1.5"
D78V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  20Q LOSS MUTATED         0    31                0
  20Q LOSS WILD-TYPE       3   527                2
D78V3, multiclass
                  clus
vv                 20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  OMENTUM                         0                  3
  OVARY                          31                527
  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, continuous
D78V5, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0  32
  20Q LOSS WILD-TYPE   3 538
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0   32
  20Q LOSS WILD-TYPE    3  538
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 0                  3
  YES               32                538
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  20Q LOSS MUTATED    0  0  0  0
  20Q LOSS WILD-TYPE 15 26  5  3
D78V6, multiclass
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q LOSS MUTATED                                  0     1
  20Q LOSS WILD-TYPE                                3    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  20Q LOSS MUTATED                           2
  20Q LOSS WILD-TYPE                        32
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20Q LOSS MUTATED                                           0    28
  20Q LOSS WILD-TYPE                                         1   448
D78V7, multiclass
                                           clus
vv                                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    1                 18
  BLACK OR AFRICAN AMERICAN                                2                 32
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   28                448
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V8, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     1  20
  20Q LOSS WILD-TYPE   9 307
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1   20
  20Q LOSS WILD-TYPE    9  307
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO               20                307
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    90 102
  21Q LOSS WILD-TYPE 178 190
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               192                368 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               102                190 
$`21Q LOSS MUTATED`
TCGA-04-1335 TCGA-04-1347 TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 
        1.81        63.09        63.98        65.46         0.53        49.28 
TCGA-04-1362 TCGA-04-1365 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1651 
       44.32        76.57        55.43        48.89        28.64        36.23 
TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 
       31.86        47.70        45.37        17.98        35.57         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-10-0926 TCGA-10-0927 TCGA-10-0930 
       63.09        39.75        12.46        25.91        81.86        34.19 
TCGA-10-0937 TCGA-13-0723 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0758 
       19.99        39.58        15.19        17.82        55.17        11.38 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0791 TCGA-13-0792 TCGA-13-0794 TCGA-13-0800 
       11.54        34.06        38.93        36.72        30.35         8.12 
TCGA-13-0803 TCGA-13-0883 TCGA-13-0886 TCGA-13-0887 TCGA-13-0891 TCGA-13-0899 
       43.86        68.94        74.27        66.67        69.01        56.15 
TCGA-13-0900 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0912 TCGA-13-0913 
       57.07        47.84        44.94        44.84        34.06        29.98 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-1404 TCGA-13-1407 
       21.17        14.89        13.81         4.64         6.61         6.05 
TCGA-13-1409 TCGA-13-1411 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 
        6.84         4.21        29.42        98.04        22.39        70.82 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1497 TCGA-13-1501 TCGA-13-1507 TCGA-13-2061 
       38.20        49.25        54.31        32.84         4.77        10.78 
TCGA-13-2065 TCGA-20-1682 TCGA-20-1684 TCGA-20-1686 TCGA-20-1687 TCGA-23-1022 
        8.75        27.52        19.10         2.93         2.66        49.68 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1113 TCGA-23-1114 TCGA-23-1124 
       29.13        18.90         2.76        31.20        68.68        58.13 
TCGA-23-2072 TCGA-23-2077 TCGA-23-2641 TCGA-24-0968 TCGA-24-0975 TCGA-24-1103 
       24.95       115.89         2.76        19.66        21.80        54.12 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1418 TCGA-24-1422 TCGA-24-1425 TCGA-24-1431 
       47.41         6.31         7.99         0.76         5.95        19.17 
TCGA-24-1434 TCGA-24-1471 TCGA-24-1548 TCGA-24-1549 TCGA-24-1557 TCGA-24-1567 
       18.67         1.18        16.21        56.58        39.88        17.23 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1846 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 
       88.37        48.33         4.37         5.79         5.52         9.80 
TCGA-24-1924 TCGA-24-1930 TCGA-24-2023 TCGA-24-2026 TCGA-24-2029 TCGA-24-2267 
       30.21        81.11        44.84        34.82        14.43        47.54 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2298 TCGA-25-1316 TCGA-25-1318 TCGA-25-1320 
       44.61         0.82        53.26        42.05        34.98        37.97 
TCGA-25-1321 TCGA-25-1625 TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 
       33.96        27.62        12.95        38.20         0.30        59.15 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-2396 
       62.17        35.87        52.04        14.96        24.99         3.02 
TCGA-29-1691 TCGA-29-1695 TCGA-29-1699 TCGA-29-1705 TCGA-29-1711 TCGA-29-1761 
       48.33        40.41        36.36        18.25        34.62        17.36 
TCGA-29-1763 TCGA-29-1769 TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1784 
       66.81        22.98        24.36        17.33        12.36         5.36 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-A5NZ TCGA-30-1714 
       36.30        86.17        65.00        62.47        35.77        38.07 
TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 TCGA-30-1866 
       51.91        36.26         2.47        15.68        48.10        36.62 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1950 TCGA-31-1956 TCGA-36-1569 TCGA-36-1575 
       30.05        48.79        18.77        44.12        29.10         8.55 
TCGA-36-1581 TCGA-36-2530 TCGA-36-2538 TCGA-36-2545 TCGA-36-2548 TCGA-36-2552 
       24.69        33.01        25.08        18.31        14.17        11.47 
TCGA-3P-A9WA TCGA-42-2587 TCGA-42-2593 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 
       13.81        23.74         1.48        25.08        25.02       180.20 
TCGA-59-2372 TCGA-59-A5PD TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 
       44.81        20.52        18.54        27.88         4.34        31.79 
TCGA-61-1734 TCGA-61-1741 TCGA-61-1899 TCGA-61-1904 TCGA-61-1913 TCGA-61-1918 
       28.47        33.67         8.42         9.07        48.92        15.75 
TCGA-61-1919 TCGA-61-2008 TCGA-61-2016 TCGA-61-2094 TCGA-61-2113 TCGA-WR-A838 
       38.17        30.64         1.18        71.74        22.22         9.99 

$`21Q LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 
       43.92        41.00        49.15         2.01        46.62         1.08 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 TCGA-04-1349 TCGA-04-1361 
