[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/15650402/transformed.cor.cli.txt"

nPatients in clinical file=590, in cluster file=466, common to both=465
[1]  23 465
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           382             83 
  TP53 MUTATED TP53 WILD-TYPE 
           382             83 
[1] "BRCA1 MUTATION ANALYSIS"
[1] 3
  BRCA1 MUTATED BRCA1 WILD-TYPE 
             19             446 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
             19             446 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           24           441 
  NF1 MUTATED NF1 WILD-TYPE 
           24           441 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           15           450 
  RB1 MUTATED RB1 WILD-TYPE 
           15           450 
[1] "BRCA2 MUTATION ANALYSIS"
[1] 3
  BRCA2 MUTATED BRCA2 WILD-TYPE 
             13             452 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
             13             452 
[1] "IL21R MUTATION ANALYSIS"
[1] 3
  IL21R MUTATED IL21R WILD-TYPE 
              8             457 
  IL21R MUTATED IL21R WILD-TYPE 
              8             457 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
             5            460 
  KRAS MUTATED KRAS WILD-TYPE 
             5            460 
[1] "YSK4 MUTATION ANALYSIS"
[1] 3
  YSK4 MUTATED YSK4 WILD-TYPE 
            10            455 
  YSK4 MUTATED YSK4 WILD-TYPE 
            10            455 
[1] "ANKRD35 MUTATION ANALYSIS"
[1] 3
  ANKRD35 MUTATED ANKRD35 WILD-TYPE 
                9               456 
  ANKRD35 MUTATED ANKRD35 WILD-TYPE 
                9               456 
[1] "C9ORF171 MUTATION ANALYSIS"
[1] 3
  C9ORF171 MUTATED C9ORF171 WILD-TYPE 
                 5                460 
  C9ORF171 MUTATED C9ORF171 WILD-TYPE 
                 5                460 
[1] "MTA2 MUTATION ANALYSIS"
[1] 3
  MTA2 MUTATED MTA2 WILD-TYPE 
             4            461 
  MTA2 MUTATED MTA2 WILD-TYPE 
             4            461 
[1] "CYP11B1 MUTATION ANALYSIS"
[1] 3
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
                8               457 
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
                8               457 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
             4            461 
  NRAS MUTATED NRAS WILD-TYPE 
             4            461 
[1] "ACBD4 MUTATION ANALYSIS"
[1] 3
  ACBD4 MUTATED ACBD4 WILD-TYPE 
              3             462 
  ACBD4 MUTATED ACBD4 WILD-TYPE 
              3             462 
[1] "EFEMP1 MUTATION ANALYSIS"
[1] 3
  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
               7              458 
  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
               7              458 
[1] "PODN MUTATION ANALYSIS"
[1] 3
  PODN MUTATED PODN WILD-TYPE 
             6            459 
  PODN MUTATED PODN WILD-TYPE 
             6            459 
[1] "TOP2A MUTATION ANALYSIS"
[1] 3
  TOP2A MUTATED TOP2A WILD-TYPE 
              8             457 
  TOP2A MUTATED TOP2A WILD-TYPE 
              8             457 
[1] "NCOA3 MUTATION ANALYSIS"
[1] 3
  NCOA3 MUTATED NCOA3 WILD-TYPE 
              5             460 
  NCOA3 MUTATED NCOA3 WILD-TYPE 
              5             460 
[1] "TP53TG5 MUTATION ANALYSIS"
[1] 3
  TP53TG5 MUTATED TP53TG5 WILD-TYPE 
                3               462 
  TP53TG5 MUTATED TP53TG5 WILD-TYPE 
                3               462 
[1] "RPGRIP1 MUTATION ANALYSIS"
[1] 3
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
                7               458 
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
                7               458 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
             5            460 
  PTEN MUTATED PTEN WILD-TYPE 
             5            460 
[1] "RB1CC1 MUTATION ANALYSIS"
[1] 3
  RB1CC1 MUTATED RB1CC1 WILD-TYPE 
               9              456 
  RB1CC1 MUTATED RB1CC1 WILD-TYPE 
               9              456 
[1] "LPAR3 MUTATION ANALYSIS"
[1] 3
  LPAR3 MUTATED LPAR3 WILD-TYPE 
              4             461 
  LPAR3 MUTATED LPAR3 WILD-TYPE 
              4             461 
[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 465 columns.

[1] "Batch" "26"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=54,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=218,	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=380,	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=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "GENDER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=0,	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=4,	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=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 24:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 25:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 26:'BATCH_NUMBER':	nDistinctValues=13,	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 465 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=54, binary=FALSE, numeric=TRUE
PRIMARY_SITE_OF_DISEASE, nv=3, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=4, binary=FALSE, numeric=TRUE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS_OF_RESECTION, nv=3, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
D1V1, survival
                sevent
clus2              0   1
  TP53 MUTATED   188 192
  TP53 WILD-TYPE  40  43
  TP53 MUTATED TP53 WILD-TYPE 
           380             83 
  TP53 MUTATED TP53 WILD-TYPE 
           192             43 
$`TP53 MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1343 
       43.92        41.00        49.15         2.01        46.62        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1361 
       65.52        63.09        48.76        21.57        63.98        32.52 
TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1369 TCGA-04-1514 
       44.32        33.67        76.57       103.40        21.11        56.55 
TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1644 
       41.59        19.99        38.37       119.08        84.20        48.89 
TCGA-04-1646 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 
       27.88        64.64        36.23        31.86        45.37        29.16 
TCGA-09-0366 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 
       57.76        35.57         9.99        38.43        89.33        41.62 
TCGA-09-1666 TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 
       57.60        30.51        17.98         3.02         8.55        97.55 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2053 TCGA-10-0926 
        6.12        35.15       112.41        71.11        39.75        25.91 
TCGA-10-0928 TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 
       18.51        32.88         6.71        35.44        19.99        20.91 
TCGA-13-0714 TCGA-13-0720 TCGA-13-0724 TCGA-13-0726 TCGA-13-0730 TCGA-13-0751 
        6.21        44.55         2.73        31.20        17.82        55.17 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 
       11.54        34.06        32.25        28.57        38.93        36.72 
TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 
       28.70        19.59         8.12         8.19        35.28        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 
       68.94       107.18        91.40        74.27        66.67        61.84 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0894 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 
       67.99        69.01        49.61        56.15        57.07        47.38 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       48.33        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-13-0924 
       29.98        21.17        14.89        13.81         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-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
        4.21         5.33        87.06        61.71        29.42        98.04 
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-13-1501 
       49.25         4.24        54.31        37.61        38.40        32.84 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1507 TCGA-13-1509 TCGA-13-1512 TCGA-13-2057 
       16.57         4.21         4.77         4.18         3.09        14.24 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2071 TCGA-20-0987 TCGA-20-0990 
       12.23         8.61        10.78         6.28        23.05        25.94 
TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 
       26.20        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-23-1028 
       47.54        49.68        40.54        15.39        26.83        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1107 TCGA-23-1110 
        8.81        29.13        18.90         2.76         0.30        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-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 
       39.09        33.47        58.13        24.95       115.89        87.48 
TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 TCGA-23-2649 TCGA-24-0966 TCGA-24-0968 
       77.00         2.76         4.70         3.81         7.63        19.66 
TCGA-24-0970 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 
       11.64        41.56         7.66        22.32        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-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        6.25         6.02         5.95         5.36         4.83        17.39 
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-24-1469 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-24-1553 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-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
       39.88        19.53        44.09        45.50        47.70        25.87 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 
       17.23        90.15        88.37        48.33        38.24         8.32 
TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 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-24-2019 TCGA-24-2024 TCGA-24-2030 TCGA-24-2254 TCGA-24-2260 
        5.52         4.87        58.16        55.92        57.07        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-25-1313 TCGA-25-1315 TCGA-25-1317 TCGA-25-1318 
       67.36        36.23        26.96        52.04         2.01        34.98 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1324 TCGA-25-1325 
       65.00        37.97        33.96         2.99        34.03        32.09 
TCGA-25-1326 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 
       41.06        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-25-1635 
       20.61        38.20         0.30        59.15        62.17        52.04 
TCGA-25-2392 TCGA-25-2396 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 
        1.02         3.02        19.99        42.02         2.96        29.03 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1691 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 
       26.99        78.90        48.33        40.41        33.93        31.20 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 
       68.32        36.36        16.93        23.93        59.67        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
       41.98        31.27        34.62        17.36        86.60        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1770 TCGA-29-1771 TCGA-29-1775 
       62.93        39.42        31.30        24.36        22.55        12.36 
TCGA-29-1776 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 
       11.84        14.93         8.38         7.23         5.36        36.30 
TCGA-29-2427 TCGA-29-2432 TCGA-29-2434 TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 
       62.47        21.47        11.47        38.07        51.91         2.47 
TCGA-30-1857 TCGA-30-1862 TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 TCGA-31-1959 
        0.26         6.12        30.05        18.77         6.71         2.20 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1575 TCGA-36-1577 
       28.77        29.10        21.53        22.85         8.55        25.74 
TCGA-36-1578 TCGA-36-1580 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
       27.85        24.23        29.49        29.82        25.91        25.08 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 
       21.60         2.24        14.17        16.18        11.47        47.57 
TCGA-42-2587 TCGA-42-2589 TCGA-42-2591 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 
       23.74        42.02        40.77        24.03        11.38        21.14 
TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 
       25.08       180.20        22.32       116.12         9.40         2.14 
TCGA-59-2363 TCGA-59-2372 TCGA-61-1725 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 
        5.42        44.81        31.43        27.88         4.34        31.79 
TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 
       48.79        44.84        35.80         2.43        33.67         1.45 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1910 
        5.79        11.41        13.02         9.07        34.13        37.05 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1919 TCGA-61-1995 
       42.51        48.92        56.61        67.76        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-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2097 TCGA-61-2101 
        1.18         4.77        51.72        71.74        60.62        55.50 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 
        6.48        76.87        44.52       125.75        22.22         6.35 
TCGA-61-2613 TCGA-61-2614 
       31.07         8.61 

$`TP53 WILD-TYPE`
TCGA-04-1342 TCGA-04-1353 TCGA-04-1356 TCGA-04-1519 TCGA-04-1638 TCGA-04-1648 
       18.51         0.53        49.28         0.79        55.43        28.64 
TCGA-09-1664 TCGA-09-1672 TCGA-09-2051 TCGA-09-2056 TCGA-10-0927 TCGA-10-0930 
       74.93         5.85        63.09        12.46        81.86        34.19 
TCGA-10-0933 TCGA-13-0717 TCGA-13-0723 TCGA-13-0727 TCGA-13-0755 TCGA-13-0801 
       14.66        24.59        39.58        15.19         2.50         8.28 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0901 TCGA-13-1408 TCGA-13-1477 TCGA-13-1506 
       43.36        57.47        19.36         5.92        54.64         4.41 
TCGA-13-1510 TCGA-13-2065 TCGA-13-2066 TCGA-20-1684 TCGA-23-1027 TCGA-23-1109 
        2.56         8.75         9.70        19.10        32.09        51.35 
TCGA-23-1120 TCGA-23-1809 TCGA-23-2079 TCGA-23-2645 TCGA-23-2647 TCGA-24-0975 
        4.27         0.53        91.66         4.50         4.44        21.80 
TCGA-24-1417 TCGA-24-1431 TCGA-24-1546 TCGA-24-1549 TCGA-24-1565 TCGA-24-2035 
        7.82        19.17        64.27        56.58        10.26        28.18 
TCGA-24-2038 TCGA-24-2280 TCGA-24-2293 TCGA-24-2298 TCGA-25-1316 TCGA-25-1328 
       44.52        70.45        16.64        53.26        42.05        66.05 
TCGA-25-1634 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2398 TCGA-25-2408 
       35.87        13.02        49.05        38.04        45.01        31.00 
TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1769 TCGA-29-1774 TCGA-29-1777 
       47.61       101.79        39.02        22.98        17.33        12.30 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2436 TCGA-30-1853 TCGA-30-1856 TCGA-36-1574 
       13.84        42.25         9.76        36.26        15.68        22.55 
TCGA-36-1576 TCGA-36-2530 TCGA-36-2540 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 
       30.08        33.01        23.80        20.98        18.31        20.52 
TCGA-42-2588 TCGA-42-2590 TCGA-57-1586 TCGA-59-2354 TCGA-61-1722 TCGA-61-1727 
       28.93        10.42        22.32        34.39         8.09        18.54 
TCGA-61-1899 TCGA-61-1907 TCGA-61-2012 TCGA-61-2095 TCGA-61-2109 
        8.42        31.30        30.64        61.64        20.68 

  TP53 MUTATED TP53 WILD-TYPE 
          0.26           0.53 
  TP53 MUTATED TP53 WILD-TYPE 
        180.20         101.79 
  TP53 MUTATED TP53 WILD-TYPE 
        29.065         22.980 
[1] "0.3 - 180.2 (29.1)" "0.5 - 101.8 (23.0)"
[1] "hr=" "1.2"
D1V2, continuous
                vv
clus             OMENTUM OVARY PERITONEUM OVARY
  TP53 MUTATED         1   380                1
  TP53 WILD-TYPE       1    82                0
D1V3, multiclass
                  clus
vv                 TP53 MUTATED TP53 WILD-TYPE
  OMENTUM                     1              1
  OVARY                     380             82
  PERITONEUM OVARY            1              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"
D1V4, continuous
D1V5, binary
                cls
clus               0   1
  TP53 MUTATED     2 380
  TP53 WILD-TYPE   1  82
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      2  380
  TP53 WILD-TYPE    1   82
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO             2              1
  YES          380             82
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2
  TP53 MUTATED    9 17  0
  TP53 WILD-TYPE  4  5  1
D1V6, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0            9              4
  R1           17              5
  R2            0              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"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TP53 MUTATED                                  1    12
  TP53 WILD-TYPE                                1     6
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED                          16   337
  TP53 WILD-TYPE                         4    66
D1V7, multiclass
                                  clus
vv                                 TP53 MUTATED TP53 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              1
  ASIAN                                      12              6
  BLACK OR AFRICAN AMERICAN                  16              4
  WHITE                                     337             66
[1] 4 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
  TP53 MUTATED     5 223
  TP53 WILD-TYPE   4  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      5  223
  TP53 WILD-TYPE    4   47
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                5              4
  NOT HISPANIC OR LATINO          223             47
[1] 2 2
[1] FALSE

Clustering(2) Variable = BRCA1 MUTATION ANALYSIS
D2V1, survival
                 sevent
clus2               0   1
  BRCA1 MUTATED    10   8
  BRCA1 WILD-TYPE 218 227
  BRCA1 MUTATED BRCA1 WILD-TYPE 
             18             445 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
              8             227 
$`BRCA1 MUTATED`
TCGA-13-0730 TCGA-13-0761 TCGA-13-0804 TCGA-13-1489 TCGA-23-1026 TCGA-24-1846 
       17.82        34.06        35.28        82.88        26.83         4.37 
TCGA-24-1847 TCGA-24-2035 TCGA-25-1625 TCGA-25-1630 TCGA-25-1632 TCGA-29-1768 
       11.28        28.18        27.62        38.20        59.15        31.30 
TCGA-29-1776 TCGA-29-2427 TCGA-30-1857 TCGA-36-2534 TCGA-42-2591 TCGA-61-1914 
       11.84        62.47         0.26        29.82        40.77        56.61 

$`BRCA1 WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       43.92        41.00        49.15         2.01        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-04-1353 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-04-1369 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 
      103.40        21.11        56.55        41.59        19.99         0.79 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
       38.37       119.08        84.20        55.43        48.89        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 
       28.64        64.64        36.23        31.86        45.37        29.16 
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-09-1666 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       41.62        57.60        30.51        17.98         5.85         3.02 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 
        8.55        97.55         6.12        35.15       112.41        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       63.09        39.75        12.46        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-13-0724 
       20.91         6.21        24.59        44.55        39.58         2.73 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0762 
       31.20        15.19        55.17         2.50        11.54        32.25 
TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 
       28.57        38.93        36.72        28.70        19.59         8.12 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 
        8.28         8.19        13.61        68.94       107.18        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-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       49.61        57.47        56.15        57.07        19.36        47.38 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       48.33        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-13-0924 
       29.98        21.17        14.89        13.81         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-13-1487 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 
       29.42        98.04        22.39        70.82        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-13-1501 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-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 
        2.56         3.09        14.24        12.23         8.61        10.78 
TCGA-13-2065 TCGA-13-2066 TCGA-13-2071 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
        8.75         9.70         6.28        23.05        25.94        26.20 
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-23-1027 TCGA-23-1028 
       47.54        49.68        40.54        15.39        32.09        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1107 TCGA-23-1109 
        8.81        29.13        18.90         2.76         0.30        51.35 
TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
       54.51         3.22        68.68         4.57        33.30        86.01 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 
      129.96         4.27        39.09        33.47        58.13         0.53 
TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2641 
       24.95       115.89        87.48        91.66        77.00         2.76 
TCGA-23-2643 TCGA-23-2645 TCGA-23-2647 TCGA-23-2649 TCGA-24-0966 TCGA-24-0968 
        4.70         4.50         4.44         3.81         7.63        19.66 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 
       11.64        21.80        41.56         7.66        22.32        54.12 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 
       63.55        47.41         6.31         6.38         7.82         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 
        7.86         0.76         6.25         6.02         5.95         5.36 
TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
        4.83        17.39        19.17        18.67        43.53         8.55 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 
       72.92        12.46        45.14         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-24-1551 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-24-1849 TCGA-24-1850 TCGA-24-2019 
        3.48         3.72         3.81         5.79         5.52         4.87 
TCGA-24-2024 TCGA-24-2030 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 
       58.16        55.92        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-24-2298 TCGA-25-1313 TCGA-25-1315 
       67.36        36.23        16.64        53.26        26.96        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-25-1324 TCGA-25-1325 TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 
        2.99        34.03        32.09        41.06        66.05        15.02 
TCGA-25-1623 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1633 
       18.58        17.03        12.95        20.61         0.30        62.17 
TCGA-25-1634 TCGA-25-1635 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 
       35.87        52.04        13.02        49.05         1.02        38.04 
TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 
        3.02        45.01        19.99        42.02         2.96        29.03 
TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 
       31.00        26.99        78.90        47.61        48.33       101.79 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
       39.02        40.41        33.93        31.20        68.32        36.36 
TCGA-29-1701 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-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1777 
       22.98        24.36        22.55        17.33        12.36        12.30 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2429 
       14.93         8.38         7.23         5.36        36.30        13.84 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-30-1714 TCGA-30-1718 
       42.25        21.47        11.47         9.76        38.07        51.91 
TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1862 TCGA-30-1891 TCGA-31-1950 
       36.26         2.47        15.68         6.12        30.05        18.77 
TCGA-31-1953 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 
        6.71         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-36-2530 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-36-2547 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-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1993 TCGA-59-2348 
       24.03        11.38        21.14        22.32        25.08       180.20 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       22.32       116.12         9.40        34.39         2.14         5.42 
TCGA-59-2372 TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 
       44.81         8.09        31.43        18.54        27.88         4.34 
TCGA-61-1733 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 
       31.79        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-61-1915 
       34.13        31.30        37.05        42.51        48.92        67.76 
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-61-2088 TCGA-61-2092 
       30.64        39.85        30.64         1.18         4.77        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 
       71.74        61.64        60.62        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 
        8.61 

  BRCA1 MUTATED BRCA1 WILD-TYPE 
           0.26            0.30 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
          82.88          180.20 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
          30.56           27.88 
[1] "0.3 - 82.9 (30.6)"  "0.3 - 180.2 (27.9)"
[1] "hr=" "1.1"
D2V2, continuous
                 vv
clus              OMENTUM OVARY PERITONEUM OVARY
  BRCA1 MUTATED         0    19                0
  BRCA1 WILD-TYPE       2   443                1
D2V3, multiclass
                  clus
vv                 BRCA1 MUTATED BRCA1 WILD-TYPE
  OMENTUM                      0               2
  OVARY                       19             443
  PERITONEUM OVARY             0               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"
D2V4, continuous
[1] "Remove cluster labels:" "BRCA1 MUTATED"         
clus
  BRCA1 MUTATED BRCA1 WILD-TYPE 
              1              63 
     TCGA-04-1346      TCGA-04-1347      TCGA-04-1356      TCGA-04-1367 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-10-0926      TCGA-13-0714      TCGA-13-0720      TCGA-13-0724 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-0755      TCGA-13-0760      TCGA-13-0762      TCGA-13-0791 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-0792      TCGA-13-0793      TCGA-13-0795      TCGA-13-0801 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-0802      TCGA-13-0885      TCGA-13-0887      TCGA-13-0889 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-0891      TCGA-13-0894      TCGA-13-0897      TCGA-13-0900 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-0901      TCGA-13-0903      TCGA-13-0904      TCGA-13-0905 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-0906      TCGA-13-0910      TCGA-13-0911      TCGA-13-0912 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-0913      TCGA-13-0919      TCGA-13-1404      TCGA-13-1405 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-1409      TCGA-13-1410      TCGA-13-1412      TCGA-13-1482 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-1483      TCGA-13-1484      TCGA-13-1488      TCGA-13-1491 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-1492      TCGA-13-1495      TCGA-13-1497      TCGA-13-1498 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-1499      TCGA-13-1501      TCGA-13-1504      TCGA-13-1506 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-1507      TCGA-13-1509      TCGA-13-1512      TCGA-13-2057 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-2059      TCGA-13-2060      TCGA-13-2061      TCGA-13-2066 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-2071      TCGA-24-1614      TCGA-61-2101 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
D2V5, binary
                 cls
clus                0   1
  BRCA1 MUTATED     0  19
  BRCA1 WILD-TYPE   3 443
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA1 MUTATED      0   19
  BRCA1 WILD-TYPE    3  443
     clus
vv    BRCA1 MUTATED BRCA1 WILD-TYPE
  NO              0               3
  YES            19             443
[1] 2 2
[1] FALSE
                 vv
clus              R0 R1 R2
  BRCA1 MUTATED    0  2  0
  BRCA1 WILD-TYPE 13 20  1
D2V6, multiclass
[1] "Remove cluster labels:" "BRCA1 MUTATED"         
clus
  BRCA1 MUTATED BRCA1 WILD-TYPE 
              2              34 
     TCGA-04-1369      TCGA-04-1516      TCGA-04-1644      TCGA-13-0807 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-0911      TCGA-29-2429      TCGA-29-2431      TCGA-29-2432 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-29-2434      TCGA-29-2436      TCGA-36-2530      TCGA-36-2532 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-36-2537      TCGA-36-2538      TCGA-36-2540      TCGA-36-2542 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-36-2543      TCGA-36-2544      TCGA-36-2545      TCGA-36-2547 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-36-2548      TCGA-36-2551      TCGA-36-2552      TCGA-42-2582 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-42-2587      TCGA-42-2588      TCGA-42-2589      TCGA-42-2590 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-57-1993      TCGA-59-2363      TCGA-59-2372      TCGA-61-2612 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-61-2613      TCGA-61-2614 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BRCA1 MUTATED                                  0     0
  BRCA1 WILD-TYPE                                2    18
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BRCA1 MUTATED                           1    15
  BRCA1 WILD-TYPE                        19   388
D2V7, multiclass
                                  clus
vv                                 BRCA1 MUTATED BRCA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              18
  BLACK OR AFRICAN AMERICAN                    1              19
  WHITE                                       15             388
[1] 4 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
  BRCA1 MUTATED     0  10
  BRCA1 WILD-TYPE   9 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA1 MUTATED      0   10
  BRCA1 WILD-TYPE    9  260
                        clus
vv                       BRCA1 MUTATED BRCA1 WILD-TYPE
  HISPANIC OR LATINO                 0               9
  NOT HISPANIC OR LATINO            10             260
[1] 2 2
[1] FALSE

