[1] "ofn"      "-oTOV-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/OV-TP/22507289/OV-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/OV-TP/22572516/transformed.cor.cli.txt"

nPatients in clinical file=590, in cluster file=466, common to both=465
[1]  21 465
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           384             81 
  TP53 MUTATED TP53 WILD-TYPE 
           384             81 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           15           450 
  RB1 MUTATED RB1 WILD-TYPE 
           15           450 
[1] "BRCA1 MUTATION ANALYSIS"
[1] 3
  BRCA1 MUTATED BRCA1 WILD-TYPE 
             18             447 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
             18             447 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           24           441 
  NF1 MUTATED NF1 WILD-TYPE 
           24           441 
[1] "CDK12 MUTATION ANALYSIS"
[1] 3
  CDK12 MUTATED CDK12 WILD-TYPE 
             15             450 
  CDK12 MUTATED CDK12 WILD-TYPE 
             15             450 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
             5            460 
  KRAS MUTATED KRAS WILD-TYPE 
             5            460 
[1] "HNF1B MUTATION ANALYSIS"
[1] 3
  HNF1B MUTATED HNF1B WILD-TYPE 
              5             460 
  HNF1B MUTATED HNF1B WILD-TYPE 
              5             460 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
             5            460 
  PTEN MUTATED PTEN WILD-TYPE 
             5            460 
[1] "LARP1 MUTATION ANALYSIS"
[1] 3
  LARP1 MUTATED LARP1 WILD-TYPE 
              4             461 
  LARP1 MUTATED LARP1 WILD-TYPE 
              4             461 
[1] "BRCA2 MUTATION ANALYSIS"
[1] 3
  BRCA2 MUTATED BRCA2 WILD-TYPE 
             13             452 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
             13             452 
[1] "EFEMP1 MUTATION ANALYSIS"
[1] 3
  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
               7              458 
  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
               7              458 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
             4            461 
  NRAS MUTATED NRAS WILD-TYPE 
             4            461 
[1] "MTA2 MUTATION ANALYSIS"
[1] 3
  MTA2 MUTATED MTA2 WILD-TYPE 
             4            461 
  MTA2 MUTATED MTA2 WILD-TYPE 
             4            461 
[1] "ERCC6 MUTATION ANALYSIS"
[1] 3
  ERCC6 MUTATED ERCC6 WILD-TYPE 
              4             461 
  ERCC6 MUTATED ERCC6 WILD-TYPE 
              4             461 
[1] "IL21R MUTATION ANALYSIS"
[1] 3
  IL21R MUTATED IL21R WILD-TYPE 
              8             457 
  IL21R MUTATED IL21R WILD-TYPE 
              8             457 
[1] "PKD1L1 MUTATION ANALYSIS"
[1] 3
  PKD1L1 MUTATED PKD1L1 WILD-TYPE 
               6              459 
  PKD1L1 MUTATED PKD1L1 WILD-TYPE 
               6              459 
[1] "SAMD9L MUTATION ANALYSIS"
[1] 3
  SAMD9L MUTATED SAMD9L WILD-TYPE 
               9              456 
  SAMD9L MUTATED SAMD9L WILD-TYPE 
               9              456 
[1] "AQP2 MUTATION ANALYSIS"
[1] 3
  AQP2 MUTATED AQP2 WILD-TYPE 
             3            462 
  AQP2 MUTATED AQP2 WILD-TYPE 
             3            462 
[1] "CREBBP MUTATION ANALYSIS"
[1] 3
  CREBBP MUTATED CREBBP WILD-TYPE 
              11              454 
  CREBBP MUTATED CREBBP WILD-TYPE 
              11              454 
[1] "C9ORF171 MUTATION ANALYSIS"
[1] 3
  C9ORF171 MUTATED C9ORF171 WILD-TYPE 
                 5                460 
  C9ORF171 MUTATED C9ORF171 WILD-TYPE 
                 5                460 
[1] "NCOA3 MUTATION ANALYSIS"
[1] 3
  NCOA3 MUTATED NCOA3 WILD-TYPE 
              5             460 
  NCOA3 MUTATED NCOA3 WILD-TYPE 
              5             460 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "KARNOFSKY_PERFORMANCE_SCORE"         
[14] "HISTOLOGICAL_TYPE"                   
[15] "TUMOR_GRADE"                         
[16] "TUMOR_STAGE"                         
[17] "DAYS_TO_TUMOR_RECURRENCE"            
[18] "CHEMO_THERAPY"                       
[19] "RESIDUAL_TUMOR"                      
[20] "ETHNICITY"                           

Input Data has 20 rows and 465 columns.

[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=248,	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=180,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGIC_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_T_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_N_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "GENDER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HISTOLOGICAL_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'TUMOR_GRADE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_GRADE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 16:'TUMOR_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 17:'DAYS_TO_TUMOR_RECURRENCE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DAYS_TO_TUMOR_RECURRENCE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 18:'CHEMO_THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "CHEMO_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 19:'RESIDUAL_TUMOR':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 465 columns, 1 survival variables, and 6 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"              "TUMOR_TISSUE_SITE"          
[3] "RADIATION_THERAPY"           "KARNOFSKY_PERFORMANCE_SCORE"
[5] "RESIDUAL_TUMOR"              "ETHNICITY"                  
YEARS_TO_BIRTH, nv=54, binary=FALSE, numeric=TRUE
TUMOR_TISSUE_SITE, nv=3, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=4, binary=FALSE, numeric=TRUE
RESIDUAL_TUMOR, nv=3, 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   160 221
  TP53 WILD-TYPE  34  47
  TP53 MUTATED TP53 WILD-TYPE 
           381             81 
  TP53 MUTATED TP53 WILD-TYPE 
           221             47 
$`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-09-1659 
       27.88        64.64        36.23        31.86        45.37         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 TCGA-09-1670 
       38.43        89.33        41.62        57.60        30.51        17.98 
TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 
        3.02         8.55        97.55         6.12        35.15       112.41 
TCGA-09-2050 TCGA-09-2053 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 
       71.11        39.75        77.10        81.17        28.54        83.31 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 TCGA-13-1482 
       57.27        81.01        17.46        32.35        87.06        61.71 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
       29.42       124.44        22.39        70.82        83.93        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
      125.56        93.90        90.38         4.24       127.27        66.15 
TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1507 TCGA-13-1509 
      115.07        43.20        34.82        65.69        65.52        80.15 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-20-0987 
       14.53        80.02        78.48        77.88        76.90        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1685 TCGA-20-1686 
       25.94        26.20        27.52        25.38        16.70         2.93 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
        2.66        47.54        49.68        40.54        15.39        26.83 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1107 
       49.41         8.81        29.13        18.90         2.76         0.30 
TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
       54.51         3.22        68.68        19.46        33.30        86.01 
TCGA-23-1119 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 
      129.96        39.09        33.47        58.13        24.95       115.89 
TCGA-23-2078 TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 TCGA-23-2649 TCGA-24-0966 
       87.48        77.00         2.76         4.70         3.81         7.63 
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-25-2042 TCGA-25-2392 TCGA-25-2396 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 
       13.02         1.02         3.02        19.99        42.02         2.96 
TCGA-25-2404 TCGA-25-2409 TCGA-29-1688 TCGA-29-1691 TCGA-29-1695 TCGA-29-1696 
       29.03        26.99        78.90        48.33        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-29-1770 TCGA-29-1771 
       66.81        62.93        39.42        31.30        24.36        22.55 
TCGA-29-1775 TCGA-29-1776 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
       12.36        11.84        14.93         8.38         7.23         5.36 
TCGA-29-1785 TCGA-29-2427 TCGA-29-2432 TCGA-29-2434 TCGA-30-1714 TCGA-30-1718 
       36.30        62.47        21.47        11.47        38.07        51.91 
TCGA-30-1855 TCGA-30-1857 TCGA-30-1862 TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 
        2.47         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-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       25.74        27.85        24.23        29.49        29.82        25.91 
TCGA-36-2538 TCGA-36-2542 TCGA-36-2543 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 
       25.08        21.60         2.24        14.17        16.18        11.47 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2589 TCGA-42-2591 TCGA-57-1582 TCGA-57-1583 
       47.57        23.74        42.02        40.77        24.03        11.38 
TCGA-57-1584 TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       21.14        25.08       180.20        22.32       116.12         9.40 
TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1725 TCGA-61-1728 TCGA-61-1730 
        2.14         5.42        44.81        31.43        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-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 
        1.45         5.79        11.41        13.02         9.07        34.13 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1919 
       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-61-2097 
       39.85         1.18         4.77        51.72        71.74        60.62 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
       55.50         6.48        76.87        44.52       125.75        22.22 
TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-09-0364 TCGA-09-0366 TCGA-09-0369 
        6.35        31.07         8.61        29.16        57.76        35.57 
TCGA-10-0926 TCGA-10-0928 TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 
       25.91        18.51        32.88         6.71        35.44        19.99 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 TCGA-13-0724 TCGA-13-0726 TCGA-13-0730 
       20.91         6.21        44.55         2.73        31.20        17.82 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0765 
       55.17         2.50        11.54        38.01       111.78        45.67 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 TCGA-13-0802 
       40.24       118.42       107.28        20.35        87.48        51.02 
TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 
       35.28        13.61        68.94       107.18       111.39       153.37 
TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0894 TCGA-13-0899 
       66.67        95.15       145.45       102.84        49.61        66.15 
TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 
      134.04       127.79        50.37       123.16       118.98       116.65 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       44.55        37.64       109.32        58.68        84.53        48.79 
TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       83.74        85.94        25.41 

$`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-13-1408 TCGA-13-1477 
       74.93         5.85        63.09        12.46        55.23        54.64 
TCGA-13-1506 TCGA-13-1510 TCGA-13-2065 TCGA-13-2066 TCGA-20-1684 TCGA-23-1027 
       34.16        44.68        65.52        70.13        19.10        32.09 
TCGA-23-1109 TCGA-23-1120 TCGA-23-1809 TCGA-23-2079 TCGA-23-2645 TCGA-23-2647 
       51.35         4.27         0.53        91.66         4.50         4.44 
TCGA-24-0975 TCGA-24-1417 TCGA-24-1431 TCGA-24-1546 TCGA-24-1549 TCGA-24-1565 
       21.80         7.82        18.64        64.27        56.58        10.26 
TCGA-24-2035 TCGA-24-2038 TCGA-24-2280 TCGA-24-2293 TCGA-24-2298 TCGA-25-1316 
       28.18        44.52        70.45        16.64        53.26        42.05 
TCGA-25-1328 TCGA-25-1634 TCGA-25-2391 TCGA-25-2393 TCGA-25-2398 TCGA-25-2408 
       66.05        35.87        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 TCGA-10-0927 
        8.42        31.30        30.64        61.64        20.68        81.86 
TCGA-10-0930 TCGA-10-0933 TCGA-13-0717 TCGA-13-0723 TCGA-13-0727 TCGA-13-0801 
       34.19        14.66        24.59        39.58        15.19        45.99 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0901 
       43.36        71.74        19.36 

  TP53 MUTATED TP53 WILD-TYPE 
          0.26           0.53 
  TP53 MUTATED TP53 WILD-TYPE 
        180.20         101.79 
  TP53 MUTATED TP53 WILD-TYPE 
         33.47          30.64 
[1] "0.3 - 180.2 (33.5)" "0.5 - 101.8 (30.6)"
[1] "hr=" "1.2"
D1V2, continuous
                vv
clus             OMENTUM OVARY PERITONEUM OVARY
  TP53 MUTATED         1   382                1
  TP53 WILD-TYPE       1    80                0
D1V3, multiclass
                  clus
vv                 TP53 MUTATED TP53 WILD-TYPE
  OMENTUM                     1              1
  OVARY                     382             80
  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, binary
                cls
clus               0   1
  TP53 MUTATED   371   3
  TP53 WILD-TYPE  75   1
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    371    3
  TP53 WILD-TYPE   75    1
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO           371             75
  YES            3              1
[1] 2 2
[1] FALSE
D1V5, continuous
                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"
D1V7, binary
                cls
clus               0   1
  TP53 MUTATED     5 225
  TP53 WILD-TYPE   4  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      5  225
  TP53 WILD-TYPE    4   45
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                5              4
  NOT HISPANIC OR LATINO          225             45
[1] 2 2
[1] FALSE

Clustering(2) Variable = RB1 MUTATION ANALYSIS
D2V1, survival
               sevent
clus2             0   1
  RB1 MUTATED     6   9
  RB1 WILD-TYPE 188 259
  RB1 MUTATED RB1 WILD-TYPE 
           15           447 
  RB1 MUTATED RB1 WILD-TYPE 
            9           259 
$`RB1 MUTATED`
TCGA-04-1350 TCGA-04-1638 TCGA-09-1665 TCGA-09-1674 TCGA-13-1489 TCGA-13-1509 
       63.98        55.43        41.62         8.55        83.93        80.15 
TCGA-23-2079 TCGA-24-1463 TCGA-24-1469 TCGA-24-1849 TCGA-25-1635 TCGA-29-1691 
       91.66        72.92         9.11         5.79        52.04        48.33 
TCGA-29-1703 TCGA-36-2538 TCGA-10-0933 
       59.67        25.08        14.66 

$`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-09-1659 TCGA-09-1661 TCGA-09-1662 
       36.23        31.86        45.37         9.99        38.43        89.33 
TCGA-09-1664 TCGA-09-1666 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       74.93        57.60        30.51        17.98         5.85         3.02 
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-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 
       39.75        12.46        77.10        81.17        28.54        83.31 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 
       55.23        57.27        81.01        17.46        32.35        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 
       87.06        61.71        29.42       124.44        22.39        70.82 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 
       52.44       125.56        93.90        90.38         4.24       127.27 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       66.15       115.07        43.20        34.82        65.69        34.16 
TCGA-13-1507 TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
       65.52        44.68        14.53        80.02        78.48        77.88 
TCGA-13-2061 TCGA-13-2065 TCGA-13-2066 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
       76.90        65.52        70.13        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        19.46        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-23-2081 TCGA-23-2641 
        0.53        24.95       115.89        87.48        77.00         2.76 
TCGA-23-2643 TCGA-23-2645 TCGA-23-2647 TCGA-23-2649 TCGA-24-0966 TCGA-24-0970 
        4.70         4.50         4.44         3.81         7.63        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 
       21.80        41.56         7.66        22.32        54.12        63.55 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       47.41         6.31         6.38         7.82         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        0.76         6.25         6.02         5.95         5.36         4.83 
TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1464 
       17.39        18.64        18.67        43.53         8.55        12.46 
TCGA-24-1466 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 
       45.14         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-24-1850 TCGA-24-2019 TCGA-24-2024 TCGA-24-2030 
        4.37        11.28         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-25-2042 TCGA-25-2391 TCGA-25-2392 
       59.15        62.17        35.87        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-29-1693 
       29.03        31.00        26.99        78.90        47.61       101.79 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
       39.02        40.41        33.93        31.20        68.32        36.36 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 
       16.93        23.93        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-30-1862 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-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 
       25.91        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 
TCGA-09-0364 TCGA-09-0366 TCGA-09-0369 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       29.16        57.76        35.57        25.91        81.86        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 
       34.19        32.88         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        38.01 
TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 
      111.78        45.67        40.24       118.42       107.28        20.35 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 
       87.48        45.99        51.02        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       111.39       153.37        66.67        95.15       145.45 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
      102.84        43.36        49.61        71.74        66.15       134.04 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 
       19.36       127.79        50.37       123.16       118.98       116.65 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       44.55        37.64       109.32        58.68        84.53        48.79 
TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       83.74        85.94        25.41 