       18.51        11.87        65.52        48.76        21.57        32.52 
TCGA-04-1364 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 
       33.67       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-04-1646 
        0.79        38.37       119.08        29.10        84.20        27.88 
TCGA-04-1649 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-1664 TCGA-09-1665 
       64.64        29.16         9.47        57.76        74.93        41.62 
TCGA-09-1666 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 
       57.60        55.36        17.98         5.85         3.02         8.55 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 TCGA-09-2054 
        6.18         6.12        35.15         4.54        71.11        20.94 
TCGA-09-2055 TCGA-10-0925 TCGA-10-0928 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       26.93        54.31        18.51        32.88        14.66         6.71 
TCGA-10-0935 TCGA-10-0936 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
       35.44        36.92        20.91         6.21        24.59        44.55 
TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0755 TCGA-13-0757 TCGA-13-0762 
        2.73        12.39        31.20         2.50        11.18        32.25 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 
       31.04        21.40         8.45        28.70        19.59         8.71 
TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
        7.79         8.28         8.19        35.28        35.31        13.61 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0893 
      107.18        91.40        70.39        61.84        67.99        43.36 
TCGA-13-0897 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0910 TCGA-13-0911 
       57.47        19.36        47.38        48.33        37.08        27.72 
TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1405 TCGA-13-1408 TCGA-13-1410 
        6.41         6.08        10.88         7.36         5.92         4.70 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1485 TCGA-13-1489 
        5.33        54.64        87.06        61.71        20.68        82.88 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 
       52.44        73.55         4.24        37.61        38.40        13.97 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
       16.57         4.21         4.41         4.18         2.56         3.91 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2071 TCGA-13-A5FT 
        3.09        14.24        12.23         8.61         6.28        54.77 
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-20-1685 TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
       16.70        47.54        40.54        15.39        26.83        32.09 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1116 
       49.41         8.81        51.35        54.51         3.22         4.57 
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-23-1809 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 
       33.47         0.53        87.48        91.66        77.00        49.84 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0979 TCGA-24-0980 
        4.70         4.50         7.63        11.64        41.56         7.66 
TCGA-24-0982 TCGA-24-1104 TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 TCGA-24-1423 
       22.32        63.55         6.38         7.82         7.86         6.25 
TCGA-24-1424 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1435 
        6.02         5.36         4.83        17.39        28.37        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-24-1550 
        3.45        22.22        26.96        57.40        64.27        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-24-1603 
       44.09        45.50        47.70        25.87        10.26        90.15 
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-24-1923 TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 TCGA-24-2020 TCGA-24-2024 
       22.68        16.44        11.05         4.87       152.02        58.16 
TCGA-24-2027 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
      109.71        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-24-2289 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-25-1317 TCGA-25-1319 TCGA-25-1322 
       26.96        33.01        52.04         2.01        65.00         2.99 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1628 TCGA-25-1877 
       12.99        15.02        18.58        17.03        20.61        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-25-2399 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-29-1696 
       26.99        78.90        47.61       101.79        39.02        33.93 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 
       31.20        68.32        16.93        23.93        59.67        41.98 
TCGA-29-1710 TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1771 
       31.27        86.60        62.93        39.42        31.30        22.55 
TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-2428 
       11.84        12.30        14.93         8.38         7.23        45.11 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-30-1857 
       13.84        42.25        21.47        11.47         9.76         0.26 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 
       44.91        34.78         6.12         1.22        57.57        24.26 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 
       45.57        30.18        22.49         6.71        42.51         2.20 
TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1576 TCGA-36-1577 
       28.77        21.53        22.85        22.55        30.08        25.74 
TCGA-36-1578 TCGA-36-1580 TCGA-36-2529 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       27.85        24.23        35.05        29.49        29.82        25.91 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2547 TCGA-36-2549 
       23.80        21.60         2.24        20.98        20.52         6.05 
TCGA-36-2551 TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
       16.18        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-59-2351 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-5X-AA5U TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
        5.42        11.87        11.11         8.09        20.94        31.43 
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-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 
        5.79        11.41        13.02        34.13        31.30        37.05 
TCGA-61-1911 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1995 TCGA-61-1998 
       42.51        56.61        67.76        43.43         2.01         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2009 TCGA-61-2012 TCGA-61-2017 
       14.50        17.98         4.01        39.85        30.64        45.96 
TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 
       45.40         4.80         4.77        51.72        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-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P 
       44.52       125.75         6.35        31.07         8.61        39.68 
TCGA-OY-A56Q TCGA-VG-A8LO 
       18.94         0.79 

  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 
            30.575             26.945 
[1] "0.3 - 180.2 (30.6)" "0.3 - 152.0 (26.9)"
[1] "hr=" "1"  
D79V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  21Q LOSS MUTATED         1   191                0
  21Q LOSS WILD-TYPE       2   367                2
D79V3, multiclass
                  clus