Clustering(3) Variable = NF1 MUTATION ANALYSIS
D3V1, survival
               sevent
clus2             0   1
  NF1 MUTATED    12  12
  NF1 WILD-TYPE 216 223
  NF1 MUTATED NF1 WILD-TYPE 
           24           439 
  NF1 MUTATED NF1 WILD-TYPE 
           12           223 
$`NF1 MUTATED`
TCGA-04-1331 TCGA-04-1367 TCGA-09-1664 TCGA-09-1670 TCGA-09-2053 TCGA-13-1483 
       43.92       103.40        74.93        17.98        39.75        29.42 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1119 TCGA-23-2078 TCGA-24-1463 TCGA-24-1470 
       32.09        49.41       129.96        87.48        72.92         3.45 
TCGA-24-1562 TCGA-29-1694 TCGA-29-1771 TCGA-29-1776 TCGA-30-1714 TCGA-30-1862 
       45.50        39.02        22.55        11.84        38.07         6.12 
TCGA-36-2534 TCGA-36-2543 TCGA-59-2363 TCGA-61-1740 TCGA-61-1895 TCGA-61-2613 
       29.82         2.24         5.42         2.43         1.45        31.07 

$`NF1 WILD-TYPE`
TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 TCGA-04-1343 
       41.00        49.15         2.01        46.62        18.51        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1353 
       65.52        63.09        48.76        21.57        63.98         0.53 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1369 
       49.28        32.52        44.32        33.67        76.57        21.11 
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-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 
       84.20        55.43        48.89        27.88        28.64        64.64 
TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 TCGA-09-0366 TCGA-09-0369 
       36.23        31.86        45.37        29.16        57.76        35.57 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 
        9.99        38.43        89.33        41.62        57.60        30.51 
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-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 
      112.41        71.11        63.09        12.46        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-13-0724 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 
        2.73        31.20        15.19        17.82        55.17         2.50 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 
       11.54        34.06        32.25        28.57        38.93        36.72 
TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 
       28.70        19.59         8.12         8.28         8.19        35.28 
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-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 
       61.84        67.99        69.01        43.36        49.61        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-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       44.94        37.08        27.72        34.06        29.98        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-13-1409 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-13-1487 
        5.33        54.64        87.06        61.71        98.04        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-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 
        4.24        54.31        37.61        38.40        32.84        16.57 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 
        4.21         4.41         4.77         4.18         2.56         3.09 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2066 
       14.24        12.23         8.61        10.78         8.75         9.70 
TCGA-13-2071 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 
        6.28        23.05        25.94        26.20        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-23-1029 TCGA-23-1030 TCGA-23-1031 
       40.54        15.39        26.83         8.81        29.13        18.90 
TCGA-23-1032 TCGA-23-1107 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 
        2.76         0.30        51.35        54.51         3.22        68.68 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 
        4.57        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-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-23-2647 TCGA-23-2649 TCGA-24-0966 
        2.76         4.70         4.50         4.44         3.81         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-24-1431 TCGA-24-1434 TCGA-24-1435 
        5.36         4.83        17.39        19.17        18.67        43.53 
TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 
        8.55        12.46        45.14         9.11         1.18        22.22 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 
       26.96        57.40        64.27        16.21        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-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       44.09        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-24-2019 
        3.81         4.37        11.28         5.79         5.52         4.87 
TCGA-24-2024 TCGA-24-2030 TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 
       58.16        55.92        28.18        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-24-2298 TCGA-25-1313 
        0.82        67.36        36.23        16.64        53.26        26.96 
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-25-1324 TCGA-25-1325 TCGA-25-1326 TCGA-25-1328 
       33.96         2.99        34.03        32.09        41.06        66.05 
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-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 
       13.02        49.05         1.02        38.04         3.02        45.01 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-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-29-1695 TCGA-29-1696 
       78.90        47.61        48.33       101.79        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-29-1770 
       66.81        62.93        39.42        31.30        22.98        24.36 
TCGA-29-1774 TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 
       17.33        12.36        12.30        14.93         8.38         7.23 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 
        5.36        36.30        62.47        13.84        42.25        21.47 
TCGA-29-2434 TCGA-29-2436 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 
       11.47         9.76        51.91        36.26         2.47        15.68 
TCGA-30-1857 TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 TCGA-31-1959 TCGA-36-1568 
        0.26        30.05        18.77         6.71         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-36-2530 TCGA-36-2532 TCGA-36-2537 
       25.74        27.85        24.23        33.01        29.49        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-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
       14.17        16.18        11.47        47.57        23.74        28.93 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 
       42.02        10.42        40.77        24.03        11.38        21.14 
TCGA-57-1586 TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       22.32        25.08       180.20        22.32       116.12         9.40 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2372 TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 
       34.39         2.14        44.81         8.09        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-61-1741 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 
       33.67         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-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       67.76        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-61-2088 
        4.01        30.64        39.85        30.64         1.18         4.77 
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-61-2104 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-61-2614 
        8.61 

  NF1 MUTATED NF1 WILD-TYPE 
         1.45          0.26 
  NF1 MUTATED NF1 WILD-TYPE 
       129.96        180.20 
  NF1 MUTATED NF1 WILD-TYPE 
        31.58         27.88 
[1] "1.4 - 130.0 (31.6)" "0.3 - 180.2 (27.9)"
[1] "hr=" "1.3"
D3V2, continuous
               vv
clus            OMENTUM OVARY PERITONEUM OVARY
  NF1 MUTATED         0    24                0
  NF1 WILD-TYPE       2   438                1
D3V3, multiclass
                  clus
vv                 NF1 MUTATED NF1 WILD-TYPE
  OMENTUM                    0             2
  OVARY                     24           438
  PERITONEUM OVARY           0             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"
D3V4, continuous
[1] "Remove cluster labels:" "NF1 MUTATED"           
clus
  NF1 MUTATED NF1 WILD-TYPE 
            2            62 
   TCGA-04-1346    TCGA-04-1347    TCGA-04-1356    TCGA-10-0926    TCGA-13-0714 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-13-0720    TCGA-13-0724    TCGA-13-0755    TCGA-13-0760    TCGA-13-0762 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-13-0791    TCGA-13-0792    TCGA-13-0793    TCGA-13-0795    TCGA-13-0801 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-13-0802    TCGA-13-0885    TCGA-13-0887    TCGA-13-0889    TCGA-13-0891 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-13-0894    TCGA-13-0897    TCGA-13-0900    TCGA-13-0901    TCGA-13-0903 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-13-0904    TCGA-13-0905    TCGA-13-0906    TCGA-13-0910    TCGA-13-0911 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-13-0912    TCGA-13-0913    TCGA-13-0919    TCGA-13-1404    TCGA-13-1405 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-13-1409    TCGA-13-1410    TCGA-13-1412    TCGA-13-1482    TCGA-13-1484 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-13-1488    TCGA-13-1489    TCGA-13-1491    TCGA-13-1492    TCGA-13-1495 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-13-1497    TCGA-13-1498    TCGA-13-1499    TCGA-13-1501    TCGA-13-1504 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-13-1506    TCGA-13-1507    TCGA-13-1509    TCGA-13-1512    TCGA-13-2057 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-13-2059    TCGA-13-2060    TCGA-13-2061    TCGA-13-2066    TCGA-13-2071 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-24-1614    TCGA-61-2101 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" 
D3V5, binary
               cls
clus              0   1
  NF1 MUTATED     1  23
  NF1 WILD-TYPE   2 439
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      1   23
  NF1 WILD-TYPE    2  439
     clus
vv    NF1 MUTATED NF1 WILD-TYPE
  NO            1             2
  YES          23           439
[1] 2 2
[1] FALSE
               vv
clus            R0 R1 R2
  NF1 MUTATED    1  3  0
  NF1 WILD-TYPE 12 19  1
D3V6, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  R0           1            12
  R1           3            19
  R2           0             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"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NF1 MUTATED                                  0     1
  NF1 WILD-TYPE                                2    17
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NF1 MUTATED                           1    21
  NF1 WILD-TYPE                        19   382
D3V7, multiclass
                                  clus
vv                                 NF1 MUTATED NF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      1            17
  BLACK OR AFRICAN AMERICAN                  1            19
  WHITE                                     21           382
[1] 4 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
  NF1 MUTATED     1  14
  NF1 WILD-TYPE   8 256
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      1   14
  NF1 WILD-TYPE    8  256
                        clus
vv                       NF1 MUTATED NF1 WILD-TYPE
  HISPANIC OR LATINO               1             8
  NOT HISPANIC OR LATINO          14           256
[1] 2 2
[1] FALSE

Clustering(4) Variable = RB1 MUTATION ANALYSIS
D4V1, survival
               sevent
clus2             0   1
  RB1 MUTATED     7   8
  RB1 WILD-TYPE 221 227
  RB1 MUTATED RB1 WILD-TYPE 
           15           448 
  RB1 MUTATED RB1 WILD-TYPE 
            8           227 
$`RB1 MUTATED`
TCGA-04-1350 TCGA-04-1638 TCGA-09-1665 TCGA-09-1674 TCGA-10-0933 TCGA-13-1489 
       63.98        55.43        41.62         8.55        14.66        82.88 
TCGA-13-1509 TCGA-23-2079 TCGA-24-1463 TCGA-24-1469 TCGA-24-1849 TCGA-25-1635 
        4.18        91.66        72.92         9.11         5.79        52.04 
TCGA-29-1691 TCGA-29-1703 TCGA-36-2538 
       48.33        59.67        25.08 

$`RB1 WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       43.92        41.00        49.15         2.01        46.62        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-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       49.28        32.52        44.32        33.67        76.57       103.40 
TCGA-04-1369 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 
       21.11        56.55        41.59        19.99         0.79        38.37 
TCGA-04-1530 TCGA-04-1542 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 
      119.08        84.20        48.89        27.88        28.64        64.64 
TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 TCGA-09-0366 TCGA-09-0369 
       36.23        31.86        45.37        29.16        57.76        35.57 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1669 
        9.99        38.43        89.33        74.93        57.60        30.51 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 
       17.98         5.85         3.02        97.55         6.12        35.15 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 
      112.41        71.11        63.09        39.75        12.46        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 
       81.86        18.51        34.19        32.88         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-13-0724 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 
        2.73        31.20        15.19        17.82        55.17         2.50 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 
       11.54        34.06        32.25        28.57        38.93        36.72 
TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 
       28.70        19.59         8.12         8.28         8.19        35.28 
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-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 
       61.84        67.99        69.01        43.36        49.61        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-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       44.94        37.08        27.72        34.06        29.98        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-13-1409 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-13-1487 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       22.39        70.82        52.44        73.55        38.20        49.25 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 
        4.24        54.31        37.61        38.40        32.84        16.57 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 
        4.21         4.41         4.77         2.56         3.09        14.24 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2066 TCGA-13-2071 
       12.23         8.61        10.78         8.75         9.70         6.28 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 
       23.05        25.94        26.20        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-23-1107 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
       18.90         2.76         0.30        51.35        54.51         3.22 
TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 
       68.68         4.57        33.30        86.01       129.96         4.27 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 
       39.09        33.47        58.13         0.53        24.95       115.89 
TCGA-23-2078 TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-23-2647 
       87.48        77.00         2.76         4.70         4.50         4.44 
TCGA-23-2649 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        3.81         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-24-1431 
        6.02         5.95         5.36         4.83        17.39        19.17 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 TCGA-24-1470 
       18.67        43.53         8.55        12.46        45.14         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-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 
       56.58        51.91        41.39        58.09        88.50        70.62 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
       39.88        19.53        44.09        45.50        47.70        25.87 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 
       10.26        17.23        90.15        88.37        48.33        38.24 
TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 
        8.32         3.48         3.72         3.81         4.37        11.28 
TCGA-24-1850 TCGA-24-2019 TCGA-24-2024 TCGA-24-2030 TCGA-24-2035 TCGA-24-2038 
        5.52         4.87        58.16        55.92        28.18        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-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
       53.26        26.96        52.04        42.05         2.01        34.98 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1324 TCGA-25-1325 
       65.00        37.97        33.96         2.99        34.03        32.09 
TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 
       41.06        66.05        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-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 
       35.87        13.02        49.05         1.02        38.04         3.02 
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-29-1695 
       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-29-1701 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-29-1711 TCGA-29-1761 TCGA-29-1762 
       18.25        41.98        31.27        34.62        17.36        86.60 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 
       66.81        62.93        39.42        31.30        22.98        24.36 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 
       22.55        17.33        12.36        11.84        12.30        14.93 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 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-29-2434 TCGA-29-2436 TCGA-30-1714 TCGA-30-1718 
       42.25        21.47        11.47         9.76        38.07        51.91 
TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1862 TCGA-30-1891 
       36.26         2.47        15.68         0.26         6.12        30.05 
TCGA-31-1950 TCGA-31-1953 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
       18.77         6.71         2.20        28.77        29.10        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 
       22.85        22.55         8.55        30.08        25.74        27.85 
TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2540 
       24.23        33.01        29.49        29.82        25.91        23.80 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 
       21.60         2.24        20.98        18.31        20.52        14.17 
TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 
       16.18        11.47        47.57        23.74        28.93        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 
       10.42        40.77        24.03        11.38        21.14        22.32 
TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 
       25.08       180.20        22.32       116.12         9.40        34.39 
TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 
        2.14         5.42        44.81         8.09        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-61-1895 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-61-1906 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-61-1919 TCGA-61-1995 TCGA-61-1998 
       48.92        56.61        67.76        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-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 
        1.18         4.77        51.72        71.74        61.64        60.62 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       55.50         6.48        76.87        20.68        44.52       125.75 
TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       22.22         6.35        31.07         8.61 

  RB1 MUTATED RB1 WILD-TYPE 
         4.18          0.26 
  RB1 MUTATED RB1 WILD-TYPE 
        91.66        180.20 
  RB1 MUTATED RB1 WILD-TYPE 
        48.33         28.03 
[1] "4.2 - 91.7 (48.3)"  "0.3 - 180.2 (28.0)"
[1] "hr=" "1.5"
D4V2, continuous
               vv
clus            OMENTUM OVARY PERITONEUM OVARY
  RB1 MUTATED         0    15                0
  RB1 WILD-TYPE       2   447                1
D4V3, multiclass
                  clus
vv                 RB1 MUTATED RB1 WILD-TYPE
  OMENTUM                    0             2
  OVARY                     15           447
  PERITONEUM OVARY           0             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"
D4V4, continuous
[1] "Remove cluster labels:" "RB1 MUTATED"           
clus
  RB1 MUTATED RB1 WILD-TYPE 
            2            62 
   TCGA-04-1346    TCGA-04-1347    TCGA-04-1356    TCGA-04-1367    TCGA-10-0926 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-0714    TCGA-13-0720    TCGA-13-0724    TCGA-13-0755    TCGA-13-0760 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-0762    TCGA-13-0791    TCGA-13-0792    TCGA-13-0793    TCGA-13-0795 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-0801    TCGA-13-0802    TCGA-13-0885    TCGA-13-0887    TCGA-13-0889 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-0891    TCGA-13-0894    TCGA-13-0897    TCGA-13-0900    TCGA-13-0901 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-0903    TCGA-13-0904    TCGA-13-0905    TCGA-13-0906    TCGA-13-0910 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-0911    TCGA-13-0912    TCGA-13-0913    TCGA-13-0919    TCGA-13-1404 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-1405    TCGA-13-1409    TCGA-13-1410    TCGA-13-1412    TCGA-13-1482 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-1483    TCGA-13-1484    TCGA-13-1488    TCGA-13-1491    TCGA-13-1492 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-1495    TCGA-13-1497    TCGA-13-1498    TCGA-13-1499    TCGA-13-1501 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-1504    TCGA-13-1506    TCGA-13-1507    TCGA-13-1512    TCGA-13-2057 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-2059    TCGA-13-2060    TCGA-13-2061    TCGA-13-2066    TCGA-13-2071 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-1614    TCGA-61-2101 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" 
D4V5, binary
               cls
clus              0   1
  RB1 MUTATED     0  15
  RB1 WILD-TYPE   3 447
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      0   15
  RB1 WILD-TYPE    3  447
     clus
vv    RB1 MUTATED RB1 WILD-TYPE
  NO            0             3
  YES          15           447
[1] 2 2
[1] FALSE
               vv
clus            R0 R1 R2
  RB1 MUTATED    0  1  0
  RB1 WILD-TYPE 13 21  1
D4V6, multiclass
[1] "Remove cluster labels:" "RB1 MUTATED"           
clus
  RB1 MUTATED RB1 WILD-TYPE 
            1            35 
   TCGA-04-1369    TCGA-04-1516    TCGA-04-1644    TCGA-13-0807    TCGA-13-0911 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-29-2427    TCGA-29-2429    TCGA-29-2431    TCGA-29-2432    TCGA-29-2434 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-29-2436    TCGA-36-2530    TCGA-36-2532    TCGA-36-2534    TCGA-36-2537 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-36-2540    TCGA-36-2542    TCGA-36-2543    TCGA-36-2544    TCGA-36-2545 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-36-2547    TCGA-36-2548    TCGA-36-2551    TCGA-36-2552    TCGA-42-2582 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-42-2587    TCGA-42-2588    TCGA-42-2589    TCGA-42-2590    TCGA-57-1993 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-59-2363    TCGA-59-2372    TCGA-61-2612    TCGA-61-2613    TCGA-61-2614 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RB1 MUTATED                                  0     0
  RB1 WILD-TYPE                                2    18
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  RB1 MUTATED                           2    12
  RB1 WILD-TYPE                        18   391
D4V7, multiclass
                                  clus
vv                                 RB1 MUTATED RB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0            18
  BLACK OR AFRICAN AMERICAN                  2            18
  WHITE                                     12           391
[1] 4 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
  RB1 MUTATED     0   8
  RB1 WILD-TYPE   9 262
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      0    8
  RB1 WILD-TYPE    9  262
                        clus
vv                       RB1 MUTATED RB1 WILD-TYPE
  HISPANIC OR LATINO               0             9
  NOT HISPANIC OR LATINO           8           262
[1] 2 2
[1] FALSE

Clustering(5) Variable = BRCA2 MUTATION ANALYSIS
D5V1, survival
                 sevent
clus2               0   1
  BRCA2 MUTATED     8   5
  BRCA2 WILD-TYPE 220 230
  BRCA2 MUTATED BRCA2 WILD-TYPE 
             13             450 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
              5             230 
$`BRCA2 MUTATED`
TCGA-04-1331 TCGA-09-2050 TCGA-13-0792 TCGA-13-0885 TCGA-13-0890 TCGA-13-1481 
       43.92        71.11        36.72        91.40        67.99        87.06 
TCGA-23-1030 TCGA-23-1120 TCGA-24-1103 TCGA-24-1555 TCGA-29-1693 TCGA-29-1762 
       29.13         4.27        54.12        88.50       101.79        86.60 
TCGA-61-1903 
       13.02 

$`BRCA2 WILD-TYPE`
TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 TCGA-04-1343 
       41.00        49.15         2.01        46.62        18.51        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1353 
       65.52        63.09        48.76        21.57        63.98         0.53 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       49.28        32.52        44.32        33.67        76.57       103.40 
TCGA-04-1369 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 
       21.11        56.55        41.59        19.99         0.79        38.37 
TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 
      119.08        84.20        55.43        48.89        27.88        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 TCGA-09-0366 
       64.64        36.23        31.86        45.37        29.16        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-09-1666 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 
       57.60        30.51        17.98         5.85         3.02         8.55 
TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2051 TCGA-09-2053 
       97.55         6.12        35.15       112.41        63.09        39.75 
TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       12.46        25.91        81.86        18.51        34.19        32.88 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
       14.66         6.71        35.44        19.99        20.91         6.21 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 
       24.59        44.55        39.58         2.73        31.20        15.19 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 
       17.82        55.17         2.50        11.54        34.06        32.25 
TCGA-13-0765 TCGA-13-0791 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 TCGA-13-0801 
       28.57        38.93        28.70        19.59         8.12         8.28 
TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 
        8.19        35.28        13.61        68.94       107.18        74.27 
TCGA-13-0887 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 
       66.67        61.84        69.01        43.36        49.61        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-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       44.94        37.08        27.72        34.06        29.98        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-13-1409 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-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 
        5.33        54.64        61.71        29.42        98.04        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-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 
        4.24        54.31        37.61        38.40        32.84        16.57 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 
        4.21         4.41         4.77         4.18         2.56         3.09 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2066 
       14.24        12.23         8.61        10.78         8.75         9.70 
TCGA-13-2071 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 
        6.28        23.05        25.94        26.20        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-23-1031 TCGA-23-1032 TCGA-23-1107 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
       18.90         2.76         0.30        51.35        54.51         3.22 
TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1122 
       68.68         4.57        33.30        86.01       129.96        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-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-23-2647 
       91.66        77.00         2.76         4.70         4.50         4.44 
TCGA-23-2649 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        3.81         7.63        19.66        11.64        21.80        41.56 
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-24-1418 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-24-1434 
        5.95         5.36         4.83        17.39        19.17        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 
       43.53         8.55        72.92        12.46        45.14         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-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1556 
       16.21        56.58        51.91        41.39        58.09        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-24-2019 TCGA-24-2024 TCGA-24-2030 TCGA-24-2035 
        5.79         5.52         4.87        58.16        55.92        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-24-2280 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-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
       16.64        53.26        26.96        52.04        42.05         2.01 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1324 
       34.98        65.00        37.97        33.96         2.99        34.03 
TCGA-25-1325 TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       32.09        41.06        66.05        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-25-2042 TCGA-25-2391 TCGA-25-2392 
       62.17        35.87        52.04        13.02        49.05         1.02 
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-29-1691 
       29.03        31.00        26.99        78.90        47.61        48.33 
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-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 
       34.62        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-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 
       12.30        14.93         8.38         7.23         5.36        36.30 
TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 
       62.47        13.84        42.25        21.47        11.47         9.76 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 
       38.07        51.91        36.26         2.47        15.68         0.26 
TCGA-30-1862 TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 TCGA-31-1959 TCGA-36-1568 
        6.12        30.05        18.77         6.71         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-36-2530 TCGA-36-2532 TCGA-36-2534 
       25.74        27.85        24.23        33.01        29.49        29.82 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 
       25.91        25.08        23.80        21.60         2.24        20.98 
TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 
       18.31        20.52        14.17        16.18        11.47        47.57 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 
       23.74        28.93        42.02        10.42        40.77        24.03 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 
       11.38        21.14        22.32        25.08       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-61-1722 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 
        8.09        31.43        18.54        27.88         4.34        31.79 
TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 
       48.79        44.84        35.80         2.43        33.67         1.45 
TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        8.42         5.79        11.41         9.07        34.13        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1919 
       37.05        42.51        48.92        56.61        67.76        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-61-2088 TCGA-61-2092 TCGA-61-2094 
       39.85        30.64         1.18         4.77        51.72        71.74 
TCGA-61-2095 TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       61.64        60.62        55.50         6.48        76.87        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       44.52       125.75        22.22         6.35        31.07         8.61 