  RB1 MUTATED RB1 WILD-TYPE 
         5.79          0.26 
  RB1 MUTATED RB1 WILD-TYPE 
        91.66        180.20 
  RB1 MUTATED RB1 WILD-TYPE 
        52.04         32.09 
[1] "5.8 - 91.7 (52.0)"  "0.3 - 180.2 (32.1)"
[1] "hr=" "1.3"
D2V2, continuous
               vv
clus            OMENTUM OVARY PERITONEUM OVARY
  RB1 MUTATED         0    15                0
  RB1 WILD-TYPE       2   447                1
D2V3, 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"
D2V4, binary
               cls
clus              0   1
  RB1 MUTATED    15   0
  RB1 WILD-TYPE 431   4
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     15    0
  RB1 WILD-TYPE  431    4
     clus
vv    RB1 MUTATED RB1 WILD-TYPE
  NO           15           431
  YES           0             4
[1] 2 2
[1] FALSE
D2V5, 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-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-24-1614 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-61-2101    TCGA-10-0926    TCGA-13-0714    TCGA-13-0720    TCGA-13-0724 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-0755    TCGA-13-0760    TCGA-13-0762    TCGA-13-0791    TCGA-13-0792 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-0793    TCGA-13-0795    TCGA-13-0801    TCGA-13-0802    TCGA-13-0885 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-0887    TCGA-13-0889    TCGA-13-0891    TCGA-13-0894    TCGA-13-0897 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-0900    TCGA-13-0901    TCGA-13-0903    TCGA-13-0904    TCGA-13-0905 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-0906    TCGA-13-0910    TCGA-13-0911    TCGA-13-0912    TCGA-13-0913 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-0919    TCGA-13-2071 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" 
               vv
clus            R0 R1 R2
  RB1 MUTATED    0  1  0
  RB1 WILD-TYPE 13 21  1
D2V6, 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-29-2427    TCGA-29-2429 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-29-2431    TCGA-29-2432    TCGA-29-2434    TCGA-29-2436    TCGA-36-2530 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-36-2532    TCGA-36-2534    TCGA-36-2537    TCGA-36-2540    TCGA-36-2542 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-36-2543    TCGA-36-2544    TCGA-36-2545    TCGA-36-2547    TCGA-36-2548 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-36-2551    TCGA-36-2552    TCGA-42-2582    TCGA-42-2587    TCGA-42-2588 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-42-2589    TCGA-42-2590    TCGA-57-1993    TCGA-59-2363    TCGA-59-2372 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-61-2612    TCGA-61-2613    TCGA-61-2614    TCGA-13-0807    TCGA-13-0911 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
D2V7, 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(3) Variable = BRCA1 MUTATION ANALYSIS
D3V1, survival
                 sevent
clus2               0   1
  BRCA1 MUTATED     7  10
  BRCA1 WILD-TYPE 187 258
  BRCA1 MUTATED BRCA1 WILD-TYPE 
             17             445 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
             10             258 
$`BRCA1 MUTATED`
TCGA-13-1489 TCGA-23-1026 TCGA-24-1846 TCGA-24-1847 TCGA-24-2035 TCGA-25-1625 
       83.93        26.83         4.37        11.28        28.18        27.62 
TCGA-25-1630 TCGA-25-1632 TCGA-29-1768 TCGA-29-1776 TCGA-29-2427 TCGA-30-1857 
       38.20        59.15        31.30        11.84        62.47         0.26 
TCGA-36-2534 TCGA-61-1914 TCGA-13-0730 TCGA-13-0761 TCGA-13-0804 
       29.82        56.61        17.82        38.01        35.28 

$`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-09-1659 
       28.64        64.64        36.23        31.86        45.37         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 
       38.43        89.33        74.93        41.62        57.60        30.51 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 
       17.98         5.85         3.02         8.55        97.55         6.12 
TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 
       35.15       112.41        71.11        63.09        39.75        12.46 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
       77.10        81.17        28.54        83.31        55.23        57.27 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 
       81.01        17.46        32.35        54.64        87.06        61.71 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 
       29.42       124.44        22.39        70.82        52.44       125.56 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 
       93.90        90.38         4.24       127.27        66.15       115.07 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       43.20        34.82        65.69        34.16        65.52        80.15 
TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 
       44.68        14.53        80.02        78.48        77.88        76.90 
TCGA-13-2065 TCGA-13-2066 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 
       65.52        70.13        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-23-1027 TCGA-23-1028 TCGA-23-1029 
       49.68        40.54        15.39        32.09        49.41         8.81 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1107 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        19.46        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-24-0970 TCGA-24-0975 
        4.50         4.44         3.81         7.63        11.64        21.80 
TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 
       41.56         7.66        22.32        54.12        63.55        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 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 
       18.64        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-24-1849 TCGA-24-1850 TCGA-24-2019 TCGA-24-2024 TCGA-24-2030 
        3.81         5.79         5.52         4.87        58.16        55.92 
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-25-1626 
       32.09        41.06        66.05        15.02        18.58        17.03 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 
       12.95        20.61         0.30        62.17        35.87        52.04 
TCGA-25-2042 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-29-1769 TCGA-29-1770 
       86.60        66.81        62.93        39.42        22.98        24.36 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 
       22.55        17.33        12.36        12.30        14.93         8.38 
TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 
        7.23         5.36        36.30        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-30-1862 TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 TCGA-31-1959 
       15.68         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-36-2537 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-61-1903 TCGA-61-1904 TCGA-61-1906 
        8.42         5.79        11.41        13.02         9.07        34.13 
TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1915 TCGA-61-1919 
       31.30        37.05        42.51        48.92        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 
TCGA-09-0364 TCGA-09-0366 TCGA-09-0369 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       29.16        57.76        35.57        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       111.78 
TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 
       45.67        40.24       118.42       107.28        20.35        87.48 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 
       45.99        51.02        13.61        68.94       107.18       111.39 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
      153.37        66.67        95.15       145.45       102.84        43.36 
TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       49.61        71.74        66.15       134.04        19.36       127.79 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       50.37       123.16       118.98       116.65        44.55        37.64 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 
      109.32        58.68        84.53        48.79        83.74        85.94 
TCGA-13-2071 
       25.41 

  BRCA1 MUTATED BRCA1 WILD-TYPE 
           0.26            0.30 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
          83.93          180.20 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
          29.82           32.88 
[1] "0.3 - 83.9 (29.8)"  "0.3 - 180.2 (32.9)"
[1] "hr=" "1.3"
D3V2, continuous
                 vv
clus              OMENTUM OVARY PERITONEUM OVARY
  BRCA1 MUTATED         0    18                0
  BRCA1 WILD-TYPE       2   444                1
D3V3, multiclass
                  clus
vv                 BRCA1 MUTATED BRCA1 WILD-TYPE
  OMENTUM                      0               2
  OVARY                       18             444
  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, binary
                 cls
clus                0   1
  BRCA1 MUTATED    17   0
  BRCA1 WILD-TYPE 429   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA1 MUTATED     17    0
  BRCA1 WILD-TYPE  429    4
     clus
vv    BRCA1 MUTATED BRCA1 WILD-TYPE
  NO             17             429
  YES             0               4
[1] 2 2
[1] FALSE
D3V5, 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-13-1404      TCGA-13-1405      TCGA-13-1409      TCGA-13-1410 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-1412      TCGA-13-1482      TCGA-13-1483      TCGA-13-1484 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-1488      TCGA-13-1491      TCGA-13-1492      TCGA-13-1495 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-1497      TCGA-13-1498      TCGA-13-1499      TCGA-13-1501 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-1504      TCGA-13-1506      TCGA-13-1507      TCGA-13-1509 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-1512      TCGA-13-2057      TCGA-13-2059      TCGA-13-2060 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-2061      TCGA-13-2066      TCGA-24-1614      TCGA-61-2101 
"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-13-2071 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
                 vv
clus              R0 R1 R2
  BRCA1 MUTATED    0  2  0
  BRCA1 WILD-TYPE 13 20  1
D3V6, 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-29-2429 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-29-2431      TCGA-29-2432      TCGA-29-2434      TCGA-29-2436 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-36-2530      TCGA-36-2532      TCGA-36-2537      TCGA-36-2538 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-36-2540      TCGA-36-2542      TCGA-36-2543      TCGA-36-2544 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-36-2545      TCGA-36-2547      TCGA-36-2548      TCGA-36-2551 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-36-2552      TCGA-42-2582      TCGA-42-2587      TCGA-42-2588 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-42-2589      TCGA-42-2590      TCGA-57-1993      TCGA-59-2363 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-59-2372      TCGA-61-2612      TCGA-61-2613      TCGA-61-2614 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-0807      TCGA-13-0911 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
D3V7, binary
                 cls
clus                0   1
  BRCA1 MUTATED     0   9
  BRCA1 WILD-TYPE   9 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA1 MUTATED      0    9
  BRCA1 WILD-TYPE    9  261
                        clus
vv                       BRCA1 MUTATED BRCA1 WILD-TYPE
  HISPANIC OR LATINO                 0               9
  NOT HISPANIC OR LATINO             9             261
[1] 2 2
[1] FALSE

Clustering(4) Variable = NF1 MUTATION ANALYSIS
D4V1, survival
               sevent
clus2             0   1
  NF1 MUTATED    12  12
  NF1 WILD-TYPE 182 256
  NF1 MUTATED NF1 WILD-TYPE 
           24           438 
  NF1 MUTATED NF1 WILD-TYPE 
           12           256 
$`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-09-1659 TCGA-09-1661 TCGA-09-1662 
       36.23        31.86        45.37         9.99        38.43        89.33 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 
       41.62        57.60        30.51         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-09-2056 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 
       12.46        77.10        81.17        28.54        83.31        55.23 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
       57.27        81.01        17.46        32.35        54.64        87.06 
TCGA-13-1482 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
       61.71       124.44        22.39        70.82        83.93        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
      125.56        93.90        90.38         4.24       127.27        66.15 
TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
      115.07        43.20        34.82        65.69        34.16        65.52 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
       80.15        44.68        14.53        80.02        78.48        77.88 
TCGA-13-2061 TCGA-13-2065 TCGA-13-2066 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
       76.90        65.52        70.13        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-23-1029 
       47.54        49.68        40.54        15.39        26.83         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-23-1120 
        3.22        68.68        19.46        33.30        86.01         4.27 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 
       39.09        33.47        58.13         0.53        24.95       115.89 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2641 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-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        3.81         7.63        11.64        21.80        41.56         7.66 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
       22.32        54.12        63.55        47.41         6.31         6.38 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
        7.82         7.99         7.86         0.76         6.25         6.02 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 
        5.95         5.36         4.83        17.39        18.64        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1471 
       43.53         8.55        12.46        45.14         9.11         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-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 
       19.53        44.09        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-24-2024 TCGA-24-2030 TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 
        4.87        58.16        55.92        28.18        44.52        57.07 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       36.16         0.79         0.36        47.54        31.63        70.45 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2298 
       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-25-1326 
       37.97        33.96         2.99        34.03        32.09        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-29-1695 
       26.99        78.90        47.61        48.33       101.79        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-29-1774 TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 
       24.36        17.33        12.36        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-30-1718 TCGA-30-1853 TCGA-30-1855 
       21.47        11.47         9.76        51.91        36.26         2.47 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 TCGA-31-1959 
       15.68         0.26        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-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 
       25.91        25.08        23.80        21.60        20.98        18.31 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2551 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-59-2372 TCGA-61-1722 TCGA-61-1725 
        9.40        34.39         2.14        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-61-1741 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 
       35.80        33.67         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-61-2614 TCGA-09-0364 TCGA-09-0366 TCGA-09-0369 TCGA-10-0926 
        6.35         8.61        29.16        57.76        35.57        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       81.86        18.51        34.19        32.88        14.66         6.71 
TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
       35.44        19.99        20.91         6.21        24.59        44.55 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
       39.58         2.73        31.20        15.19        17.82        55.17 
TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 
        2.50        11.54        38.01       111.78        45.67        40.24 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 
      118.42       107.28        20.35        87.48        45.99        51.02 
TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 
       35.28        13.61        68.94       107.18       111.39       153.37 
TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 
       66.67        95.15       145.45       102.84        43.36        49.61 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 
       71.74        66.15       134.04        19.36       127.79        50.37 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
      123.16       118.98       116.65        44.55        37.64       109.32 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       58.68        84.53        48.79        83.74        85.94        25.41 

