[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"      "-oTOV-TP"
[1] "opt"                    "-OPAGGREGRATED_CLUSTER"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/OV-TP/10006099/OV-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/OV-TP/10671262/OV-TP.mergedcluster.txt"

nPatients in clinical file=586, in cluster file=586, common to both=578
[1]  13 578
[1] "MRNA_CNMF"
[1] 3
  1   2   3 
219 214 129 
  1   2   3 
219 214 129 
[1] "MRNA_CHIERARCHICAL"
[1] 3
  1   2   3 
313 160  89 
  1   2   3 
313 160  89 
[1] "MIR_CNMF"
[1] 3
  1   2   3 
157 165 238 
  1   2   3 
157 165 238 
[1] "MIR_CHIERARCHICAL"
[1] 3
 1 10  2  3  4  5  6  7  8  9 
82 57 58 86 35 75 36 36 51 44 
 1 10  2  3  4  5  6  7  8  9 
82 57 58 86 35 75 36 36 51 44 
[1] "CN_CNMF"
[1] 3
  1   2   3 
173 201 188 
  1   2   3 
173 201 188 
[1] "RPPA_CNMF"
[1] 3
  1   2   3 
123 199  85 
  1   2   3 
123 199  85 
[1] "RPPA_CHIERARCHICAL"
[1] 3
  1   2   3   4 
120  98 130  59 
  1   2   3   4 
120  98 130  59 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3 
102  67  92 
  1   2   3 
102  67  92 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
107 117  37 
  1   2   3 
107 117  37 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
124 185 144 
  1   2   3 
124 185 144 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
105  73 169 106 
  1   2   3   4 
105  73 169 106 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3 
 98 198 157 
  1   2   3 
 98 198 157 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3 
173 176 104 
  1   2   3 
173 176 104 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                                      
 [2] "VITALSTATUS"                                       
 [3] "DAYSTODEATH"                                       
 [4] "DAYSTOLASTFOLLOWUP"                                
 [5] "PRIMARYSITEOFDESEASE"                              
 [6] "NEOPLASM.DISEASESTAGE"                             
 [7] "PATHOLOGY.T.STAGE"                                 
 [8] "PATHOLOGY.N.STAGE"                                 
 [9] "PATHOLOGY.M.STAGE"                                 
[10] "DCCUPLOADDATE"                                     
[11] "GENDER"                                            
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"                  
[13] "RADIATIONTHERAPY"                                  
[14] "KARNOFSKYPERFORMANCESCORE"                         
[15] "EXAMINATIONS.EXAMINATION.KARNOFSKYPERFORMANCESCORE"
[16] "HISTOLOGICALTYPE"                                  
[17] "TUMORGRADE"                                        
[18] "TUMORSTAGE"                                        
[19] "PATIENTTUMORRECURRENCESTATUS"                      
[20] "DAYSTOTUMORRECURRENCE"                             
[21] "CHEMOTHERAPY"                                      
[22] "RADIATIONS.RADIATION.REGIMENINDICATION"            
[23] "COMPLETENESS.OF.RESECTION"                         
[24] "RACE"                                              
[25] "ETHNICITY"                                         
[26] "BATCHNUMBER"                                       

Input Data has 26 rows and 578 columns.