  BRCA2 MUTATED BRCA2 WILD-TYPE 
           4.27            0.26 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
         101.79          180.20 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
         67.990          27.785 
[1] "4.3 - 101.8 (68.0)" "0.3 - 180.2 (27.8)"
[1] "hr=" "3.2"
D5V2, continuous
                 vv
clus              OMENTUM OVARY PERITONEUM OVARY
  BRCA2 MUTATED         0    13                0
  BRCA2 WILD-TYPE       2   449                1
D5V3, multiclass
                  clus
vv                 BRCA2 MUTATED BRCA2 WILD-TYPE
  OMENTUM                      0               2
  OVARY                       13             449
  PERITONEUM OVARY             0               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
[1] "Remove cluster labels:" "BRCA2 MUTATED"         
clus
  BRCA2 MUTATED BRCA2 WILD-TYPE 
              2              62 
     TCGA-04-1346      TCGA-04-1347      TCGA-04-1356      TCGA-04-1367 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-10-0926      TCGA-13-0714      TCGA-13-0720      TCGA-13-0724 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-0755      TCGA-13-0760      TCGA-13-0762      TCGA-13-0791 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-0793      TCGA-13-0795      TCGA-13-0801      TCGA-13-0802 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-0887      TCGA-13-0889      TCGA-13-0891      TCGA-13-0894 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-0897      TCGA-13-0900      TCGA-13-0901      TCGA-13-0903 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-0904      TCGA-13-0905      TCGA-13-0906      TCGA-13-0910 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-0911      TCGA-13-0912      TCGA-13-0913      TCGA-13-0919 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-1404      TCGA-13-1405      TCGA-13-1409      TCGA-13-1410 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-1412      TCGA-13-1482      TCGA-13-1483      TCGA-13-1484 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-1488      TCGA-13-1489      TCGA-13-1491      TCGA-13-1492 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-1495      TCGA-13-1497      TCGA-13-1498      TCGA-13-1499 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-1501      TCGA-13-1504      TCGA-13-1506      TCGA-13-1507 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-1509      TCGA-13-1512      TCGA-13-2057      TCGA-13-2059 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-2060      TCGA-13-2061      TCGA-13-2066      TCGA-13-2071 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-24-1614      TCGA-61-2101 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
D5V5, binary
                 cls
clus                0   1
  BRCA2 MUTATED     0  13
  BRCA2 WILD-TYPE   3 449
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA2 MUTATED      0   13
  BRCA2 WILD-TYPE    3  449
     clus
vv    BRCA2 MUTATED BRCA2 WILD-TYPE
  NO              0               3
  YES            13             449
[1] 2 2
[1] FALSE
                 vv
clus              R0 R1 R2
  BRCA2 MUTATED    0  0  0
  BRCA2 WILD-TYPE 13 22  1
D5V6, multiclass
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BRCA2 MUTATED                                  0     0
  BRCA2 WILD-TYPE                                2    18
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BRCA2 MUTATED                           1    12
  BRCA2 WILD-TYPE                        19   391
D5V7, multiclass
                                  clus
vv                                 BRCA2 MUTATED BRCA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              18
  BLACK OR AFRICAN AMERICAN                    1              19
  WHITE                                       12             391
[1] 4 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
  BRCA2 MUTATED     0   8
  BRCA2 WILD-TYPE   9 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA2 MUTATED      0    8
  BRCA2 WILD-TYPE    9  262
                        clus
vv                       BRCA2 MUTATED BRCA2 WILD-TYPE
  HISPANIC OR LATINO                 0               9
  NOT HISPANIC OR LATINO             8             262
[1] 2 2
[1] FALSE

Clustering(6) Variable = IL21R MUTATION ANALYSIS
D6V1, survival
                 sevent
clus2               0   1
  IL21R MUTATED     4   3
  IL21R WILD-TYPE 224 232
  IL21R MUTATED IL21R WILD-TYPE 
              7             456 
  IL21R MUTATED IL21R WILD-TYPE 
              3             232 
$`IL21R MUTATED`
TCGA-09-2044 TCGA-24-1417 TCGA-24-1842 TCGA-25-2398 TCGA-29-2432 TCGA-30-1855 
        6.12         7.82         8.32        45.01        21.47         2.47 
TCGA-36-2545 
       18.31 

$`IL21R WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       43.92        41.00        49.15         2.01        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-04-1353 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-04-1369 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 
      103.40        21.11        56.55        41.59        19.99         0.79 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
       38.37       119.08        84.20        55.43        48.89        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 
       28.64        64.64        36.23        31.86        45.37        29.16 
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-09-1666 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       41.62        57.60        30.51        17.98         5.85         3.02 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
        8.55        97.55        35.15       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       39.75        12.46        25.91        81.86        18.51        34.19 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 
       32.88        14.66         6.71        35.44        19.99        20.91 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 
        6.21        24.59        44.55        39.58         2.73        31.20 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 
       15.19        17.82        55.17         2.50        11.54        34.06 
TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 
       32.25        28.57        38.93        36.72        28.70        19.59 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 
        8.12         8.28         8.19        35.28        13.61        68.94 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 
      107.18        91.40        74.27        66.67        61.84        67.99 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       69.01        43.36        49.61        57.47        56.15        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-13-0911 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-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 
        5.92         6.84         4.70         4.21         5.33        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 
       87.06        61.71        29.42        98.04        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-13-1501 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-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 
        4.41         4.77         4.18         2.56         3.09        14.24 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2066 TCGA-13-2071 
       12.23         8.61        10.78         8.75         9.70         6.28 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 
       23.05        25.94        26.20        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-23-1107 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
       18.90         2.76         0.30        51.35        54.51         3.22 
TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 
       68.68         4.57        33.30        86.01       129.96         4.27 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 
       39.09        33.47        58.13         0.53        24.95       115.89 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 
       87.48        91.66        77.00         2.76         4.70         4.50 
TCGA-23-2647 TCGA-23-2649 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 
        4.44         3.81         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-24-1428 TCGA-24-1431 
        6.02         5.95         5.36         4.83        17.39        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-24-1469 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-24-1551 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-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 
       48.33        38.24         3.48         3.72         3.81         4.37 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-2019 TCGA-24-2024 TCGA-24-2030 
       11.28         5.79         5.52         4.87        58.16        55.92 
TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 
       28.18        44.52        57.07        36.16         0.79         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 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-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 
       36.23        16.64        53.26        26.96        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-25-1324 TCGA-25-1325 TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 
       34.03        32.09        41.06        66.05        15.02        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
       27.62        17.03        12.95        20.61        38.20         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-2042 TCGA-25-2391 
       59.15        62.17        35.87        52.04        13.02        49.05 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 
        1.02        38.04         3.02        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-29-1695 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-29-1705 TCGA-29-1707 
       36.36        16.93        23.93        59.67        18.25        41.98 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 
       31.27        34.62        17.36        86.60        66.81        62.93 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
       39.42        31.30        22.98        24.36        22.55        17.33 
TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 
       12.36        11.84        12.30        14.93         8.38         7.23 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 
        5.36        36.30        62.47        13.84        42.25        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-30-1862 TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 TCGA-31-1959 TCGA-36-1568 
        6.12        30.05        18.77         6.71         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-36-2530 TCGA-36-2532 TCGA-36-2534 
       25.74        27.85        24.23        33.01        29.49        29.82 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 
       25.91        25.08        23.80        21.60         2.24        20.98 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 
       20.52        14.17        16.18        11.47        47.57        23.74 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 TCGA-57-1583 
       28.93        42.02        10.42        40.77        24.03        11.38 
TCGA-57-1584 TCGA-57-1586 TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 
       21.14        22.32        25.08       180.20        22.32       116.12 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1722 
        9.40        34.39         2.14         5.42        44.81         8.09 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 
       31.43        18.54        27.88         4.34        31.79        48.79 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 
       44.84        35.80         2.43        33.67         1.45         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        5.79        11.41        13.02         9.07        34.13        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1919 
       37.05        42.51        48.92        56.61        67.76        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-61-2088 TCGA-61-2092 TCGA-61-2094 
       39.85        30.64         1.18         4.77        51.72        71.74 
TCGA-61-2095 TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       61.64        60.62        55.50         6.48        76.87        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       44.52       125.75        22.22         6.35        31.07         8.61 

  IL21R MUTATED IL21R WILD-TYPE 
           2.47            0.26 
  IL21R MUTATED IL21R WILD-TYPE 
          45.01          180.20 
  IL21R MUTATED IL21R WILD-TYPE 
          8.320          28.735 
[1] "2.5 - 45.0 (8.3)"   "0.3 - 180.2 (28.7)"
[1] "hr=" "2.3"
D6V2, continuous
                 vv
clus              OMENTUM OVARY PERITONEUM OVARY
  IL21R MUTATED         0     8                0
  IL21R WILD-TYPE       2   454                1
D6V3, multiclass
                  clus
vv                 IL21R MUTATED IL21R WILD-TYPE
  OMENTUM                      0               2
  OVARY                        8             454
  PERITONEUM OVARY             0               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"
D6V4, continuous
D6V5, binary
                 cls
clus                0   1
  IL21R MUTATED     0   8
  IL21R WILD-TYPE   3 454
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL21R MUTATED      0    8
  IL21R WILD-TYPE    3  454
     clus
vv    IL21R MUTATED IL21R WILD-TYPE
  NO              0               3
  YES             8             454
[1] 2 2
[1] FALSE
                 vv
clus              R0 R1 R2
  IL21R MUTATED    1  1  0
  IL21R WILD-TYPE 12 21  1
D6V6, multiclass
[1] "Remove cluster labels:" "IL21R MUTATED"         
clus
  IL21R MUTATED IL21R WILD-TYPE 
              2              34 
     TCGA-04-1369      TCGA-04-1516      TCGA-04-1644      TCGA-13-0807 
"IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" 
     TCGA-13-0911      TCGA-29-2427      TCGA-29-2429      TCGA-29-2431 
"IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" 
     TCGA-29-2434      TCGA-29-2436      TCGA-36-2530      TCGA-36-2532 
"IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" 
     TCGA-36-2534      TCGA-36-2537      TCGA-36-2538      TCGA-36-2540 
"IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" 
     TCGA-36-2542      TCGA-36-2543      TCGA-36-2544      TCGA-36-2547 
"IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" 
     TCGA-36-2548      TCGA-36-2551      TCGA-36-2552      TCGA-42-2582 
"IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" 
     TCGA-42-2587      TCGA-42-2588      TCGA-42-2589      TCGA-42-2590 
"IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" 
     TCGA-57-1993      TCGA-59-2363      TCGA-59-2372      TCGA-61-2612 
"IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" 
     TCGA-61-2613      TCGA-61-2614 
"IL21R WILD-TYPE" "IL21R WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IL21R MUTATED                                  0     1
  IL21R WILD-TYPE                                2    17
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IL21R MUTATED                           0     5
  IL21R WILD-TYPE                        20   398
D6V7, multiclass
                                  clus
vv                                 IL21R MUTATED IL21R WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1              17
  BLACK OR AFRICAN AMERICAN                    0              20
  WHITE                                        5             398
[1] 4 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
  IL21R MUTATED     0   3
  IL21R WILD-TYPE   9 267
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL21R MUTATED      0    3
  IL21R WILD-TYPE    9  267
                        clus
vv                       IL21R MUTATED IL21R WILD-TYPE
  HISPANIC OR LATINO                 0               9
  NOT HISPANIC OR LATINO             3             267
[1] 2 2
[1] FALSE

Clustering(7) Variable = KRAS MUTATION ANALYSIS
D7V1, survival
                sevent
clus2              0   1
  KRAS MUTATED     1   4
  KRAS WILD-TYPE 227 231
  KRAS MUTATED KRAS WILD-TYPE 
             5            458 
  KRAS MUTATED KRAS WILD-TYPE 
             4            231 
$`KRAS MUTATED`
TCGA-09-1664 TCGA-09-1672 TCGA-24-2038 TCGA-25-1316 TCGA-29-1696 
       74.93         5.85        44.52        42.05        33.93 

$`KRAS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       43.92        41.00        49.15         2.01        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-04-1353 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-04-1369 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 
      103.40        21.11        56.55        41.59        19.99         0.79 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
       38.37       119.08        84.20        55.43        48.89        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 
       28.64        64.64        36.23        31.86        45.37        29.16 
TCGA-09-0366 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 
       57.76        35.57         9.99        38.43        89.33        41.62 
TCGA-09-1666 TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 
       57.60        30.51        17.98         3.02         8.55        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-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       12.46        25.91        81.86        18.51        34.19        32.88 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
       14.66         6.71        35.44        19.99        20.91         6.21 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 
       24.59        44.55        39.58         2.73        31.20        15.19 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 
       17.82        55.17         2.50        11.54        34.06        32.25 
TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 
       28.57        38.93        36.72        28.70        19.59         8.12 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
        8.28         8.19        35.28        13.61        68.94       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-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
       43.36        49.61        57.47        56.15        57.07        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 
       47.38        48.33        47.84        44.94        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-13-1487 TCGA-13-1488 TCGA-13-1489 
       61.71        29.42        98.04        22.39        70.82        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-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       37.61        38.40        32.84        16.57         4.21         4.41 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 
        4.77         4.18         2.56         3.09        14.24        12.23 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2066 TCGA-13-2071 TCGA-20-0987 
        8.61        10.78         8.75         9.70         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-23-1022 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-23-1107 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 
        2.76         0.30        51.35        54.51         3.22        68.68 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 
        4.57        33.30        86.01       129.96         4.27        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-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-23-2647 
       91.66        77.00         2.76         4.70         4.50         4.44 
TCGA-23-2649 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        3.81         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-24-1431 
        6.02         5.95         5.36         4.83        17.39        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-24-1469 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-24-1551 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-24-1849 TCGA-24-1850 TCGA-24-2019 TCGA-24-2024 
        4.37        11.28         5.79         5.52         4.87        58.16 
TCGA-24-2030 TCGA-24-2035 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 
       55.92        28.18        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-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1317 
       36.23        16.64        53.26        26.96        52.04         2.01 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1324 
       34.98        65.00        37.97        33.96         2.99        34.03 
TCGA-25-1325 TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       32.09        41.06        66.05        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-25-2042 TCGA-25-2391 TCGA-25-2392 
       62.17        35.87        52.04        13.02        49.05         1.02 
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-29-1691 
       29.03        31.00        26.99        78.90        47.61        48.33 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
      101.79        39.02        40.41        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-29-1774 TCGA-29-1775 
       31.30        22.98        24.36        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-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 
       36.30        62.47        13.84        42.25        21.47        11.47 
TCGA-29-2436 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 
        9.76        38.07        51.91        36.26         2.47        15.68 
TCGA-30-1857 TCGA-30-1862 TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 TCGA-31-1959 
        0.26         6.12        30.05        18.77         6.71         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-36-2543 
       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-36-2551 TCGA-36-2552 
       20.98        18.31        20.52        14.17        16.18        11.47 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
       47.57        23.74        28.93        42.02        10.42        40.77 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1993 TCGA-59-2348 
       24.03        11.38        21.14        22.32        25.08       180.20 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       22.32       116.12         9.40        34.39         2.14         5.42 
TCGA-59-2372 TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 
       44.81         8.09        31.43        18.54        27.88         4.34 
TCGA-61-1733 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 
       31.79        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-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       67.76        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-61-2088 
        4.01        30.64        39.85        30.64         1.18         4.77 
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-61-2104 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 
       31.07         8.61 

  KRAS MUTATED KRAS WILD-TYPE 
          5.85           0.26 
  KRAS MUTATED KRAS WILD-TYPE 
         74.93         180.20 
  KRAS MUTATED KRAS WILD-TYPE 
         42.05          28.03 
[1] "5.8 - 74.9 (42.0)"  "0.3 - 180.2 (28.0)"
[1] "hr=" "1.2"
D7V2, continuous
                vv
clus             OMENTUM OVARY PERITONEUM OVARY
  KRAS MUTATED         0     5                0
  KRAS WILD-TYPE       2   457                1
D7V3, multiclass
                  clus
vv                 KRAS MUTATED KRAS WILD-TYPE
  OMENTUM                     0              2
  OVARY                       5            457
  PERITONEUM OVARY            0              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
  KRAS MUTATED     0   5
  KRAS WILD-TYPE   3 457
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      0    5
  KRAS WILD-TYPE    3  457
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO             0              3
  YES            5            457
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2
  KRAS MUTATED    0  0  0
  KRAS WILD-TYPE 13 22  1
D7V6, multiclass
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRAS MUTATED                                  0     0
  KRAS WILD-TYPE                                2    18
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KRAS MUTATED                           0     5
  KRAS WILD-TYPE                        20   398
D7V7, multiclass
                                  clus
vv                                 KRAS MUTATED KRAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             18
  BLACK OR AFRICAN AMERICAN                   0             20
  WHITE                                       5            398
[1] 4 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
  KRAS MUTATED     0   3
  KRAS WILD-TYPE   9 267
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      0    3
  KRAS WILD-TYPE    9  267
                        clus
vv                       KRAS MUTATED KRAS WILD-TYPE
  HISPANIC OR LATINO                0              9
  NOT HISPANIC OR LATINO            3            267
[1] 2 2
[1] FALSE

Clustering(8) Variable = YSK4 MUTATION ANALYSIS
D8V1, survival
                sevent
clus2              0   1
  YSK4 MUTATED     5   5
  YSK4 WILD-TYPE 223 230
  YSK4 MUTATED YSK4 WILD-TYPE 
            10            453 
  YSK4 MUTATED YSK4 WILD-TYPE 
             5            230 
$`YSK4 MUTATED`
TCGA-04-1348 TCGA-13-1489 TCGA-23-1026 TCGA-24-1549 TCGA-24-2035 TCGA-24-2254 
       48.76        82.88        26.83        56.58        28.18        57.07 
TCGA-25-1326 TCGA-29-1784 TCGA-29-2434 TCGA-36-2537 
       41.06         5.36        11.47        25.91 

$`YSK4 WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       43.92        41.00        49.15         2.01        46.62        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1353 
       11.87        65.52        63.09        21.57        63.98         0.53 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       49.28        32.52        44.32        33.67        76.57       103.40 
TCGA-04-1369 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 
       21.11        56.55        41.59        19.99         0.79        38.37 
TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 
      119.08        84.20        55.43        48.89        27.88        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 TCGA-09-0366 
       64.64        36.23        31.86        45.37        29.16        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-09-1666 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 
       57.60        30.51        17.98         5.85         3.02         8.55 
TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
       97.55         6.12        35.15       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       39.75        12.46        25.91        81.86        18.51        34.19 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 
       32.88        14.66         6.71        35.44        19.99        20.91 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 
        6.21        24.59        44.55        39.58         2.73        31.20 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 
       15.19        17.82        55.17         2.50        11.54        34.06 
TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 
       32.25        28.57        38.93        36.72        28.70        19.59 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 
        8.12         8.28         8.19        35.28        13.61        68.94 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 
      107.18        91.40        74.27        66.67        61.84        67.99 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       69.01        43.36        49.61        57.47        56.15        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-13-0911 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-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 
        5.92         6.84         4.70         4.21         5.33        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 
       87.06        61.71        29.42        98.04        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-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       37.61        38.40        32.84        16.57         4.21         4.41 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 
        4.77         4.18         2.56         3.09        14.24        12.23 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2066 TCGA-13-2071 TCGA-20-0987 
        8.61        10.78         8.75         9.70         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-23-1022 TCGA-23-1023 TCGA-23-1024 
        2.93         2.66        47.54        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-23-1107 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 
        0.30        51.35        54.51         3.22        68.68         4.57 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 
       33.30        86.01       129.96         4.27        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-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-23-2647 TCGA-23-2649 
       77.00         2.76         4.70         4.50         4.44         3.81 
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-24-1431 TCGA-24-1434 
        5.95         5.36         4.83        17.39        19.17        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 
       43.53         8.55        72.92        12.46        45.14         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-24-1551 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-24-1560 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-24-2019 TCGA-24-2024 TCGA-24-2030 TCGA-24-2038 
        5.79         5.52         4.87        58.16        55.92        44.52 
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-24-2298 
       44.61         0.82        67.36        36.23        16.64        53.26 
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-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1324 TCGA-25-1325 TCGA-25-1328 
       37.97        33.96         2.99        34.03        32.09        66.05 
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-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 
       13.02        49.05         1.02        38.04         3.02        45.01 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-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-29-1785 TCGA-29-2427 TCGA-29-2429 
       14.93         8.38         7.23        36.30        62.47        13.84 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2436 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 
       42.25        21.47         9.76        38.07        51.91        36.26 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1862 TCGA-30-1891 TCGA-31-1950 
        2.47        15.68         0.26         6.12        30.05        18.77 
TCGA-31-1953 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 
        6.71         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-36-2530 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-36-2543 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-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1993 
       40.77        24.03        11.38        21.14        22.32        25.08 
TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 
      180.20        22.32       116.12         9.40        34.39         2.14 
TCGA-59-2363 TCGA-59-2372 TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 
        5.42        44.81         8.09        31.43        18.54        27.88 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 
        4.34        31.79        48.79        44.84        35.80         2.43 
TCGA-61-1741 TCGA-61-1895 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-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       56.61        67.76        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-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 TCGA-61-2101 
        4.77        51.72        71.74        61.64        60.62        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 
        6.35        31.07         8.61 

  YSK4 MUTATED YSK4 WILD-TYPE 
          5.36           0.26 
  YSK4 MUTATED YSK4 WILD-TYPE 
         82.88         180.20 
  YSK4 MUTATED YSK4 WILD-TYPE 
         34.62          28.57 
[1] "5.4 - 82.9 (34.6)"  "0.3 - 180.2 (28.6)"
[1] "hr=" "1.2"
D8V2, continuous
                vv
clus             OMENTUM OVARY PERITONEUM OVARY
  YSK4 MUTATED         0    10                0
  YSK4 WILD-TYPE       2   452                1
D8V3, multiclass
                  clus
vv                 YSK4 MUTATED YSK4 WILD-TYPE
  OMENTUM                     0              2
  OVARY                      10            452
  PERITONEUM OVARY            0              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"
D8V4, continuous
[1] "Remove cluster labels:" "YSK4 MUTATED"          
clus
  YSK4 MUTATED YSK4 WILD-TYPE 
             1             63 
    TCGA-04-1346     TCGA-04-1347     TCGA-04-1356     TCGA-04-1367 
"YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" 
    TCGA-10-0926     TCGA-13-0714     TCGA-13-0720     TCGA-13-0724 
"YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" 
    TCGA-13-0755     TCGA-13-0760     TCGA-13-0762     TCGA-13-0791 
"YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" 
    TCGA-13-0792     TCGA-13-0793     TCGA-13-0795     TCGA-13-0801 
"YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" 
    TCGA-13-0802     TCGA-13-0885     TCGA-13-0887     TCGA-13-0889 
"YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" 
    TCGA-13-0891     TCGA-13-0894     TCGA-13-0897     TCGA-13-0900 
"YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" 
    TCGA-13-0901     TCGA-13-0903     TCGA-13-0904     TCGA-13-0905 
"YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" 
    TCGA-13-0906     TCGA-13-0910     TCGA-13-0911     TCGA-13-0912 
"YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" 
    TCGA-13-0913     TCGA-13-0919     TCGA-13-1404     TCGA-13-1405 
"YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" 
    TCGA-13-1409     TCGA-13-1410     TCGA-13-1412     TCGA-13-1482 
"YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" 
    TCGA-13-1483     TCGA-13-1484     TCGA-13-1488     TCGA-13-1491 
"YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" 
    TCGA-13-1492     TCGA-13-1495     TCGA-13-1497     TCGA-13-1498 
"YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" 
    TCGA-13-1499     TCGA-13-1501     TCGA-13-1504     TCGA-13-1506 
"YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" 
    TCGA-13-1507     TCGA-13-1509     TCGA-13-1512     TCGA-13-2057 
"YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" 
    TCGA-13-2059     TCGA-13-2060     TCGA-13-2061     TCGA-13-2066 
"YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" 
    TCGA-13-2071     TCGA-24-1614     TCGA-61-2101 
"YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" 
D8V5, binary
                cls
clus               0   1
  YSK4 MUTATED     0  10
  YSK4 WILD-TYPE   3 452
[1] "tbl2"
                cls
clus             [,1] [,2]
  YSK4 MUTATED      0   10
  YSK4 WILD-TYPE    3  452
     clus
vv    YSK4 MUTATED YSK4 WILD-TYPE
  NO             0              3
  YES           10            452
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2
  YSK4 MUTATED    1  1  0
  YSK4 WILD-TYPE 12 21  1
D8V6, multiclass
[1] "Remove cluster labels:" "YSK4 MUTATED"          
clus
  YSK4 MUTATED YSK4 WILD-TYPE 
             2             34 
    TCGA-04-1369     TCGA-04-1516     TCGA-04-1644     TCGA-13-0807 
"YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" 
    TCGA-13-0911     TCGA-29-2427     TCGA-29-2429     TCGA-29-2431 
"YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" 
    TCGA-29-2432     TCGA-29-2436     TCGA-36-2530     TCGA-36-2532 
"YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" 
    TCGA-36-2534     TCGA-36-2538     TCGA-36-2540     TCGA-36-2542 
"YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" 
    TCGA-36-2543     TCGA-36-2544     TCGA-36-2545     TCGA-36-2547 
"YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" 
    TCGA-36-2548     TCGA-36-2551     TCGA-36-2552     TCGA-42-2582 
"YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" 
    TCGA-42-2587     TCGA-42-2588     TCGA-42-2589     TCGA-42-2590 
"YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" 
    TCGA-57-1993     TCGA-59-2363     TCGA-59-2372     TCGA-61-2612 
"YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" "YSK4 WILD-TYPE" 
    TCGA-61-2613     TCGA-61-2614 
"YSK4 WILD-TYPE" "YSK4 WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  YSK4 MUTATED                                  0     0
  YSK4 WILD-TYPE                                2    18
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  YSK4 MUTATED                           0     9
  YSK4 WILD-TYPE                        20   394
D8V7, multiclass
                                  clus
vv                                 YSK4 MUTATED YSK4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             18
  BLACK OR AFRICAN AMERICAN                   0             20
  WHITE                                       9            394
[1] 4 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
  YSK4 MUTATED     2   3
  YSK4 WILD-TYPE   7 267
[1] "tbl2"
                cls
clus             [,1] [,2]
  YSK4 MUTATED      2    3
  YSK4 WILD-TYPE    7  267
                        clus
vv                       YSK4 MUTATED YSK4 WILD-TYPE
  HISPANIC OR LATINO                2              7
  NOT HISPANIC OR LATINO            3            267
[1] 2 2
[1] FALSE