  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         32.70 
[1] "1.4 - 130.0 (31.6)" "0.3 - 180.2 (32.7)"
[1] "hr=" "1.2"
D4V2, continuous
               vv
clus            OMENTUM OVARY PERITONEUM OVARY
  NF1 MUTATED         0    24                0
  NF1 WILD-TYPE       2   438                1
D4V3, 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"
D4V4, binary
               cls
clus              0   1
  NF1 MUTATED    24   0
  NF1 WILD-TYPE 422   4
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     24    0
  NF1 WILD-TYPE  422    4
     clus
vv    NF1 MUTATED NF1 WILD-TYPE
  NO           24           422
  YES           0             4
[1] 2 2
[1] FALSE
D4V5, 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-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-24-1614 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-61-2101    TCGA-10-0926    TCGA-13-0714    TCGA-13-0720    TCGA-13-0724 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-13-0755    TCGA-13-0760    TCGA-13-0762    TCGA-13-0791    TCGA-13-0792 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-13-0793    TCGA-13-0795    TCGA-13-0801    TCGA-13-0802    TCGA-13-0885 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-13-0887    TCGA-13-0889    TCGA-13-0891    TCGA-13-0894    TCGA-13-0897 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-13-0900    TCGA-13-0901    TCGA-13-0903    TCGA-13-0904    TCGA-13-0905 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-13-0906    TCGA-13-0910    TCGA-13-0911    TCGA-13-0912    TCGA-13-0913 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-13-0919    TCGA-13-2071 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" 
               vv
clus            R0 R1 R2
  NF1 MUTATED    1  3  0
  NF1 WILD-TYPE 12 19  1
D4V6, 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"
D4V7, 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(5) Variable = CDK12 MUTATION ANALYSIS
D5V1, survival
                 sevent
clus2               0   1
  CDK12 MUTATED     6   9
  CDK12 WILD-TYPE 188 259
  CDK12 MUTATED CDK12 WILD-TYPE 
             15             447 
  CDK12 MUTATED CDK12 WILD-TYPE 
              9             259 
$`CDK12 MUTATED`
TCGA-04-1369 TCGA-09-1673 TCGA-13-1495 TCGA-20-0987 TCGA-20-1684 TCGA-24-1466 
       21.11         3.02        90.38        23.05        19.10        45.14 
TCGA-24-1842 TCGA-25-1322 TCGA-25-2392 TCGA-29-1696 TCGA-29-1711 TCGA-31-1953 
        8.32         2.99         1.02        33.93        34.62         6.71 
TCGA-59-2351 TCGA-13-0791 TCGA-13-0891 
      116.12        40.24       102.84 

$`CDK12 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-09-1659 TCGA-09-1661 
       64.64        36.23        31.86        45.37         9.99        38.43 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 TCGA-09-1670 
       89.33        74.93        41.62        57.60        30.51        17.98 
TCGA-09-1672 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 
        5.85         8.55        97.55         6.12        35.15       112.41 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 
       71.11        63.09        39.75        12.46        77.10        81.17 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
       28.54        83.31        55.23        57.27        81.01        17.46 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
       32.35        54.64        87.06        61.71        29.42       124.44 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       22.39        70.82        83.93        52.44       125.56        93.90 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 
        4.24       127.27        66.15       115.07        43.20        34.82 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 
       65.69        34.16        65.52        80.15        44.68        14.53 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2066 
       80.02        78.48        77.88        76.90        65.52        70.13 
TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1685 TCGA-20-1686 
       25.94        26.20        27.52        25.38        16.70         2.93 
TCGA-20-1687 TCGA-23-1021 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        19.46 
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-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
        7.63        11.64        21.80        41.56         7.66        22.32 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 
       54.12        63.55        47.41         6.31         6.38         7.82 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 
        7.99         7.86         0.76         6.25         6.02         5.95 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 
        5.36         4.83        17.39        18.64        18.67        43.53 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 
        8.55        72.92        12.46         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-24-1843 
       17.23        90.15        88.37        48.33        38.24         3.48 
TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 
        3.72         3.81         4.37        11.28         5.79         5.52 
TCGA-24-2019 TCGA-24-2024 TCGA-24-2030 TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 
        4.87        58.16        55.92        28.18        44.52        57.07 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       36.16         0.79         0.36        47.54        31.63        70.45 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2298 
       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-25-1324 TCGA-25-1325 TCGA-25-1326 TCGA-25-1328 
       37.97        33.96        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-25-2393 TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 
       13.02        49.05        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-29-1697 
       47.61        48.33       101.79        39.02        40.41        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-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 
       41.98        31.27        17.36        86.60        66.81        62.93 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
       39.42        31.30        22.98        24.36        22.55        17.33 
TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 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-31-1959 
       15.68         0.26         6.12        30.05        18.77         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-61-1728 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-61-1903 TCGA-61-1904 TCGA-61-1906 
        8.42         5.79        11.41        13.02         9.07        34.13 
TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 
       31.30        37.05        42.51        48.92        56.61        67.76 
TCGA-61-1919 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 TCGA-09-0364 TCGA-09-0366 TCGA-09-0369 TCGA-10-0926 TCGA-10-0927 
        8.61        29.16        57.76        35.57        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-13-0792 TCGA-13-0793 
       11.54        38.01       111.78        45.67       118.42       107.28 
TCGA-13-0795 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 
       20.35        87.48        45.99        51.02        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       111.39       153.37        66.67        95.15 
TCGA-13-0890 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
      145.45        43.36        49.61        71.74        66.15       134.04 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 
       19.36       127.79        50.37       123.16       118.98       116.65 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       44.55        37.64       109.32        58.68        84.53        48.79 
TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       83.74        85.94        25.41 

  CDK12 MUTATED CDK12 WILD-TYPE 
           1.02            0.26 
  CDK12 MUTATED CDK12 WILD-TYPE 
         116.12          180.20 
  CDK12 MUTATED CDK12 WILD-TYPE 
          23.05           32.52 
[1] "1.0 - 116.1 (23.1)" "0.3 - 180.2 (32.5)"
[1] "hr=" "1.1"
D5V2, continuous
                 vv
clus              OMENTUM OVARY PERITONEUM OVARY
  CDK12 MUTATED         0    15                0
  CDK12 WILD-TYPE       2   447                1
D5V3, multiclass
                  clus
vv                 CDK12 MUTATED CDK12 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"
D5V4, binary
                 cls
clus                0   1
  CDK12 MUTATED    14   0
  CDK12 WILD-TYPE 432   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED     14    0
  CDK12 WILD-TYPE  432    4
     clus
vv    CDK12 MUTATED CDK12 WILD-TYPE
  NO             14             432
  YES             0               4
[1] 2 2
[1] FALSE
D5V5, continuous
                 vv
clus              R0 R1 R2
  CDK12 MUTATED    0  1  0
  CDK12 WILD-TYPE 13 21  1
D5V6, multiclass
[1] "Remove cluster labels:" "CDK12 MUTATED"         
clus
  CDK12 MUTATED CDK12 WILD-TYPE 
              1              35 
     TCGA-04-1516      TCGA-04-1644      TCGA-29-2427      TCGA-29-2429 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-29-2431      TCGA-29-2432      TCGA-29-2434      TCGA-29-2436 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-36-2530      TCGA-36-2532      TCGA-36-2534      TCGA-36-2537 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-36-2538      TCGA-36-2540      TCGA-36-2542      TCGA-36-2543 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-36-2544      TCGA-36-2545      TCGA-36-2547      TCGA-36-2548 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-36-2551      TCGA-36-2552      TCGA-42-2582      TCGA-42-2587 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-42-2588      TCGA-42-2589      TCGA-42-2590      TCGA-57-1993 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-59-2363      TCGA-59-2372      TCGA-61-2612      TCGA-61-2613 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-61-2614      TCGA-13-0807      TCGA-13-0911 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
D5V7, binary
                 cls
clus                0   1
  CDK12 MUTATED     0  11
  CDK12 WILD-TYPE   9 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED      0   11
  CDK12 WILD-TYPE    9  259
                        clus
vv                       CDK12 MUTATED CDK12 WILD-TYPE
  HISPANIC OR LATINO                 0               9
  NOT HISPANIC OR LATINO            11             259
[1] 2 2
[1] FALSE

Clustering(6) Variable = KRAS MUTATION ANALYSIS
D6V1, survival
                sevent
clus2              0   1
  KRAS MUTATED     1   4
  KRAS WILD-TYPE 193 264
  KRAS MUTATED KRAS WILD-TYPE 
             5            457 
  KRAS MUTATED KRAS WILD-TYPE 
             4            264 
$`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-09-1659 
       28.64        64.64        36.23        31.86        45.37         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 TCGA-09-1670 
       38.43        89.33        41.62        57.60        30.51        17.98 
TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 
        3.02         8.55        97.55         6.12        35.15       112.41 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 
       71.11        63.09        39.75        12.46        77.10        81.17 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
       28.54        83.31        55.23        57.27        81.01        17.46 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
       32.35        54.64        87.06        61.71        29.42       124.44 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       22.39        70.82        83.93        52.44       125.56        93.90 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 
       90.38         4.24       127.27        66.15       115.07        43.20 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 
       34.82        65.69        34.16        65.52        80.15        44.68 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 
       14.53        80.02        78.48        77.88        76.90        65.52 
TCGA-13-2066 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 
       70.13        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        19.46        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-24-0970 TCGA-24-0975 
        4.50         4.44         3.81         7.63        11.64        21.80 
TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 
       41.56         7.66        22.32        54.12        63.55        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 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 
       18.64        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-24-2254 TCGA-24-2260 TCGA-24-2261 
       58.16        55.92        28.18        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-25-1317 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-29-1697 TCGA-29-1698 
       48.33       101.79        39.02        40.41        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-36-1574 
        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 TCGA-09-0364 TCGA-09-0366 TCGA-09-0369 
        6.35        31.07         8.61        29.16        57.76        35.57 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 
       25.91        81.86        18.51        34.19        32.88        14.66 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
        6.71        35.44        19.99        20.91         6.21        24.59 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 
       44.55        39.58         2.73        31.20        15.19        17.82 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0765 
       55.17         2.50        11.54        38.01       111.78        45.67 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 TCGA-13-0801 
       40.24       118.42       107.28        20.35        87.48        45.99 
TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 
       51.02        35.28        13.61        68.94       107.18       111.39 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
      153.37        66.67        95.15       145.45       102.84        43.36 
TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       49.61        71.74        66.15       134.04        19.36       127.79 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       50.37       123.16       118.98       116.65        44.55        37.64 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 
      109.32        58.68        84.53        48.79        83.74        85.94 
TCGA-13-2071 
       25.41 

  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          32.09 
[1] "5.8 - 74.9 (42.0)"  "0.3 - 180.2 (32.1)"
[1] "hr=" "1.3"
D6V2, continuous
                vv
clus             OMENTUM OVARY PERITONEUM OVARY
  KRAS MUTATED         0     5                0
  KRAS WILD-TYPE       2   457                1
D6V3, 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"
D6V4, binary
                cls
clus               0   1
  KRAS MUTATED     5   0
  KRAS WILD-TYPE 441   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      5    0
  KRAS WILD-TYPE  441    4
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO             5            441
  YES            0              4
[1] 2 2
[1] FALSE
D6V5, continuous
                vv
clus             R0 R1 R2
  KRAS MUTATED    0  0  0
  KRAS WILD-TYPE 13 22  1
D6V6, multiclass
D6V7, 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(7) Variable = HNF1B MUTATION ANALYSIS
D7V1, survival
                 sevent
clus2               0   1
  HNF1B MUTATED     3   2
  HNF1B WILD-TYPE 191 266
  HNF1B MUTATED HNF1B WILD-TYPE 
              5             457 
  HNF1B MUTATED HNF1B WILD-TYPE 
              2             266 
$`HNF1B MUTATED`
TCGA-04-1338 TCGA-25-1632 TCGA-29-1783 TCGA-61-1914 TCGA-13-0904 
       46.62        59.15         7.23        56.61        50.37 

$`HNF1B WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 
       43.92        41.00        49.15         2.01        18.51        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1353 
       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-09-1659 TCGA-09-1661 
       64.64        36.23        31.86        45.37         9.99        38.43 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 TCGA-09-1670 
       89.33        74.93        41.62        57.60        30.51        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 
        5.85         3.02         8.55        97.55         6.12        35.15 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-13-1403 
      112.41        71.11        63.09        39.75        12.46        77.10 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
       81.17        28.54        83.31        55.23        57.27        81.01 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
       17.46        32.35        54.64        87.06        61.71        29.42 
TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
      124.44        22.39        70.82        83.93        52.44       125.56 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 
       93.90        90.38         4.24       127.27        66.15       115.07 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       43.20        34.82        65.69        34.16        65.52        80.15 
TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 
       44.68        14.53        80.02        78.48        77.88        76.90 
TCGA-13-2065 TCGA-13-2066 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 
       65.52        70.13        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-23-1030 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        19.46        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-24-0970 
        4.70         4.50         4.44         3.81         7.63        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 
       21.80        41.56         7.66        22.32        54.12        63.55 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       47.41         6.31         6.38         7.82         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        0.76         6.25         6.02         5.95         5.36         4.83 
TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 
       17.39        18.64        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-24-2024 TCGA-24-2030 TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 
        4.87        58.16        55.92        28.18        44.52        57.07 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       36.16         0.79         0.36        47.54        31.63        70.45 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2298 
       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-25-1326 
       37.97        33.96         2.99        34.03        32.09        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-25-1633 TCGA-25-1634 TCGA-25-1635 
       20.61        38.20         0.30        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-29-1784 TCGA-29-1785 TCGA-29-2427 TCGA-29-2429 
       14.93         8.38         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-61-1915 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
       42.51        48.92        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 TCGA-09-0364 TCGA-09-0366 
       22.22         6.35        31.07         8.61        29.16        57.76 
TCGA-09-0369 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       35.57        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        38.01       111.78 
TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 
       45.67        40.24       118.42       107.28        20.35        87.48 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
       45.99        51.02        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 
      111.39       153.37        66.67        95.15       145.45       102.84 
TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
       43.36        49.61        71.74        66.15       134.04        19.36 
TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
      127.79       123.16       118.98       116.65        44.55        37.64 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 
      109.32        58.68        84.53        48.79        83.74        85.94 
TCGA-13-2071 
       25.41 