vv                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  OMENTUM                         1                  2
  OVARY                         191                367
  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, continuous
D79V5, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     1 194
  21Q LOSS WILD-TYPE   2 376
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1  194
  21Q LOSS WILD-TYPE    2  376
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 1                  2
  YES              194                376
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  21Q LOSS MUTATED    4  8  1  1
  21Q LOSS WILD-TYPE 11 18  4  2
D79V6, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0                4                 11
  R1                8                 18
  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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q LOSS MUTATED                                  1     4
  21Q LOSS WILD-TYPE                                2    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  21Q LOSS MUTATED                          12
  21Q LOSS WILD-TYPE                        22
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  21Q LOSS MUTATED                                           1   166
  21Q LOSS WILD-TYPE                                         0   310
D79V7, multiclass
                                           clus
vv                                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  2
  ASIAN                                                    4                 15
  BLACK OR AFRICAN AMERICAN                               12                 22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  166                310
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V8, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     3 120
  21Q LOSS WILD-TYPE   7 207
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      3  120
  21Q LOSS WILD-TYPE    7  207
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  7
  NOT HISPANIC OR LATINO              120                207
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED   193 226
  22Q LOSS WILD-TYPE  75  66
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               419                141 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               226                 66 
$`22Q LOSS MUTATED`
TCGA-04-1331 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 
       43.92        49.15         2.01        46.62         1.08        18.51 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 
       65.52        63.09        21.57        63.98        65.46        49.28 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 
       32.52        44.32        76.57       103.40        82.39        56.55 
TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 
       19.99         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-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 
       45.37        29.16         9.47        57.76        17.98        35.57 
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-09-1668 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-09-2044 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 
        6.12         4.54       112.41        71.11        63.09        39.75 
TCGA-09-2054 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       20.94        12.46        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        34.06        21.40        38.93 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 
       30.35        19.59         7.79         8.12         8.28         8.19 
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 
       91.40        74.27        66.67        70.39        61.84        67.99 
TCGA-13-0891 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 
       69.01        57.47        57.07        19.36        47.38        48.33 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
       44.94        44.84        37.08        27.72        34.06        29.98 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1404 
       21.17        14.89         4.64         6.41         6.08         6.61 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
        6.05         5.92         6.84         4.70         4.21         5.33 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1489 
       87.06        61.71        29.42        98.04        22.39        82.88 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 
       52.44        73.55        38.20        49.25         4.24        54.31 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       37.61        38.40        13.97        16.57         4.21         4.41 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
        4.77         4.18         3.09        14.24        12.23         8.61 
TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 
       10.78         8.75         6.28        54.77         8.42        25.94 
TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1687 
       26.20        27.52        25.38        19.10        16.70         2.66 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1024 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 
       47.54        49.68        15.39        32.09        49.41         8.81 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 
       29.13        18.90         2.76        51.35        54.51        31.20 
TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1122 TCGA-23-1123 TCGA-23-2072 
       68.68         4.57        33.30        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-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0982 
        7.63        19.66        11.64        21.80        41.56        22.32 
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-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
        4.83        17.39        19.17        18.67        43.53         8.55 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 
       12.46        45.14         1.18        22.22        26.96        57.40 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1552 TCGA-24-1555 TCGA-24-1557 
       16.21        56.58        41.06        41.39        88.50        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-24-1604 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-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1930 
        4.37         5.52         9.80        22.68        30.21        81.11 
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-24-2030 TCGA-24-2033 TCGA-24-2036 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 
       55.92        18.48        64.01        57.07        36.16         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2288 TCGA-24-2293 
        0.36        47.54        31.63        70.45         0.82        16.64 
TCGA-24-2295 TCGA-24-2298 TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 
       33.11        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-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 
       15.02        18.58        17.03        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-25-2042 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-25-2399 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-29-1693 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-29-1711 
       16.93        23.93        59.67        18.25        41.98        34.62 
TCGA-29-1761 TCGA-29-1763 TCGA-29-1766 TCGA-29-1769 TCGA-29-1774 TCGA-29-1775 
       17.36        66.81        39.42        22.98        17.33        12.36 