[1] "Batch" "26"   
[1] "Last Follow UP"
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
        1224         1247           55         1495           NA         1418 
TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 
          NA           NA           NA         1993         1919           NA 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1357 TCGA-04-1360 
          NA           NA         1991           NA           NA           NA 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1369 
         989           NA           NA         2329         2174           NA 
TCGA-04-1370 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 
        1824         2506           NA         1265           NA           NA 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 
        1167           NA           NA           NA           NA           NA 
TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 
          NA           NA         1966           NA           NA           NA 
TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 
          NA           NA           NA           NA           NA           NA 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 
          NA           NA           NA           NA           NA         1752 
TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
        1882         1684          928          547          178           92 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 
         260         2967          188          186           NA           NA 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 
        3419         2163         1919         1209          637          819 
TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
         379         1652          788         2478          563         1011 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 
         982          356          119         1078         1089          460 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 
         604          189          748         1355         1204           83 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 
         377          946          462          542         1678           76 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 
         340          346          351         1036          981          944 
TCGA-13-0765 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
         869          651          257         1184         1117          873 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
         923          596          265          237          247          252 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
         249         1334         1073         1073          414         2097 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 
        3260         2780         2259         2028         2141         1881 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 
        2068         2099         1319         1509         1748         1708 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
        1736          589         1441         1470         1455         1367 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
        1364         1128          843         1036          912          644 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 
         453          420          141          195          185          331 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
         201          224          184          180          208          143 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
         128          162         1662         2648         1877          895 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
        2982          629          681         2154         2521         1595 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
        2237         1162         1498          129         1652         1144 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
        1168          425          999          504          128          134 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 
         145          127           78          119           94          433 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2066 TCGA-13-2071 
         372          262          328          266          295          191 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 
          NA          789          797         2196          837          772 
TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 
         581          508           89           81         1446         1294 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 
        1233          468          816          966         1503          268 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1107 TCGA-23-1109 TCGA-23-1110 
         886          575           68            9         1562         1658 
TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
          98          949         2089          139         1013         2616 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 
        3953          130          194         1189         1018         1768 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
          16          759         3525         2661         2788         2342 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-23-2647 TCGA-23-2649 
        1516           84          143          137          135          116 
TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
         232          598          354          663         1264          233 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