  HNF1B MUTATED HNF1B WILD-TYPE 
           7.23            0.26 
  HNF1B MUTATED HNF1B WILD-TYPE 
          59.15          180.20 
  HNF1B MUTATED HNF1B WILD-TYPE 
          50.37           32.09 
[1] "7.2 - 59.1 (50.4)"  "0.3 - 180.2 (32.1)"
[1] "hr=" "1.9"
D7V2, continuous
                 vv
clus              OMENTUM OVARY PERITONEUM OVARY
  HNF1B MUTATED         0     5                0
  HNF1B WILD-TYPE       2   457                1
D7V3, multiclass
                  clus
vv                 HNF1B MUTATED HNF1B 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, binary
                 cls
clus                0   1
  HNF1B MUTATED     5   0
  HNF1B WILD-TYPE 441   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1B MUTATED      5    0
  HNF1B WILD-TYPE  441    4
     clus
vv    HNF1B MUTATED HNF1B WILD-TYPE
  NO              5             441
  YES             0               4
[1] 2 2
[1] FALSE
D7V5, continuous
[1] "Remove cluster labels:" "HNF1B MUTATED"         
clus
  HNF1B MUTATED HNF1B WILD-TYPE 
              1              63 
     TCGA-04-1346      TCGA-04-1347      TCGA-04-1356      TCGA-04-1367 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-13-1404      TCGA-13-1405      TCGA-13-1409      TCGA-13-1410 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-13-1412      TCGA-13-1482      TCGA-13-1483      TCGA-13-1484 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-13-1488      TCGA-13-1489      TCGA-13-1491      TCGA-13-1492 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-13-1495      TCGA-13-1497      TCGA-13-1498      TCGA-13-1499 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-13-1501      TCGA-13-1504      TCGA-13-1506      TCGA-13-1507 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-13-1509      TCGA-13-1512      TCGA-13-2057      TCGA-13-2059 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-13-2060      TCGA-13-2061      TCGA-13-2066      TCGA-24-1614 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-61-2101      TCGA-10-0926      TCGA-13-0714      TCGA-13-0720 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-13-0724      TCGA-13-0755      TCGA-13-0760      TCGA-13-0762 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-13-0791      TCGA-13-0792      TCGA-13-0793      TCGA-13-0795 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-13-0801      TCGA-13-0802      TCGA-13-0885      TCGA-13-0887 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-13-0889      TCGA-13-0891      TCGA-13-0894      TCGA-13-0897 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-13-0900      TCGA-13-0901      TCGA-13-0903      TCGA-13-0905 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-13-0906      TCGA-13-0910      TCGA-13-0911      TCGA-13-0912 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-13-0913      TCGA-13-0919      TCGA-13-2071 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
                 vv
clus              R0 R1 R2
  HNF1B MUTATED    0  0  0
  HNF1B WILD-TYPE 13 22  1
D7V6, multiclass
D7V7, binary
                 cls
clus                0   1
  HNF1B MUTATED     0   3
  HNF1B WILD-TYPE   9 267
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1B MUTATED      0    3
  HNF1B WILD-TYPE    9  267
                        clus
vv                       HNF1B MUTATED HNF1B WILD-TYPE
  HISPANIC OR LATINO                 0               9
  NOT HISPANIC OR LATINO             3             267
[1] 2 2
[1] FALSE

Clustering(8) Variable = PTEN MUTATION ANALYSIS
D8V1, survival
                sevent
clus2              0   1
  PTEN MUTATED     2   3
  PTEN WILD-TYPE 192 265
  PTEN MUTATED PTEN WILD-TYPE 
             5            457 
  PTEN MUTATED PTEN WILD-TYPE 
             3            265 
$`PTEN MUTATED`
TCGA-13-1492 TCGA-61-1737 TCGA-61-1740 TCGA-61-1900 TCGA-10-0930 
      125.56        44.84         2.43         5.79        34.19 

$`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-09-1659 
       28.64        64.64        36.23        31.86        45.37         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 
       38.43        89.33        74.93        41.62        57.60        30.51 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 
       17.98         5.85         3.02         8.55        97.55         6.12 
TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 
       35.15       112.41        71.11        63.09        39.75        12.46 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
       77.10        81.17        28.54        83.31        55.23        57.27 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 
       81.01        17.46        32.35        54.64        87.06        61.71 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
       29.42       124.44        22.39        70.82        83.93        52.44 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 
       93.90        90.38         4.24       127.27        66.15       115.07 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       43.20        34.82        65.69        34.16        65.52        80.15 
TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 
       44.68        14.53        80.02        78.48        77.88        76.90 
TCGA-13-2065 TCGA-13-2066 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 
       65.52        70.13        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-23-1030 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        19.46        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-24-0970 
        4.70         4.50         4.44         3.81         7.63        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 
       21.80        41.56         7.66        22.32        54.12        63.55 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       47.41         6.31         6.38         7.82         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        0.76         6.25         6.02         5.95         5.36         4.83 
TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 
       17.39        18.64        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-24-2024 TCGA-24-2030 TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 
        4.87        58.16        55.92        28.18        44.52        57.07 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       36.16         0.79         0.36        47.54        31.63        70.45 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2298 
       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-25-1326 
       37.97        33.96         2.99        34.03        32.09        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-30-1862 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-61-1738 TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 TCGA-61-1901 
       48.79        35.80        33.67         1.45         8.42        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 TCGA-09-0364 TCGA-09-0366 
       22.22         6.35        31.07         8.61        29.16        57.76 
TCGA-09-0369 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0933 
       35.57        25.91        81.86        18.51        32.88        14.66 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
        6.71        35.44        19.99        20.91         6.21        24.59 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 
       44.55        39.58         2.73        31.20        15.19        17.82 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0765 
       55.17         2.50        11.54        38.01       111.78        45.67 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 TCGA-13-0801 
       40.24       118.42       107.28        20.35        87.48        45.99 
TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 
       51.02        35.28        13.61        68.94       107.18       111.39 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
      153.37        66.67        95.15       145.45       102.84        43.36 
TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       49.61        71.74        66.15       134.04        19.36       127.79 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       50.37       123.16       118.98       116.65        44.55        37.64 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 
      109.32        58.68        84.53        48.79        83.74        85.94 
TCGA-13-2071 
       25.41 

  PTEN MUTATED PTEN WILD-TYPE 
          2.43           0.26 
  PTEN MUTATED PTEN WILD-TYPE 
        125.56         180.20 
  PTEN MUTATED PTEN WILD-TYPE 
         34.19          32.35 
[1] "2.4 - 125.6 (34.2)" "0.3 - 180.2 (32.4)"
[1] "hr=" "1.1"
D8V2, continuous
                vv
clus             OMENTUM OVARY PERITONEUM OVARY
  PTEN MUTATED         0     5                0
  PTEN WILD-TYPE       2   457                1
D8V3, 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"
D8V4, binary
                cls
clus               0   1
  PTEN MUTATED     5   0
  PTEN WILD-TYPE 441   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      5    0
  PTEN WILD-TYPE  441    4
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO             5            441
  YES            0              4
[1] 2 2
[1] FALSE
D8V5, 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-13-1404     TCGA-13-1405     TCGA-13-1409     TCGA-13-1410 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-13-1412     TCGA-13-1482     TCGA-13-1483     TCGA-13-1484 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-13-1488     TCGA-13-1489     TCGA-13-1491     TCGA-13-1495 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-13-1497     TCGA-13-1498     TCGA-13-1499     TCGA-13-1501 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-13-1504     TCGA-13-1506     TCGA-13-1507     TCGA-13-1509 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-13-1512     TCGA-13-2057     TCGA-13-2059     TCGA-13-2060 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-13-2061     TCGA-13-2066     TCGA-24-1614     TCGA-61-2101 
"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-13-2071 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
                vv
clus             R0 R1 R2
  PTEN MUTATED    0  0  0
  PTEN WILD-TYPE 13 22  1
D8V6, multiclass
D8V7, 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(9) Variable = LARP1 MUTATION ANALYSIS
D9V1, survival
                 sevent
clus2               0   1
  LARP1 MUTATED     3   1
  LARP1 WILD-TYPE 191 267
  LARP1 MUTATED LARP1 WILD-TYPE 
              4             458 
  LARP1 MUTATED LARP1 WILD-TYPE 
              1             267 
$`LARP1 MUTATED`
TCGA-04-1338 TCGA-09-2050 TCGA-30-1718 TCGA-36-1577 
       46.62        71.11        51.91        25.74 

$`LARP1 WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 
       43.92        41.00        49.15         2.01        18.51        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1353 
       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-09-1659 TCGA-09-1661 
       64.64        36.23        31.86        45.37         9.99        38.43 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 TCGA-09-1670 
       89.33        74.93        41.62        57.60        30.51        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 
        5.85         3.02         8.55        97.55         6.12        35.15 
TCGA-09-2049 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 
      112.41        63.09        39.75        12.46        77.10        81.17 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
       28.54        83.31        55.23        57.27        81.01        17.46 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
       32.35        54.64        87.06        61.71        29.42       124.44 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       22.39        70.82        83.93        52.44       125.56        93.90 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 
       90.38         4.24       127.27        66.15       115.07        43.20 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 
       34.82        65.69        34.16        65.52        80.15        44.68 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 
       14.53        80.02        78.48        77.88        76.90        65.52 
TCGA-13-2066 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 
       70.13        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        19.46        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-24-0970 TCGA-24-0975 
        4.50         4.44         3.81         7.63        11.64        21.80 
TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 
       41.56         7.66        22.32        54.12        63.55        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 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 
       18.64        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-30-1853 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-36-1578 TCGA-36-1580 
       22.85        22.55         8.55        30.08        27.85        24.23 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 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 TCGA-09-0364 TCGA-09-0366 
       22.22         6.35        31.07         8.61        29.16        57.76 
TCGA-09-0369 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       35.57        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        38.01       111.78 
TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 
       45.67        40.24       118.42       107.28        20.35        87.48 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
       45.99        51.02        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 
      111.39       153.37        66.67        95.15       145.45       102.84 
TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
       43.36        49.61        71.74        66.15       134.04        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 
      127.79        50.37       123.16       118.98       116.65        44.55 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 
       37.64       109.32        58.68        84.53        48.79        83.74 
TCGA-13-0924 TCGA-13-2071 
       85.94        25.41 

  LARP1 MUTATED LARP1 WILD-TYPE 
          25.74            0.26 
  LARP1 MUTATED LARP1 WILD-TYPE 
          71.11          180.20 
  LARP1 MUTATED LARP1 WILD-TYPE 
         49.265          32.220 
[1] "25.7 - 71.1 (49.3)" "0.3 - 180.2 (32.2)"
[1] "hr=" "3.2"
D9V2, continuous
                 vv
clus              OMENTUM OVARY PERITONEUM OVARY
  LARP1 MUTATED         0     4                0
  LARP1 WILD-TYPE       2   458                1
D9V3, multiclass
                  clus
vv                 LARP1 MUTATED LARP1 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"
D9V4, binary
                 cls
clus                0   1
  LARP1 MUTATED     3   1
  LARP1 WILD-TYPE 443   3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP1 MUTATED      3    1
  LARP1 WILD-TYPE  443    3
     clus
vv    LARP1 MUTATED LARP1 WILD-TYPE
  NO              3             443
  YES             1               3
[1] 2 2
[1] FALSE
D9V5, continuous
                 vv
clus              R0 R1 R2
  LARP1 MUTATED    0  0  0
  LARP1 WILD-TYPE 13 22  1
D9V6, multiclass
D9V7, binary
                 cls
clus                0   1
  LARP1 MUTATED     0   3
  LARP1 WILD-TYPE   9 267
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP1 MUTATED      0    3
  LARP1 WILD-TYPE    9  267
                        clus
vv                       LARP1 MUTATED LARP1 WILD-TYPE
  HISPANIC OR LATINO                 0               9
  NOT HISPANIC OR LATINO             3             267
[1] 2 2
[1] FALSE

Clustering(10) Variable = BRCA2 MUTATION ANALYSIS
D10V1, survival
                 sevent
clus2               0   1
  BRCA2 MUTATED     8   5
  BRCA2 WILD-TYPE 186 263
  BRCA2 MUTATED BRCA2 WILD-TYPE 
             13             449 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
              5             263 
$`BRCA2 MUTATED`
TCGA-04-1331 TCGA-09-2050 TCGA-13-1481 TCGA-23-1030 TCGA-23-1120 TCGA-24-1103 
       43.92        71.11        87.06        29.13         4.27        54.12 
TCGA-24-1555 TCGA-29-1693 TCGA-29-1762 TCGA-61-1903 TCGA-13-0792 TCGA-13-0885 
       88.50       101.79        86.60        13.02       118.42       111.39 
TCGA-13-0890 
      145.45 

$`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-09-1659 TCGA-09-1661 
       64.64        36.23        31.86        45.37         9.99        38.43 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 TCGA-09-1670 
       89.33        74.93        41.62        57.60        30.51        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 
        5.85         3.02         8.55        97.55         6.12        35.15 
TCGA-09-2049 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-13-1403 TCGA-13-1404 
      112.41        63.09        39.75        12.46        77.10        81.17 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
       28.54        83.31        55.23        57.27        81.01        17.46 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 
       32.35        54.64        61.71        29.42       124.44        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       70.82        83.93        52.44       125.56        93.90        90.38 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 
        4.24       127.27        66.15       115.07        43.20        34.82 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 
       65.69        34.16        65.52        80.15        44.68        14.53 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2066 
       80.02        78.48        77.88        76.90        65.52        70.13 
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-23-1031 
       15.39        26.83        32.09        49.41         8.81        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-23-1122 TCGA-23-1123 
       19.46        33.30        86.01       129.96        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-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
        7.63        11.64        21.80        41.56         7.66        22.32 
TCGA-24-1104 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        18.64        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-24-1556 TCGA-24-1557 TCGA-24-1558 
       51.91        41.39        58.09        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-24-2024 TCGA-24-2030 TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 
        4.87        58.16        55.92        28.18        44.52        57.07 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       36.16         0.79         0.36        47.54        31.63        70.45 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2298 
       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-25-1326 
       37.97        33.96         2.99        34.03        32.09        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-29-1694 TCGA-29-1695 
       26.99        78.90        47.61        48.33        39.02        40.41 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 
       33.93        31.20        68.32        36.36        16.93        23.93 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 
       59.67        18.25        41.98        31.27        34.62        17.36 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 
       66.81        62.93        39.42        31.30        22.98        24.36 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 
       22.55        17.33        12.36        11.84        12.30        14.93 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 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-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 
       11.41         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 TCGA-09-0364 TCGA-09-0366 
       22.22         6.35        31.07         8.61        29.16        57.76 
TCGA-09-0369 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       35.57        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        38.01       111.78 
TCGA-13-0765 TCGA-13-0791 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 TCGA-13-0801 
       45.67        40.24       107.28        20.35        87.48        45.99 
TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 
       51.02        35.28        13.61        68.94       107.18       153.37 
TCGA-13-0887 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 
       66.67        95.15       102.84        43.36        49.61        71.74 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       66.15       134.04        19.36       127.79        50.37       123.16 
TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
      118.98       116.65        44.55        37.64       109.32        58.68 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       84.53        48.79        83.74        85.94        25.41 