Clustering(9) Variable = ANKRD35 MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  ANKRD35 MUTATED     4   5
  ANKRD35 WILD-TYPE 224 230
  ANKRD35 MUTATED ANKRD35 WILD-TYPE 
                9               454 
  ANKRD35 MUTATED ANKRD35 WILD-TYPE 
                5               230 
$`ANKRD35 MUTATED`
TCGA-13-0883 TCGA-13-1497 TCGA-24-0980 TCGA-24-2280 TCGA-29-1761 TCGA-29-1764 
       68.94        54.31         7.66        70.45        17.36        62.93 
TCGA-29-1785 TCGA-61-1730 TCGA-61-1913 
       36.30         4.34        48.92 

$`ANKRD35 WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       43.92        41.00        49.15         2.01        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-04-1353 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-04-1369 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 
      103.40        21.11        56.55        41.59        19.99         0.79 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
       38.37       119.08        84.20        55.43        48.89        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 
       28.64        64.64        36.23        31.86        45.37        29.16 
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-09-1666 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       41.62        57.60        30.51        17.98         5.85         3.02 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 
        8.55        97.55         6.12        35.15       112.41        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       63.09        39.75        12.46        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-13-0724 
       20.91         6.21        24.59        44.55        39.58         2.73 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 
       31.20        15.19        17.82        55.17         2.50        11.54 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       34.06        32.25        28.57        38.93        36.72        28.70 
TCGA-13-0795 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 
       19.59         8.12         8.28         8.19        35.28        13.61 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 
      107.18        91.40        74.27        66.67        61.84        67.99 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       69.01        43.36        49.61        57.47        56.15        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-13-0911 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-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 
        5.92         6.84         4.70         4.21         5.33        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 
       87.06        61.71        29.42        98.04        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-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       37.61        38.40        32.84        16.57         4.21         4.41 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 
        4.77         4.18         2.56         3.09        14.24        12.23 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2066 TCGA-13-2071 TCGA-20-0987 
        8.61        10.78         8.75         9.70         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-23-1022 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-23-1107 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 
        2.76         0.30        51.35        54.51         3.22        68.68 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 
        4.57        33.30        86.01       129.96         4.27        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-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-23-2647 
       91.66        77.00         2.76         4.70         4.50         4.44 
TCGA-23-2649 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        3.81         7.63        19.66        11.64        21.80        41.56 
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-24-1434 
        5.95         5.36         4.83        17.39        19.17        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 
       43.53         8.55        72.92        12.46        45.14         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-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       16.21        56.58        51.91        41.39        58.09        88.50 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       70.62        39.88        19.53        44.09        45.50        47.70 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 
       25.87        10.26        17.23        90.15        88.37        48.33 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 
       38.24         8.32         3.48         3.72         3.81         4.37 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-2019 TCGA-24-2024 TCGA-24-2030 
       11.28         5.79         5.52         4.87        58.16        55.92 
TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 
       28.18        44.52        57.07        36.16         0.79         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 
       47.54        31.63        44.61         0.82        67.36        36.23 
TCGA-24-2293 TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
       16.64        53.26        26.96        52.04        42.05         2.01 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1324 
       34.98        65.00        37.97        33.96         2.99        34.03 
TCGA-25-1325 TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       32.09        41.06        66.05        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-25-2042 TCGA-25-2391 TCGA-25-2392 
       62.17        35.87        52.04        13.02        49.05         1.02 
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-29-1691 
       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-29-1697 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-29-1705 TCGA-29-1707 
       36.36        16.93        23.93        59.67        18.25        41.98 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1762 TCGA-29-1763 TCGA-29-1766 TCGA-29-1768 
       31.27        34.62        86.60        66.81        39.42        31.30 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 
       22.98        24.36        22.55        17.33        12.36        11.84 
TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-2427 
       12.30        14.93         8.38         7.23         5.36        62.47 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-30-1714 
       13.84        42.25        21.47        11.47         9.76        38.07 
TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1862 
       51.91        36.26         2.47        15.68         0.26         6.12 
TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 
       30.05        18.77         6.71         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-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       27.85        24.23        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-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 
       20.52        14.17        16.18        11.47        47.57        23.74 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 TCGA-57-1583 
       28.93        42.02        10.42        40.77        24.03        11.38 
TCGA-57-1584 TCGA-57-1586 TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 
       21.14        22.32        25.08       180.20        22.32       116.12 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1722 
        9.40        34.39         2.14         5.42        44.81         8.09 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 TCGA-61-1736 TCGA-61-1737 
       31.43        18.54        27.88        31.79        48.79        44.84 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
       35.80         2.43        33.67         1.45         8.42         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 
       11.41        13.02         9.07        34.13        31.30        37.05 
TCGA-61-1911 TCGA-61-1914 TCGA-61-1915 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
       42.51        56.61        67.76        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-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 
        1.18         4.77        51.72        71.74        61.64        60.62 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       55.50         6.48        76.87        20.68        44.52       125.75 
TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       22.22         6.35        31.07         8.61 

  ANKRD35 MUTATED ANKRD35 WILD-TYPE 
             4.34              0.26 
  ANKRD35 MUTATED ANKRD35 WILD-TYPE 
            70.45            180.20 
  ANKRD35 MUTATED ANKRD35 WILD-TYPE 
            48.92             28.03 
[1] "4.3 - 70.5 (48.9)"  "0.3 - 180.2 (28.0)"
[1] "hr=" "1.3"
D9V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  ANKRD35 MUTATED         0     9                0
  ANKRD35 WILD-TYPE       2   453                1
D9V3, multiclass
                  clus
vv                 ANKRD35 MUTATED ANKRD35 WILD-TYPE
  OMENTUM                        0                 2
  OVARY                          9               453
  PERITONEUM OVARY               0                 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"
D9V4, continuous
[1] "Remove cluster labels:" "ANKRD35 MUTATED"       
clus
  ANKRD35 MUTATED ANKRD35 WILD-TYPE 
                1                63 
       TCGA-04-1346        TCGA-04-1347        TCGA-04-1356        TCGA-04-1367 
"ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" 
       TCGA-10-0926        TCGA-13-0714        TCGA-13-0720        TCGA-13-0724 
"ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" 
       TCGA-13-0755        TCGA-13-0760        TCGA-13-0762        TCGA-13-0791 
"ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" 
       TCGA-13-0792        TCGA-13-0793        TCGA-13-0795        TCGA-13-0801 
"ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" 
       TCGA-13-0802        TCGA-13-0885        TCGA-13-0887        TCGA-13-0889 
"ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" 
       TCGA-13-0891        TCGA-13-0894        TCGA-13-0897        TCGA-13-0900 
"ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" 
       TCGA-13-0901        TCGA-13-0903        TCGA-13-0904        TCGA-13-0905 
"ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" 
       TCGA-13-0906        TCGA-13-0910        TCGA-13-0911        TCGA-13-0912 
"ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" 
       TCGA-13-0913        TCGA-13-0919        TCGA-13-1404        TCGA-13-1405 
"ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" 
       TCGA-13-1409        TCGA-13-1410        TCGA-13-1412        TCGA-13-1482 
"ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" 
       TCGA-13-1483        TCGA-13-1484        TCGA-13-1488        TCGA-13-1489 
"ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" 
       TCGA-13-1491        TCGA-13-1492        TCGA-13-1495        TCGA-13-1498 
"ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" 
       TCGA-13-1499        TCGA-13-1501        TCGA-13-1504        TCGA-13-1506 
"ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" 
       TCGA-13-1507        TCGA-13-1509        TCGA-13-1512        TCGA-13-2057 
"ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" 
       TCGA-13-2059        TCGA-13-2060        TCGA-13-2061        TCGA-13-2066 
"ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" 
       TCGA-13-2071        TCGA-24-1614        TCGA-61-2101 
"ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" "ANKRD35 WILD-TYPE" 
D9V5, binary
                   cls
clus                  0   1
  ANKRD35 MUTATED     0   9
  ANKRD35 WILD-TYPE   3 453
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD35 MUTATED      0    9
  ANKRD35 WILD-TYPE    3  453
     clus
vv    ANKRD35 MUTATED ANKRD35 WILD-TYPE
  NO                0                 3
  YES               9               453
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2
  ANKRD35 MUTATED    0  0  0
  ANKRD35 WILD-TYPE 13 22  1
D9V6, multiclass
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANKRD35 MUTATED                                  0     1
  ANKRD35 WILD-TYPE                                2    17
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ANKRD35 MUTATED                           0     8
  ANKRD35 WILD-TYPE                        20   395
D9V7, multiclass
                                  clus
vv                                 ANKRD35 MUTATED ANKRD35 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                17
  BLACK OR AFRICAN AMERICAN                      0                20
  WHITE                                          8               395
[1] 4 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
  ANKRD35 MUTATED     0   4
  ANKRD35 WILD-TYPE   9 266
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD35 MUTATED      0    4
  ANKRD35 WILD-TYPE    9  266
                        clus
vv                       ANKRD35 MUTATED ANKRD35 WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO               4               266
[1] 2 2
[1] FALSE

Clustering(10) Variable = C9ORF171 MUTATION ANALYSIS
D10V1, survival
                    sevent
clus2                  0   1
  C9ORF171 MUTATED     4   1
  C9ORF171 WILD-TYPE 224 234
  C9ORF171 MUTATED C9ORF171 WILD-TYPE 
                 5                458 
  C9ORF171 MUTATED C9ORF171 WILD-TYPE 
                 1                234 
$`C9ORF171 MUTATED`
TCGA-13-0793 TCGA-13-1404 TCGA-13-1408 TCGA-13-1412 TCGA-24-2035 
       28.70         6.61         5.92         5.33        28.18 

$`C9ORF171 WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       43.92        41.00        49.15         2.01        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-04-1353 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-04-1369 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 
      103.40        21.11        56.55        41.59        19.99         0.79 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
       38.37       119.08        84.20        55.43        48.89        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 
       28.64        64.64        36.23        31.86        45.37        29.16 
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-09-1666 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       41.62        57.60        30.51        17.98         5.85         3.02 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 
        8.55        97.55         6.12        35.15       112.41        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       63.09        39.75        12.46        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-13-0724 
       20.91         6.21        24.59        44.55        39.58         2.73 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 
       31.20        15.19        17.82        55.17         2.50        11.54 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0795 
       34.06        32.25        28.57        38.93        36.72        19.59 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 
        8.12         8.28         8.19        35.28        13.61        68.94 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 
      107.18        91.40        74.27        66.67        61.84        67.99 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       69.01        43.36        49.61        57.47        56.15        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-13-0911 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-13-1405 TCGA-13-1407 TCGA-13-1409 
        6.41         6.08        10.88         7.36         6.05         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-13-1487 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-13-1501 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-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 
        2.56         3.09        14.24        12.23         8.61        10.78 
TCGA-13-2065 TCGA-13-2066 TCGA-13-2071 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
        8.75         9.70         6.28        23.05        25.94        26.20 
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-23-1107 
       49.41         8.81        29.13        18.90         2.76         0.30 
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-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 
       86.01       129.96         4.27        39.09        33.47        58.13 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
        0.53        24.95       115.89        87.48        91.66        77.00 
TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-23-2647 TCGA-23-2649 TCGA-24-0966 
        2.76         4.70         4.50         4.44         3.81         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-24-1431 TCGA-24-1434 TCGA-24-1435 
        5.36         4.83        17.39        19.17        18.67        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-24-1471 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-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 
       56.58        51.91        41.39        58.09        88.50        70.62 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
       39.88        19.53        44.09        45.50        47.70        25.87 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 
       10.26        17.23        90.15        88.37        48.33        38.24 
TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 
        8.32         3.48         3.72         3.81         4.37        11.28 
TCGA-24-1849 TCGA-24-1850 TCGA-24-2019 TCGA-24-2024 TCGA-24-2030 TCGA-24-2038 
        5.79         5.52         4.87        58.16        55.92        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-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
       53.26        26.96        52.04        42.05         2.01        34.98 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1324 TCGA-25-1325 
       65.00        37.97        33.96         2.99        34.03        32.09 
TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 
       41.06        66.05        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-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 
       35.87        52.04        13.02        49.05         1.02        38.04 
TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 
        3.02        45.01        19.99        42.02         2.96        29.03 
TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 
       31.00        26.99        78.90        47.61        48.33       101.79 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
       39.02        40.41        33.93        31.20        68.32        36.36 
TCGA-29-1701 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-29-1774 TCGA-29-1775 
       31.30        22.98        24.36        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-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 
       36.30        62.47        13.84        42.25        21.47        11.47 
TCGA-29-2436 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 
        9.76        38.07        51.91        36.26         2.47        15.68 
TCGA-30-1857 TCGA-30-1862 TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 TCGA-31-1959 
        0.26         6.12        30.05        18.77         6.71         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-36-2543 
       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-36-2551 TCGA-36-2552 
       20.98        18.31        20.52        14.17        16.18        11.47 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
       47.57        23.74        28.93        42.02        10.42        40.77 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1993 TCGA-59-2348 
       24.03        11.38        21.14        22.32        25.08       180.20 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       22.32       116.12         9.40        34.39         2.14         5.42 
TCGA-59-2372 TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 
       44.81         8.09        31.43        18.54        27.88         4.34 
TCGA-61-1733 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 
       31.79        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-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       67.76        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-61-2088 
        4.01        30.64        39.85        30.64         1.18         4.77 
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-61-2104 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 
       31.07         8.61 

  C9ORF171 MUTATED C9ORF171 WILD-TYPE 
              5.33               0.26 
  C9ORF171 MUTATED C9ORF171 WILD-TYPE 
              28.7              180.2 
  C9ORF171 MUTATED C9ORF171 WILD-TYPE 
             6.610             28.705 
[1] "5.3 - 28.7 (6.6)"   "0.3 - 180.2 (28.7)"
[1] "hr=" "1.3"
D10V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  C9ORF171 MUTATED         0     5                0
  C9ORF171 WILD-TYPE       2   457                1
D10V3, multiclass
                  clus
vv                 C9ORF171 MUTATED C9ORF171 WILD-TYPE
  OMENTUM                         0                  2
  OVARY                           5                457
  PERITONEUM OVARY                0                  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
  C9ORF171 MUTATED     0   5
  C9ORF171 WILD-TYPE   3 457
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF171 MUTATED      0    5
  C9ORF171 WILD-TYPE    3  457
     clus
vv    C9ORF171 MUTATED C9ORF171 WILD-TYPE
  NO                 0                  3
  YES                5                457
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2
  C9ORF171 MUTATED    0  0  0
  C9ORF171 WILD-TYPE 13 22  1
D10V6, multiclass
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C9ORF171 MUTATED                                  0     0
  C9ORF171 WILD-TYPE                                2    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C9ORF171 MUTATED                           0     5
  C9ORF171 WILD-TYPE                        20   398
D10V7, multiclass
                                  clus
vv                                 C9ORF171 MUTATED C9ORF171 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 18
  BLACK OR AFRICAN AMERICAN                       0                 20
  WHITE                                           5                398
[1] 4 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
  C9ORF171 MUTATED     0   4
  C9ORF171 WILD-TYPE   9 266
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF171 MUTATED      0    4
  C9ORF171 WILD-TYPE    9  266
                        clus
vv                       C9ORF171 MUTATED C9ORF171 WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                4                266
[1] 2 2
[1] FALSE

Clustering(11) Variable = MTA2 MUTATION ANALYSIS
D11V1, survival
                sevent
clus2              0   1
  MTA2 MUTATED     1   3
  MTA2 WILD-TYPE 227 232
  MTA2 MUTATED MTA2 WILD-TYPE 
             4            459 
  MTA2 MUTATED MTA2 WILD-TYPE 
             3            232 
$`MTA2 MUTATED`
TCGA-04-1369 TCGA-20-1683 TCGA-25-2400 TCGA-36-2543 
       21.11        25.38        42.02         2.24 

$`MTA2 WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       43.92        41.00        49.15         2.01        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-04-1353 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-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 
      103.40        56.55        41.59        19.99         0.79        38.37 
TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 
      119.08        84.20        55.43        48.89        27.88        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 TCGA-09-0366 
       64.64        36.23        31.86        45.37        29.16        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-09-1666 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 
       57.60        30.51        17.98         5.85         3.02         8.55 
TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
       97.55         6.12        35.15       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       39.75        12.46        25.91        81.86        18.51        34.19 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 
       32.88        14.66         6.71        35.44        19.99        20.91 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 
        6.21        24.59        44.55        39.58         2.73        31.20 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 
       15.19        17.82        55.17         2.50        11.54        34.06 
TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 
       32.25        28.57        38.93        36.72        28.70        19.59 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 
        8.12         8.28         8.19        35.28        13.61        68.94 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 
      107.18        91.40        74.27        66.67        61.84        67.99 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       69.01        43.36        49.61        57.47        56.15        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-13-0911 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-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 
        5.92         6.84         4.70         4.21         5.33        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 
       87.06        61.71        29.42        98.04        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-13-1501 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-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 
        4.41         4.77         4.18         2.56         3.09        14.24 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2066 TCGA-13-2071 
       12.23         8.61        10.78         8.75         9.70         6.28 
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-23-1022 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-23-1107 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 
        2.76         0.30        51.35        54.51         3.22        68.68 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 
        4.57        33.30        86.01       129.96         4.27        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-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-23-2647 
       91.66        77.00         2.76         4.70         4.50         4.44 
TCGA-23-2649 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        3.81         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-24-1431 
        6.02         5.95         5.36         4.83        17.39        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-24-1469 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-24-1551 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-24-1849 TCGA-24-1850 TCGA-24-2019 TCGA-24-2024 
        4.37        11.28         5.79         5.52         4.87        58.16 
TCGA-24-2030 TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 
       55.92        28.18        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-24-2298 TCGA-25-1313 TCGA-25-1315 
       67.36        36.23        16.64        53.26        26.96        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-25-1324 TCGA-25-1325 TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 
        2.99        34.03        32.09        41.06        66.05        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-25-2042 
        0.30        59.15        62.17        35.87        52.04        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-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 
        2.96        29.03        31.00        26.99        78.90        47.61 
TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 
       48.33       101.79        39.02        40.41        33.93        31.20 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 
       68.32        36.36        16.93        23.93        59.67        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
       41.98        31.27        34.62        17.36        86.60        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 
       62.93        39.42        31.30        22.98        24.36        22.55 
TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 
       17.33        12.36        11.84        12.30        14.93         8.38 
TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 
        7.23         5.36        36.30        62.47        13.84        42.25 
TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 
       21.47        11.47         9.76        38.07        51.91        36.26 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1862 TCGA-30-1891 TCGA-31-1950 
        2.47        15.68         0.26         6.12        30.05        18.77 
TCGA-31-1953 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 
        6.71         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-36-2530 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-36-2548 TCGA-36-2551 
       21.60        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-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1993 
       40.77        24.03        11.38        21.14        22.32        25.08 
TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 
      180.20        22.32       116.12         9.40        34.39         2.14 
TCGA-59-2363 TCGA-59-2372 TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 
        5.42        44.81         8.09        31.43        18.54        27.88 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 
        4.34        31.79        48.79        44.84        35.80         2.43 
TCGA-61-1741 TCGA-61-1895 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-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       56.61        67.76        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-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 TCGA-61-2101 
        4.77        51.72        71.74        61.64        60.62        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 
        6.35        31.07         8.61 

  MTA2 MUTATED MTA2 WILD-TYPE 
          2.24           0.26 
  MTA2 MUTATED MTA2 WILD-TYPE 
         42.02         180.20 
  MTA2 MUTATED MTA2 WILD-TYPE 
        23.245         28.640 
[1] "2.2 - 42.0 (23.2)"  "0.3 - 180.2 (28.6)"
[1] "hr=" "2.7"
D11V2, continuous
                vv
clus             OMENTUM OVARY PERITONEUM OVARY
  MTA2 MUTATED         0     4                0
  MTA2 WILD-TYPE       2   458                1
D11V3, multiclass
                  clus
vv                 MTA2 MUTATED MTA2 WILD-TYPE
  OMENTUM                     0              2
  OVARY                       4            458
  PERITONEUM OVARY            0              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
  MTA2 MUTATED     0   4
  MTA2 WILD-TYPE   3 458
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTA2 MUTATED      0    4
  MTA2 WILD-TYPE    3  458
     clus
vv    MTA2 MUTATED MTA2 WILD-TYPE
  NO             0              3
  YES            4            458
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2
  MTA2 MUTATED    0  2  0
  MTA2 WILD-TYPE 13 20  1
D11V6, multiclass
[1] "Remove cluster labels:" "MTA2 MUTATED"          
clus
  MTA2 MUTATED MTA2 WILD-TYPE 
             2             34 
    TCGA-04-1516     TCGA-04-1644     TCGA-13-0807     TCGA-13-0911 
"MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" 
    TCGA-29-2427     TCGA-29-2429     TCGA-29-2431     TCGA-29-2432 
"MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" 
    TCGA-29-2434     TCGA-29-2436     TCGA-36-2530     TCGA-36-2532 
"MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" 
    TCGA-36-2534     TCGA-36-2537     TCGA-36-2538     TCGA-36-2540 
"MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" 
    TCGA-36-2542     TCGA-36-2544     TCGA-36-2545     TCGA-36-2547 
"MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" 
    TCGA-36-2548     TCGA-36-2551     TCGA-36-2552     TCGA-42-2582 
"MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" 
    TCGA-42-2587     TCGA-42-2588     TCGA-42-2589     TCGA-42-2590 
"MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" 
    TCGA-57-1993     TCGA-59-2363     TCGA-59-2372     TCGA-61-2612 
"MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" 
    TCGA-61-2613     TCGA-61-2614 
"MTA2 WILD-TYPE" "MTA2 WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MTA2 MUTATED                                  0     0
  MTA2 WILD-TYPE                                2    18
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MTA2 MUTATED                           0     3
  MTA2 WILD-TYPE                        20   400
D11V7, multiclass
                                  clus
vv                                 MTA2 MUTATED MTA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             18
  BLACK OR AFRICAN AMERICAN                   0             20
  WHITE                                       3            400
[1] 4 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
  MTA2 MUTATED     0   3
  MTA2 WILD-TYPE   9 267
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTA2 MUTATED      0    3
  MTA2 WILD-TYPE    9  267
                        clus
vv                       MTA2 MUTATED MTA2 WILD-TYPE
  HISPANIC OR LATINO                0              9
  NOT HISPANIC OR LATINO            3            267
[1] 2 2
[1] FALSE

Clustering(12) Variable = CYP11B1 MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  CYP11B1 MUTATED     4   4
  CYP11B1 WILD-TYPE 224 231
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
                8               455 
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
                4               231 
$`CYP11B1 MUTATED`
TCGA-09-0366 TCGA-13-0893 TCGA-23-1122 TCGA-29-1777 TCGA-59-2355 TCGA-61-1737 
       57.76        43.36        39.09        12.30         2.14        44.84 
TCGA-61-1907 TCGA-61-2012 
       31.30        30.64 