TCGA-29-1776 TCGA-29-1778 TCGA-29-1783 TCGA-29-1785 TCGA-29-2428 TCGA-29-2429 
       11.84        14.93         7.23        36.30        45.11        13.84 
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-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 
       15.68        48.10        44.91         6.12        36.62         1.22 
TCGA-30-1880 TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 TCGA-31-1951 TCGA-31-1953 
       57.57        24.26        48.79        45.57        22.49         6.71 
TCGA-31-1955 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1571 TCGA-36-1575 
       42.51         2.20        28.77        29.10        22.85         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-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 
       29.49        29.82        25.08        23.80        21.60         2.24 
TCGA-36-2544 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2588 
       20.98        14.17        16.18        11.47        13.81        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-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2350 
       21.14        29.00        25.08        25.02       180.20        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-5X-AA5U TCGA-61-1722 TCGA-61-1725 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 
       11.87         8.09        31.43        27.88         4.34        31.79 
TCGA-61-1736 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1899 
       48.79        35.80         2.43        33.67        43.69         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1913 
        5.79        11.41        34.13        31.30        37.05        48.92 
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-61-2003 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2018 
       14.50         4.01        39.85        30.64         1.18        45.40 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2102 
        4.80         4.77        58.39        60.62        65.52         6.48 
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 
        8.61        39.68        18.94         0.79         9.99 

$`22Q LOSS WILD-TYPE`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1343 TCGA-04-1348 TCGA-04-1353 TCGA-04-1364 
       41.00         1.81        11.87        48.76         0.53        33.67 
TCGA-04-1516 TCGA-04-1536 TCGA-04-1654 TCGA-09-1665 TCGA-09-1672 TCGA-09-2043 
       41.59        29.10        47.70        41.62         5.85         6.18 
TCGA-09-2045 TCGA-09-2055 TCGA-10-0930 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 
       35.15        26.93        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        32.25        31.04         8.45 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0797 TCGA-13-0893 TCGA-13-0899 TCGA-13-0905 
       36.72        28.70         8.71        43.36        56.15        47.84 
TCGA-13-0920 TCGA-13-1403 TCGA-13-1405 TCGA-13-1477 TCGA-13-1485 TCGA-13-1488 
       13.81        10.88         7.36        54.64        20.68        70.82 
TCGA-13-1501 TCGA-13-1510 TCGA-13-1511 TCGA-20-0987 TCGA-20-0996 TCGA-20-1686 
       32.84         2.56         3.91        23.05        72.20         2.93 
TCGA-23-1023 TCGA-23-1026 TCGA-23-1111 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 
       40.54        26.83         3.22        86.01       129.96         4.27 
TCGA-23-1121 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2079 TCGA-24-0980 
        6.38        58.13         0.53       115.89        91.66         7.66 
TCGA-24-1103 TCGA-24-1430 TCGA-24-1463 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 
       54.12        28.37        72.92       105.99         9.11         3.45 
TCGA-24-1546 TCGA-24-1551 TCGA-24-1553 TCGA-24-1556 TCGA-24-1558 TCGA-24-1563 
       64.27        51.91        58.09        70.62        19.53        47.70 
TCGA-24-1845 TCGA-24-1847 TCGA-24-1849 TCGA-24-1927 TCGA-24-1928 TCGA-24-2024 
        3.81        11.28         5.79        16.44        11.05        58.16 
TCGA-24-2035 TCGA-24-2038 TCGA-24-2281 TCGA-24-2289 TCGA-24-2290 TCGA-24-2297 
       28.18        44.52        44.61        67.36        36.23        55.86 
TCGA-25-1313 TCGA-25-1323 TCGA-25-1625 TCGA-25-1627 TCGA-25-1630 TCGA-25-2396 
       26.96        12.99        27.62        12.95        38.20         3.02 
TCGA-25-2401 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1699 TCGA-29-1710 
        2.96        78.90        47.61        48.33        36.36        31.27 
TCGA-29-1762 TCGA-29-1764 TCGA-29-1768 TCGA-29-1770 TCGA-29-1771 TCGA-29-1777 
       86.60        62.93        31.30        24.36        22.55        12.30 
TCGA-29-1781 TCGA-29-1784 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2431 
        8.38         5.36        86.17        65.00        62.47        42.25 
TCGA-29-2434 TCGA-29-2436 TCGA-30-1857 TCGA-30-1861 TCGA-30-1891 TCGA-31-1946 
       11.47         9.76         0.26        34.78        30.05        30.18 
TCGA-31-1950 TCGA-31-1956 TCGA-36-1570 TCGA-36-1574 TCGA-36-2529 TCGA-36-2537 
       18.77        44.12        21.53        22.55        35.05        25.91 
TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 TCGA-42-2582 TCGA-42-2587 TCGA-57-1585 
       18.31        20.52         6.05        47.57        23.74         1.74 
TCGA-57-1586 TCGA-59-2349 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1724 TCGA-61-1727 
       22.32        80.12        20.52        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-61-2104 
       61.64        55.50        76.87 

  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 
             27.88              30.05 
[1] "0.3 - 180.2 (27.9)" "0.3 - 130.0 (30.1)"
[1] "hr=" "1.2"
D80V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  22Q LOSS MUTATED         2   417                1
  22Q LOSS WILD-TYPE       1   141                1
D80V3, multiclass
                  clus
vv                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  OMENTUM                         2                  1
  OVARY                         417                141
  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, continuous
D80V5, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     3 425
  22Q LOSS WILD-TYPE   0 145
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      3  425
  22Q LOSS WILD-TYPE    0  145
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 3                  0
  YES              425                145
[1] 2 2
[1] FALSE
                    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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q LOSS MUTATED                                  3    14
  22Q LOSS WILD-TYPE                                0     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  22Q LOSS MUTATED                          26
  22Q LOSS WILD-TYPE                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  22Q LOSS MUTATED                                           1   357
  22Q LOSS WILD-TYPE                                         0   119
D80V7, multiclass
                                           clus
vv                                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         3                  0
  ASIAN                                                   14                  5
  BLACK OR AFRICAN AMERICAN                               26                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  357                119
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V8, 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   146 168