         679         1646         1933         1442          192          194 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
         238          243          239           23          190          183 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 
         181          163          147          529          863          583 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 
         568         1324          260         2218          379         1373 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
        3224          277          105           36          676          820 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 
        1746         1955          493         1721         1249         1579 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 
        1259         1767         2692         2148         1213          594 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 
        1341         1384         1451          787          312          524 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 
        2742         2688         1470         1163          253          106 
TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 
         113          116          133          343          176          168 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 
         298          690          919          500          336         2467 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 
         148         4624         1364         1769         1059         3337 
TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
         439         1641          562          857         1947         1354 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 
        1736         1100           24           11         1446          962 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 
        2143         1357           25         2049         1102          506 
TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 
        1007         1699         1620           31          820          974 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 
        1553         1126           31         1064         1977         1124 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1324 TCGA-25-1325 TCGA-25-1326 
        1033           91          365         1035          976          945 
TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 
        1979           90          565          548          481           11 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
         627          239            9         1732         1843         1081 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 
        1558          455          760          549         2587          396 
TCGA-25-2390 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 
          NA         1492           31         1157           92          365 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 
        1369          608         1278           90          883          943 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 
         821         2400         1360         1435         3096         1172 
TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 
          24         1025          949         2078           16          514 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 
         568         1815          555         1277          889         1053 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 
         517         2606         2032         1914         1190          950 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 
         699          741          686          527          376          360 
TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 
         374          454          255          220          163         1053 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 
        2621         1977         1900         1372          149         1285 
TCGA-29-2432 TCGA-29-2434 TCGA-29-2435 TCGA-29-2436 TCGA-30-1714 TCGA-30-1718 
         360          349           34          297         1158         1579 
TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 
        1103           75          477            8         1463         1366 
TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1869 TCGA-30-1880 
        1058          186         1114           37         1563         1751 
TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 
         738          914         1484         1386          918          571 
TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 
         684          204         1293         1342           67          875 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 
         885          655          695          686          260          915 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 
         783          847          737          751         1066         1004 
TCGA-36-2532 TCGA-36-2533 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
         897           NA          907          788          763          724 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 
         657           68          638          557          624          431 
TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
         184          492          349          792          722          287 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 
        1278          227         1240           NA          731          346 
TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 
         643           53          679          882          763          761 
TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 