$`CYP11B1 WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       43.92        41.00        49.15         2.01        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-04-1353 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-04-1369 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 
      103.40        21.11        56.55        41.59        19.99         0.79 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
       38.37       119.08        84.20        55.43        48.89        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 
       28.64        64.64        36.23        31.86        45.37        29.16 
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-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 
       57.60        30.51        17.98         5.85         3.02         8.55 
TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
       97.55         6.12        35.15       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       39.75        12.46        25.91        81.86        18.51        34.19 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 
       32.88        14.66         6.71        35.44        19.99        20.91 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 
        6.21        24.59        44.55        39.58         2.73        31.20 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 
       15.19        17.82        55.17         2.50        11.54        34.06 
TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 
       32.25        28.57        38.93        36.72        28.70        19.59 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 
        8.12         8.28         8.19        35.28        13.61        68.94 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 
      107.18        91.40        74.27        66.67        61.84        67.99 
TCGA-13-0891 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
       69.01        49.61        57.47        56.15        57.07        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 
       47.38        48.33        47.84        44.94        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-13-1487 TCGA-13-1488 TCGA-13-1489 
       61.71        29.42        98.04        22.39        70.82        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-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       37.61        38.40        32.84        16.57         4.21         4.41 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 
        4.77         4.18         2.56         3.09        14.24        12.23 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2066 TCGA-13-2071 TCGA-20-0987 
        8.61        10.78         8.75         9.70         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-23-1022 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-23-1107 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 
        2.76         0.30        51.35        54.51         3.22        68.68 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1123 
        4.57        33.30        86.01       129.96         4.27        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-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-23-2647 TCGA-23-2649 
       77.00         2.76         4.70         4.50         4.44         3.81 
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-24-1431 TCGA-24-1434 
        5.95         5.36         4.83        17.39        19.17        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 
       43.53         8.55        72.92        12.46        45.14         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-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       16.21        56.58        51.91        41.39        58.09        88.50 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       70.62        39.88        19.53        44.09        45.50        47.70 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 
       25.87        10.26        17.23        90.15        88.37        48.33 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 
       38.24         8.32         3.48         3.72         3.81         4.37 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-2019 TCGA-24-2024 TCGA-24-2030 
       11.28         5.79         5.52         4.87        58.16        55.92 
TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 
       28.18        44.52        57.07        36.16         0.79         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 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-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 
       36.23        16.64        53.26        26.96        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-25-1324 TCGA-25-1325 TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 
       34.03        32.09        41.06        66.05        15.02        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
       27.62        17.03        12.95        20.61        38.20         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-2042 TCGA-25-2391 
       59.15        62.17        35.87        52.04        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-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 
        2.96        29.03        31.00        26.99        78.90        47.61 
TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 
       48.33       101.79        39.02        40.41        33.93        31.20 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 
       68.32        36.36        16.93        23.93        59.67        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
       41.98        31.27        34.62        17.36        86.60        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 
       62.93        39.42        31.30        22.98        24.36        22.55 
TCGA-29-1774 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-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 
        5.36        36.30        62.47        13.84        42.25        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-30-1856 TCGA-30-1857 TCGA-30-1862 TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 
       15.68         0.26         6.12        30.05        18.77         6.71 
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-36-2530 
        8.55        30.08        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-36-2551 
        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-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1993 
       40.77        24.03        11.38        21.14        22.32        25.08 
TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 
      180.20        22.32       116.12         9.40        34.39         5.42 
TCGA-59-2372 TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 
       44.81         8.09        31.43        18.54        27.88         4.34 
TCGA-61-1733 TCGA-61-1736 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 
       31.79        48.79        35.80         2.43        33.67         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-61-1915 TCGA-61-1919 
       37.05        42.51        48.92        56.61        67.76        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-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       39.85         1.18         4.77        51.72        71.74        61.64 
TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       60.62        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 
      125.75        22.22         6.35        31.07         8.61 

  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
             2.14              0.26 
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
            57.76            180.20 
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
           35.195            27.880 
[1] "2.1 - 57.8 (35.2)"  "0.3 - 180.2 (27.9)"
[1] "hr=" "1"  
D12V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  CYP11B1 MUTATED         0     8                0
  CYP11B1 WILD-TYPE       2   454                1
D12V3, multiclass
                  clus
vv                 CYP11B1 MUTATED CYP11B1 WILD-TYPE
  OMENTUM                        0                 2
  OVARY                          8               454
  PERITONEUM OVARY               0                 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"
D12V4, continuous
D12V5, binary
                   cls
clus                  0   1
  CYP11B1 MUTATED     1   7
  CYP11B1 WILD-TYPE   2 455
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP11B1 MUTATED      1    7
  CYP11B1 WILD-TYPE    2  455
     clus
vv    CYP11B1 MUTATED CYP11B1 WILD-TYPE
  NO                1                 2
  YES               7               455
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2
  CYP11B1 MUTATED    0  0  0
  CYP11B1 WILD-TYPE 13 22  1
D12V6, multiclass
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYP11B1 MUTATED                                  0     0
  CYP11B1 WILD-TYPE                                2    18
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CYP11B1 MUTATED                           1     7
  CYP11B1 WILD-TYPE                        19   396
D12V7, multiclass
                                  clus
vv                                 CYP11B1 MUTATED CYP11B1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                18
  BLACK OR AFRICAN AMERICAN                      1                19
  WHITE                                          7               396
[1] 4 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
  CYP11B1 MUTATED     0   5
  CYP11B1 WILD-TYPE   9 265
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP11B1 MUTATED      0    5
  CYP11B1 WILD-TYPE    9  265
                        clus
vv                       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO               5               265
[1] 2 2
[1] FALSE

Clustering(13) Variable = NRAS MUTATION ANALYSIS
D13V1, survival
                sevent
clus2              0   1
  NRAS MUTATED     2   2
  NRAS WILD-TYPE 226 233
  NRAS MUTATED NRAS WILD-TYPE 
             4            459 
  NRAS MUTATED NRAS WILD-TYPE 
             2            233 
$`NRAS MUTATED`
TCGA-23-2645 TCGA-61-1913 TCGA-61-2016 TCGA-61-2095 
        4.50        48.92         1.18        61.64 

$`NRAS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       43.92        41.00        49.15         2.01        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-04-1353 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-04-1369 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 
      103.40        21.11        56.55        41.59        19.99         0.79 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
       38.37       119.08        84.20        55.43        48.89        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 
       28.64        64.64        36.23        31.86        45.37        29.16 
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-09-1666 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       41.62        57.60        30.51        17.98         5.85         3.02 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 
        8.55        97.55         6.12        35.15       112.41        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       63.09        39.75        12.46        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-13-0724 
       20.91         6.21        24.59        44.55        39.58         2.73 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 
       31.20        15.19        17.82        55.17         2.50        11.54 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       34.06        32.25        28.57        38.93        36.72        28.70 
TCGA-13-0795 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 
       19.59         8.12         8.28         8.19        35.28        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 
       68.94       107.18        91.40        74.27        66.67        61.84 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 
       67.99        69.01        43.36        49.61        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-13-0910 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-13-1487 
       54.64        87.06        61.71        29.42        98.04        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-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 
        4.24        54.31        37.61        38.40        32.84        16.57 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 
        4.21         4.41         4.77         4.18         2.56         3.09 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2066 
       14.24        12.23         8.61        10.78         8.75         9.70 
TCGA-13-2071 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 
        6.28        23.05        25.94        26.20        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-23-1107 TCGA-23-1109 TCGA-23-1110 
       29.13        18.90         2.76         0.30        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-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 
        4.27        39.09        33.47        58.13         0.53        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-23-2647 TCGA-23-2649 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 
        4.44         3.81         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-24-1428 
        6.25         6.02         5.95         5.36         4.83        17.39 
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-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
       45.14         9.11         3.45         1.18        22.22        26.96 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 
       57.40        64.27        16.21        56.58        51.91        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 
       58.09        88.50        70.62        39.88        19.53        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       45.50        47.70        25.87        10.26        17.23        90.15 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
       88.37        48.33        38.24         8.32         3.48         3.72 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-2019 
        3.81         4.37        11.28         5.79         5.52         4.87 
TCGA-24-2024 TCGA-24-2030 TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 
       58.16        55.92        28.18        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-24-2298 TCGA-25-1313 
        0.82        67.36        36.23        16.64        53.26        26.96 
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-25-1324 TCGA-25-1325 TCGA-25-1326 TCGA-25-1328 
       33.96         2.99        34.03        32.09        41.06        66.05 
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-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 
       13.02        49.05         1.02        38.04         3.02        45.01 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-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-29-2427 
       14.93         8.38         7.23         5.36        36.30        62.47 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-30-1714 
       13.84        42.25        21.47        11.47         9.76        38.07 
TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1862 
       51.91        36.26         2.47        15.68         0.26         6.12 
TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 
       30.05        18.77         6.71         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-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       27.85        24.23        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-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 
       20.52        14.17        16.18        11.47        47.57        23.74 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 TCGA-57-1583 
       28.93        42.02        10.42        40.77        24.03        11.38 
TCGA-57-1584 TCGA-57-1586 TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 
       21.14        22.32        25.08       180.20        22.32       116.12 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1722 
        9.40        34.39         2.14         5.42        44.81         8.09 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 
       31.43        18.54        27.88         4.34        31.79        48.79 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 
       44.84        35.80         2.43        33.67         1.45         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        5.79        11.41        13.02         9.07        34.13        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1914 TCGA-61-1915 TCGA-61-1919 TCGA-61-1995 
       37.05        42.51        56.61        67.76        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-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2097 TCGA-61-2101 
       30.64         4.77        51.72        71.74        60.62        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 
        6.35        31.07         8.61 

  NRAS MUTATED NRAS WILD-TYPE 
          1.18           0.26 
  NRAS MUTATED NRAS WILD-TYPE 
         61.64         180.20 
  NRAS MUTATED NRAS WILD-TYPE 
         26.71          28.57 
[1] "1.2 - 61.6 (26.7)"  "0.3 - 180.2 (28.6)"
[1] "hr=" "1.1"
D13V2, continuous
                vv
clus             OMENTUM OVARY PERITONEUM OVARY
  NRAS MUTATED         0     4                0
  NRAS WILD-TYPE       2   458                1
D13V3, multiclass
                  clus
vv                 NRAS MUTATED NRAS WILD-TYPE
  OMENTUM                     0              2
  OVARY                       4            458
  PERITONEUM OVARY            0              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"
D13V4, continuous
D13V5, binary
                cls
clus               0   1
  NRAS MUTATED     0   4
  NRAS WILD-TYPE   3 458
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      0    4
  NRAS WILD-TYPE    3  458
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  NO             0              3
  YES            4            458
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2
  NRAS MUTATED    0  0  0
  NRAS WILD-TYPE 13 22  1
D13V6, multiclass
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NRAS MUTATED                                  0     1
  NRAS WILD-TYPE                                2    17
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NRAS MUTATED                           0     3
  NRAS WILD-TYPE                        20   400
D13V7, multiclass
                                  clus
vv                                 NRAS MUTATED NRAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       1             17
  BLACK OR AFRICAN AMERICAN                   0             20
  WHITE                                       3            400
[1] 4 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
  NRAS MUTATED     0   4
  NRAS WILD-TYPE   9 266
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      0    4
  NRAS WILD-TYPE    9  266
                        clus
vv                       NRAS MUTATED NRAS WILD-TYPE
  HISPANIC OR LATINO                0              9
  NOT HISPANIC OR LATINO            4            266
[1] 2 2
[1] FALSE

Clustering(14) Variable = ACBD4 MUTATION ANALYSIS
D14V1, survival
                 sevent
clus2               0   1
  ACBD4 MUTATED     2   1
  ACBD4 WILD-TYPE 226 234
  ACBD4 MUTATED ACBD4 WILD-TYPE 
              3             460 
  ACBD4 MUTATED ACBD4 WILD-TYPE 
              1             234 
$`ACBD4 MUTATED`
TCGA-09-0369 TCGA-13-0906 TCGA-13-1408 
       35.57        44.94         5.92 

$`ACBD4 WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       43.92        41.00        49.15         2.01        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-04-1353 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-04-1369 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 
      103.40        21.11        56.55        41.59        19.99         0.79 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
       38.37       119.08        84.20        55.43        48.89        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 
       28.64        64.64        36.23        31.86        45.37        29.16 
TCGA-09-0366 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       57.76         9.99        38.43        89.33        74.93        41.62 
TCGA-09-1666 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 
       57.60        30.51        17.98         5.85         3.02         8.55 
TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
       97.55         6.12        35.15       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       39.75        12.46        25.91        81.86        18.51        34.19 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 
       32.88        14.66         6.71        35.44        19.99        20.91 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 
        6.21        24.59        44.55        39.58         2.73        31.20 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 
       15.19        17.82        55.17         2.50        11.54        34.06 
TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 
       32.25        28.57        38.93        36.72        28.70        19.59 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 
        8.12         8.28         8.19        35.28        13.61        68.94 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 
      107.18        91.40        74.27        66.67        61.84        67.99 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       69.01        43.36        49.61        57.47        56.15        57.07 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0910 TCGA-13-0911 
       19.36        47.38        48.33        47.84        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-13-1409 
        6.08        10.88         6.61         7.36         6.05         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-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
       29.42        98.04        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-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
       38.40        32.84        16.57         4.21         4.41         4.77 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
        4.18         2.56         3.09        14.24        12.23         8.61 
TCGA-13-2061 TCGA-13-2065 TCGA-13-2066 TCGA-13-2071 TCGA-20-0987 TCGA-20-0990 
       10.78         8.75         9.70         6.28        23.05        25.94 
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-23-1021 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-23-1107 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 
        0.30        51.35        54.51         3.22        68.68         4.57 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 
       33.30        86.01       129.96         4.27        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-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-23-2647 TCGA-23-2649 
       77.00         2.76         4.70         4.50         4.44         3.81 
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-24-1431 TCGA-24-1434 
        5.95         5.36         4.83        17.39        19.17        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 
       43.53         8.55        72.92        12.46        45.14         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-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       16.21        56.58        51.91        41.39        58.09        88.50 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       70.62        39.88        19.53        44.09        45.50        47.70 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 
       25.87        10.26        17.23        90.15        88.37        48.33 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 
       38.24         8.32         3.48         3.72         3.81         4.37 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-2019 TCGA-24-2024 TCGA-24-2030 
       11.28         5.79         5.52         4.87        58.16        55.92 
TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 
       28.18        44.52        57.07        36.16         0.79         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 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-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 
       36.23        16.64        53.26        26.96        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-25-1324 TCGA-25-1325 TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 
       34.03        32.09        41.06        66.05        15.02        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
       27.62        17.03        12.95        20.61        38.20         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-2042 TCGA-25-2391 
       59.15        62.17        35.87        52.04        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-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 
        2.96        29.03        31.00        26.99        78.90        47.61 
TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 
       48.33       101.79        39.02        40.41        33.93        31.20 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 
       68.32        36.36        16.93        23.93        59.67        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
       41.98        31.27        34.62        17.36        86.60        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 
       62.93        39.42        31.30        22.98        24.36        22.55 
TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 
       17.33        12.36        11.84        12.30        14.93         8.38 
TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 
        7.23         5.36        36.30        62.47        13.84        42.25 
TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 
       21.47        11.47         9.76        38.07        51.91        36.26 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1862 TCGA-30-1891 TCGA-31-1950 
        2.47        15.68         0.26         6.12        30.05        18.77 
TCGA-31-1953 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 
        6.71         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-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       33.01        29.49        29.82        25.91        25.08        23.80 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 
       21.60         2.24        20.98        18.31        20.52        14.17 
TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 
       16.18        11.47        47.57        23.74        28.93        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 
       10.42        40.77        24.03        11.38        21.14        22.32 
TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 
       25.08       180.20        22.32       116.12         9.40        34.39 
TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 
        2.14         5.42        44.81         8.09        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-61-1895 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-61-1906 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-61-1919 TCGA-61-1995 TCGA-61-1998 
       48.92        56.61        67.76        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-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 
        1.18         4.77        51.72        71.74        61.64        60.62 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       55.50         6.48        76.87        20.68        44.52       125.75 
TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       22.22         6.35        31.07         8.61 

  ACBD4 MUTATED ACBD4 WILD-TYPE 
           5.92            0.26 
  ACBD4 MUTATED ACBD4 WILD-TYPE 
          44.94          180.20 
  ACBD4 MUTATED ACBD4 WILD-TYPE 
         35.570          28.375 
[1] "5.9 - 44.9 (35.6)"  "0.3 - 180.2 (28.4)"
[1] "hr=" "1.2"
D14V2, continuous
                 vv
clus              OMENTUM OVARY PERITONEUM OVARY
  ACBD4 MUTATED         0     3                0
  ACBD4 WILD-TYPE       2   459                1
D14V3, multiclass
                  clus
vv                 ACBD4 MUTATED ACBD4 WILD-TYPE
  OMENTUM                      0               2
  OVARY                        3             459
  PERITONEUM OVARY             0               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
[1] "Remove cluster labels:" "ACBD4 MUTATED"         
clus
  ACBD4 MUTATED ACBD4 WILD-TYPE 
              1              63 
     TCGA-04-1346      TCGA-04-1347      TCGA-04-1356      TCGA-04-1367 
"ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" 
     TCGA-10-0926      TCGA-13-0714      TCGA-13-0720      TCGA-13-0724 
"ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" 
     TCGA-13-0755      TCGA-13-0760      TCGA-13-0762      TCGA-13-0791 
"ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" 
     TCGA-13-0792      TCGA-13-0793      TCGA-13-0795      TCGA-13-0801 
"ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" 
     TCGA-13-0802      TCGA-13-0885      TCGA-13-0887      TCGA-13-0889 
"ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" 
     TCGA-13-0891      TCGA-13-0894      TCGA-13-0897      TCGA-13-0900 
"ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" 
     TCGA-13-0901      TCGA-13-0903      TCGA-13-0904      TCGA-13-0905 
"ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" 
     TCGA-13-0910      TCGA-13-0911      TCGA-13-0912      TCGA-13-0913 
"ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" 
     TCGA-13-0919      TCGA-13-1404      TCGA-13-1405      TCGA-13-1409 
"ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" 
     TCGA-13-1410      TCGA-13-1412      TCGA-13-1482      TCGA-13-1483 
"ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" 
     TCGA-13-1484      TCGA-13-1488      TCGA-13-1489      TCGA-13-1491 
"ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" 
     TCGA-13-1492      TCGA-13-1495      TCGA-13-1497      TCGA-13-1498 
"ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" 
     TCGA-13-1499      TCGA-13-1501      TCGA-13-1504      TCGA-13-1506 
"ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" 
     TCGA-13-1507      TCGA-13-1509      TCGA-13-1512      TCGA-13-2057 
"ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" 
     TCGA-13-2059      TCGA-13-2060      TCGA-13-2061      TCGA-13-2066 
"ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" 
     TCGA-13-2071      TCGA-24-1614      TCGA-61-2101 
"ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" "ACBD4 WILD-TYPE" 
D14V5, binary
                 cls
clus                0   1
  ACBD4 MUTATED     0   3
  ACBD4 WILD-TYPE   3 459
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACBD4 MUTATED      0    3
  ACBD4 WILD-TYPE    3  459
     clus
vv    ACBD4 MUTATED ACBD4 WILD-TYPE
  NO              0               3
  YES             3             459
[1] 2 2
[1] FALSE
                 vv
clus              R0 R1 R2
  ACBD4 MUTATED    0  0  0
  ACBD4 WILD-TYPE 13 22  1
D14V6, multiclass
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACBD4 MUTATED                                  0     0
  ACBD4 WILD-TYPE                                2    18
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ACBD4 MUTATED                           0     3
  ACBD4 WILD-TYPE                        20   400
D14V7, multiclass
                                  clus
vv                                 ACBD4 MUTATED ACBD4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              18
  BLACK OR AFRICAN AMERICAN                    0              20
  WHITE                                        3             400
[1] 4 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
  ACBD4 MUTATED     0   3
  ACBD4 WILD-TYPE   9 267
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACBD4 MUTATED      0    3
  ACBD4 WILD-TYPE    9  267
                        clus
vv                       ACBD4 MUTATED ACBD4 WILD-TYPE
  HISPANIC OR LATINO                 0               9
  NOT HISPANIC OR LATINO             3             267
[1] 2 2
[1] FALSE

Clustering(15) Variable = EFEMP1 MUTATION ANALYSIS
D15V1, survival
                  sevent
clus2                0   1
  EFEMP1 MUTATED     4   3
  EFEMP1 WILD-TYPE 224 232
  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
               7              456 
  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
               3              232 
$`EFEMP1 MUTATED`
TCGA-09-1669 TCGA-13-0887 TCGA-13-1408 TCGA-24-1614 TCGA-36-1574 TCGA-61-1906 
       30.51        66.67         5.92        48.33        22.55        34.13 
TCGA-61-1915 
       67.76 

$`EFEMP1 WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       43.92        41.00        49.15         2.01        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-04-1353 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-04-1369 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 
      103.40        21.11        56.55        41.59        19.99         0.79 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
       38.37       119.08        84.20        55.43        48.89        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 
       28.64        64.64        36.23        31.86        45.37        29.16 
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-09-1666 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 
       41.62        57.60        17.98         5.85         3.02         8.55 
TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
       97.55         6.12        35.15       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       39.75        12.46        25.91        81.86        18.51        34.19 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 
       32.88        14.66         6.71        35.44        19.99        20.91 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 
        6.21        24.59        44.55        39.58         2.73        31.20 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 
       15.19        17.82        55.17         2.50        11.54        34.06 
TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 
       32.25        28.57        38.93        36.72        28.70        19.59 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 
        8.12         8.28         8.19        35.28        13.61        68.94 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 
      107.18        91.40        74.27        61.84        67.99        69.01 
TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
       43.36        49.61        57.47        56.15        57.07        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 
       47.38        48.33        47.84        44.94        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-13-1409 
        6.08        10.88         6.61         7.36         6.05         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-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
       29.42        98.04        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-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
       38.40        32.84        16.57         4.21         4.41         4.77 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
        4.18         2.56         3.09        14.24        12.23         8.61 
TCGA-13-2061 TCGA-13-2065 TCGA-13-2066 TCGA-13-2071 TCGA-20-0987 TCGA-20-0990 
       10.78         8.75         9.70         6.28        23.05        25.94 
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-23-1021 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-23-1107 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 
        0.30        51.35        54.51         3.22        68.68         4.57 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 
       33.30        86.01       129.96         4.27        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-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-23-2647 TCGA-23-2649 
       77.00         2.76         4.70         4.50         4.44         3.81 
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-24-1431 TCGA-24-1434 
        5.95         5.36         4.83        17.39        19.17        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 
       43.53         8.55        72.92        12.46        45.14         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-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       16.21        56.58        51.91        41.39        58.09        88.50 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       70.62        39.88        19.53        44.09        45.50        47.70 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 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-24-1847 
        8.32         3.48         3.72         3.81         4.37        11.28 
TCGA-24-1849 TCGA-24-1850 TCGA-24-2019 TCGA-24-2024 TCGA-24-2030 TCGA-24-2035 
        5.79         5.52         4.87        58.16        55.92        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-24-2280 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-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
       16.64        53.26        26.96        52.04        42.05         2.01 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1324 
       34.98        65.00        37.97        33.96         2.99        34.03 
TCGA-25-1325 TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       32.09        41.06        66.05        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-25-2042 TCGA-25-2391 TCGA-25-2392 
       62.17        35.87        52.04        13.02        49.05         1.02 
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-29-1691 
       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-29-1697 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-29-1705 TCGA-29-1707 
       36.36        16.93        23.93        59.67        18.25        41.98 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 
       31.27        34.62        17.36        86.60        66.81        62.93 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
       39.42        31.30        22.98        24.36        22.55        17.33 
TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 
       12.36        11.84        12.30        14.93         8.38         7.23 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 
        5.36        36.30        62.47        13.84        42.25        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-30-1856 TCGA-30-1857 TCGA-30-1862 TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 
       15.68         0.26         6.12        30.05        18.77         6.71 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1575 
        2.20        28.77        29.10        21.53        22.85         8.55 
TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-2530 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-36-2543 
       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-36-2551 TCGA-36-2552 
       20.98        18.31        20.52        14.17        16.18        11.47 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
       47.57        23.74        28.93        42.02        10.42        40.77 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1993 TCGA-59-2348 
       24.03        11.38        21.14        22.32        25.08       180.20 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       22.32       116.12         9.40        34.39         2.14         5.42 
TCGA-59-2372 TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 
       44.81         8.09        31.43        18.54        27.88         4.34 
TCGA-61-1733 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 
       31.79        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-61-1907 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-61-2000 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-61-2088 TCGA-61-2092 TCGA-61-2094 
       39.85        30.64         1.18         4.77        51.72        71.74 
TCGA-61-2095 TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       61.64        60.62        55.50         6.48        76.87        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       44.52       125.75        22.22         6.35        31.07         8.61 