  XP LOSS WILD-TYPE 122 124
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              314               246 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              168               124 
$`XP LOSS MUTATED`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 
       43.92         1.81        49.15        65.52        63.09        48.76 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 
       32.52        44.32        33.67        76.57       103.40        56.55 
TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1638 
       19.99         0.79        38.37       119.08        29.10        55.43 
TCGA-04-1644 TCGA-04-1648 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 
       48.89        28.64        36.23        31.86        47.70        45.37 
TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       57.76        17.98        35.57         9.99        38.43        89.33 
TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 TCGA-09-1673 TCGA-09-1675 
       74.93        57.60        61.87        30.51         3.02        97.55 
TCGA-09-2044 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 
        6.12       112.41        71.11        63.09        39.75        20.94 
TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       26.93        12.46        54.31        25.91        81.86        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 
       34.19        32.88        19.99        20.91         6.21        44.55 
TCGA-13-0725 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 
       12.39         2.50        11.18        11.38        11.54        34.06 
TCGA-13-0766 TCGA-13-0792 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 
       21.40        36.72        30.35        19.59         8.71         7.79 
TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
        8.28        43.86        35.28        35.31        13.61        68.94 
TCGA-13-0887 TCGA-13-0889 TCGA-13-0891 TCGA-13-0900 TCGA-13-0903 TCGA-13-0905 
       66.67        61.84        69.01        57.07        47.38        47.84 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0913 TCGA-13-0919 TCGA-13-0920 
       44.94        44.84        37.08        29.98        14.89        13.81 
TCGA-13-0924 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1412 TCGA-13-1482 
        6.08         6.61         7.36         6.05         5.33        61.71 
TCGA-13-1483 TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       29.42        22.39        82.88        52.44        73.55        38.20 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1500 TCGA-13-1504 TCGA-13-1505 
       49.25         4.24        37.61        13.97        16.57         4.21 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2059 TCGA-13-2061 TCGA-20-0987 
        4.18         2.56         3.09        12.23        10.78        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-24-1419 TCGA-24-1422 
       47.41         6.31         6.38         7.82         7.86         0.76 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 
        6.25         6.02         5.36         4.83        17.39        28.37 
TCGA-24-1431 TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 TCGA-24-1469 TCGA-24-1546 
       19.17        43.53        72.92        12.46         9.11        64.27 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1552 TCGA-24-1555 TCGA-24-1560 
       16.21        56.58        41.06        41.39        88.50        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1567 TCGA-24-1603 TCGA-24-1614 TCGA-24-1845 
       45.50        47.70        17.23        90.15        48.33         3.81 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1930 TCGA-24-2023 TCGA-24-2024 
        4.37        11.28         5.79        81.11        44.84        58.16 
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-24-2254 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-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2297 TCGA-24-2298 TCGA-25-1314 
        0.82        67.36        36.23        55.86        53.26        33.01 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1320 TCGA-25-1322 TCGA-25-1625 TCGA-25-1630 
       52.04        42.05        37.97         2.99        27.62        38.20 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 
        0.30        59.15        52.04        14.96        24.99        85.05 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 
       13.02        49.05         1.02         3.02        12.00        19.99 
TCGA-25-2400 TCGA-25-2409 TCGA-29-1688 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 
       42.02        26.99        78.90       101.79        39.02        33.93 
TCGA-29-1697 TCGA-29-1699 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
       31.20        36.36        23.93        59.67        18.25        41.98 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1769 TCGA-29-1771 
       31.27        34.62        17.36        86.60        22.98        22.55 
TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1784 TCGA-29-2414 
       12.36        12.30        14.93         8.38         5.36        86.17 
TCGA-29-2427 TCGA-29-2431 TCGA-29-2432 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 
       62.47        42.25        21.47        35.77        38.07        51.91 
TCGA-30-1853 TCGA-30-1857 TCGA-30-1866 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 
       36.26         0.26        36.62        57.57        24.26        30.05 
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-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-36-1580 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-36-2542 TCGA-36-2545 TCGA-36-2547 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2591 
       21.60        18.31        20.52        13.81        47.57        40.77 
TCGA-42-2593 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1994 
        1.48        21.14         1.74        22.32        29.00        25.02 
TCGA-59-2350 TCGA-59-2354 TCGA-59-2363 TCGA-59-A5PD TCGA-61-1724 TCGA-61-1725 
       22.32        34.39         5.42        20.52        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 
       31.07         8.61 

$`XP LOSS WILD-TYPE`
TCGA-04-1332 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 
       41.00         2.01        46.62         1.08        18.51        11.87 
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-04-1542 TCGA-04-1646 TCGA-04-1649 TCGA-09-0364 TCGA-09-0365 
       41.59        84.20        27.88        64.64        29.16         9.47 
TCGA-09-1665 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 TCGA-09-2043 
       41.62        55.36        17.98         5.85         8.55         6.18 
TCGA-09-2045 TCGA-09-2048 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 
       35.15         4.54        14.66         6.71        35.44        36.92 
TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 
       24.59        39.58         2.73        31.20        15.19        17.82 
TCGA-13-0751 TCGA-13-0762 TCGA-13-0764 TCGA-13-0768 TCGA-13-0791 TCGA-13-0793 
       55.17        32.25        31.04         8.45        38.93        28.70 
TCGA-13-0800 TCGA-13-0802 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0888 
        8.12         8.19       107.18        91.40        74.27        70.39 
TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0901 TCGA-13-0904 
       67.99        43.36        57.47        56.15        19.36        48.33 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 TCGA-13-0921 TCGA-13-0923 TCGA-13-1403 