        5481           NA           NA         3532           NA           NA 
TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 
          NA          165           NA          338          246          637 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 
         956          564          848          132          967          866 
TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 
        1484         1364         1089           74         1024         1329 
TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 
          44          256          176          347          396          276 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 
        1038          952         1127         1293         1488         1722 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
        2061         1321          479         1161           61          168 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 
         441          547          122          932         1212          932 
TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 
          36         1398         1381          146          145         1573 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 
        2182         1875         1776         1844         1993         1688 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
         197         2338          629         1354         3825          676 
TCGA-61-2610 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-72-4231 TCGA-72-4232 
        1579          193          945          262           NA           NA 
TCGA-72-4233 TCGA-72-4234 TCGA-72-4235 TCGA-72-4236 TCGA-72-4237 TCGA-72-4238 
          NA           NA           NA           NA           NA           NA 
TCGA-72-4240 TCGA-72-4241 
          NA           NA 
Variable 1:'AGE':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=270,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=457,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'EXAMINATIONS.EXAMINATION.KARNOFSKYPERFORMANCESCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'TUMOR.GRADE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'TUMOR.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 19:'PATIENTTUMORRECURRENCESTATUS':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 20:'DAYSTOTUMORRECURRENCE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 21:'CHEMOTHERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 22:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'COMPLETENESS.OF.RESECTION':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 24:'RACE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 25:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 26:'BATCH.NUMBER':	nDistinctValues=17,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "PRIMARY.SITE.OF.DISEASE"               
[3] "KARNOFSKY.PERFORMANCE.SCORE"           
[4] "RADIATIONS.RADIATION.REGIMENINDICATION"
[5] "COMPLETENESS.OF.RESECTION"             
[6] "RACE"                                  
[7] "ETHNICITY"                             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 578 columns, 1 survival variables, and 7 non-survival variables.
AGE, nv=55, binary=FALSE, numeric=TRUE
PRIMARY.SITE.OF.DISEASE, nv=3, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=4, binary=FALSE, numeric=TRUE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=3, binary=FALSE, numeric=FALSE
RACE, nv=5, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
          sevent
clus2        0   1
  subtype1  92 124
  subtype2 119  93
  subtype3  53  76
subtype1 subtype2 subtype3 
     216      212      129 
subtype1 subtype2 subtype3 
     124       93       76 
$subtype1
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1342 TCGA-04-1347 TCGA-04-1350 
       40.24        41.00         1.81        18.51        63.09        63.98 
TCGA-04-1351 TCGA-04-1356 TCGA-04-1364 TCGA-04-1367 TCGA-04-1369 TCGA-04-1371 
       65.46        49.28        33.67        71.47        21.11        82.39 
TCGA-04-1514 TCGA-04-1517 TCGA-04-1525 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 
       56.55        19.99        38.37        84.20        55.43        48.89 
TCGA-04-1646 TCGA-04-1648 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 
       27.88        28.64        31.86        45.37        29.16         9.47 
TCGA-09-0369 TCGA-09-1661 TCGA-09-1664 TCGA-09-1669 TCGA-09-1672 TCGA-09-1673 
       35.57        38.43        74.93        30.51         5.85         3.02 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2053 
        8.55        97.55         4.54       112.41        71.11        39.75 
TCGA-09-2054 TCGA-09-2055 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       20.94        26.93        54.31        25.91        81.47        18.51 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0938 TCGA-13-0717 TCGA-13-0724 
       11.70         3.91        35.44        19.86        24.59         2.73 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0762 TCGA-13-0766 
       15.19        17.82        55.17        11.18        32.25        21.40 
TCGA-13-0794 TCGA-13-0799 TCGA-13-0800 TCGA-13-0802 TCGA-13-0883 TCGA-13-0887 
       30.35         7.79         8.12         8.19        68.94        66.67 
TCGA-13-0888 TCGA-13-0891 TCGA-13-0899 TCGA-13-0901 TCGA-13-0906 TCGA-13-0910 
       70.39        69.01        56.15        19.36        44.94        37.08 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0923 TCGA-13-1403 
       34.06        29.98        21.17        13.81         6.41        10.88 
TCGA-13-1407 TCGA-13-1409 TCGA-13-1477 TCGA-13-1482 TCGA-13-1487 TCGA-13-1489 