  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
            5.92             0.26 
  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
           67.76           180.20 
  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
           34.13            28.03 
[1] "5.9 - 67.8 (34.1)"  "0.3 - 180.2 (28.0)"
[1] "hr=" "1.5"
D15V2, continuous
                  vv
clus               OMENTUM OVARY PERITONEUM OVARY
  EFEMP1 MUTATED         0     7                0
  EFEMP1 WILD-TYPE       2   455                1
D15V3, multiclass
                  clus
vv                 EFEMP1 MUTATED EFEMP1 WILD-TYPE
  OMENTUM                       0                2
  OVARY                         7              455
  PERITONEUM OVARY              0                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
[1] "Remove cluster labels:" "EFEMP1 MUTATED"        
clus
  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
               2               62 
      TCGA-04-1346       TCGA-04-1347       TCGA-04-1356       TCGA-04-1367 
"EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" 
      TCGA-10-0926       TCGA-13-0714       TCGA-13-0720       TCGA-13-0724 
"EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" 
      TCGA-13-0755       TCGA-13-0760       TCGA-13-0762       TCGA-13-0791 
"EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" 
      TCGA-13-0792       TCGA-13-0793       TCGA-13-0795       TCGA-13-0801 
"EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" 
      TCGA-13-0802       TCGA-13-0885       TCGA-13-0889       TCGA-13-0891 
"EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" 
      TCGA-13-0894       TCGA-13-0897       TCGA-13-0900       TCGA-13-0901 
"EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" 
      TCGA-13-0903       TCGA-13-0904       TCGA-13-0905       TCGA-13-0906 
"EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" 
      TCGA-13-0910       TCGA-13-0911       TCGA-13-0912       TCGA-13-0913 
"EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" 
      TCGA-13-0919       TCGA-13-1404       TCGA-13-1405       TCGA-13-1409 
"EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" 
      TCGA-13-1410       TCGA-13-1412       TCGA-13-1482       TCGA-13-1483 
"EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" 
      TCGA-13-1484       TCGA-13-1488       TCGA-13-1489       TCGA-13-1491 
"EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" 
      TCGA-13-1492       TCGA-13-1495       TCGA-13-1497       TCGA-13-1498 
"EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" 
      TCGA-13-1499       TCGA-13-1501       TCGA-13-1504       TCGA-13-1506 
"EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" 
      TCGA-13-1507       TCGA-13-1509       TCGA-13-1512       TCGA-13-2057 
"EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" 
      TCGA-13-2059       TCGA-13-2060       TCGA-13-2061       TCGA-13-2066 
"EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" 
      TCGA-13-2071       TCGA-61-2101 
"EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" 
D15V5, binary
                  cls
clus                 0   1
  EFEMP1 MUTATED     0   7
  EFEMP1 WILD-TYPE   3 455
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EFEMP1 MUTATED      0    7
  EFEMP1 WILD-TYPE    3  455
     clus
vv    EFEMP1 MUTATED EFEMP1 WILD-TYPE
  NO               0                3
  YES              7              455
[1] 2 2
[1] FALSE
                  vv
clus               R0 R1 R2
  EFEMP1 MUTATED    0  0  0
  EFEMP1 WILD-TYPE 13 22  1
D15V6, multiclass
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EFEMP1 MUTATED                                  0     1
  EFEMP1 WILD-TYPE                                2    17
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  EFEMP1 MUTATED                           0     6
  EFEMP1 WILD-TYPE                        20   397
D15V7, multiclass
                                  clus
vv                                 EFEMP1 MUTATED EFEMP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         1               17
  BLACK OR AFRICAN AMERICAN                     0               20
  WHITE                                         6              397
[1] 4 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
  EFEMP1 MUTATED     0   4
  EFEMP1 WILD-TYPE   9 266
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EFEMP1 MUTATED      0    4
  EFEMP1 WILD-TYPE    9  266
                        clus
vv                       EFEMP1 MUTATED EFEMP1 WILD-TYPE
  HISPANIC OR LATINO                  0                9
  NOT HISPANIC OR LATINO              4              266
[1] 2 2
[1] FALSE

Clustering(16) Variable = PODN MUTATION ANALYSIS
D16V1, survival
                sevent
clus2              0   1
  PODN MUTATED     6   0
  PODN WILD-TYPE 222 235
  PODN MUTATED PODN WILD-TYPE 
             6            457 
  PODN MUTATED PODN WILD-TYPE 
             0            235 
$`PODN MUTATED`
TCGA-09-1675 TCGA-13-2060 TCGA-20-1687 TCGA-29-2434 TCGA-36-2552 TCGA-61-1913 
       97.55         8.61         2.66        11.47        11.47        48.92 

$`PODN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       43.92        41.00        49.15         2.01        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-04-1353 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-04-1369 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 
      103.40        21.11        56.55        41.59        19.99         0.79 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
       38.37       119.08        84.20        55.43        48.89        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 
       28.64        64.64        36.23        31.86        45.37        29.16 
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-09-1666 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       41.62        57.60        30.51        17.98         5.85         3.02 
TCGA-09-1674 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
        8.55         6.12        35.15       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       39.75        12.46        25.91        81.86        18.51        34.19 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 
       32.88        14.66         6.71        35.44        19.99        20.91 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 
        6.21        24.59        44.55        39.58         2.73        31.20 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 
       15.19        17.82        55.17         2.50        11.54        34.06 
TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 
       32.25        28.57        38.93        36.72        28.70        19.59 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 
        8.12         8.28         8.19        35.28        13.61        68.94 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 
      107.18        91.40        74.27        66.67        61.84        67.99 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       69.01        43.36        49.61        57.47        56.15        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-13-0911 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-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 
        5.92         6.84         4.70         4.21         5.33        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 
       87.06        61.71        29.42        98.04        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-13-1501 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-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 
        4.41         4.77         4.18         2.56         3.09        14.24 
TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 TCGA-13-2066 TCGA-13-2071 TCGA-20-0987 
       12.23        10.78         8.75         9.70         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-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
        2.93        47.54        49.68        40.54        15.39        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       32.09        49.41         8.81        29.13        18.90         2.76 
TCGA-23-1107 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 
        0.30        51.35        54.51         3.22        68.68         4.57 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 
       33.30        86.01       129.96         4.27        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-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-23-2647 TCGA-23-2649 
       77.00         2.76         4.70         4.50         4.44         3.81 
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-24-1431 TCGA-24-1434 
        5.95         5.36         4.83        17.39        19.17        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 
       43.53         8.55        72.92        12.46        45.14         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-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       16.21        56.58        51.91        41.39        58.09        88.50 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       70.62        39.88        19.53        44.09        45.50        47.70 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 
       25.87        10.26        17.23        90.15        88.37        48.33 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 
       38.24         8.32         3.48         3.72         3.81         4.37 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-2019 TCGA-24-2024 TCGA-24-2030 
       11.28         5.79         5.52         4.87        58.16        55.92 
TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 
       28.18        44.52        57.07        36.16         0.79         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 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-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 
       36.23        16.64        53.26        26.96        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-25-1324 TCGA-25-1325 TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 
       34.03        32.09        41.06        66.05        15.02        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
       27.62        17.03        12.95        20.61        38.20         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-2042 TCGA-25-2391 
       59.15        62.17        35.87        52.04        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-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 
        2.96        29.03        31.00        26.99        78.90        47.61 
TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 
       48.33       101.79        39.02        40.41        33.93        31.20 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 
       68.32        36.36        16.93        23.93        59.67        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
       41.98        31.27        34.62        17.36        86.60        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 
       62.93        39.42        31.30        22.98        24.36        22.55 
TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 
       17.33        12.36        11.84        12.30        14.93         8.38 
TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 
        7.23         5.36        36.30        62.47        13.84        42.25 
TCGA-29-2432 TCGA-29-2436 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 
       21.47         9.76        38.07        51.91        36.26         2.47 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1862 TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 
       15.68         0.26         6.12        30.05        18.77         6.71 
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-36-2530 
        8.55        30.08        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-36-2551 
        2.24        20.98        18.31        20.52        14.17        16.18 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
       47.57        23.74        28.93        42.02        10.42        40.77 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1993 TCGA-59-2348 
       24.03        11.38        21.14        22.32        25.08       180.20 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       22.32       116.12         9.40        34.39         2.14         5.42 
TCGA-59-2372 TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 
       44.81         8.09        31.43        18.54        27.88         4.34 
TCGA-61-1733 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 
       31.79        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-61-1914 TCGA-61-1915 
       34.13        31.30        37.05        42.51        56.61        67.76 
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-61-2088 TCGA-61-2092 
       30.64        39.85        30.64         1.18         4.77        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 
       71.74        61.64        60.62        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 
        8.61 

  PODN MUTATED PODN WILD-TYPE 
          2.66           0.26 
  PODN MUTATED PODN WILD-TYPE 
         97.55         180.20 
  PODN MUTATED PODN WILD-TYPE 
         11.47          28.64 
[1] "2.7 - 97.5 (11.5)"  "0.3 - 180.2 (28.6)"
[1] "hr="     "9200000"
D16V2, continuous
                vv
clus             OMENTUM OVARY PERITONEUM OVARY
  PODN MUTATED         0     6                0
  PODN WILD-TYPE       2   456                1
D16V3, multiclass
                  clus
vv                 PODN MUTATED PODN WILD-TYPE
  OMENTUM                     0              2
  OVARY                       6            456
  PERITONEUM OVARY            0              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"
D16V4, continuous
[1] "Remove cluster labels:" "PODN MUTATED"          
clus
  PODN MUTATED PODN WILD-TYPE 
             1             63 
    TCGA-04-1346     TCGA-04-1347     TCGA-04-1356     TCGA-04-1367 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-10-0926     TCGA-13-0714     TCGA-13-0720     TCGA-13-0724 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-13-0755     TCGA-13-0760     TCGA-13-0762     TCGA-13-0791 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-13-0792     TCGA-13-0793     TCGA-13-0795     TCGA-13-0801 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-13-0802     TCGA-13-0885     TCGA-13-0887     TCGA-13-0889 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-13-0891     TCGA-13-0894     TCGA-13-0897     TCGA-13-0900 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-13-0901     TCGA-13-0903     TCGA-13-0904     TCGA-13-0905 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-13-0906     TCGA-13-0910     TCGA-13-0911     TCGA-13-0912 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-13-0913     TCGA-13-0919     TCGA-13-1404     TCGA-13-1405 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-13-1409     TCGA-13-1410     TCGA-13-1412     TCGA-13-1482 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-13-1483     TCGA-13-1484     TCGA-13-1488     TCGA-13-1489 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-13-1491     TCGA-13-1492     TCGA-13-1495     TCGA-13-1497 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-13-1498     TCGA-13-1499     TCGA-13-1501     TCGA-13-1504 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-13-1506     TCGA-13-1507     TCGA-13-1509     TCGA-13-1512 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-13-2057     TCGA-13-2059     TCGA-13-2061     TCGA-13-2066 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-13-2071     TCGA-24-1614     TCGA-61-2101 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
D16V5, binary
                cls
clus               0   1
  PODN MUTATED     0   6
  PODN WILD-TYPE   3 456
[1] "tbl2"
                cls
clus             [,1] [,2]
  PODN MUTATED      0    6
  PODN WILD-TYPE    3  456
     clus
vv    PODN MUTATED PODN WILD-TYPE
  NO             0              3
  YES            6            456
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2
  PODN MUTATED    2  0  0
  PODN WILD-TYPE 11 22  1
D16V6, multiclass
[1] "Remove cluster labels:" "PODN MUTATED"          
clus
  PODN MUTATED PODN WILD-TYPE 
             2             34 
    TCGA-04-1369     TCGA-04-1516     TCGA-04-1644     TCGA-13-0807 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-13-0911     TCGA-29-2427     TCGA-29-2429     TCGA-29-2431 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-29-2432     TCGA-29-2436     TCGA-36-2530     TCGA-36-2532 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-36-2534     TCGA-36-2537     TCGA-36-2538     TCGA-36-2540 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-36-2542     TCGA-36-2543     TCGA-36-2544     TCGA-36-2545 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-36-2547     TCGA-36-2548     TCGA-36-2551     TCGA-42-2582 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-42-2587     TCGA-42-2588     TCGA-42-2589     TCGA-42-2590 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-57-1993     TCGA-59-2363     TCGA-59-2372     TCGA-61-2612 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-61-2613     TCGA-61-2614 
"PODN WILD-TYPE" "PODN WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PODN MUTATED                                  0     0
  PODN WILD-TYPE                                2    18
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PODN MUTATED                           0     4
  PODN WILD-TYPE                        20   399
D16V7, multiclass
                                  clus
vv                                 PODN MUTATED PODN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             18
  BLACK OR AFRICAN AMERICAN                   0             20
  WHITE                                       4            399
[1] 4 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
  PODN MUTATED     1   3
  PODN WILD-TYPE   8 267
[1] "tbl2"
                cls
clus             [,1] [,2]
  PODN MUTATED      1    3
  PODN WILD-TYPE    8  267
                        clus
vv                       PODN MUTATED PODN WILD-TYPE
  HISPANIC OR LATINO                1              8
  NOT HISPANIC OR LATINO            3            267
[1] 2 2
[1] FALSE

Clustering(17) Variable = TOP2A MUTATION ANALYSIS
D17V1, survival
                 sevent
clus2               0   1
  TOP2A MUTATED     4   3
  TOP2A WILD-TYPE 224 232
  TOP2A MUTATED TOP2A WILD-TYPE 
              7             456 
  TOP2A MUTATED TOP2A WILD-TYPE 
              3             232 
$`TOP2A MUTATED`
TCGA-13-0761 TCGA-13-0791 TCGA-13-0919 TCGA-23-1028 TCGA-24-1105 TCGA-25-1325 
       34.06        38.93        14.89        49.41        47.41        32.09 
TCGA-30-1862 
        6.12 

$`TOP2A WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       43.92        41.00        49.15         2.01        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-04-1353 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-04-1369 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 
      103.40        21.11        56.55        41.59        19.99         0.79 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
       38.37       119.08        84.20        55.43        48.89        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 
       28.64        64.64        36.23        31.86        45.37        29.16 
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-09-1666 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       41.62        57.60        30.51        17.98         5.85         3.02 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 
        8.55        97.55         6.12        35.15       112.41        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       63.09        39.75        12.46        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-13-0724 
       20.91         6.21        24.59        44.55        39.58         2.73 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 
       31.20        15.19        17.82        55.17         2.50        11.54 
TCGA-13-0762 TCGA-13-0765 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 
       32.25        28.57        36.72        28.70        19.59         8.12 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
        8.28         8.19        35.28        13.61        68.94       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-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
       43.36        49.61        57.47        56.15        57.07        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 
       47.38        48.33        47.84        44.94        37.08        27.72 
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-13-1404 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-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
       29.42        98.04        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-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
       38.40        32.84        16.57         4.21         4.41         4.77 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
        4.18         2.56         3.09        14.24        12.23         8.61 
TCGA-13-2061 TCGA-13-2065 TCGA-13-2066 TCGA-13-2071 TCGA-20-0987 TCGA-20-0990 
       10.78         8.75         9.70         6.28        23.05        25.94 
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-23-1021 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-23-1107 
       32.09         8.81        29.13        18.90         2.76         0.30 
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-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 
       86.01       129.96         4.27        39.09        33.47        58.13 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
        0.53        24.95       115.89        87.48        91.66        77.00 
TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-23-2647 TCGA-23-2649 TCGA-24-0966 
        2.76         4.70         4.50         4.44         3.81         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-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 
       54.12        63.55         6.31         6.38         7.82         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 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-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 
       72.92        12.46        45.14         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-24-1551 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-24-2019 TCGA-24-2024 TCGA-24-2030 TCGA-24-2035 TCGA-24-2038 
        5.52         4.87        58.16        55.92        28.18        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-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
       53.26        26.96        52.04        42.05         2.01        34.98 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1324 TCGA-25-1326 
       65.00        37.97        33.96         2.99        34.03        41.06 
TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 
       66.05        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-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 
       52.04        13.02        49.05         1.02        38.04         3.02 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 
       45.01        19.99        42.02         2.96        29.03        31.00 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 
       26.99        78.90        47.61        48.33       101.79        39.02 
TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 
       40.41        33.93        31.20        68.32        36.36        16.93 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 
       23.93        59.67        18.25        41.98        31.27        34.62 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 
       17.36        86.60        66.81        62.93        39.42        31.30 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 
       22.98        24.36        22.55        17.33        12.36        11.84 
TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 
       12.30        14.93         8.38         7.23         5.36        36.30 
TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 
       62.47        13.84        42.25        21.47        11.47         9.76 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 
       38.07        51.91        36.26         2.47        15.68         0.26 
TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 
       30.05        18.77         6.71         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-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       27.85        24.23        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-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 
       20.52        14.17        16.18        11.47        47.57        23.74 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 TCGA-57-1583 
       28.93        42.02        10.42        40.77        24.03        11.38 
TCGA-57-1584 TCGA-57-1586 TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 
       21.14        22.32        25.08       180.20        22.32       116.12 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1722 
        9.40        34.39         2.14         5.42        44.81         8.09 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 
       31.43        18.54        27.88         4.34        31.79        48.79 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 
       44.84        35.80         2.43        33.67         1.45         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        5.79        11.41        13.02         9.07        34.13        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1919 
       37.05        42.51        48.92        56.61        67.76        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-61-2088 TCGA-61-2092 TCGA-61-2094 
       39.85        30.64         1.18         4.77        51.72        71.74 
TCGA-61-2095 TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       61.64        60.62        55.50         6.48        76.87        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       44.52       125.75        22.22         6.35        31.07         8.61 

  TOP2A MUTATED TOP2A WILD-TYPE 
           6.12            0.26 
  TOP2A MUTATED TOP2A WILD-TYPE 
          49.41          180.20 
  TOP2A MUTATED TOP2A WILD-TYPE 
          34.06           28.03 
[1] "6.1 - 49.4 (34.1)"  "0.3 - 180.2 (28.0)"
[1] "hr=" "1"  
D17V2, continuous
                 vv
clus              OMENTUM OVARY PERITONEUM OVARY
  TOP2A MUTATED         0     8                0
  TOP2A WILD-TYPE       2   454                1
D17V3, multiclass
                  clus
vv                 TOP2A MUTATED TOP2A WILD-TYPE
  OMENTUM                      0               2
  OVARY                        8             454
  PERITONEUM OVARY             0               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"
D17V4, continuous
[1] "Remove cluster labels:" "TOP2A MUTATED"         
clus
  TOP2A MUTATED TOP2A WILD-TYPE 
              2              62 
     TCGA-04-1346      TCGA-04-1347      TCGA-04-1356      TCGA-04-1367 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-10-0926      TCGA-13-0714      TCGA-13-0720      TCGA-13-0724 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-13-0755      TCGA-13-0760      TCGA-13-0762      TCGA-13-0792 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-13-0793      TCGA-13-0795      TCGA-13-0801      TCGA-13-0802 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-13-0885      TCGA-13-0887      TCGA-13-0889      TCGA-13-0891 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-13-0894      TCGA-13-0897      TCGA-13-0900      TCGA-13-0901 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-13-0903      TCGA-13-0904      TCGA-13-0905      TCGA-13-0906 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-13-0910      TCGA-13-0911      TCGA-13-0912      TCGA-13-0913 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-13-1404      TCGA-13-1405      TCGA-13-1409      TCGA-13-1410 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-13-1412      TCGA-13-1482      TCGA-13-1483      TCGA-13-1484 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-13-1488      TCGA-13-1489      TCGA-13-1491      TCGA-13-1492 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-13-1495      TCGA-13-1497      TCGA-13-1498      TCGA-13-1499 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-13-1501      TCGA-13-1504      TCGA-13-1506      TCGA-13-1507 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-13-1509      TCGA-13-1512      TCGA-13-2057      TCGA-13-2059 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-13-2060      TCGA-13-2061      TCGA-13-2066      TCGA-13-2071 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-24-1614      TCGA-61-2101 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
D17V5, binary
                 cls
clus                0   1
  TOP2A MUTATED     0   8
  TOP2A WILD-TYPE   3 454
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOP2A MUTATED      0    8
  TOP2A WILD-TYPE    3  454
     clus
vv    TOP2A MUTATED TOP2A WILD-TYPE
  NO              0               3
  YES             8             454
[1] 2 2
[1] FALSE
                 vv
clus              R0 R1 R2
  TOP2A MUTATED    0  0  0
  TOP2A WILD-TYPE 13 22  1
D17V6, multiclass
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TOP2A MUTATED                                  0     0
  TOP2A WILD-TYPE                                2    18
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TOP2A MUTATED                           0     7
  TOP2A WILD-TYPE                        20   396
D17V7, multiclass
                                  clus
vv                                 TOP2A MUTATED TOP2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              18
  BLACK OR AFRICAN AMERICAN                    0              20
  WHITE                                        7             396
[1] 4 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
  TOP2A MUTATED     1   5
  TOP2A WILD-TYPE   8 265
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOP2A MUTATED      1    5
  TOP2A WILD-TYPE    8  265
                        clus
vv                       TOP2A MUTATED TOP2A WILD-TYPE
  HISPANIC OR LATINO                 1               8
  NOT HISPANIC OR LATINO             5             265
[1] 2 2
[1] FALSE

Clustering(18) Variable = NCOA3 MUTATION ANALYSIS
D18V1, survival
                 sevent
clus2               0   1
  NCOA3 MUTATED     5   0
  NCOA3 WILD-TYPE 223 235
  NCOA3 MUTATED NCOA3 WILD-TYPE 
              5             458 
  NCOA3 MUTATED NCOA3 WILD-TYPE 
              0             235 
$`NCOA3 MUTATED`
TCGA-04-1365 TCGA-13-0890 TCGA-13-0904 TCGA-23-1118 TCGA-24-1845 
       76.57        67.99        48.33        86.01         3.81 

$`NCOA3 WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       43.92        41.00        49.15         2.01        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-04-1353 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1367 
        0.53        49.28        32.52        44.32        33.67       103.40 
TCGA-04-1369 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 
       21.11        56.55        41.59        19.99         0.79        38.37 
TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 
      119.08        84.20        55.43        48.89        27.88        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 TCGA-09-0366 
       64.64        36.23        31.86        45.37        29.16        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-09-1666 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 
       57.60        30.51        17.98         5.85         3.02         8.55 
TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
       97.55         6.12        35.15       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       39.75        12.46        25.91        81.86        18.51        34.19 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 
       32.88        14.66         6.71        35.44        19.99        20.91 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 
        6.21        24.59        44.55        39.58         2.73        31.20 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 
       15.19        17.82        55.17         2.50        11.54        34.06 
TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 
       32.25        28.57        38.93        36.72        28.70        19.59 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 
        8.12         8.28         8.19        35.28        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-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
       43.36        49.61        57.47        56.15        57.07        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-13-0924 
       29.98        21.17        14.89        13.81         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-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
       29.42        98.04        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-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
       38.40        32.84        16.57         4.21         4.41         4.77 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
        4.18         2.56         3.09        14.24        12.23         8.61 
TCGA-13-2061 TCGA-13-2065 TCGA-13-2066 TCGA-13-2071 TCGA-20-0987 TCGA-20-0990 
       10.78         8.75         9.70         6.28        23.05        25.94 
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-23-1021 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-23-1107 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 
        0.30        51.35        54.51         3.22        68.68         4.57 
TCGA-23-1117 TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 
       33.30       129.96         4.27        39.09        33.47        58.13 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
        0.53        24.95       115.89        87.48        91.66        77.00 
TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-23-2647 TCGA-23-2649 TCGA-24-0966 
        2.76         4.70         4.50         4.44         3.81         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-24-1431 TCGA-24-1434 TCGA-24-1435 
        5.36         4.83        17.39        19.17        18.67        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-24-1471 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-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 
       56.58        51.91        41.39        58.09        88.50        70.62 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
       39.88        19.53        44.09        45.50        47.70        25.87 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 
       10.26        17.23        90.15        88.37        48.33        38.24 
TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 
        8.32         3.48         3.72         4.37        11.28         5.79 
TCGA-24-1850 TCGA-24-2019 TCGA-24-2024 TCGA-24-2030 TCGA-24-2035 TCGA-24-2038 
        5.52         4.87        58.16        55.92        28.18        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-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
       53.26        26.96        52.04        42.05         2.01        34.98 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1324 TCGA-25-1325 
       65.00        37.97        33.96         2.99        34.03        32.09 
TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 
       41.06        66.05        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-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 
       35.87        52.04        13.02        49.05         1.02        38.04 
TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 
        3.02        45.01        19.99        42.02         2.96        29.03 
TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 
       31.00        26.99        78.90        47.61        48.33       101.79 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
       39.02        40.41        33.93        31.20        68.32        36.36 
TCGA-29-1701 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-29-1774 TCGA-29-1775 
       31.30        22.98        24.36        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-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 
       36.30        62.47        13.84        42.25        21.47        11.47 
TCGA-29-2436 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 
        9.76        38.07        51.91        36.26         2.47        15.68 
TCGA-30-1857 TCGA-30-1862 TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 TCGA-31-1959 
        0.26         6.12        30.05        18.77         6.71         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-36-2543 
       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-36-2551 TCGA-36-2552 
       20.98        18.31        20.52        14.17        16.18        11.47 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
       47.57        23.74        28.93        42.02        10.42        40.77 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1993 TCGA-59-2348 
       24.03        11.38        21.14        22.32        25.08       180.20 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       22.32       116.12         9.40        34.39         2.14         5.42 
TCGA-59-2372 TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 
       44.81         8.09        31.43        18.54        27.88         4.34 
TCGA-61-1733 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 
       31.79        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-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       67.76        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-61-2088 
        4.01        30.64        39.85        30.64         1.18         4.77 
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-61-2104 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 
       31.07         8.61 