       27.72        34.06        21.17         4.64         6.41        10.88 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1477 TCGA-13-1481 
        5.92         6.84         4.70         4.21        54.64        87.06 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1488 TCGA-13-1497 TCGA-13-1499 TCGA-13-1501 
       98.04        20.68        70.82        54.31        38.40        32.84 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1511 TCGA-13-2057 TCGA-13-2060 TCGA-13-2065 
        4.41         4.77         3.91        14.24         8.61         8.75 
TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-0996 TCGA-23-1021 
        6.28        54.77         8.42        25.94        72.20        47.54 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1110 TCGA-23-1114 TCGA-23-1116 
       40.54        15.39        26.83        54.51        68.68         4.57 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1121 TCGA-23-1122 TCGA-23-1124 
       33.30        86.01       129.96         6.38        39.09        58.13 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2078 TCGA-23-2084 TCGA-23-2643 TCGA-23-2645 
        0.53        24.95        87.48        49.84         4.70         4.50 
TCGA-24-0968 TCGA-24-0982 TCGA-24-1418 TCGA-24-1425 TCGA-24-1434 TCGA-24-1436 
       19.66        22.32         7.99         5.95        18.67         8.55 
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-24-1551 TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 
       57.40        51.91        58.09        70.62        39.88        19.53 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 
       25.87        10.26        88.37        38.24         8.32         3.48 
TCGA-24-1844 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 
        3.72         5.52         9.80        22.68        30.21        16.44 
TCGA-24-1928 TCGA-24-2019 TCGA-24-2020 TCGA-24-2026 TCGA-24-2038 TCGA-24-2261 
       11.05         4.87       152.02        34.82        44.52         0.79 
TCGA-24-2281 TCGA-24-2293 TCGA-24-2295 TCGA-25-1312 TCGA-25-1313 TCGA-25-1317 
       44.61        16.64        33.11         1.02        26.96         2.01 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
       34.98        65.00        33.96        12.99        15.02        18.58 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1633 TCGA-25-1634 TCGA-25-1877 
       17.03        12.95        20.61        62.17        35.87        24.00 
TCGA-25-2393 TCGA-25-2398 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-29-1690 
       38.04        45.01         2.96        29.03        31.00        47.61 
TCGA-29-1691 TCGA-29-1695 TCGA-29-1698 TCGA-29-1701 TCGA-29-1763 TCGA-29-1764 
       48.33        40.41        68.32        16.93        66.81        62.93 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1770 TCGA-29-1774 TCGA-29-1776 TCGA-29-1783 
       39.42        31.30        24.36        17.33        11.84         7.23 
TCGA-29-1785 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 TCGA-29-2434 TCGA-29-2436 
       36.30        65.00        45.11        13.84        11.47         9.76 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 
        2.47        15.68        48.10        44.91        34.78         6.12 
TCGA-30-1867 TCGA-30-1892 TCGA-31-1946 TCGA-31-1959 TCGA-36-1568 TCGA-36-1571 
        1.22        48.79        30.18         2.20        28.77        22.85 
TCGA-36-1576 TCGA-36-1581 TCGA-36-2529 TCGA-36-2540 TCGA-36-2543 TCGA-36-2544 
       30.08        24.69        35.05        23.80         2.24        20.98 
TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 TCGA-42-2588 
       14.17         6.05        16.18        11.47        23.74        28.93 
TCGA-42-2589 TCGA-42-2590 TCGA-57-1582 TCGA-57-1583 TCGA-57-1993 TCGA-59-2348 
       42.02        10.42        24.03        11.38        25.08       180.20 
TCGA-59-2349 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2372 TCGA-5X-AA5U 
       80.12       116.12         9.40         2.14        44.81        11.87 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1730 TCGA-61-1734 TCGA-61-1740 TCGA-61-1741 
       11.11         8.09         4.34        28.47         2.43        33.67 
TCGA-61-1900 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 
        5.79         9.07        34.13        31.30        37.05        42.51 
TCGA-61-1917 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2009 TCGA-61-2017 
       43.43         2.01         5.52        14.50        39.85        45.96 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 
       51.72        71.74        61.64        60.62        55.50         6.48 
TCGA-61-2109 TCGA-61-2111 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       20.68       125.75        39.68        18.94         0.79         9.99 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.26              0.53 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           119.08            180.20 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           29.900            25.905 
[1] "0.3 - 119.1 (29.9)" "0.5 - 180.2 (25.9)"
[1] "hr=" "1"  
D81V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  XP LOSS MUTATED         2   312                0
  XP LOSS WILD-TYPE       1   246                2
D81V3, multiclass
                  clus
vv                 XP LOSS MUTATED XP LOSS WILD-TYPE
  OMENTUM                        2                 1
  OVARY                        312               246
  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, continuous
D81V5, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     3 319
  XP LOSS WILD-TYPE   0 251
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      3  319
  XP LOSS WILD-TYPE    0  251
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO                3                 0
  YES             319               251
[1] 2 2
[1] FALSE
                   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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP LOSS MUTATED                                  2    13
  XP LOSS WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN
  XP LOSS MUTATED                          17
  XP LOSS WILD-TYPE                        17
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XP LOSS MUTATED                                           1   266
  XP LOSS WILD-TYPE                                         0   210
D81V7, multiclass
                                           clus
vv                                          XP LOSS MUTATED XP LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        2                 1
  ASIAN                                                  13                 6
  BLACK OR AFRICAN AMERICAN                              17                17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 266               210
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V8, 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   127 143
  XQ LOSS WILD-TYPE 141 149
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              270               290 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              143               149 
$`XQ LOSS MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1341 TCGA-04-1343 TCGA-04-1347 
       43.92        41.00        49.15         1.08        11.87        63.09 
TCGA-04-1348 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       48.76        32.52        44.32        33.67        76.57       103.40 