        6.05         6.84        54.64        61.71        22.39        82.88 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1495 TCGA-13-1505 TCGA-13-1506 TCGA-13-1510 
       52.44        73.55        49.25         4.21         4.41         2.56 
TCGA-13-2057 TCGA-13-2066 TCGA-20-0990 TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 
       14.24         9.70        25.94        72.20        25.38        19.10 
TCGA-20-1686 TCGA-23-1021 TCGA-23-1022 TCGA-23-1024 TCGA-23-1029 TCGA-23-1030 
        2.93        47.54        42.54        15.39         8.81        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1107 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
       18.90         2.24         0.30        51.35        54.51         3.22 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1119 TCGA-23-1121 TCGA-23-1122 TCGA-23-1809 
       31.20        68.68       129.96         6.38        39.09         0.53 
TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0979 TCGA-24-0982 
        2.76         4.70         4.50         7.63        41.56        22.32 
TCGA-24-1103 TCGA-24-1413 TCGA-24-1419 TCGA-24-1423 TCGA-24-1424 TCGA-24-1426 
       54.12         6.31         7.86         6.25         6.02         5.36 
TCGA-24-1430 TCGA-24-1464 TCGA-24-1467 TCGA-24-1469 TCGA-24-1544 TCGA-24-1548 
       28.37        12.46       105.99         9.11        26.96        16.21 
TCGA-24-1552 TCGA-24-1555 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1567 
       41.39        88.50        39.88        19.53        44.09        17.23 
TCGA-24-1603 TCGA-24-1614 TCGA-24-1616 TCGA-24-1844 TCGA-24-1923 TCGA-24-2019 
       90.15        48.33        38.24         3.72        22.68         4.87 
TCGA-24-2020 TCGA-24-2024 TCGA-24-2027 TCGA-24-2030 TCGA-24-2033 TCGA-24-2036 
      152.02        58.16       109.71        53.95        18.48        64.01 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 
       44.52        57.07        36.16        33.11        55.86         1.02 
TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1321 TCGA-25-1323 
       32.02        51.06        37.02         1.02        33.96        12.00 
TCGA-25-1324 TCGA-25-1325 TCGA-25-1627 TCGA-25-1631 TCGA-25-1632 TCGA-25-1634 
       34.03        32.09         0.36         0.30        56.94        35.54 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-2393 TCGA-25-2400 TCGA-29-1691 
       14.96        24.99        18.05        38.04        42.02        47.18 
TCGA-29-1697 TCGA-29-1702 TCGA-29-1703 TCGA-29-1762 TCGA-29-1763 TCGA-29-1774 
       31.20        18.67        59.67        85.68        66.81        17.33 
TCGA-29-1775 TCGA-29-2414 TCGA-29-2425 TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 
       12.36        86.17        65.00         4.90        42.25        11.47 
TCGA-30-1714 TCGA-30-1853 TCGA-30-1859 TCGA-30-1866 TCGA-31-1955 TCGA-36-1571 
       38.07        36.26        48.10        36.62        42.51        22.85 
TCGA-36-1575 TCGA-36-1577 TCGA-36-2537 TCGA-36-2538 TCGA-36-2544 TCGA-36-2547 
        8.55        25.74        25.91        25.08        20.98        20.52 
TCGA-36-2552 TCGA-42-2591 TCGA-57-1582 TCGA-57-1583 TCGA-57-1586 TCGA-57-1992 
       11.47        40.77        24.03        11.38        22.32        29.00 
TCGA-59-2350 TCGA-59-2352 TCGA-59-2363 TCGA-59-2372 TCGA-61-1728 TCGA-61-1730 
       22.32         9.40         5.42        44.81        27.88         4.34 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1900 TCGA-61-1910 TCGA-61-1917 TCGA-61-2088 
       33.67        43.69         5.79        37.05        43.43         4.77 
TCGA-61-2092 TCGA-61-2096 TCGA-61-2098 TCGA-61-2101 TCGA-61-2110 TCGA-61-2111 
       51.72        58.39        65.52        55.50        44.52       125.75 

$subtype2
TCGA-04-1336 TCGA-04-1346 TCGA-04-1348 TCGA-04-1349 TCGA-04-1361 TCGA-04-1362 
       49.15        65.52        48.76        21.57        32.52        44.32 
TCGA-04-1365 TCGA-04-1516 TCGA-04-1536 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 
       76.57        41.59        29.10        64.64        36.23        47.70 
TCGA-09-0366 TCGA-09-0367 TCGA-09-1659 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 
       57.76        17.98         9.99        89.33        41.62        57.60 
TCGA-09-1667 TCGA-09-1668 TCGA-09-1670 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 
       61.87        55.36        17.98         6.18         6.12        35.15 
TCGA-09-2051 TCGA-09-2056 TCGA-10-0931 TCGA-10-0936 TCGA-10-0937 TCGA-13-0720 
       63.09        12.46        32.28        35.80        15.12        44.55 
TCGA-13-0723 TCGA-13-0725 TCGA-13-0755 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 
       39.58        12.39         2.50        11.38        11.54        34.06 
TCGA-13-0764 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0795 TCGA-13-0797 
       31.04        28.57        38.93        36.72        19.59         8.71 
TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0884 TCGA-13-0885 TCGA-13-0893 
        8.28        43.86        35.28       107.18        91.40        43.36 
TCGA-13-0897 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0921 TCGA-13-0924 
       57.47        47.38        48.33        47.84         4.64         6.08 
TCGA-13-1410 TCGA-13-1484 TCGA-13-1488 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
        4.70        98.04        70.82         4.24        54.31        37.61 
TCGA-13-1500 TCGA-13-1507 TCGA-13-1511 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 
       13.97         4.77         3.91        12.23         8.61        10.78 