  BRCA2 MUTATED BRCA2 WILD-TYPE 
           4.27            0.26 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
         145.45          180.20 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
          86.60           31.86 
[1] "4.3 - 145.4 (86.6)" "0.3 - 180.2 (31.9)"
[1] "hr=" "3.2"
D10V2, continuous
                 vv
clus              OMENTUM OVARY PERITONEUM OVARY
  BRCA2 MUTATED         0    13                0
  BRCA2 WILD-TYPE       2   449                1
D10V3, 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"
D10V4, binary
                 cls
clus                0   1
  BRCA2 MUTATED    13   0
  BRCA2 WILD-TYPE 433   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA2 MUTATED     13    0
  BRCA2 WILD-TYPE  433    4
     clus
vv    BRCA2 MUTATED BRCA2 WILD-TYPE
  NO             13             433
  YES             0               4
[1] 2 2
[1] FALSE
D10V5, 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-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-24-1614 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-61-2101      TCGA-10-0926      TCGA-13-0714      TCGA-13-0720 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-0724      TCGA-13-0755      TCGA-13-0760      TCGA-13-0762 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-0791      TCGA-13-0793      TCGA-13-0795      TCGA-13-0801 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-0802      TCGA-13-0887      TCGA-13-0889      TCGA-13-0891 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-0894      TCGA-13-0897      TCGA-13-0900      TCGA-13-0901 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-0903      TCGA-13-0904      TCGA-13-0905      TCGA-13-0906 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-0910      TCGA-13-0911      TCGA-13-0912      TCGA-13-0913 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-0919      TCGA-13-2071 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
                 vv
clus              R0 R1 R2
  BRCA2 MUTATED    0  0  0
  BRCA2 WILD-TYPE 13 22  1
D10V6, multiclass
D10V7, 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(11) Variable = EFEMP1 MUTATION ANALYSIS
D11V1, survival
                  sevent
clus2                0   1
  EFEMP1 MUTATED     3   4
  EFEMP1 WILD-TYPE 191 264
  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
               7              455 
  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
               4              264 
$`EFEMP1 MUTATED`
TCGA-09-1669 TCGA-13-1408 TCGA-24-1614 TCGA-36-1574 TCGA-61-1906 TCGA-61-1915 
       30.51        55.23        48.33        22.55        34.13        67.76 
TCGA-13-0887 
       66.67 

$`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-09-1659 
       28.64        64.64        36.23        31.86        45.37         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1670 
       38.43        89.33        74.93        41.62        57.60        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 
        5.85         3.02         8.55        97.55         6.12        35.15 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-13-1403 
      112.41        71.11        63.09        39.75        12.46        77.10 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
       81.17        28.54        83.31        57.27        81.01        17.46 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
       32.35        54.64        87.06        61.71        29.42       124.44 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       22.39        70.82        83.93        52.44       125.56        93.90 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 
       90.38         4.24       127.27        66.15       115.07        43.20 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 
       34.82        65.69        34.16        65.52        80.15        44.68 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 
       14.53        80.02        78.48        77.88        76.90        65.52 
TCGA-13-2066 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 
       70.13        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        19.46        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-24-0970 TCGA-24-0975 
        4.50         4.44         3.81         7.63        11.64        21.80 
TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 
       41.56         7.66        22.32        54.12        63.55        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 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 
       18.64        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-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 
       88.37        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-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 
       22.85         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-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 
       13.02         9.07        31.30        37.05        42.51        48.92 
TCGA-61-1914 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       56.61        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 TCGA-09-0364 TCGA-09-0366 TCGA-09-0369 TCGA-10-0926 
       31.07         8.61        29.16        57.76        35.57        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       81.86        18.51        34.19        32.88        14.66         6.71 
TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
       35.44        19.99        20.91         6.21        24.59        44.55 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
       39.58         2.73        31.20        15.19        17.82        55.17 
TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 
        2.50        11.54        38.01       111.78        45.67        40.24 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 
      118.42       107.28        20.35        87.48        45.99        51.02 
TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 
       35.28        13.61        68.94       107.18       111.39       153.37 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 
       95.15       145.45       102.84        43.36        49.61        71.74 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       66.15       134.04        19.36       127.79        50.37       123.16 
TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
      118.98       116.65        44.55        37.64       109.32        58.68 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       84.53        48.79        83.74        85.94        25.41 

  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
           22.55             0.26 
  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
           67.76           180.20 
  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
           48.33            32.09 
[1] "22.6 - 67.8 (48.3)" "0.3 - 180.2 (32.1)"
[1] "hr=" "1.3"
D11V2, continuous
                  vv
clus               OMENTUM OVARY PERITONEUM OVARY
  EFEMP1 MUTATED         0     7                0
  EFEMP1 WILD-TYPE       2   455                1
D11V3, 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"
D11V4, binary
                  cls
clus                 0   1
  EFEMP1 MUTATED     7   0
  EFEMP1 WILD-TYPE 439   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EFEMP1 MUTATED      7    0
  EFEMP1 WILD-TYPE  439    4
     clus
vv    EFEMP1 MUTATED EFEMP1 WILD-TYPE
  NO               7              439
  YES              0                4
[1] 2 2
[1] FALSE
D11V5, 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-13-1404       TCGA-13-1405       TCGA-13-1409       TCGA-13-1410 
"EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" 
      TCGA-13-1412       TCGA-13-1482       TCGA-13-1483       TCGA-13-1484 
"EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" 
      TCGA-13-1488       TCGA-13-1489       TCGA-13-1491       TCGA-13-1492 
"EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" 
      TCGA-13-1495       TCGA-13-1497       TCGA-13-1498       TCGA-13-1499 
"EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" 
      TCGA-13-1501       TCGA-13-1504       TCGA-13-1506       TCGA-13-1507 
"EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" 
      TCGA-13-1509       TCGA-13-1512       TCGA-13-2057       TCGA-13-2059 
"EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" 
      TCGA-13-2060       TCGA-13-2061       TCGA-13-2066       TCGA-61-2101 
"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-13-2071 
"EFEMP1 WILD-TYPE" "EFEMP1 WILD-TYPE" 
                  vv
clus               R0 R1 R2
  EFEMP1 MUTATED    0  0  0
  EFEMP1 WILD-TYPE 13 22  1
D11V6, multiclass
D11V7, 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(12) Variable = NRAS MUTATION ANALYSIS
D12V1, survival
                sevent
clus2              0   1
  NRAS MUTATED     2   2
  NRAS WILD-TYPE 192 266
  NRAS MUTATED NRAS WILD-TYPE 
             4            458 
  NRAS MUTATED NRAS WILD-TYPE 
             2            266 
$`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-09-1659 
       28.64        64.64        36.23        31.86        45.37         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 
       38.43        89.33        74.93        41.62        57.60        30.51 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 
       17.98         5.85         3.02         8.55        97.55         6.12 
TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 
       35.15       112.41        71.11        63.09        39.75        12.46 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
       77.10        81.17        28.54        83.31        55.23        57.27 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 
       81.01        17.46        32.35        54.64        87.06        61.71 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
       29.42       124.44        22.39        70.82        83.93        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
      125.56        93.90        90.38         4.24       127.27        66.15 
TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
      115.07        43.20        34.82        65.69        34.16        65.52 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
       80.15        44.68        14.53        80.02        78.48        77.88 
TCGA-13-2061 TCGA-13-2065 TCGA-13-2066 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
       76.90        65.52        70.13        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        19.46        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-23-2647 TCGA-23-2649 TCGA-24-0966 TCGA-24-0970 
        2.76         4.70         4.44         3.81         7.63        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 
       21.80        41.56         7.66        22.32        54.12        63.55 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       47.41         6.31         6.38         7.82         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        0.76         6.25         6.02         5.95         5.36         4.83 
TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 
       17.39        18.64        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-24-2024 TCGA-24-2030 TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 
        4.87        58.16        55.92        28.18        44.52        57.07 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       36.16         0.79         0.36        47.54        31.63        70.45 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2298 
       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-25-1326 
       37.97        33.96         2.99        34.03        32.09        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-30-1862 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-61-1903 TCGA-61-1904 TCGA-61-1906 
        8.42         5.79        11.41        13.02         9.07        34.13 
TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1914 TCGA-61-1915 TCGA-61-1919 
       31.30        37.05        42.51        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-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2097 
       39.85        30.64         4.77        51.72        71.74        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 TCGA-09-0364 TCGA-09-0366 
       22.22         6.35        31.07         8.61        29.16        57.76 
TCGA-09-0369 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       35.57        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        38.01       111.78 
TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 
       45.67        40.24       118.42       107.28        20.35        87.48 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
       45.99        51.02        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 
      111.39       153.37        66.67        95.15       145.45       102.84 
TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
       43.36        49.61        71.74        66.15       134.04        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 
      127.79        50.37       123.16       118.98       116.65        44.55 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 
       37.64       109.32        58.68        84.53        48.79        83.74 
TCGA-13-0924 TCGA-13-2071 
       85.94        25.41 

  NRAS MUTATED NRAS WILD-TYPE 
          1.18           0.26 
  NRAS MUTATED NRAS WILD-TYPE 
         61.64         180.20 
  NRAS MUTATED NRAS WILD-TYPE 
        26.710         32.435 
[1] "1.2 - 61.6 (26.7)"  "0.3 - 180.2 (32.4)"
[1] "hr=" "1"  
D12V2, continuous
                vv
clus             OMENTUM OVARY PERITONEUM OVARY
  NRAS MUTATED         0     4                0
  NRAS WILD-TYPE       2   458                1
D12V3, 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"
D12V4, binary
                cls
clus               0   1
  NRAS MUTATED     4   0
  NRAS WILD-TYPE 442   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      4    0
  NRAS WILD-TYPE  442    4
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  NO             4            442
  YES            0              4
[1] 2 2
[1] FALSE
D12V5, continuous
                vv
clus             R0 R1 R2
  NRAS MUTATED    0  0  0
  NRAS WILD-TYPE 13 22  1
D12V6, multiclass
D12V7, 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(13) Variable = MTA2 MUTATION ANALYSIS
D13V1, survival
                sevent
clus2              0   1
  MTA2 MUTATED     1   3
  MTA2 WILD-TYPE 193 265
  MTA2 MUTATED MTA2 WILD-TYPE 
             4            458 
  MTA2 MUTATED MTA2 WILD-TYPE 
             3            265 
$`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-09-1659 TCGA-09-1661 
       64.64        36.23        31.86        45.37         9.99        38.43 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 TCGA-09-1670 
       89.33        74.93        41.62        57.60        30.51        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 
        5.85         3.02         8.55        97.55         6.12        35.15 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-13-1403 
      112.41        71.11        63.09        39.75        12.46        77.10 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
       81.17        28.54        83.31        55.23        57.27        81.01 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
       17.46        32.35        54.64        87.06        61.71        29.42 
TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
      124.44        22.39        70.82        83.93        52.44       125.56 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 
       93.90        90.38         4.24       127.27        66.15       115.07 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       43.20        34.82        65.69        34.16        65.52        80.15 
TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 
       44.68        14.53        80.02        78.48        77.88        76.90 
TCGA-13-2065 TCGA-13-2066 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 
       65.52        70.13        23.05        25.94        26.20        27.52 
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        19.46        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-24-0970 TCGA-24-0975 
        4.50         4.44         3.81         7.63        11.64        21.80 
TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 
       41.56         7.66        22.32        54.12        63.55        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 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 
       18.64        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-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 
       19.99         2.96        29.03        31.00        26.99        78.90 
TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       47.61        48.33       101.79        39.02        40.41        33.93 
TCGA-29-1697 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-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 
       23.80        21.60        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 TCGA-09-0364 TCGA-09-0366 
       22.22         6.35        31.07         8.61        29.16        57.76 
TCGA-09-0369 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       35.57        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        38.01       111.78 
TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 
       45.67        40.24       118.42       107.28        20.35        87.48 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
       45.99        51.02        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 
      111.39       153.37        66.67        95.15       145.45       102.84 
TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
       43.36        49.61        71.74        66.15       134.04        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 
      127.79        50.37       123.16       118.98       116.65        44.55 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 
       37.64       109.32        58.68        84.53        48.79        83.74 
TCGA-13-0924 TCGA-13-2071 
       85.94        25.41 

  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         32.700 
[1] "2.2 - 42.0 (23.2)"  "0.3 - 180.2 (32.7)"
[1] "hr=" "2.8"
D13V2, continuous
                vv
clus             OMENTUM OVARY PERITONEUM OVARY
  MTA2 MUTATED         0     4                0
  MTA2 WILD-TYPE       2   458                1
D13V3, 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"
D13V4, binary
                cls
clus               0   1
  MTA2 MUTATED     4   0
  MTA2 WILD-TYPE 442   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTA2 MUTATED      4    0
  MTA2 WILD-TYPE  442    4
     clus
vv    MTA2 MUTATED MTA2 WILD-TYPE
  NO             4            442
  YES            0              4
[1] 2 2
[1] FALSE
D13V5, continuous
                vv
clus             R0 R1 R2
  MTA2 MUTATED    0  2  0
  MTA2 WILD-TYPE 13 20  1
D13V6, multiclass
[1] "Remove cluster labels:" "MTA2 MUTATED"          
clus
  MTA2 MUTATED MTA2 WILD-TYPE 
             2             34 
    TCGA-04-1516     TCGA-04-1644     TCGA-29-2427     TCGA-29-2429 
"MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" 
    TCGA-29-2431     TCGA-29-2432     TCGA-29-2434     TCGA-29-2436 
"MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" 
    TCGA-36-2530     TCGA-36-2532     TCGA-36-2534     TCGA-36-2537 
"MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" 
    TCGA-36-2538     TCGA-36-2540     TCGA-36-2542     TCGA-36-2544 
"MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" 
    TCGA-36-2545     TCGA-36-2547     TCGA-36-2548     TCGA-36-2551 
"MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" 
    TCGA-36-2552     TCGA-42-2582     TCGA-42-2587     TCGA-42-2588 
"MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" 
    TCGA-42-2589     TCGA-42-2590     TCGA-57-1993     TCGA-59-2363 
"MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" 
    TCGA-59-2372     TCGA-61-2612     TCGA-61-2613     TCGA-61-2614 
"MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" "MTA2 WILD-TYPE" 
    TCGA-13-0807     TCGA-13-0911 
"MTA2 WILD-TYPE" "MTA2 WILD-TYPE" 
D13V7, 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(14) Variable = ERCC6 MUTATION ANALYSIS
D14V1, survival
                 sevent
clus2               0   1
  ERCC6 MUTATED     2   2
  ERCC6 WILD-TYPE 192 266
  ERCC6 MUTATED ERCC6 WILD-TYPE 
              4             458 
  ERCC6 MUTATED ERCC6 WILD-TYPE 
              2             266 
$`ERCC6 MUTATED`
TCGA-04-1332 TCGA-24-1104 TCGA-29-1698 TCGA-61-2008 
       41.00        63.55        68.32        30.64 