TCGA-04-1514 TCGA-04-1517 TCGA-04-1519 TCGA-04-1530 TCGA-04-1536 TCGA-04-1638 
       56.55        19.99         0.79       119.08        29.10        55.43 
TCGA-04-1644 TCGA-04-1648 TCGA-04-1651 TCGA-04-1654 TCGA-09-0366 TCGA-09-0367 
       48.89        28.64        36.23        47.70        57.76        17.98 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 
       35.57         9.99        38.43        89.33        74.93        57.60 
TCGA-09-1667 TCGA-09-1673 TCGA-09-1675 TCGA-09-2044 TCGA-09-2049 TCGA-09-2050 
       61.87         3.02        97.55         6.12       112.41        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 
       63.09        39.75        20.94        26.93        12.46        54.31 
TCGA-10-0926 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0937 TCGA-10-0938 
       25.91        18.51        34.19        32.88        19.99        20.91 
TCGA-13-0714 TCGA-13-0725 TCGA-13-0726 TCGA-13-0758 TCGA-13-0760 TCGA-13-0766 
        6.21        12.39        31.20        11.38        11.54        21.40 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0799 TCGA-13-0801 TCGA-13-0803 
       38.93        36.72        28.70         7.79         8.28        43.86 
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        61.84        69.01 
TCGA-13-0900 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
       57.07        47.38        47.84        44.94        44.84        37.08 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 
       34.06        29.98        14.89        13.81         6.41         6.08 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1412 TCGA-13-1482 TCGA-13-1483 
        7.36         6.05         5.92         5.33        61.71        29.42 
TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1495 TCGA-13-1496 
       22.39        82.88        52.44        73.55        49.25         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 
       54.31        37.61        13.97         4.77         4.18         2.56 
TCGA-13-1512 TCGA-13-2059 TCGA-13-2061 TCGA-13-2071 TCGA-20-1682 TCGA-20-1684 
        3.09        12.23        10.78         6.28        27.52        19.10 
TCGA-23-1022 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 
       49.68        32.09        49.41         8.81        29.13        18.90 
TCGA-23-1032 TCGA-23-1113 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-2081 
        2.76        31.20         4.27        39.09        33.47        77.00 
TCGA-23-2641 TCGA-24-0966 TCGA-24-0970 TCGA-24-0980 TCGA-24-1103 TCGA-24-1105 
        2.76         7.63        11.64         7.66        54.12        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 TCGA-24-1423 TCGA-24-1425 
        6.31         6.38         7.82         7.86         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        19.17        43.53 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 TCGA-24-1546 
       72.92        12.46        45.14         9.11         3.45        64.27 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1552 TCGA-24-1560 TCGA-24-1562 
       16.21        56.58        41.06        41.39        44.09        45.50 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1845 TCGA-24-1849 
       17.23        90.15        88.37        48.33         3.81         5.79 
TCGA-24-1930 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 
       81.11        44.84        58.16       109.71        14.43        55.92 
TCGA-24-2035 TCGA-24-2036 TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 TCGA-24-2271 
       28.18        64.01        57.07        36.16         0.36        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-25-1322 TCGA-25-1625 TCGA-25-1630 
       33.01        52.04        42.05         2.99        27.62        38.20 
TCGA-25-1631 TCGA-25-1633 TCGA-25-1635 TCGA-25-1870 TCGA-25-1878 TCGA-25-2042 
        0.30        62.17        52.04        14.96        85.05        13.02 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2396 TCGA-25-2399 TCGA-25-2409 TCGA-29-1688 
       49.05         1.02         3.02        19.99        26.99        78.90 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1702 TCGA-29-1703 
      101.79        39.02        33.93        31.20        23.93        59.67 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1769 
       18.25        41.98        34.62        17.36        86.60        22.98 
TCGA-29-1771 TCGA-29-1775 TCGA-29-1777 TCGA-29-1781 TCGA-29-1784 TCGA-29-2414 
       22.55        12.36        12.30         8.38         5.36        86.17 
TCGA-29-2427 TCGA-29-2431 TCGA-29-2432 TCGA-30-1714 TCGA-30-1853 TCGA-30-1857 
       62.47        42.25        21.47        38.07        36.26         0.26 
TCGA-30-1866 TCGA-30-1880 TCGA-30-1891 TCGA-31-1944 TCGA-31-1953 TCGA-31-1955 
       36.62        57.57        30.05        45.57         6.71        42.51 
TCGA-31-1956 TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 
       44.12        29.10        21.53        22.55         8.55        25.74 
TCGA-36-1578 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
       27.85        33.01        29.49        29.82        25.91        25.08 
TCGA-36-2542 TCGA-36-2545 TCGA-36-2547 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2589 
       21.60        18.31        20.52        13.81        47.57        42.02 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1585 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 
       40.77         1.48         1.74        29.00        25.08        25.02 
TCGA-59-2350 TCGA-59-2354 TCGA-59-2363 TCGA-59-A5PD TCGA-61-1724 TCGA-61-1725 
       22.32        34.39         5.42        20.52        20.94        31.43 
TCGA-61-1727 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1743 TCGA-61-1901 
       18.54        48.79        44.84        35.80        43.69        11.41 
TCGA-61-1903 TCGA-61-1913 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-2002 
       13.02        48.92        15.75        38.17         2.01        17.98 
TCGA-61-2008 TCGA-61-2012 TCGA-61-2016 TCGA-61-2018 TCGA-61-2088 TCGA-61-2094 
       30.64        30.64         1.18        45.40         4.77        71.74 
TCGA-61-2096 TCGA-61-2098 TCGA-61-2104 TCGA-61-2110 TCGA-61-2113 TCGA-61-2613 
       58.39        65.52        76.87        44.52        22.22        31.07 

$`XQ LOSS WILD-TYPE`
TCGA-04-1335 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 TCGA-04-1346 TCGA-04-1349 
        1.81         2.01        46.62        18.51        65.52        21.57 
TCGA-04-1350 TCGA-04-1351 TCGA-04-1353 TCGA-04-1356 TCGA-04-1371 TCGA-04-1516 
       63.98        65.46         0.53        49.28        82.39        41.59 
TCGA-04-1525 TCGA-04-1542 TCGA-04-1646 TCGA-04-1649 TCGA-04-1652 TCGA-04-1655 
       38.37        84.20        27.88        64.64        31.86        45.37 
TCGA-09-0364 TCGA-09-0365 TCGA-09-1665 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 
       29.16         9.47        41.62        55.36        30.51        17.98 
TCGA-09-1672 TCGA-09-1674 TCGA-09-2043 TCGA-09-2045 TCGA-09-2048 TCGA-10-0927 
        5.85         8.55         6.18        35.15         4.54        81.86 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-13-0717 TCGA-13-0720 
       14.66         6.71        35.44        36.92        24.59        44.55 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 
       39.58         2.73        15.19        17.82        55.17         2.50 
TCGA-13-0757 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0768 TCGA-13-0794 