TCGA-13-2065 TCGA-20-0987 TCGA-20-0991 TCGA-20-1685 TCGA-20-1687 TCGA-23-1026 
        8.75        23.05        26.20        16.70         2.66        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1118 TCGA-23-1120 TCGA-23-1123 TCGA-23-1124 
       31.76        49.41        86.01         4.27        33.47        58.13 
TCGA-23-2072 TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2649 
       24.95       115.89        91.66        77.00        49.84         3.81 
TCGA-24-0968 TCGA-24-0980 TCGA-24-1104 TCGA-24-1416 TCGA-24-1417 TCGA-24-1428 
       19.66         7.66        63.55         6.38         7.82        17.39 
TCGA-24-1431 TCGA-24-1436 TCGA-24-1466 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 
       19.17         8.55        45.14         3.45         1.18        22.22 
TCGA-24-1549 TCGA-24-1551 TCGA-24-1553 TCGA-24-1556 TCGA-24-1565 TCGA-24-1604 
       56.58        51.91        58.09        70.62        10.26        88.37 
TCGA-24-1842 TCGA-24-1843 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1920 
        8.32         3.48         3.81         4.37        11.28         9.80 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 TCGA-24-2023 TCGA-24-2026 TCGA-24-2261 
       30.21        16.44        81.11        44.84        34.82         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 TCGA-24-2290 TCGA-25-1313 
        0.36        47.54        31.63        44.61        36.23        26.96 
TCGA-25-1319 TCGA-25-1322 TCGA-25-1625 TCGA-25-1630 TCGA-25-1878 TCGA-25-2391 
       65.00         2.99        18.02         7.86        85.05        49.05 
TCGA-25-2392 TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 TCGA-25-2409 TCGA-29-1688 
        1.02         3.02        12.00        19.99        26.99        78.90 
TCGA-29-1694 TCGA-29-1696 TCGA-29-1699 TCGA-29-1707 TCGA-29-1711 TCGA-29-1761 
       38.53        33.70         0.53        41.98        34.62        17.00 
TCGA-29-1769 TCGA-29-1771 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 
       22.98        22.55        11.84        12.30        14.93         8.38 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2427 TCGA-29-2428 TCGA-30-1856 TCGA-30-1860 
        5.36        34.62        62.47        45.11        15.68        44.91 
TCGA-30-1880 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1953 TCGA-36-1568 
       57.57        45.57        30.18        18.77         6.71        28.77 
TCGA-36-1570 TCGA-36-1574 TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 
       21.53        22.55        27.85        24.69        35.05        33.01 
TCGA-36-2532 TCGA-36-2534 TCGA-36-2542 TCGA-36-2543 TCGA-36-2545 TCGA-36-2549 
       29.49        29.82        21.60         2.24        18.31         6.05 
TCGA-36-2551 TCGA-42-2582 TCGA-42-2589 TCGA-42-2590 TCGA-57-1584 TCGA-57-1993 
       16.18        26.04        42.02         7.46        21.14        25.08 
TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2351 TCGA-59-2355 TCGA-61-1722 
       25.02       180.20        80.12       116.12         2.14         8.09 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1734 TCGA-61-1736 TCGA-61-1738 
       20.94        31.43        18.54        28.47        48.79        35.80 
TCGA-61-1740 TCGA-61-1895 TCGA-61-1899 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 
        2.43         1.45         8.42        11.41        13.02         9.07 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 
       34.13        31.30        42.51        48.92        56.61        67.76 
TCGA-61-1918 TCGA-61-1995 TCGA-61-2000 TCGA-61-2002 TCGA-61-2008 TCGA-61-2012 
       15.75         2.01        14.50        17.98        30.64        30.64 
TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2094 TCGA-61-2097 
        1.18        45.96        45.40         4.80        71.74        60.62 
TCGA-61-2104 TCGA-61-2109 
       76.87        20.68 

$subtype3
TCGA-04-1337 TCGA-04-1338 TCGA-04-1343 TCGA-04-1530 TCGA-10-0930 TCGA-13-0714 
        2.01        46.62        11.87       119.08        33.24         6.21 
TCGA-13-0726 TCGA-13-0768 TCGA-13-0793 TCGA-13-0805 TCGA-13-0807 TCGA-13-0886 
       31.10         8.45        28.70        35.28        13.61        74.27 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0894 TCGA-13-0900 TCGA-13-0908 TCGA-13-0911 
       61.84        67.99        49.61        57.07        44.84        27.72 
TCGA-13-0919 TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1411 TCGA-13-1412 
       14.89         6.61         7.36         5.92         4.21         5.33 
TCGA-13-1481 TCGA-13-1483 TCGA-13-1485 TCGA-13-1494 TCGA-13-1499 TCGA-13-1501 
       87.06        29.42        20.68        38.20        38.40        32.84 
TCGA-13-1504 TCGA-13-1509 TCGA-13-1512 TCGA-13-2071 TCGA-20-1682 TCGA-23-1023 
       16.57         4.18         3.09         6.28        27.52        40.54 
TCGA-23-1116 TCGA-23-1117 TCGA-23-2078 TCGA-23-2647 TCGA-24-0970 TCGA-24-0975 
        4.57        33.30        87.48         4.44        11.64        21.80 
TCGA-24-1105 TCGA-24-1418 TCGA-24-1422 TCGA-24-1425 TCGA-24-1427 TCGA-24-1434 
       47.41         7.99         0.76         5.95         4.83        18.67 
TCGA-24-1435 TCGA-24-1463 TCGA-24-1545 TCGA-24-1546 TCGA-24-1550 TCGA-24-1562 
       43.53        72.92        57.40        64.27        41.06        45.50 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1849 TCGA-24-1850 TCGA-24-1928 TCGA-24-2029 
       47.70        25.87         5.79         5.52        11.05        14.43 
TCGA-24-2035 TCGA-24-2280 TCGA-24-2288 TCGA-24-2289 TCGA-24-2293 TCGA-24-2298 
       28.18        70.45         0.82        67.36        16.64        53.26 