$`ERCC6 WILD-TYPE`
TCGA-04-1331 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 TCGA-04-1343 
       43.92        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-09-1659 TCGA-09-1661 
       64.64        36.23        31.86        45.37         9.99        38.43 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 TCGA-09-1670 
       89.33        74.93        41.62        57.60        30.51        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 
        5.85         3.02         8.55        97.55         6.12        35.15 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-13-1403 
      112.41        71.11        63.09        39.75        12.46        77.10 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
       81.17        28.54        83.31        55.23        57.27        81.01 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
       17.46        32.35        54.64        87.06        61.71        29.42 
TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
      124.44        22.39        70.82        83.93        52.44       125.56 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 
       93.90        90.38         4.24       127.27        66.15       115.07 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       43.20        34.82        65.69        34.16        65.52        80.15 
TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 
       44.68        14.53        80.02        78.48        77.88        76.90 
TCGA-13-2065 TCGA-13-2066 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 
       65.52        70.13        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-23-1030 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        19.46        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-24-0970 
        4.70         4.50         4.44         3.81         7.63        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1105 
       21.80        41.56         7.66        22.32        54.12        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 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 
       18.64        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-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 
       33.93        31.20        36.36        16.93        23.93        59.67 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 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-61-2009 TCGA-61-2012 
        5.52        14.50        17.98         4.01        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 TCGA-09-0364 TCGA-09-0366 
       22.22         6.35        31.07         8.61        29.16        57.76 
TCGA-09-0369 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       35.57        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        38.01       111.78 
TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 
       45.67        40.24       118.42       107.28        20.35        87.48 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
       45.99        51.02        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 
      111.39       153.37        66.67        95.15       145.45       102.84 
TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
       43.36        49.61        71.74        66.15       134.04        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 
      127.79        50.37       123.16       118.98       116.65        44.55 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 
       37.64       109.32        58.68        84.53        48.79        83.74 
TCGA-13-0924 TCGA-13-2071 
       85.94        25.41 

  ERCC6 MUTATED ERCC6 WILD-TYPE 
          30.64            0.26 
  ERCC6 MUTATED ERCC6 WILD-TYPE 
          68.32          180.20 
  ERCC6 MUTATED ERCC6 WILD-TYPE 
         52.275          32.220 
[1] "30.6 - 68.3 (52.3)" "0.3 - 180.2 (32.2)"
[1] "hr=" "1.6"
D14V2, continuous
                 vv
clus              OMENTUM OVARY PERITONEUM OVARY
  ERCC6 MUTATED         0     4                0
  ERCC6 WILD-TYPE       2   458                1
D14V3, multiclass
                  clus
vv                 ERCC6 MUTATED ERCC6 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"
D14V4, binary
                 cls
clus                0   1
  ERCC6 MUTATED     4   0
  ERCC6 WILD-TYPE 442   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC6 MUTATED      4    0
  ERCC6 WILD-TYPE  442    4
     clus
vv    ERCC6 MUTATED ERCC6 WILD-TYPE
  NO              4             442
  YES             0               4
[1] 2 2
[1] FALSE
D14V5, continuous
                 vv
clus              R0 R1 R2
  ERCC6 MUTATED    0  0  0
  ERCC6 WILD-TYPE 13 22  1
D14V6, multiclass
D14V7, binary
                 cls
clus                0   1
  ERCC6 MUTATED     0   2
  ERCC6 WILD-TYPE   9 268
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC6 MUTATED      0    2
  ERCC6 WILD-TYPE    9  268
                        clus
vv                       ERCC6 MUTATED ERCC6 WILD-TYPE
  HISPANIC OR LATINO                 0               9
  NOT HISPANIC OR LATINO             2             268
[1] 2 2
[1] FALSE

Clustering(15) Variable = IL21R MUTATION ANALYSIS
D15V1, survival
                 sevent
clus2               0   1
  IL21R MUTATED     4   3
  IL21R WILD-TYPE 190 265
  IL21R MUTATED IL21R WILD-TYPE 
              7             455 
  IL21R MUTATED IL21R WILD-TYPE 
              3             265 
$`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-09-1659 
       28.64        64.64        36.23        31.86        45.37         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 
       38.43        89.33        74.93        41.62        57.60        30.51 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2045 
       17.98         5.85         3.02         8.55        97.55        35.15 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-13-1403 
      112.41        71.11        63.09        39.75        12.46        77.10 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
       81.17        28.54        83.31        55.23        57.27        81.01 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
       17.46        32.35        54.64        87.06        61.71        29.42 
TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
      124.44        22.39        70.82        83.93        52.44       125.56 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 
       93.90        90.38         4.24       127.27        66.15       115.07 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       43.20        34.82        65.69        34.16        65.52        80.15 
TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 
       44.68        14.53        80.02        78.48        77.88        76.90 
TCGA-13-2065 TCGA-13-2066 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 
       65.52        70.13        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-23-1030 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        19.46        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-24-0970 
        4.70         4.50         4.44         3.81         7.63        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 
       21.80        41.56         7.66        22.32        54.12        63.55 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1418 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-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 
       18.64        18.67        43.53         8.55        72.92        12.46 
TCGA-24-1466 TCGA-24-1469 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-24-1843 TCGA-24-1844 TCGA-24-1845 
       88.37        48.33        38.24         3.48         3.72         3.81 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 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-25-2399 TCGA-25-2400 
       49.05         1.02        38.04         3.02        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-29-2434 TCGA-29-2436 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1856 
       11.47         9.76        38.07        51.91        36.26        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-36-2547 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 
       20.98        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-61-1903 TCGA-61-1904 TCGA-61-1906 
        8.42         5.79        11.41        13.02         9.07        34.13 
TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 
       31.30        37.05        42.51        48.92        56.61        67.76 
TCGA-61-1919 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 TCGA-09-0364 TCGA-09-0366 TCGA-09-0369 TCGA-10-0926 TCGA-10-0927 
        8.61        29.16        57.76        35.57        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        38.01       111.78        45.67        40.24       118.42 
TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 
      107.28        20.35        87.48        45.99        51.02        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       111.39       153.37        66.67 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 
       95.15       145.45       102.84        43.36        49.61        71.74 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       66.15       134.04        19.36       127.79        50.37       123.16 
TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
      118.98       116.65        44.55        37.64       109.32        58.68 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       84.53        48.79        83.74        85.94        25.41 

  IL21R MUTATED IL21R WILD-TYPE 
           2.47            0.26 
  IL21R MUTATED IL21R WILD-TYPE 
          45.01          180.20 
  IL21R MUTATED IL21R WILD-TYPE 
           8.32           33.01 
[1] "2.5 - 45.0 (8.3)"   "0.3 - 180.2 (33.0)"
[1] "hr=" "2.4"
D15V2, continuous
                 vv
clus              OMENTUM OVARY PERITONEUM OVARY
  IL21R MUTATED         0     8                0
  IL21R WILD-TYPE       2   454                1
D15V3, 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"
D15V4, binary
                 cls
clus                0   1
  IL21R MUTATED     7   0
  IL21R WILD-TYPE 439   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL21R MUTATED      7    0
  IL21R WILD-TYPE  439    4
     clus
vv    IL21R MUTATED IL21R WILD-TYPE
  NO              7             439
  YES             0               4
[1] 2 2
[1] FALSE
D15V5, continuous
                 vv
clus              R0 R1 R2
  IL21R MUTATED    1  1  0
  IL21R WILD-TYPE 12 21  1
D15V6, 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-29-2427 
"IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" 
     TCGA-29-2429      TCGA-29-2431      TCGA-29-2434      TCGA-29-2436 
"IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" 
     TCGA-36-2530      TCGA-36-2532      TCGA-36-2534      TCGA-36-2537 
"IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" 
     TCGA-36-2538      TCGA-36-2540      TCGA-36-2542      TCGA-36-2543 
"IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" 
     TCGA-36-2544      TCGA-36-2547      TCGA-36-2548      TCGA-36-2551 
"IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" 
     TCGA-36-2552      TCGA-42-2582      TCGA-42-2587      TCGA-42-2588 
"IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" 
     TCGA-42-2589      TCGA-42-2590      TCGA-57-1993      TCGA-59-2363 
"IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" 
     TCGA-59-2372      TCGA-61-2612      TCGA-61-2613      TCGA-61-2614 
"IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" "IL21R WILD-TYPE" 
     TCGA-13-0807      TCGA-13-0911 
"IL21R WILD-TYPE" "IL21R WILD-TYPE" 
D15V7, 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(16) Variable = PKD1L1 MUTATION ANALYSIS
D16V1, survival
                  sevent
clus2                0   1
  PKD1L1 MUTATED     3   3
  PKD1L1 WILD-TYPE 191 265
  PKD1L1 MUTATED PKD1L1 WILD-TYPE 
               6              456 
  PKD1L1 MUTATED PKD1L1 WILD-TYPE 
               3              265 
$`PKD1L1 MUTATED`
TCGA-04-1362 TCGA-13-1509 TCGA-23-1120 TCGA-24-1544 TCGA-25-2400 TCGA-13-0923 
       44.32        80.15         4.27        26.96        42.02        83.74 

$`PKD1L1 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-04-1364 TCGA-04-1365 TCGA-04-1367 
        0.53        49.28        32.52        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-09-1659 TCGA-09-1661 
       64.64        36.23        31.86        45.37         9.99        38.43 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 TCGA-09-1670 
       89.33        74.93        41.62        57.60        30.51        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 
        5.85         3.02         8.55        97.55         6.12        35.15 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-13-1403 
      112.41        71.11        63.09        39.75        12.46        77.10 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
       81.17        28.54        83.31        55.23        57.27        81.01 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
       17.46        32.35        54.64        87.06        61.71        29.42 
TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
      124.44        22.39        70.82        83.93        52.44       125.56 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 
       93.90        90.38         4.24       127.27        66.15       115.07 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1510 
       43.20        34.82        65.69        34.16        65.52        44.68 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 
       14.53        80.02        78.48        77.88        76.90        65.52 
TCGA-13-2066 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 
       70.13        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        19.46        33.30        86.01       129.96 
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-24-0970 TCGA-24-0975 TCGA-24-0979 
        4.44         3.81         7.63        11.64        21.80        41.56 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 
        7.66        22.32        54.12        63.55        47.41         6.31 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 
        6.38         7.82         7.99         7.86         0.76         6.25 
TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 
        6.02         5.95         5.36         4.83        17.39        18.64 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 
       18.67        43.53         8.55        72.92        12.46        45.14 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1545 TCGA-24-1546 
        9.11         3.45         1.18        22.22        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-25-2401 
        1.02        38.04         3.02        45.01        19.99         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-36-1574 
        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 TCGA-09-0364 TCGA-09-0366 TCGA-09-0369 
        6.35        31.07         8.61        29.16        57.76        35.57 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 
       25.91        81.86        18.51        34.19        32.88        14.66 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
        6.71        35.44        19.99        20.91         6.21        24.59 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 
       44.55        39.58         2.73        31.20        15.19        17.82 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0765 
       55.17         2.50        11.54        38.01       111.78        45.67 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 TCGA-13-0801 
       40.24       118.42       107.28        20.35        87.48        45.99 
TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 
       51.02        35.28        13.61        68.94       107.18       111.39 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
      153.37        66.67        95.15       145.45       102.84        43.36 
TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       49.61        71.74        66.15       134.04        19.36       127.79 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       50.37       123.16       118.98       116.65        44.55        37.64 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0924 TCGA-13-2071 
      109.32        58.68        84.53        48.79        85.94        25.41 

  PKD1L1 MUTATED PKD1L1 WILD-TYPE 
            4.27             0.26 
  PKD1L1 MUTATED PKD1L1 WILD-TYPE 
           83.74           180.20 
  PKD1L1 MUTATED PKD1L1 WILD-TYPE 
           43.17            32.22 
[1] "4.3 - 83.7 (43.2)"  "0.3 - 180.2 (32.2)"
[1] "hr=" "1.5"
D16V2, continuous
                  vv
clus               OMENTUM OVARY PERITONEUM OVARY
  PKD1L1 MUTATED         0     6                0
  PKD1L1 WILD-TYPE       2   456                1
D16V3, multiclass
                  clus
vv                 PKD1L1 MUTATED PKD1L1 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, binary
                  cls
clus                 0   1
  PKD1L1 MUTATED     6   0
  PKD1L1 WILD-TYPE 440   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PKD1L1 MUTATED      6    0
  PKD1L1 WILD-TYPE  440    4
     clus
vv    PKD1L1 MUTATED PKD1L1 WILD-TYPE
  NO               6              440
  YES              0                4
[1] 2 2
[1] FALSE
D16V5, continuous
[1] "Remove cluster labels:" "PKD1L1 MUTATED"        
clus
  PKD1L1 MUTATED PKD1L1 WILD-TYPE 
               1               63 
      TCGA-04-1346       TCGA-04-1347       TCGA-04-1356       TCGA-04-1367 
"PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" 
      TCGA-13-1404       TCGA-13-1405       TCGA-13-1409       TCGA-13-1410 
"PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" 
      TCGA-13-1412       TCGA-13-1482       TCGA-13-1483       TCGA-13-1484 
"PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" 
      TCGA-13-1488       TCGA-13-1489       TCGA-13-1491       TCGA-13-1492 
"PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" 
      TCGA-13-1495       TCGA-13-1497       TCGA-13-1498       TCGA-13-1499 
"PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" 
      TCGA-13-1501       TCGA-13-1504       TCGA-13-1506       TCGA-13-1507 
"PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" 
      TCGA-13-1512       TCGA-13-2057       TCGA-13-2059       TCGA-13-2060 
"PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" 
      TCGA-13-2061       TCGA-13-2066       TCGA-24-1614       TCGA-61-2101 
"PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" 
      TCGA-10-0926       TCGA-13-0714       TCGA-13-0720       TCGA-13-0724 
"PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" 
      TCGA-13-0755       TCGA-13-0760       TCGA-13-0762       TCGA-13-0791 
"PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" 
      TCGA-13-0792       TCGA-13-0793       TCGA-13-0795       TCGA-13-0801 
"PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" 
      TCGA-13-0802       TCGA-13-0885       TCGA-13-0887       TCGA-13-0889 
"PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" 
      TCGA-13-0891       TCGA-13-0894       TCGA-13-0897       TCGA-13-0900 
"PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" 
      TCGA-13-0901       TCGA-13-0903       TCGA-13-0904       TCGA-13-0905 
"PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" 
      TCGA-13-0906       TCGA-13-0910       TCGA-13-0911       TCGA-13-0912 
"PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" 
      TCGA-13-0913       TCGA-13-0919       TCGA-13-2071 
"PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" "PKD1L1 WILD-TYPE" 
                  vv
clus               R0 R1 R2
  PKD1L1 MUTATED    0  0  0
  PKD1L1 WILD-TYPE 13 22  1
D16V6, multiclass
D16V7, binary
                  cls
clus                 0   1
  PKD1L1 MUTATED     0   4
  PKD1L1 WILD-TYPE   9 266
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PKD1L1 MUTATED      0    4
  PKD1L1 WILD-TYPE    9  266
                        clus
vv                       PKD1L1 MUTATED PKD1L1 WILD-TYPE
  HISPANIC OR LATINO                  0                9
  NOT HISPANIC OR LATINO              4              266
[1] 2 2
[1] FALSE