  NCOA3 MUTATED NCOA3 WILD-TYPE 
           3.81            0.26 
  NCOA3 MUTATED NCOA3 WILD-TYPE 
          86.01          180.20 
  NCOA3 MUTATED NCOA3 WILD-TYPE 
          67.99           28.03 
[1] "3.8 - 86.0 (68.0)"  "0.3 - 180.2 (28.0)"
[1] "hr="     "9300000"
D18V2, continuous
                 vv
clus              OMENTUM OVARY PERITONEUM OVARY
  NCOA3 MUTATED         0     5                0
  NCOA3 WILD-TYPE       2   457                1
D18V3, multiclass
                  clus
vv                 NCOA3 MUTATED NCOA3 WILD-TYPE
  OMENTUM                      0               2
  OVARY                        5             457
  PERITONEUM OVARY             0               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"
D18V4, continuous
[1] "Remove cluster labels:" "NCOA3 MUTATED"         
clus
  NCOA3 MUTATED NCOA3 WILD-TYPE 
              1              63 
     TCGA-04-1346      TCGA-04-1347      TCGA-04-1356      TCGA-04-1367 
"NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" 
     TCGA-10-0926      TCGA-13-0714      TCGA-13-0720      TCGA-13-0724 
"NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" 
     TCGA-13-0755      TCGA-13-0760      TCGA-13-0762      TCGA-13-0791 
"NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" 
     TCGA-13-0792      TCGA-13-0793      TCGA-13-0795      TCGA-13-0801 
"NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" 
     TCGA-13-0802      TCGA-13-0885      TCGA-13-0887      TCGA-13-0889 
"NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" 
     TCGA-13-0891      TCGA-13-0894      TCGA-13-0897      TCGA-13-0900 
"NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" 
     TCGA-13-0901      TCGA-13-0903      TCGA-13-0905      TCGA-13-0906 
"NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" 
     TCGA-13-0910      TCGA-13-0911      TCGA-13-0912      TCGA-13-0913 
"NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" 
     TCGA-13-0919      TCGA-13-1404      TCGA-13-1405      TCGA-13-1409 
"NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" 
     TCGA-13-1410      TCGA-13-1412      TCGA-13-1482      TCGA-13-1483 
"NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" 
     TCGA-13-1484      TCGA-13-1488      TCGA-13-1489      TCGA-13-1491 
"NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" 
     TCGA-13-1492      TCGA-13-1495      TCGA-13-1497      TCGA-13-1498 
"NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" 
     TCGA-13-1499      TCGA-13-1501      TCGA-13-1504      TCGA-13-1506 
"NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" 
     TCGA-13-1507      TCGA-13-1509      TCGA-13-1512      TCGA-13-2057 
"NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" 
     TCGA-13-2059      TCGA-13-2060      TCGA-13-2061      TCGA-13-2066 
"NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" 
     TCGA-13-2071      TCGA-24-1614      TCGA-61-2101 
"NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" 
D18V5, binary
                 cls
clus                0   1
  NCOA3 MUTATED     0   5
  NCOA3 WILD-TYPE   3 457
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA3 MUTATED      0    5
  NCOA3 WILD-TYPE    3  457
     clus
vv    NCOA3 MUTATED NCOA3 WILD-TYPE
  NO              0               3
  YES             5             457
[1] 2 2
[1] FALSE
                 vv
clus              R0 R1 R2
  NCOA3 MUTATED    0  0  0
  NCOA3 WILD-TYPE 13 22  1
D18V6, multiclass
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NCOA3 MUTATED                                  0     0
  NCOA3 WILD-TYPE                                2    18
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NCOA3 MUTATED                           0     5
  NCOA3 WILD-TYPE                        20   398
D18V7, multiclass
                                  clus
vv                                 NCOA3 MUTATED NCOA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              18
  BLACK OR AFRICAN AMERICAN                    0              20
  WHITE                                        5             398
[1] 4 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
  NCOA3 MUTATED     0   4
  NCOA3 WILD-TYPE   9 266
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA3 MUTATED      0    4
  NCOA3 WILD-TYPE    9  266
                        clus
vv                       NCOA3 MUTATED NCOA3 WILD-TYPE
  HISPANIC OR LATINO                 0               9
  NOT HISPANIC OR LATINO             4             266
[1] 2 2
[1] FALSE

Clustering(19) Variable = TP53TG5 MUTATION ANALYSIS
D19V1, survival
                   sevent
clus2                 0   1
  TP53TG5 MUTATED     1   2
  TP53TG5 WILD-TYPE 227 233
  TP53TG5 MUTATED TP53TG5 WILD-TYPE 
                3               460 
  TP53TG5 MUTATED TP53TG5 WILD-TYPE 
                2               233 
$`TP53TG5 MUTATED`
TCGA-13-2057 TCGA-29-1697 TCGA-61-2614 
       14.24        31.20         8.61 

$`TP53TG5 WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       43.92        41.00        49.15         2.01        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-04-1353 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-04-1369 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 
      103.40        21.11        56.55        41.59        19.99         0.79 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
       38.37       119.08        84.20        55.43        48.89        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 
       28.64        64.64        36.23        31.86        45.37        29.16 
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-09-1666 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       41.62        57.60        30.51        17.98         5.85         3.02 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 
        8.55        97.55         6.12        35.15       112.41        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       63.09        39.75        12.46        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-13-0724 
       20.91         6.21        24.59        44.55        39.58         2.73 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 
       31.20        15.19        17.82        55.17         2.50        11.54 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       34.06        32.25        28.57        38.93        36.72        28.70 
TCGA-13-0795 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 
       19.59         8.12         8.28         8.19        35.28        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 
       68.94       107.18        91.40        74.27        66.67        61.84 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 
       67.99        69.01        43.36        49.61        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-13-0910 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-13-1487 
       54.64        87.06        61.71        29.42        98.04        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-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 
        4.24        54.31        37.61        38.40        32.84        16.57 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 
        4.21         4.41         4.77         4.18         2.56         3.09 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2066 TCGA-13-2071 
       12.23         8.61        10.78         8.75         9.70         6.28 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 
       23.05        25.94        26.20        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-23-1107 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
       18.90         2.76         0.30        51.35        54.51         3.22 
TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 
       68.68         4.57        33.30        86.01       129.96         4.27 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 
       39.09        33.47        58.13         0.53        24.95       115.89 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 
       87.48        91.66        77.00         2.76         4.70         4.50 
TCGA-23-2647 TCGA-23-2649 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 
        4.44         3.81         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-24-1428 
        6.25         6.02         5.95         5.36         4.83        17.39 
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-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
       45.14         9.11         3.45         1.18        22.22        26.96 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 
       57.40        64.27        16.21        56.58        51.91        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 
       58.09        88.50        70.62        39.88        19.53        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       45.50        47.70        25.87        10.26        17.23        90.15 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
       88.37        48.33        38.24         8.32         3.48         3.72 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-2019 
        3.81         4.37        11.28         5.79         5.52         4.87 
TCGA-24-2024 TCGA-24-2030 TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 
       58.16        55.92        28.18        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-24-2298 TCGA-25-1313 
        0.82        67.36        36.23        16.64        53.26        26.96 
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-25-1324 TCGA-25-1325 TCGA-25-1326 TCGA-25-1328 
       33.96         2.99        34.03        32.09        41.06        66.05 
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-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 
       13.02        49.05         1.02        38.04         3.02        45.01 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-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-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 
       33.93        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-29-1770 
       66.81        62.93        39.42        31.30        22.98        24.36 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 
       22.55        17.33        12.36        11.84        12.30        14.93 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 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-29-2434 TCGA-29-2436 TCGA-30-1714 TCGA-30-1718 
       42.25        21.47        11.47         9.76        38.07        51.91 
TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1862 TCGA-30-1891 
       36.26         2.47        15.68         0.26         6.12        30.05 
TCGA-31-1950 TCGA-31-1953 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
       18.77         6.71         2.20        28.77        29.10        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 
       22.85        22.55         8.55        30.08        25.74        27.85 
TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
       24.23        33.01        29.49        29.82        25.91        25.08 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 
       23.80        21.60         2.24        20.98        18.31        20.52 
TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
       14.17        16.18        11.47        47.57        23.74        28.93 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 
       42.02        10.42        40.77        24.03        11.38        21.14 
TCGA-57-1586 TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       22.32        25.08       180.20        22.32       116.12         9.40 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1722 TCGA-61-1725 
       34.39         2.14         5.42        44.81         8.09        31.43 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 TCGA-61-1737 
       18.54        27.88         4.34        31.79        48.79        44.84 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
       35.80         2.43        33.67         1.45         8.42         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 
       11.41        13.02         9.07        34.13        31.30        37.05 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1919 TCGA-61-1995 
       42.51        48.92        56.61        67.76        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-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       30.64         1.18         4.77        51.72        71.74        61.64 
TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       60.62        55.50         6.48        76.87        20.68        44.52 
TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 
      125.75        22.22         6.35        31.07 

  TP53TG5 MUTATED TP53TG5 WILD-TYPE 
             8.61              0.26 
  TP53TG5 MUTATED TP53TG5 WILD-TYPE 
             31.2             180.2 
  TP53TG5 MUTATED TP53TG5 WILD-TYPE 
           14.240            28.605 
[1] "8.6 - 31.2 (14.2)"  "0.3 - 180.2 (28.6)"
[1] "hr=" "3.9"
D19V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  TP53TG5 MUTATED         0     3                0
  TP53TG5 WILD-TYPE       2   459                1
D19V3, multiclass
                  clus
vv                 TP53TG5 MUTATED TP53TG5 WILD-TYPE
  OMENTUM                        0                 2
  OVARY                          3               459
  PERITONEUM OVARY               0                 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"
D19V4, continuous
[1] "Remove cluster labels:" "TP53TG5 MUTATED"       
clus
  TP53TG5 MUTATED TP53TG5 WILD-TYPE 
                1                63 
       TCGA-04-1346        TCGA-04-1347        TCGA-04-1356        TCGA-04-1367 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-10-0926        TCGA-13-0714        TCGA-13-0720        TCGA-13-0724 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-13-0755        TCGA-13-0760        TCGA-13-0762        TCGA-13-0791 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-13-0792        TCGA-13-0793        TCGA-13-0795        TCGA-13-0801 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-13-0802        TCGA-13-0885        TCGA-13-0887        TCGA-13-0889 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-13-0891        TCGA-13-0894        TCGA-13-0897        TCGA-13-0900 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-13-0901        TCGA-13-0903        TCGA-13-0904        TCGA-13-0905 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-13-0906        TCGA-13-0910        TCGA-13-0911        TCGA-13-0912 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-13-0913        TCGA-13-0919        TCGA-13-1404        TCGA-13-1405 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-13-1409        TCGA-13-1410        TCGA-13-1412        TCGA-13-1482 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-13-1483        TCGA-13-1484        TCGA-13-1488        TCGA-13-1489 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-13-1491        TCGA-13-1492        TCGA-13-1495        TCGA-13-1497 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-13-1498        TCGA-13-1499        TCGA-13-1501        TCGA-13-1504 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-13-1506        TCGA-13-1507        TCGA-13-1509        TCGA-13-1512 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-13-2059        TCGA-13-2060        TCGA-13-2061        TCGA-13-2066 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-13-2071        TCGA-24-1614        TCGA-61-2101 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
D19V5, binary
                   cls
clus                  0   1
  TP53TG5 MUTATED     0   3
  TP53TG5 WILD-TYPE   3 459
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TP53TG5 MUTATED      0    3
  TP53TG5 WILD-TYPE    3  459
     clus
vv    TP53TG5 MUTATED TP53TG5 WILD-TYPE
  NO                0                 3
  YES               3               459
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2
  TP53TG5 MUTATED    0  1  0
  TP53TG5 WILD-TYPE 13 21  1
D19V6, multiclass
[1] "Remove cluster labels:" "TP53TG5 MUTATED"       
clus
  TP53TG5 MUTATED TP53TG5 WILD-TYPE 
                1                35 
       TCGA-04-1369        TCGA-04-1516        TCGA-04-1644        TCGA-13-0807 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-13-0911        TCGA-29-2427        TCGA-29-2429        TCGA-29-2431 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-29-2432        TCGA-29-2434        TCGA-29-2436        TCGA-36-2530 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-36-2532        TCGA-36-2534        TCGA-36-2537        TCGA-36-2538 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-36-2540        TCGA-36-2542        TCGA-36-2543        TCGA-36-2544 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-36-2545        TCGA-36-2547        TCGA-36-2548        TCGA-36-2551 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-36-2552        TCGA-42-2582        TCGA-42-2587        TCGA-42-2588 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-42-2589        TCGA-42-2590        TCGA-57-1993        TCGA-59-2363 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-59-2372        TCGA-61-2612        TCGA-61-2613 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TP53TG5 MUTATED                                  0     0
  TP53TG5 WILD-TYPE                                2    18
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TP53TG5 MUTATED                           0     3
  TP53TG5 WILD-TYPE                        20   400
D19V7, multiclass
                                  clus
vv                                 TP53TG5 MUTATED TP53TG5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                18
  BLACK OR AFRICAN AMERICAN                      0                20
  WHITE                                          3               400
[1] 4 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
  TP53TG5 MUTATED     0   0
  TP53TG5 WILD-TYPE   9 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TP53TG5 MUTATED      0    0
  TP53TG5 WILD-TYPE    9  270

Clustering(20) Variable = RPGRIP1 MUTATION ANALYSIS
D20V1, survival
                   sevent
clus2                 0   1
  RPGRIP1 MUTATED     5   2
  RPGRIP1 WILD-TYPE 223 233
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
                7               456 
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
                2               233 
$`RPGRIP1 MUTATED`
TCGA-13-1410 TCGA-24-1417 TCGA-24-1844 TCGA-24-2298 TCGA-29-1702 TCGA-59-2351 
        4.70         7.82         3.72        53.26        23.93       116.12 
TCGA-61-1728 
       27.88 

$`RPGRIP1 WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       43.92        41.00        49.15         2.01        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-04-1353 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-04-1369 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 
      103.40        21.11        56.55        41.59        19.99         0.79 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
       38.37       119.08        84.20        55.43        48.89        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 
       28.64        64.64        36.23        31.86        45.37        29.16 
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-09-1666 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       41.62        57.60        30.51        17.98         5.85         3.02 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 
        8.55        97.55         6.12        35.15       112.41        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       63.09        39.75        12.46        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-13-0724 
       20.91         6.21        24.59        44.55        39.58         2.73 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 
       31.20        15.19        17.82        55.17         2.50        11.54 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       34.06        32.25        28.57        38.93        36.72        28.70 
TCGA-13-0795 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 
       19.59         8.12         8.28         8.19        35.28        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 
       68.94       107.18        91.40        74.27        66.67        61.84 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 
       67.99        69.01        43.36        49.61        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-13-0910 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-13-1411 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-13-1487 TCGA-13-1488 
       87.06        61.71        29.42        98.04        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-13-1501 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-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 
        4.41         4.77         4.18         2.56         3.09        14.24 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2066 TCGA-13-2071 
       12.23         8.61        10.78         8.75         9.70         6.28 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 
       23.05        25.94        26.20        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-23-1107 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
       18.90         2.76         0.30        51.35        54.51         3.22 
TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 
       68.68         4.57        33.30        86.01       129.96         4.27 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 
       39.09        33.47        58.13         0.53        24.95       115.89 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 
       87.48        91.66        77.00         2.76         4.70         4.50 
TCGA-23-2647 TCGA-23-2649 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 
        4.44         3.81         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-24-1428 TCGA-24-1431 
        6.02         5.95         5.36         4.83        17.39        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-24-1469 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-24-1551 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-24-1845 TCGA-24-1846 
       48.33        38.24         8.32         3.48         3.81         4.37 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-2019 TCGA-24-2024 TCGA-24-2030 
       11.28         5.79         5.52         4.87        58.16        55.92 
TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 
       28.18        44.52        57.07        36.16         0.79         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 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-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
       36.23        16.64        26.96        52.04        42.05         2.01 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1324 
       34.98        65.00        37.97        33.96         2.99        34.03 
TCGA-25-1325 TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       32.09        41.06        66.05        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-25-2042 TCGA-25-2391 TCGA-25-2392 
       62.17        35.87        52.04        13.02        49.05         1.02 
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-29-1691 
       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-29-1697 TCGA-29-1698 
      101.79        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-29-1711 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-29-1774 TCGA-29-1775 
       31.30        22.98        24.36        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-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 
       36.30        62.47        13.84        42.25        21.47        11.47 
TCGA-29-2436 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 
        9.76        38.07        51.91        36.26         2.47        15.68 
TCGA-30-1857 TCGA-30-1862 TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 TCGA-31-1959 
        0.26         6.12        30.05        18.77         6.71         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-36-2543 
       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-36-2551 TCGA-36-2552 
       20.98        18.31        20.52        14.17        16.18        11.47 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
       47.57        23.74        28.93        42.02        10.42        40.77 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1993 TCGA-59-2348 
       24.03        11.38        21.14        22.32        25.08       180.20 
TCGA-59-2350 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 
       22.32         9.40        34.39         2.14         5.42        44.81 
TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 
        8.09        31.43        18.54         4.34        31.79        48.79 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 
       44.84        35.80         2.43        33.67         1.45         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        5.79        11.41        13.02         9.07        34.13        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1919 
       37.05        42.51        48.92        56.61        67.76        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-61-2088 TCGA-61-2092 TCGA-61-2094 
       39.85        30.64         1.18         4.77        51.72        71.74 
TCGA-61-2095 TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       61.64        60.62        55.50         6.48        76.87        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       44.52       125.75        22.22         6.35        31.07         8.61 

  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
             3.72              0.26 
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
           116.12            180.20 
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
            23.93             28.67 
[1] "3.7 - 116.1 (23.9)" "0.3 - 180.2 (28.7)"
[1] "hr=" "1.9"
D20V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  RPGRIP1 MUTATED         0     7                0
  RPGRIP1 WILD-TYPE       2   455                1
D20V3, multiclass
                  clus
vv                 RPGRIP1 MUTATED RPGRIP1 WILD-TYPE
  OMENTUM                        0                 2
  OVARY                          7               455
  PERITONEUM OVARY               0                 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
[1] "Remove cluster labels:" "RPGRIP1 MUTATED"       
clus
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
                1                63 
       TCGA-04-1346        TCGA-04-1347        TCGA-04-1356        TCGA-04-1367 
"RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" 
       TCGA-10-0926        TCGA-13-0714        TCGA-13-0720        TCGA-13-0724 
"RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" 
       TCGA-13-0755        TCGA-13-0760        TCGA-13-0762        TCGA-13-0791 
"RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" 
       TCGA-13-0792        TCGA-13-0793        TCGA-13-0795        TCGA-13-0801 
"RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" 
       TCGA-13-0802        TCGA-13-0885        TCGA-13-0887        TCGA-13-0889 
"RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" 
       TCGA-13-0891        TCGA-13-0894        TCGA-13-0897        TCGA-13-0900 
"RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" 
       TCGA-13-0901        TCGA-13-0903        TCGA-13-0904        TCGA-13-0905 
"RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" 
       TCGA-13-0906        TCGA-13-0910        TCGA-13-0911        TCGA-13-0912 
"RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" 
       TCGA-13-0913        TCGA-13-0919        TCGA-13-1404        TCGA-13-1405 
"RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" 
       TCGA-13-1409        TCGA-13-1412        TCGA-13-1482        TCGA-13-1483 
"RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" 
       TCGA-13-1484        TCGA-13-1488        TCGA-13-1489        TCGA-13-1491 
"RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" 
       TCGA-13-1492        TCGA-13-1495        TCGA-13-1497        TCGA-13-1498 
"RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" 
       TCGA-13-1499        TCGA-13-1501        TCGA-13-1504        TCGA-13-1506 
"RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" 
       TCGA-13-1507        TCGA-13-1509        TCGA-13-1512        TCGA-13-2057 
"RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" 
       TCGA-13-2059        TCGA-13-2060        TCGA-13-2061        TCGA-13-2066 
"RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" 
       TCGA-13-2071        TCGA-24-1614        TCGA-61-2101 
"RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" 
D20V5, binary
                   cls
clus                  0   1
  RPGRIP1 MUTATED     0   7
  RPGRIP1 WILD-TYPE   3 455
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPGRIP1 MUTATED      0    7
  RPGRIP1 WILD-TYPE    3  455
     clus
vv    RPGRIP1 MUTATED RPGRIP1 WILD-TYPE
  NO                0                 3
  YES               7               455
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2
  RPGRIP1 MUTATED    0  0  0
  RPGRIP1 WILD-TYPE 13 22  1
D20V6, multiclass
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RPGRIP1 MUTATED                                  0     0
  RPGRIP1 WILD-TYPE                                2    18
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  RPGRIP1 MUTATED                           0     7
  RPGRIP1 WILD-TYPE                        20   396
D20V7, multiclass
                                  clus
vv                                 RPGRIP1 MUTATED RPGRIP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                18
  BLACK OR AFRICAN AMERICAN                      0                20
  WHITE                                          7               396
[1] 4 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
  RPGRIP1 MUTATED     0   3
  RPGRIP1 WILD-TYPE   9 267
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPGRIP1 MUTATED      0    3
  RPGRIP1 WILD-TYPE    9  267
                        clus
vv                       RPGRIP1 MUTATED RPGRIP1 WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO               3               267
[1] 2 2
[1] FALSE

Clustering(21) Variable = PTEN MUTATION ANALYSIS
D21V1, survival
                sevent
clus2              0   1
  PTEN MUTATED     3   2
  PTEN WILD-TYPE 225 233
  PTEN MUTATED PTEN WILD-TYPE 
             5            458 
  PTEN MUTATED PTEN WILD-TYPE 
             2            233 
$`PTEN MUTATED`
TCGA-10-0930 TCGA-13-1492 TCGA-61-1737 TCGA-61-1740 TCGA-61-1900 
       34.19        73.55        44.84         2.43         5.79 