       11.18        34.06        32.25        31.04         8.45        30.35 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0800 TCGA-13-0802 TCGA-13-0804 TCGA-13-0884 
       19.59         8.71         8.12         8.19        35.28       107.18 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0888 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 
       91.40        74.27        70.39        67.99        43.36        57.47 
TCGA-13-0899 TCGA-13-0901 TCGA-13-0904 TCGA-13-0911 TCGA-13-0916 TCGA-13-0921 
       56.15        19.36        48.33        27.72        21.17         4.64 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1477 
       10.88         6.61         6.84         4.70         4.21        54.64 
TCGA-13-1481 TCGA-13-1484 TCGA-13-1485 TCGA-13-1488 TCGA-13-1494 TCGA-13-1499 
       87.06        98.04        20.68        70.82        38.20        38.40 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1511 TCGA-13-2057 
       32.84        16.57         4.21         4.41         3.91        14.24 
TCGA-13-2060 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
        8.61         8.75        54.77         8.42        23.05        25.94 
TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 
       26.20        72.20        25.38        16.70         2.93         2.66 
TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1109 TCGA-23-1110 
       47.54        40.54        15.39        26.83        51.35        54.51 
TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 
        3.22        68.68         4.57        33.30        86.01       129.96 
TCGA-23-1121 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 
        6.38        58.13         0.53        24.95       115.89        87.48 
TCGA-23-2079 TCGA-23-2084 TCGA-23-2643 TCGA-23-2645 TCGA-24-0968 TCGA-24-0975 
       91.66        49.84         4.70         4.50        19.66        21.80 
TCGA-24-0979 TCGA-24-0982 TCGA-24-1104 TCGA-24-1418 TCGA-24-1422 TCGA-24-1424 
       41.56        22.32        63.55         7.99         0.76         6.02 
TCGA-24-1434 TCGA-24-1436 TCGA-24-1467 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
       18.67         8.55       105.99         1.18        22.22        26.96 
TCGA-24-1545 TCGA-24-1551 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       57.40        51.91        58.09        88.50        70.62        39.88 
TCGA-24-1558 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1616 TCGA-24-1842 
       19.53        47.70        25.87        10.26        38.24         8.32 
TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 
        3.48         3.72         4.37        11.28         5.52         9.80 
TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 TCGA-24-2020 
       22.68        30.21        16.44        11.05         4.87       152.02 
TCGA-24-2026 TCGA-24-2033 TCGA-24-2038 TCGA-24-2261 TCGA-24-2267 TCGA-24-2281 
       34.82        18.48        44.52         0.79        47.54        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-25-1320 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-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1632 TCGA-25-1634 TCGA-25-1871 
       17.03        12.95        20.61        59.15        35.87        24.99 
TCGA-25-1877 TCGA-25-2393 TCGA-25-2397 TCGA-25-2398 TCGA-25-2400 TCGA-25-2401 
       24.00        38.04        12.00        45.01        42.02         2.96 
TCGA-25-2404 TCGA-25-2408 TCGA-29-1690 TCGA-29-1691 TCGA-29-1695 TCGA-29-1698 
       29.03        31.00        47.61        48.33        40.41        68.32 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1710 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 
       36.36        16.93        31.27        66.81        62.93        39.42 
TCGA-29-1768 TCGA-29-1770 TCGA-29-1774 TCGA-29-1776 TCGA-29-1778 TCGA-29-1783 
       31.30        24.36        17.33        11.84        14.93         7.23 
TCGA-29-1785 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 TCGA-29-2434 TCGA-29-2436 
       36.30        65.00        45.11        13.84        11.47         9.76 
TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 TCGA-30-1860 
       35.77        51.91         2.47        15.68        48.10        44.91 
TCGA-30-1861 TCGA-30-1862 TCGA-30-1867 TCGA-30-1887 TCGA-30-1892 TCGA-31-1946 
       34.78         6.12         1.22        24.26        48.79        30.18 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1959 TCGA-36-1568 TCGA-36-1571 TCGA-36-1576 
       18.77        22.49         2.20        28.77        22.85        30.08 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2540 TCGA-36-2543 TCGA-36-2544 
       24.23        24.69        35.05        23.80         2.24        20.98 
TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 TCGA-42-2588 
       14.17         6.05        16.18        11.47        23.74        28.93 
TCGA-42-2590 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-59-2348 
       10.42        24.03        11.38        21.14        22.32       180.20 
TCGA-59-2349 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2372 TCGA-5X-AA5U 
       80.12       116.12         9.40         2.14        44.81        11.87 
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 
        0.79         9.99 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.26              0.53 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           119.08            180.20 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           30.855            24.970 
[1] "0.3 - 119.1 (30.9)" "0.5 - 180.2 (25.0)"
[1] "hr=" "1.1"
D82V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  XQ LOSS MUTATED         1   269                0
  XQ LOSS WILD-TYPE       2   289                2
D82V3, multiclass
                  clus
vv                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  OMENTUM                        1                 2
  OVARY                        269               289
  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, continuous
D82V5, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     3 274
  XQ LOSS WILD-TYPE   0 296
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3  274
  XQ LOSS WILD-TYPE    0  296
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                3                 0
  YES             274               296
[1] 2 2
[1] FALSE
                   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"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ LOSS MUTATED                                  2    13
  XQ LOSS WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN
  XQ LOSS MUTATED                          13
  XQ LOSS WILD-TYPE                        21
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XQ LOSS MUTATED                                           1   230
  XQ LOSS WILD-TYPE                                         0   246
D82V7, multiclass
                                           clus
vv                                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        2                 1
  ASIAN                                                  13                 6
  BLACK OR AFRICAN AMERICAN                              13                21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 230               246
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     4 157
  XQ LOSS WILD-TYPE   6 170
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      4  157
  XQ LOSS WILD-TYPE    6  170
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 6
  NOT HISPANIC OR LATINO             157               170
[1] 2 2
[1] FALSE