Clustering(17) Variable = SAMD9L MUTATION ANALYSIS
D17V1, survival
                  sevent
clus2                0   1
  SAMD9L MUTATED     4   5
  SAMD9L WILD-TYPE 190 263
  SAMD9L MUTATED SAMD9L WILD-TYPE 
               9              453 
  SAMD9L MUTATED SAMD9L WILD-TYPE 
               5              263 
$`SAMD9L MUTATED`
TCGA-20-1682 TCGA-24-1845 TCGA-24-1850 TCGA-25-1625 TCGA-25-2400 TCGA-30-1891 
       27.52         3.81         5.52        27.62        42.02        30.05 
TCGA-36-2543 TCGA-36-2544 TCGA-10-0927 
        2.24        20.98        81.86 

$`SAMD9L 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-09-1659 
       28.64        64.64        36.23        31.86        45.37         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 
       38.43        89.33        74.93        41.62        57.60        30.51 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 
       17.98         5.85         3.02         8.55        97.55         6.12 
TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 
       35.15       112.41        71.11        63.09        39.75        12.46 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
       77.10        81.17        28.54        83.31        55.23        57.27 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 
       81.01        17.46        32.35        54.64        87.06        61.71 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
       29.42       124.44        22.39        70.82        83.93        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
      125.56        93.90        90.38         4.24       127.27        66.15 
TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
      115.07        43.20        34.82        65.69        34.16        65.52 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
       80.15        44.68        14.53        80.02        78.48        77.88 
TCGA-13-2061 TCGA-13-2065 TCGA-13-2066 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
       76.90        65.52        70.13        23.05        25.94        26.20 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 
       25.38        19.10        16.70         2.93         2.66        47.54 
TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       49.68        40.54        15.39        26.83        32.09        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1107 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        19.46        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-24-0970 
        4.70         4.50         4.44         3.81         7.63        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 
       21.80        41.56         7.66        22.32        54.12        63.55 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       47.41         6.31         6.38         7.82         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        0.76         6.25         6.02         5.95         5.36         4.83 
TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 
       17.39        18.64        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-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-2019 TCGA-24-2024 
        3.72         4.37        11.28         5.79         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-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
       18.58        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-25-2401 
        1.02        38.04         3.02        45.01        19.99         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-31-1950 TCGA-31-1953 TCGA-31-1959 
       15.68         0.26         6.12        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-36-2545 
       29.82        25.91        25.08        23.80        21.60        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 
TCGA-09-0364 TCGA-09-0366 TCGA-09-0369 TCGA-10-0926 TCGA-10-0928 TCGA-10-0930 
       29.16        57.76        35.57        25.91        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        38.01 
TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 
      111.78        45.67        40.24       118.42       107.28        20.35 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 
       87.48        45.99        51.02        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       111.39       153.37        66.67        95.15       145.45 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
      102.84        43.36        49.61        71.74        66.15       134.04 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 
       19.36       127.79        50.37       123.16       118.98       116.65 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       44.55        37.64       109.32        58.68        84.53        48.79 
TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       83.74        85.94        25.41 

  SAMD9L MUTATED SAMD9L WILD-TYPE 
            2.24             0.26 
  SAMD9L MUTATED SAMD9L WILD-TYPE 
           81.86           180.20 
  SAMD9L MUTATED SAMD9L WILD-TYPE 
           27.52            33.01 
[1] "2.2 - 81.9 (27.5)"  "0.3 - 180.2 (33.0)"
[1] "hr=" "1.6"
D17V2, continuous
                  vv
clus               OMENTUM OVARY PERITONEUM OVARY
  SAMD9L MUTATED         0     9                0
  SAMD9L WILD-TYPE       2   453                1
D17V3, multiclass
                  clus
vv                 SAMD9L MUTATED SAMD9L 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"
D17V4, binary
                  cls
clus                 0   1
  SAMD9L MUTATED     9   0
  SAMD9L WILD-TYPE 437   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD9L MUTATED      9    0
  SAMD9L WILD-TYPE  437    4
     clus
vv    SAMD9L MUTATED SAMD9L WILD-TYPE
  NO               9              437
  YES              0                4
[1] 2 2
[1] FALSE
D17V5, continuous
                  vv
clus               R0 R1 R2
  SAMD9L MUTATED    0  2  0
  SAMD9L WILD-TYPE 13 20  1
D17V6, multiclass
[1] "Remove cluster labels:" "SAMD9L MUTATED"        
clus
  SAMD9L MUTATED SAMD9L WILD-TYPE 
               2               34 
      TCGA-04-1369       TCGA-04-1516       TCGA-04-1644       TCGA-29-2427 
"SAMD9L WILD-TYPE" "SAMD9L WILD-TYPE" "SAMD9L WILD-TYPE" "SAMD9L WILD-TYPE" 
      TCGA-29-2429       TCGA-29-2431       TCGA-29-2432       TCGA-29-2434 
"SAMD9L WILD-TYPE" "SAMD9L WILD-TYPE" "SAMD9L WILD-TYPE" "SAMD9L WILD-TYPE" 
      TCGA-29-2436       TCGA-36-2530       TCGA-36-2532       TCGA-36-2534 
"SAMD9L WILD-TYPE" "SAMD9L WILD-TYPE" "SAMD9L WILD-TYPE" "SAMD9L WILD-TYPE" 
      TCGA-36-2537       TCGA-36-2538       TCGA-36-2540       TCGA-36-2542 
"SAMD9L WILD-TYPE" "SAMD9L WILD-TYPE" "SAMD9L WILD-TYPE" "SAMD9L WILD-TYPE" 
      TCGA-36-2545       TCGA-36-2547       TCGA-36-2548       TCGA-36-2551 
"SAMD9L WILD-TYPE" "SAMD9L WILD-TYPE" "SAMD9L WILD-TYPE" "SAMD9L WILD-TYPE" 
      TCGA-36-2552       TCGA-42-2582       TCGA-42-2587       TCGA-42-2588 
"SAMD9L WILD-TYPE" "SAMD9L WILD-TYPE" "SAMD9L WILD-TYPE" "SAMD9L WILD-TYPE" 
      TCGA-42-2589       TCGA-42-2590       TCGA-57-1993       TCGA-59-2363 
"SAMD9L WILD-TYPE" "SAMD9L WILD-TYPE" "SAMD9L WILD-TYPE" "SAMD9L WILD-TYPE" 
      TCGA-59-2372       TCGA-61-2612       TCGA-61-2613       TCGA-61-2614 
"SAMD9L WILD-TYPE" "SAMD9L WILD-TYPE" "SAMD9L WILD-TYPE" "SAMD9L WILD-TYPE" 
      TCGA-13-0807       TCGA-13-0911 
"SAMD9L WILD-TYPE" "SAMD9L WILD-TYPE" 
D17V7, binary
                  cls
clus                 0   1
  SAMD9L MUTATED     1   4
  SAMD9L WILD-TYPE   8 266
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD9L MUTATED      1    4
  SAMD9L WILD-TYPE    8  266
                        clus
vv                       SAMD9L MUTATED SAMD9L WILD-TYPE
  HISPANIC OR LATINO                  1                8
  NOT HISPANIC OR LATINO              4              266
[1] 2 2
[1] FALSE

Clustering(18) Variable = AQP2 MUTATION ANALYSIS
D18V1, survival
                sevent
clus2              0   1
  AQP2 MUTATED     2   1
  AQP2 WILD-TYPE 192 267
  AQP2 MUTATED AQP2 WILD-TYPE 
             3            459 
  AQP2 MUTATED AQP2 WILD-TYPE 
             1            267 
$`AQP2 MUTATED`
TCGA-09-2049 TCGA-29-1695 TCGA-42-2587 
      112.41        40.41        23.74 

$`AQP2 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-09-1659 
       28.64        64.64        36.23        31.86        45.37         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 
       38.43        89.33        74.93        41.62        57.60        30.51 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 
       17.98         5.85         3.02         8.55        97.55         6.12 
TCGA-09-2045 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-13-1403 
       35.15        71.11        63.09        39.75        12.46        77.10 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
       81.17        28.54        83.31        55.23        57.27        81.01 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
       17.46        32.35        54.64        87.06        61.71        29.42 
TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
      124.44        22.39        70.82        83.93        52.44       125.56 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 
       93.90        90.38         4.24       127.27        66.15       115.07 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       43.20        34.82        65.69        34.16        65.52        80.15 
TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 
       44.68        14.53        80.02        78.48        77.88        76.90 
TCGA-13-2065 TCGA-13-2066 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 
       65.52        70.13        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-23-1030 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        19.46        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-24-0970 
        4.70         4.50         4.44         3.81         7.63        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 
       21.80        41.56         7.66        22.32        54.12        63.55 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       47.41         6.31         6.38         7.82         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        0.76         6.25         6.02         5.95         5.36         4.83 
TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 
       17.39        18.64        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-24-2024 TCGA-24-2030 TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 
        4.87        58.16        55.92        28.18        44.52        57.07 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       36.16         0.79         0.36        47.54        31.63        70.45 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2298 
       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-25-1326 
       37.97        33.96         2.99        34.03        32.09        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-29-1696 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-42-2588 
       20.52        14.17        16.18        11.47        47.57        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 TCGA-61-2614 TCGA-09-0364 
      125.75        22.22         6.35        31.07         8.61        29.16 
TCGA-09-0366 TCGA-09-0369 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       57.76        35.57        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        38.01 
TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 
      111.78        45.67        40.24       118.42       107.28        20.35 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 
       87.48        45.99        51.02        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       111.39       153.37        66.67        95.15       145.45 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
      102.84        43.36        49.61        71.74        66.15       134.04 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 
       19.36       127.79        50.37       123.16       118.98       116.65 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       44.55        37.64       109.32        58.68        84.53        48.79 
TCGA-13-0923 TCGA-13-0924 TCGA-13-2071 
       83.74        85.94        25.41 

  AQP2 MUTATED AQP2 WILD-TYPE 
         23.74           0.26 
  AQP2 MUTATED AQP2 WILD-TYPE 
        112.41         180.20 
  AQP2 MUTATED AQP2 WILD-TYPE 
         40.41          32.35 
[1] "23.7 - 112.4 (40.4)" "0.3 - 180.2 (32.4)" 
[1] "hr=" "2.6"
D18V2, continuous
                vv
clus             OMENTUM OVARY PERITONEUM OVARY
  AQP2 MUTATED         0     3                0
  AQP2 WILD-TYPE       2   459                1
D18V3, multiclass
                  clus
vv                 AQP2 MUTATED AQP2 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"
D18V4, binary
                cls
clus               0   1
  AQP2 MUTATED     3   0
  AQP2 WILD-TYPE 443   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  AQP2 MUTATED      3    0
  AQP2 WILD-TYPE  443    4
     clus
vv    AQP2 MUTATED AQP2 WILD-TYPE
  NO             3            443
  YES            0              4
[1] 2 2
[1] FALSE
D18V5, continuous
                vv
clus             R0 R1 R2
  AQP2 MUTATED    0  1  0
  AQP2 WILD-TYPE 13 21  1
D18V6, multiclass
[1] "Remove cluster labels:" "AQP2 MUTATED"          
clus
  AQP2 MUTATED AQP2 WILD-TYPE 
             1             35 
    TCGA-04-1369     TCGA-04-1516     TCGA-04-1644     TCGA-29-2427 
"AQP2 WILD-TYPE" "AQP2 WILD-TYPE" "AQP2 WILD-TYPE" "AQP2 WILD-TYPE" 
    TCGA-29-2429     TCGA-29-2431     TCGA-29-2432     TCGA-29-2434 
"AQP2 WILD-TYPE" "AQP2 WILD-TYPE" "AQP2 WILD-TYPE" "AQP2 WILD-TYPE" 
    TCGA-29-2436     TCGA-36-2530     TCGA-36-2532     TCGA-36-2534 
"AQP2 WILD-TYPE" "AQP2 WILD-TYPE" "AQP2 WILD-TYPE" "AQP2 WILD-TYPE" 
    TCGA-36-2537     TCGA-36-2538     TCGA-36-2540     TCGA-36-2542 
"AQP2 WILD-TYPE" "AQP2 WILD-TYPE" "AQP2 WILD-TYPE" "AQP2 WILD-TYPE" 
    TCGA-36-2543     TCGA-36-2544     TCGA-36-2545     TCGA-36-2547 
"AQP2 WILD-TYPE" "AQP2 WILD-TYPE" "AQP2 WILD-TYPE" "AQP2 WILD-TYPE" 
    TCGA-36-2548     TCGA-36-2551     TCGA-36-2552     TCGA-42-2582 
"AQP2 WILD-TYPE" "AQP2 WILD-TYPE" "AQP2 WILD-TYPE" "AQP2 WILD-TYPE" 
    TCGA-42-2588     TCGA-42-2589     TCGA-42-2590     TCGA-57-1993 
"AQP2 WILD-TYPE" "AQP2 WILD-TYPE" "AQP2 WILD-TYPE" "AQP2 WILD-TYPE" 
    TCGA-59-2363     TCGA-59-2372     TCGA-61-2612     TCGA-61-2613 
"AQP2 WILD-TYPE" "AQP2 WILD-TYPE" "AQP2 WILD-TYPE" "AQP2 WILD-TYPE" 
    TCGA-61-2614     TCGA-13-0807     TCGA-13-0911 
"AQP2 WILD-TYPE" "AQP2 WILD-TYPE" "AQP2 WILD-TYPE" 
D18V7, binary
                cls
clus               0   1
  AQP2 MUTATED     0   2
  AQP2 WILD-TYPE   9 268
[1] "tbl2"
                cls
clus             [,1] [,2]
  AQP2 MUTATED      0    2
  AQP2 WILD-TYPE    9  268
                        clus
vv                       AQP2 MUTATED AQP2 WILD-TYPE
  HISPANIC OR LATINO                0              9
  NOT HISPANIC OR LATINO            2            268
[1] 2 2
[1] FALSE

Clustering(19) Variable = CREBBP MUTATION ANALYSIS
D19V1, survival
                  sevent
clus2                0   1
  CREBBP MUTATED     3   8
  CREBBP WILD-TYPE 191 260
  CREBBP MUTATED CREBBP WILD-TYPE 
              11              451 
  CREBBP MUTATED CREBBP WILD-TYPE 
               8              260 
$`CREBBP MUTATED`
TCGA-04-1338 TCGA-04-1350 TCGA-04-1525 TCGA-24-0966 TCGA-25-1631 TCGA-29-1699 
       46.62        63.98        38.37         7.63         0.30        36.36 
TCGA-29-1703 TCGA-29-1705 TCGA-31-1950 TCGA-61-1740 TCGA-13-0724 
       59.67        18.25        18.77         2.43         2.73 