$`PTEN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       43.92        41.00        49.15         2.01        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-04-1353 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-04-1369 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 
      103.40        21.11        56.55        41.59        19.99         0.79 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
       38.37       119.08        84.20        55.43        48.89        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 
       28.64        64.64        36.23        31.86        45.37        29.16 
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-09-1666 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       41.62        57.60        30.51        17.98         5.85         3.02 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 
        8.55        97.55         6.12        35.15       112.41        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       63.09        39.75        12.46        25.91        81.86        18.51 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 
       32.88        14.66         6.71        35.44        19.99        20.91 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 
        6.21        24.59        44.55        39.58         2.73        31.20 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 
       15.19        17.82        55.17         2.50        11.54        34.06 
TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 
       32.25        28.57        38.93        36.72        28.70        19.59 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 
        8.12         8.28         8.19        35.28        13.61        68.94 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 
      107.18        91.40        74.27        66.67        61.84        67.99 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       69.01        43.36        49.61        57.47        56.15        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-13-0911 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-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 
        5.92         6.84         4.70         4.21         5.33        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 
       87.06        61.71        29.42        98.04        22.39        70.82 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 
       82.88        52.44        38.20        49.25         4.24        54.31 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       37.61        38.40        32.84        16.57         4.21         4.41 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 
        4.77         4.18         2.56         3.09        14.24        12.23 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2066 TCGA-13-2071 TCGA-20-0987 
        8.61        10.78         8.75         9.70         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-23-1022 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-23-1107 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 
        2.76         0.30        51.35        54.51         3.22        68.68 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 
        4.57        33.30        86.01       129.96         4.27        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-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-23-2647 
       91.66        77.00         2.76         4.70         4.50         4.44 
TCGA-23-2649 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        3.81         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-24-1431 
        6.02         5.95         5.36         4.83        17.39        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-24-1469 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-24-1551 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-24-1849 TCGA-24-1850 TCGA-24-2019 TCGA-24-2024 
        4.37        11.28         5.79         5.52         4.87        58.16 
TCGA-24-2030 TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 
       55.92        28.18        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-24-2298 TCGA-25-1313 TCGA-25-1315 
       67.36        36.23        16.64        53.26        26.96        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-25-1324 TCGA-25-1325 TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 
        2.99        34.03        32.09        41.06        66.05        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-25-2042 
        0.30        59.15        62.17        35.87        52.04        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-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-29-1702 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-29-1770 
       66.81        62.93        39.42        31.30        22.98        24.36 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 
       22.55        17.33        12.36        11.84        12.30        14.93 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 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-29-2434 TCGA-29-2436 TCGA-30-1714 TCGA-30-1718 
       42.25        21.47        11.47         9.76        38.07        51.91 
TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1862 TCGA-30-1891 
       36.26         2.47        15.68         0.26         6.12        30.05 
TCGA-31-1950 TCGA-31-1953 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
       18.77         6.71         2.20        28.77        29.10        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 
       22.85        22.55         8.55        30.08        25.74        27.85 
TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
       24.23        33.01        29.49        29.82        25.91        25.08 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 
       23.80        21.60         2.24        20.98        18.31        20.52 
TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
       14.17        16.18        11.47        47.57        23.74        28.93 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 
       42.02        10.42        40.77        24.03        11.38        21.14 
TCGA-57-1586 TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       22.32        25.08       180.20        22.32       116.12         9.40 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1722 TCGA-61-1725 
       34.39         2.14         5.42        44.81         8.09        31.43 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 TCGA-61-1738 
       18.54        27.88         4.34        31.79        48.79        35.80 
TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 
       33.67         1.45         8.42        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-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       67.76        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-61-2088 
        4.01        30.64        39.85        30.64         1.18         4.77 
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-61-2104 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 
       31.07         8.61 

  PTEN MUTATED PTEN WILD-TYPE 
          2.43           0.26 
  PTEN MUTATED PTEN WILD-TYPE 
         73.55         180.20 
  PTEN MUTATED PTEN WILD-TYPE 
        34.190         28.375 
[1] "2.4 - 73.5 (34.2)"  "0.3 - 180.2 (28.4)"
[1] "hr=" "1.4"
D21V2, continuous
                vv
clus             OMENTUM OVARY PERITONEUM OVARY
  PTEN MUTATED         0     5                0
  PTEN WILD-TYPE       2   457                1
D21V3, multiclass
                  clus
vv                 PTEN MUTATED PTEN WILD-TYPE
  OMENTUM                     0              2
  OVARY                       5            457
  PERITONEUM OVARY            0              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"
D21V4, continuous
[1] "Remove cluster labels:" "PTEN MUTATED"          
clus
  PTEN MUTATED PTEN WILD-TYPE 
             1             63 
    TCGA-04-1346     TCGA-04-1347     TCGA-04-1356     TCGA-04-1367 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-10-0926     TCGA-13-0714     TCGA-13-0720     TCGA-13-0724 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-13-0755     TCGA-13-0760     TCGA-13-0762     TCGA-13-0791 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-13-0792     TCGA-13-0793     TCGA-13-0795     TCGA-13-0801 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-13-0802     TCGA-13-0885     TCGA-13-0887     TCGA-13-0889 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-13-0891     TCGA-13-0894     TCGA-13-0897     TCGA-13-0900 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-13-0901     TCGA-13-0903     TCGA-13-0904     TCGA-13-0905 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-13-0906     TCGA-13-0910     TCGA-13-0911     TCGA-13-0912 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-13-0913     TCGA-13-0919     TCGA-13-1404     TCGA-13-1405 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-13-1409     TCGA-13-1410     TCGA-13-1412     TCGA-13-1482 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-13-1483     TCGA-13-1484     TCGA-13-1488     TCGA-13-1489 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-13-1491     TCGA-13-1495     TCGA-13-1497     TCGA-13-1498 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-13-1499     TCGA-13-1501     TCGA-13-1504     TCGA-13-1506 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-13-1507     TCGA-13-1509     TCGA-13-1512     TCGA-13-2057 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-13-2059     TCGA-13-2060     TCGA-13-2061     TCGA-13-2066 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-13-2071     TCGA-24-1614     TCGA-61-2101 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
D21V5, binary
                cls
clus               0   1
  PTEN MUTATED     0   5
  PTEN WILD-TYPE   3 457
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      0    5
  PTEN WILD-TYPE    3  457
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO             0              3
  YES            5            457
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2
  PTEN MUTATED    0  0  0
  PTEN WILD-TYPE 13 22  1
D21V6, multiclass
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTEN MUTATED                                  0     0
  PTEN WILD-TYPE                                2    18
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED                           1     4
  PTEN WILD-TYPE                        19   399
D21V7, multiclass
                                  clus
vv                                 PTEN MUTATED PTEN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             18
  BLACK OR AFRICAN AMERICAN                   1             19
  WHITE                                       4            399
[1] 4 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
  PTEN MUTATED     0   4
  PTEN WILD-TYPE   9 266
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      0    4
  PTEN WILD-TYPE    9  266
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                0              9
  NOT HISPANIC OR LATINO            4            266
[1] 2 2
[1] FALSE

Clustering(22) Variable = RB1CC1 MUTATION ANALYSIS
D22V1, survival
                  sevent
clus2                0   1
  RB1CC1 MUTATED     4   5
  RB1CC1 WILD-TYPE 224 230
  RB1CC1 MUTATED RB1CC1 WILD-TYPE 
               9              454 
  RB1CC1 MUTATED RB1CC1 WILD-TYPE 
               5              230 
$`RB1CC1 MUTATED`
TCGA-04-1349 TCGA-09-1664 TCGA-13-0885 TCGA-13-1496 TCGA-13-1498 TCGA-23-1030 
       21.57        74.93        91.40         4.24        37.61        29.13 
TCGA-24-2024 TCGA-25-2393 TCGA-29-1764 
       58.16        38.04        62.93 

$`RB1CC1 WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       43.92        41.00        49.15         2.01        46.62        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1350 TCGA-04-1353 
       11.87        65.52        63.09        48.76        63.98         0.53 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       49.28        32.52        44.32        33.67        76.57       103.40 
TCGA-04-1369 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 
       21.11        56.55        41.59        19.99         0.79        38.37 
TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 
      119.08        84.20        55.43        48.89        27.88        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 TCGA-09-0366 
       64.64        36.23        31.86        45.37        29.16        57.76 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 
       35.57         9.99        38.43        89.33        41.62        57.60 
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-09-2044 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-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       12.46        25.91        81.86        18.51        34.19        32.88 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
       14.66         6.71        35.44        19.99        20.91         6.21 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 
       24.59        44.55        39.58         2.73        31.20        15.19 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 
       17.82        55.17         2.50        11.54        34.06        32.25 
TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 
       28.57        38.93        36.72        28.70        19.59         8.12 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
        8.28         8.19        35.28        13.61        68.94       107.18 
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-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       49.61        57.47        56.15        57.07        19.36        47.38 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       48.33        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-13-0924 
       29.98        21.17        14.89        13.81         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-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
       29.42        98.04        22.39        70.82        82.88        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1497 TCGA-13-1499 TCGA-13-1501 
       73.55        38.20        49.25        54.31        38.40        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-13-1512 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-13-2066 TCGA-13-2071 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 
        9.70         6.28        23.05        25.94        26.20        27.52 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 
       25.38        19.10        16.70         2.93         2.66        47.54 
TCGA-23-1022 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-23-1031 TCGA-23-1032 TCGA-23-1107 TCGA-23-1109 TCGA-23-1110 
        8.81        18.90         2.76         0.30        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-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 
        4.27        39.09        33.47        58.13         0.53        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-23-2647 TCGA-23-2649 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 
        4.50         4.44         3.81         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-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        0.76         6.25         6.02         5.95         5.36         4.83 
TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 
       17.39        19.17        18.67        43.53         8.55        72.92 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 
       12.46        45.14         9.11         3.45         1.18        22.22 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 
       26.96        57.40        64.27        16.21        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-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 
        3.72         3.81         4.37        11.28         5.79         5.52 
TCGA-24-2019 TCGA-24-2030 TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 
        4.87        55.92        28.18        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-24-2298 TCGA-25-1313 
        0.82        67.36        36.23        16.64        53.26        26.96 
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-25-1324 TCGA-25-1325 TCGA-25-1326 TCGA-25-1328 
       33.96         2.99        34.03        32.09        41.06        66.05 
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-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 
       13.02        49.05         1.02         3.02        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-29-1702 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-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 
       66.81        39.42        31.30        22.98        24.36        22.55 
TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 
       17.33        12.36        11.84        12.30        14.93         8.38 
TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 
        7.23         5.36        36.30        62.47        13.84        42.25 
TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 
       21.47        11.47         9.76        38.07        51.91        36.26 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1862 TCGA-30-1891 TCGA-31-1950 
        2.47        15.68         0.26         6.12        30.05        18.77 
TCGA-31-1953 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 
        6.71         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-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       33.01        29.49        29.82        25.91        25.08        23.80 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 
       21.60         2.24        20.98        18.31        20.52        14.17 
TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 
       16.18        11.47        47.57        23.74        28.93        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 
       10.42        40.77        24.03        11.38        21.14        22.32 
TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 
       25.08       180.20        22.32       116.12         9.40        34.39 
TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 
        2.14         5.42        44.81         8.09        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-61-1895 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-61-1906 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-61-1919 TCGA-61-1995 TCGA-61-1998 
       48.92        56.61        67.76        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-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 
        1.18         4.77        51.72        71.74        61.64        60.62 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       55.50         6.48        76.87        20.68        44.52       125.75 
TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       22.22         6.35        31.07         8.61 

  RB1CC1 MUTATED RB1CC1 WILD-TYPE 
            4.24             0.26 
  RB1CC1 MUTATED RB1CC1 WILD-TYPE 
            91.4            180.2 
  RB1CC1 MUTATED RB1CC1 WILD-TYPE 
           38.04            27.88 
[1] "4.2 - 91.4 (38.0)"  "0.3 - 180.2 (27.9)"
[1] "hr=" "1.5"
D22V2, continuous
                  vv
clus               OMENTUM OVARY PERITONEUM OVARY
  RB1CC1 MUTATED         0     9                0
  RB1CC1 WILD-TYPE       2   453                1
D22V3, multiclass
                  clus
vv                 RB1CC1 MUTATED RB1CC1 WILD-TYPE
  OMENTUM                       0                2
  OVARY                         9              453
  PERITONEUM OVARY              0                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"
D22V4, continuous
[1] "Remove cluster labels:" "RB1CC1 MUTATED"        
clus
  RB1CC1 MUTATED RB1CC1 WILD-TYPE 
               2               62 
      TCGA-04-1346       TCGA-04-1347       TCGA-04-1356       TCGA-04-1367 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-10-0926       TCGA-13-0714       TCGA-13-0720       TCGA-13-0724 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-13-0755       TCGA-13-0760       TCGA-13-0762       TCGA-13-0791 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-13-0792       TCGA-13-0793       TCGA-13-0795       TCGA-13-0801 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-13-0802       TCGA-13-0887       TCGA-13-0889       TCGA-13-0891 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-13-0894       TCGA-13-0897       TCGA-13-0900       TCGA-13-0901 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-13-0903       TCGA-13-0904       TCGA-13-0905       TCGA-13-0906 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-13-0910       TCGA-13-0911       TCGA-13-0912       TCGA-13-0913 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-13-0919       TCGA-13-1404       TCGA-13-1405       TCGA-13-1409 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-13-1410       TCGA-13-1412       TCGA-13-1482       TCGA-13-1483 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-13-1484       TCGA-13-1488       TCGA-13-1489       TCGA-13-1491 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-13-1492       TCGA-13-1495       TCGA-13-1497       TCGA-13-1499 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-13-1501       TCGA-13-1504       TCGA-13-1506       TCGA-13-1507 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-13-1509       TCGA-13-1512       TCGA-13-2057       TCGA-13-2059 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-13-2060       TCGA-13-2061       TCGA-13-2066       TCGA-13-2071 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-24-1614       TCGA-61-2101 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
D22V5, binary
                  cls
clus                 0   1
  RB1CC1 MUTATED     0   9
  RB1CC1 WILD-TYPE   3 453
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RB1CC1 MUTATED      0    9
  RB1CC1 WILD-TYPE    3  453
     clus
vv    RB1CC1 MUTATED RB1CC1 WILD-TYPE
  NO               0                3
  YES              9              453
[1] 2 2
[1] FALSE
                  vv
clus               R0 R1 R2
  RB1CC1 MUTATED    0  0  0
  RB1CC1 WILD-TYPE 13 22  1
D22V6, multiclass
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RB1CC1 MUTATED                                  0     0
  RB1CC1 WILD-TYPE                                2    18
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RB1CC1 MUTATED                           1     8
  RB1CC1 WILD-TYPE                        19   395
D22V7, multiclass
                                  clus
vv                                 RB1CC1 MUTATED RB1CC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               18
  BLACK OR AFRICAN AMERICAN                     1               19
  WHITE                                         8              395
[1] 4 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
  RB1CC1 MUTATED     0   7
  RB1CC1 WILD-TYPE   9 263
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RB1CC1 MUTATED      0    7
  RB1CC1 WILD-TYPE    9  263
                        clus
vv                       RB1CC1 MUTATED RB1CC1 WILD-TYPE
  HISPANIC OR LATINO                  0                9
  NOT HISPANIC OR LATINO              7              263
[1] 2 2
[1] FALSE

Clustering(23) Variable = LPAR3 MUTATION ANALYSIS
D23V1, survival
                 sevent
clus2               0   1
  LPAR3 MUTATED     3   1
  LPAR3 WILD-TYPE 225 234
  LPAR3 MUTATED LPAR3 WILD-TYPE 
              4             459 
  LPAR3 MUTATED LPAR3 WILD-TYPE 
              1             234 
$`LPAR3 MUTATED`
TCGA-13-1410 TCGA-24-1844 TCGA-29-1781 TCGA-29-2429 
        4.70         3.72         8.38        13.84 

$`LPAR3 WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       43.92        41.00        49.15         2.01        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-04-1353 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-04-1369 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 
      103.40        21.11        56.55        41.59        19.99         0.79 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
       38.37       119.08        84.20        55.43        48.89        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 
       28.64        64.64        36.23        31.86        45.37        29.16 
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-09-1666 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       41.62        57.60        30.51        17.98         5.85         3.02 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 
        8.55        97.55         6.12        35.15       112.41        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       63.09        39.75        12.46        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-13-0724 
       20.91         6.21        24.59        44.55        39.58         2.73 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 
       31.20        15.19        17.82        55.17         2.50        11.54 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       34.06        32.25        28.57        38.93        36.72        28.70 
TCGA-13-0795 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 
       19.59         8.12         8.28         8.19        35.28        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 
       68.94       107.18        91.40        74.27        66.67        61.84 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 
       67.99        69.01        43.36        49.61        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-13-0910 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-13-1411 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-13-1487 TCGA-13-1488 
       87.06        61.71        29.42        98.04        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-13-1501 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-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 
        4.41         4.77         4.18         2.56         3.09        14.24 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2066 TCGA-13-2071 
       12.23         8.61        10.78         8.75         9.70         6.28 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 
       23.05        25.94        26.20        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-23-1107 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
       18.90         2.76         0.30        51.35        54.51         3.22 
TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 
       68.68         4.57        33.30        86.01       129.96         4.27 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 
       39.09        33.47        58.13         0.53        24.95       115.89 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 
       87.48        91.66        77.00         2.76         4.70         4.50 
TCGA-23-2647 TCGA-23-2649 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 
        4.44         3.81         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-24-1428 
        6.25         6.02         5.95         5.36         4.83        17.39 
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-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
       45.14         9.11         3.45         1.18        22.22        26.96 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 
       57.40        64.27        16.21        56.58        51.91        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 
       58.09        88.50        70.62        39.88        19.53        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       45.50        47.70        25.87        10.26        17.23        90.15 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1845 
       88.37        48.33        38.24         8.32         3.48         3.81 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-2019 TCGA-24-2024 
        4.37        11.28         5.79         5.52         4.87        58.16 
TCGA-24-2030 TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 
       55.92        28.18        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-24-2298 TCGA-25-1313 TCGA-25-1315 
       67.36        36.23        16.64        53.26        26.96        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-25-1324 TCGA-25-1325 TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 
        2.99        34.03        32.09        41.06        66.05        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-25-2042 
        0.30        59.15        62.17        35.87        52.04        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-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-29-1702 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-29-1770 
       66.81        62.93        39.42        31.30        22.98        24.36 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 
       22.55        17.33        12.36        11.84        12.30        14.93 
TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2427 TCGA-29-2431 TCGA-29-2432 
        7.23         5.36        36.30        62.47        42.25        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-30-1856 TCGA-30-1857 TCGA-30-1862 TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 
       15.68         0.26         6.12        30.05        18.77         6.71 
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-36-2530 
        8.55        30.08        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-36-2551 
        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-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1993 
       40.77        24.03        11.38        21.14        22.32        25.08 
TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 
      180.20        22.32       116.12         9.40        34.39         2.14 
TCGA-59-2363 TCGA-59-2372 TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 
        5.42        44.81         8.09        31.43        18.54        27.88 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 
        4.34        31.79        48.79        44.84        35.80         2.43 
TCGA-61-1741 TCGA-61-1895 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-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       56.61        67.76        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-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 TCGA-61-2101 
        4.77        51.72        71.74        61.64        60.62        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 
        6.35        31.07         8.61 

  LPAR3 MUTATED LPAR3 WILD-TYPE 
           3.72            0.26 
  LPAR3 MUTATED LPAR3 WILD-TYPE 
          13.84          180.20 
  LPAR3 MUTATED LPAR3 WILD-TYPE 
           6.54           28.70 
[1] "3.7 - 13.8 (6.5)"   "0.3 - 180.2 (28.7)"
[1] "hr=" "3.6"
D23V2, continuous
                 vv
clus              OMENTUM OVARY PERITONEUM OVARY
  LPAR3 MUTATED         0     4                0
  LPAR3 WILD-TYPE       2   458                1
D23V3, multiclass
                  clus
vv                 LPAR3 MUTATED LPAR3 WILD-TYPE
  OMENTUM                      0               2
  OVARY                        4             458
  PERITONEUM OVARY             0               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"
D23V4, continuous
[1] "Remove cluster labels:" "LPAR3 MUTATED"         
clus
  LPAR3 MUTATED LPAR3 WILD-TYPE 
              1              63 
     TCGA-04-1346      TCGA-04-1347      TCGA-04-1356      TCGA-04-1367 
"LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" 
     TCGA-10-0926      TCGA-13-0714      TCGA-13-0720      TCGA-13-0724 
"LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" 
     TCGA-13-0755      TCGA-13-0760      TCGA-13-0762      TCGA-13-0791 
"LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" 
     TCGA-13-0792      TCGA-13-0793      TCGA-13-0795      TCGA-13-0801 
"LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" 
     TCGA-13-0802      TCGA-13-0885      TCGA-13-0887      TCGA-13-0889 
"LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" 
     TCGA-13-0891      TCGA-13-0894      TCGA-13-0897      TCGA-13-0900 
"LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" 
     TCGA-13-0901      TCGA-13-0903      TCGA-13-0904      TCGA-13-0905 
"LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" 
     TCGA-13-0906      TCGA-13-0910      TCGA-13-0911      TCGA-13-0912 
"LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" 
     TCGA-13-0913      TCGA-13-0919      TCGA-13-1404      TCGA-13-1405 
"LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" 
     TCGA-13-1409      TCGA-13-1412      TCGA-13-1482      TCGA-13-1483 
"LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" 
     TCGA-13-1484      TCGA-13-1488      TCGA-13-1489      TCGA-13-1491 
"LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" 
     TCGA-13-1492      TCGA-13-1495      TCGA-13-1497      TCGA-13-1498 
"LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" 
     TCGA-13-1499      TCGA-13-1501      TCGA-13-1504      TCGA-13-1506 
"LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" 
     TCGA-13-1507      TCGA-13-1509      TCGA-13-1512      TCGA-13-2057 
"LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" 
     TCGA-13-2059      TCGA-13-2060      TCGA-13-2061      TCGA-13-2066 
"LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" 
     TCGA-13-2071      TCGA-24-1614      TCGA-61-2101 
"LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" 
D23V5, binary
                 cls
clus                0   1
  LPAR3 MUTATED     0   4
  LPAR3 WILD-TYPE   3 458
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPAR3 MUTATED      0    4
  LPAR3 WILD-TYPE    3  458
     clus
vv    LPAR3 MUTATED LPAR3 WILD-TYPE
  NO              0               3
  YES             4             458
[1] 2 2
[1] FALSE
                 vv
clus              R0 R1 R2
  LPAR3 MUTATED    0  1  0
  LPAR3 WILD-TYPE 13 21  1
D23V6, multiclass
[1] "Remove cluster labels:" "LPAR3 MUTATED"         
clus
  LPAR3 MUTATED LPAR3 WILD-TYPE 
              1              35 
     TCGA-04-1369      TCGA-04-1516      TCGA-04-1644      TCGA-13-0807 
"LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" 
     TCGA-13-0911      TCGA-29-2427      TCGA-29-2431      TCGA-29-2432 
"LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" 
     TCGA-29-2434      TCGA-29-2436      TCGA-36-2530      TCGA-36-2532 
"LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" 
     TCGA-36-2534      TCGA-36-2537      TCGA-36-2538      TCGA-36-2540 
"LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" 
     TCGA-36-2542      TCGA-36-2543      TCGA-36-2544      TCGA-36-2545 
"LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" 
     TCGA-36-2547      TCGA-36-2548      TCGA-36-2551      TCGA-36-2552 
"LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" 
     TCGA-42-2582      TCGA-42-2587      TCGA-42-2588      TCGA-42-2589 
"LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" 
     TCGA-42-2590      TCGA-57-1993      TCGA-59-2363      TCGA-59-2372 
"LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" 
     TCGA-61-2612      TCGA-61-2613      TCGA-61-2614 
"LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" "LPAR3 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LPAR3 MUTATED                                  0     0
  LPAR3 WILD-TYPE                                2    18
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LPAR3 MUTATED                           0     4
  LPAR3 WILD-TYPE                        20   399
D23V7, multiclass
                                  clus
vv                                 LPAR3 MUTATED LPAR3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              18
  BLACK OR AFRICAN AMERICAN                    0              20
  WHITE                                        4             399
[1] 4 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
  LPAR3 MUTATED     0   1
  LPAR3 WILD-TYPE   9 269
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPAR3 MUTATED      0    1
  LPAR3 WILD-TYPE    9  269
                        clus
vv                       LPAR3 MUTATED LPAR3 WILD-TYPE
  HISPANIC OR LATINO                 0               9
  NOT HISPANIC OR LATINO             1             269
[1] 2 2
[1] FALSE