$`CREBBP WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 
       43.92        41.00        49.15         2.01        18.51        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1353 TCGA-04-1356 
       65.52        63.09        48.76        21.57         0.53        49.28 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1369 
       32.52        44.32        33.67        76.57       103.40        21.11 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1530 TCGA-04-1542 
       56.55        41.59        19.99         0.79       119.08        84.20 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 
       55.43        48.89        27.88        28.64        64.64        36.23 
TCGA-04-1652 TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       31.86        45.37         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-13-1403 TCGA-13-1404 TCGA-13-1405 
       63.09        39.75        12.46        77.10        81.17        28.54 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
       83.31        55.23        57.27        81.01        17.46        32.35 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 
       54.64        87.06        61.71        29.42       124.44        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       70.82        83.93        52.44       125.56        93.90        90.38 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 
        4.24       127.27        66.15       115.07        43.20        34.82 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 
       65.69        34.16        65.52        80.15        44.68        14.53 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2066 
       80.02        78.48        77.88        76.90        65.52        70.13 
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        19.46        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-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        4.44         3.81        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        18.64        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-25-1632 
       27.62        17.03        12.95        20.61        38.20        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-29-1701 TCGA-29-1702 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 
       16.93        23.93        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-31-1953 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
       30.05         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-61-1741 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 
       35.80        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 TCGA-09-0364 TCGA-09-0366 
       22.22         6.35        31.07         8.61        29.16        57.76 
TCGA-09-0369 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       35.57        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-13-0726 TCGA-13-0727 TCGA-13-0730 
       24.59        44.55        39.58        31.20        15.19        17.82 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0765 
       55.17         2.50        11.54        38.01       111.78        45.67 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 TCGA-13-0801 
       40.24       118.42       107.28        20.35        87.48        45.99 
TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 
       51.02        35.28        13.61        68.94       107.18       111.39 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
      153.37        66.67        95.15       145.45       102.84        43.36 
TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       49.61        71.74        66.15       134.04        19.36       127.79 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       50.37       123.16       118.98       116.65        44.55        37.64 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 
      109.32        58.68        84.53        48.79        83.74        85.94 
TCGA-13-2071 
       25.41 

  CREBBP MUTATED CREBBP WILD-TYPE 
            0.30             0.26 
  CREBBP MUTATED CREBBP WILD-TYPE 
           63.98           180.20 
  CREBBP MUTATED CREBBP WILD-TYPE 
           18.77            32.52 
[1] "0.3 - 64.0 (18.8)"  "0.3 - 180.2 (32.5)"
[1] "hr=" "1.9"
D19V2, continuous
                  vv
clus               OMENTUM OVARY PERITONEUM OVARY
  CREBBP MUTATED         0    11                0
  CREBBP WILD-TYPE       2   451                1
D19V3, multiclass
                  clus
vv                 CREBBP MUTATED CREBBP WILD-TYPE
  OMENTUM                       0                2
  OVARY                        11              451
  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, binary
                  cls
clus                 0   1
  CREBBP MUTATED    10   0
  CREBBP WILD-TYPE 436   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED     10    0
  CREBBP WILD-TYPE  436    4
     clus
vv    CREBBP MUTATED CREBBP WILD-TYPE
  NO              10              436
  YES              0                4
[1] 2 2
[1] FALSE
D19V5, continuous
[1] "Remove cluster labels:" "CREBBP MUTATED"        
clus
  CREBBP MUTATED CREBBP WILD-TYPE 
               1               63 
      TCGA-04-1346       TCGA-04-1347       TCGA-04-1356       TCGA-04-1367 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-13-1404       TCGA-13-1405       TCGA-13-1409       TCGA-13-1410 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-13-1412       TCGA-13-1482       TCGA-13-1483       TCGA-13-1484 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-13-1488       TCGA-13-1489       TCGA-13-1491       TCGA-13-1492 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-13-1495       TCGA-13-1497       TCGA-13-1498       TCGA-13-1499 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-13-1501       TCGA-13-1504       TCGA-13-1506       TCGA-13-1507 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-13-1509       TCGA-13-1512       TCGA-13-2057       TCGA-13-2059 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-13-2060       TCGA-13-2061       TCGA-13-2066       TCGA-24-1614 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-61-2101       TCGA-10-0926       TCGA-13-0714       TCGA-13-0720 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-13-0755       TCGA-13-0760       TCGA-13-0762       TCGA-13-0791 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-13-0792       TCGA-13-0793       TCGA-13-0795       TCGA-13-0801 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-13-0802       TCGA-13-0885       TCGA-13-0887       TCGA-13-0889 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-13-0891       TCGA-13-0894       TCGA-13-0897       TCGA-13-0900 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-13-0901       TCGA-13-0903       TCGA-13-0904       TCGA-13-0905 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-13-0906       TCGA-13-0910       TCGA-13-0911       TCGA-13-0912 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
      TCGA-13-0913       TCGA-13-0919       TCGA-13-2071 
"CREBBP WILD-TYPE" "CREBBP WILD-TYPE" "CREBBP WILD-TYPE" 
                  vv
clus               R0 R1 R2
  CREBBP MUTATED    0  0  0
  CREBBP WILD-TYPE 13 22  1
D19V6, multiclass
D19V7, binary
                  cls
clus                 0   1
  CREBBP MUTATED     1   6
  CREBBP WILD-TYPE   8 264
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED      1    6
  CREBBP WILD-TYPE    8  264
                        clus
vv                       CREBBP MUTATED CREBBP WILD-TYPE
  HISPANIC OR LATINO                  1                8
  NOT HISPANIC OR LATINO              6              264
[1] 2 2
[1] FALSE

Clustering(20) Variable = C9ORF171 MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  C9ORF171 MUTATED     2   3
  C9ORF171 WILD-TYPE 192 265
  C9ORF171 MUTATED C9ORF171 WILD-TYPE 
                 5                457 
  C9ORF171 MUTATED C9ORF171 WILD-TYPE 
                 3                265 
$`C9ORF171 MUTATED`
TCGA-13-1404 TCGA-13-1408 TCGA-13-1412 TCGA-24-2035 TCGA-13-0793 
       81.17        55.23        32.35        28.18       107.28 

$`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-09-1659 
       28.64        64.64        36.23        31.86        45.37         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 
       38.43        89.33        74.93        41.62        57.60        30.51 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 
       17.98         5.85         3.02         8.55        97.55         6.12 
TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 
       35.15       112.41        71.11        63.09        39.75        12.46 
TCGA-13-1403 TCGA-13-1405 TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
       77.10        28.54        83.31        57.27        81.01        17.46 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 
       54.64        87.06        61.71        29.42       124.44        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       70.82        83.93        52.44       125.56        93.90        90.38 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 
        4.24       127.27        66.15       115.07        43.20        34.82 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 
       65.69        34.16        65.52        80.15        44.68        14.53 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2066 
       80.02        78.48        77.88        76.90        65.52        70.13 
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        19.46        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-24-0970 TCGA-24-0975 TCGA-24-0979 
        4.44         3.81         7.63        11.64        21.80        41.56 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 
        7.66        22.32        54.12        63.55        47.41         6.31 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 
        6.38         7.82         7.99         7.86         0.76         6.25 
TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 
        6.02         5.95         5.36         4.83        17.39        18.64 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 
       18.67        43.53         8.55        72.92        12.46        45.14 
TCGA-24-1469 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-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 
       55.92        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 TCGA-09-0364 TCGA-09-0366 
       22.22         6.35        31.07         8.61        29.16        57.76 
TCGA-09-0369 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       35.57        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        38.01       111.78 
TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0795 TCGA-13-0800 TCGA-13-0801 
       45.67        40.24       118.42        20.35        87.48        45.99 
TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 
       51.02        35.28        13.61        68.94       107.18       111.39 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
      153.37        66.67        95.15       145.45       102.84        43.36 
TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       49.61        71.74        66.15       134.04        19.36       127.79 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       50.37       123.16       118.98       116.65        44.55        37.64 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 
      109.32        58.68        84.53        48.79        83.74        85.94 
TCGA-13-2071 
       25.41 

  C9ORF171 MUTATED C9ORF171 WILD-TYPE 
             28.18               0.26 
  C9ORF171 MUTATED C9ORF171 WILD-TYPE 
            107.28             180.20 
  C9ORF171 MUTATED C9ORF171 WILD-TYPE 
             55.23              32.09 
[1] "28.2 - 107.3 (55.2)" "0.3 - 180.2 (32.1)" 
[1] "hr=" "1.6"
D20V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  C9ORF171 MUTATED         0     5                0
  C9ORF171 WILD-TYPE       2   457                1
D20V3, 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"
D20V4, binary
                    cls
clus                   0   1
  C9ORF171 MUTATED     5   0
  C9ORF171 WILD-TYPE 441   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF171 MUTATED      5    0
  C9ORF171 WILD-TYPE  441    4
     clus
vv    C9ORF171 MUTATED C9ORF171 WILD-TYPE
  NO                 5                441
  YES                0                  4
[1] 2 2
[1] FALSE
D20V5, continuous
                    vv
clus                 R0 R1 R2
  C9ORF171 MUTATED    0  0  0
  C9ORF171 WILD-TYPE 13 22  1
D20V6, multiclass
D20V7, 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(21) Variable = NCOA3 MUTATION ANALYSIS
D21V1, survival
                 sevent
clus2               0   1
  NCOA3 MUTATED     4   1
  NCOA3 WILD-TYPE 190 267
  NCOA3 MUTATED NCOA3 WILD-TYPE 
              5             457 
  NCOA3 MUTATED NCOA3 WILD-TYPE 
              1             267 
$`NCOA3 MUTATED`
TCGA-04-1365 TCGA-23-1118 TCGA-24-1845 TCGA-13-0890 TCGA-13-0904 
       76.57        86.01         3.81       145.45        50.37 

$`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-09-1659 TCGA-09-1661 
       64.64        36.23        31.86        45.37         9.99        38.43 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 TCGA-09-1670 
       89.33        74.93        41.62        57.60        30.51        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 
        5.85         3.02         8.55        97.55         6.12        35.15 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-13-1403 
      112.41        71.11        63.09        39.75        12.46        77.10 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
       81.17        28.54        83.31        55.23        57.27        81.01 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
       17.46        32.35        54.64        87.06        61.71        29.42 
TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
      124.44        22.39        70.82        83.93        52.44       125.56 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 
       93.90        90.38         4.24       127.27        66.15       115.07 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       43.20        34.82        65.69        34.16        65.52        80.15 
TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 
       44.68        14.53        80.02        78.48        77.88        76.90 
TCGA-13-2065 TCGA-13-2066 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 
       65.52        70.13        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-23-1030 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-23-1119 
       54.51         3.22        68.68        19.46        33.30       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-24-0970 TCGA-24-0975 
        4.50         4.44         3.81         7.63        11.64        21.80 
TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 
       41.56         7.66        22.32        54.12        63.55        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 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 
       18.64        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-24-1846 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-61-1737 
       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 TCGA-61-2614 TCGA-09-0364 
      125.75        22.22         6.35        31.07         8.61        29.16 
TCGA-09-0366 TCGA-09-0369 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       57.76        35.57        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        38.01 
TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 
      111.78        45.67        40.24       118.42       107.28        20.35 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 
       87.48        45.99        51.02        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       111.39       153.37        66.67        95.15       102.84 
TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
       43.36        49.61        71.74        66.15       134.04        19.36 
TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
      127.79       123.16       118.98       116.65        44.55        37.64 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 
      109.32        58.68        84.53        48.79        83.74        85.94 
TCGA-13-2071 
       25.41 

  NCOA3 MUTATED NCOA3 WILD-TYPE 
           3.81            0.26 
  NCOA3 MUTATED NCOA3 WILD-TYPE 
         145.45          180.20 
  NCOA3 MUTATED NCOA3 WILD-TYPE 
          76.57           32.09 
[1] "3.8 - 145.4 (76.6)" "0.3 - 180.2 (32.1)"
[1] "hr=" "6"  
D21V2, continuous
                 vv
clus              OMENTUM OVARY PERITONEUM OVARY
  NCOA3 MUTATED         0     5                0
  NCOA3 WILD-TYPE       2   457                1
D21V3, 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"
D21V4, binary
                 cls
clus                0   1
  NCOA3 MUTATED     5   0
  NCOA3 WILD-TYPE 441   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA3 MUTATED      5    0
  NCOA3 WILD-TYPE  441    4
     clus
vv    NCOA3 MUTATED NCOA3 WILD-TYPE
  NO              5             441
  YES             0               4
[1] 2 2
[1] FALSE
D21V5, 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-13-1404      TCGA-13-1405      TCGA-13-1409      TCGA-13-1410 
"NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" 
     TCGA-13-1412      TCGA-13-1482      TCGA-13-1483      TCGA-13-1484 
"NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" 
     TCGA-13-1488      TCGA-13-1489      TCGA-13-1491      TCGA-13-1492 
"NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" 
     TCGA-13-1495      TCGA-13-1497      TCGA-13-1498      TCGA-13-1499 
"NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" 
     TCGA-13-1501      TCGA-13-1504      TCGA-13-1506      TCGA-13-1507 
"NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" 
     TCGA-13-1509      TCGA-13-1512      TCGA-13-2057      TCGA-13-2059 
"NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" 
     TCGA-13-2060      TCGA-13-2061      TCGA-13-2066      TCGA-24-1614 
"NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" 
     TCGA-61-2101      TCGA-10-0926      TCGA-13-0714      TCGA-13-0720 
"NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" 
     TCGA-13-0724      TCGA-13-0755      TCGA-13-0760      TCGA-13-0762 
"NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" 
     TCGA-13-0791      TCGA-13-0792      TCGA-13-0793      TCGA-13-0795 
"NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" 
     TCGA-13-0801      TCGA-13-0802      TCGA-13-0885      TCGA-13-0887 
"NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" 
     TCGA-13-0889      TCGA-13-0891      TCGA-13-0894      TCGA-13-0897 
"NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" 
     TCGA-13-0900      TCGA-13-0901      TCGA-13-0903      TCGA-13-0905 
"NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" 
     TCGA-13-0906      TCGA-13-0910      TCGA-13-0911      TCGA-13-0912 
"NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" 
     TCGA-13-0913      TCGA-13-0919      TCGA-13-2071 
"NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" "NCOA3 WILD-TYPE" 
                 vv
clus              R0 R1 R2
  NCOA3 MUTATED    0  0  0
  NCOA3 WILD-TYPE 13 22  1
D21V6, multiclass
D21V7, 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