TCGA-25-1318 TCGA-25-1320 TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 
       34.98        36.95        31.07        65.06         2.96        18.58 
TCGA-25-1626 TCGA-25-1628 TCGA-25-1633 TCGA-25-1635 TCGA-25-2042 TCGA-25-2398 
       15.81        20.61        60.59        51.22        13.02        45.01 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-29-1690 TCGA-29-1693 TCGA-29-1695 
        2.96        29.03        31.00        44.71       101.79         0.79 
TCGA-29-1698 TCGA-29-1701 TCGA-29-1705 TCGA-29-1710 TCGA-29-1764 TCGA-29-1766 
       68.32        16.90        18.25        29.23        62.93        39.12 
TCGA-29-1768 TCGA-29-1770 TCGA-29-1783 TCGA-29-2432 TCGA-29-2436 TCGA-30-1718 
       31.23        24.36         7.23        11.84         9.76        51.91 
TCGA-30-1855 TCGA-30-1857 TCGA-30-1861 TCGA-30-1862 TCGA-30-1867 TCGA-30-1887 
        2.47         0.26        34.78         6.12         1.22        24.26 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1951 TCGA-31-1956 TCGA-31-1959 TCGA-36-1569 
       30.05        48.79        22.49        44.12         2.20        29.10 
TCGA-36-1576 TCGA-36-1580 TCGA-36-2540 TCGA-36-2548 TCGA-42-2587 TCGA-42-2588 
       30.08        24.23        23.80        14.17        23.74         9.44 
TCGA-57-1585 TCGA-59-2354 TCGA-61-1721 TCGA-61-1733 TCGA-61-1737 TCGA-61-1919 
        1.74        34.39        11.11        31.79        44.84        38.17 
TCGA-61-1998 TCGA-61-2003 TCGA-61-2009 TCGA-61-2095 TCGA-61-2102 TCGA-61-2113 
        5.52         4.01        39.85        61.64         6.48        22.22 
TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
        6.35        31.07         8.61 

subtype1 subtype2 subtype3 
    0.30     0.36     0.26 
subtype1 subtype2 subtype3 
  152.02   180.20   119.08 
subtype1 subtype2 subtype3 
  30.165   28.160   25.870 
[1] "0.3 - 152.0 (30.2)" "0.4 - 180.2 (28.2)" "0.3 - 119.1 (25.9)"
D1V2, continuous
          vv
clus       OMENTUM OVARY PERITONEUM OVARY
  subtype1       0   219                0
  subtype2       1   212                1
  subtype3       1   127                1
D1V3, multiclass
                  clus
vv                 subtype1 subtype2 subtype3
  OMENTUM                 0        1        1
  OVARY                 219      212      127
  PERITONEUM OVARY        0        1        1
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V4, continuous
D1V5, binary
          cls
clus         0   1
  subtype1   2 217
  subtype2   1 213
  subtype3   0 129
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  217
  subtype2    1  213
  subtype3    0  129
     clus
vv    subtype1 subtype2 subtype3
  NO         2        1        0
  YES      217      213      129
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2
  subtype1  6  9  0
  subtype2  7  9  0
  subtype3  1  9  1
D1V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0        6        7        1
  R1        9        9        9
  R2        0        0        1
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     7                        12
  subtype2                                0    11                         9
  subtype3                                2     1                         3
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0   186
  subtype2                                         1   181
  subtype3                                         0   118
D1V7, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 0        0        2
  ASIAN                                            7       11        1
  BLACK OR AFRICAN AMERICAN                       12        9        3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        1        0
  WHITE                                          186      181      118
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
          cls
clus         0   1
  subtype1   6 130
  subtype2   5 120
  subtype3   0  78
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  130
  subtype2    5  120
  subtype3    0   78
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            6        5        0
  NOT HISPANIC OR LATINO      130      120       78
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = MRNA_CHIERARCHICAL
D2V1, survival
          sevent
clus2        0   1
  subtype1 154 155
  subtype2  73  87
  subtype3  37  51
subtype1 subtype2 subtype3 
     309      160       88 
subtype1 subtype2 subtype3 
     155       87       51 
$subtype1
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 
       40.24         1.81        49.15        18.51        11.87        65.52 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 
       48.76        21.57        49.28        32.52        44.32        76.57 
TCGA-04-1367 TCGA-04-1369 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1536 
       71.47        21.11        41.59        19.99        38.37        29.10 
TCGA-04-1638 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-09-0366 
       55.43        28.64        64.64        36.23        47.70        57.76 
TCGA-09-0367 TCGA-09-1659 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 
       17.98         9.99        89.33        74.93        41.62        57.60 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 
       17.98         5.85         3.02        97.55         6.18         6.12 
TCGA-09-2045 TCGA-09-2051 TCGA-09-2053 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 
       35.15        63.09        39.75        26.93        12.46        54.31 
TCGA-10-0926 TCGA-10-0931 TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 TCGA-13-0714 
       25.91        32.28         3.91        35.80        15.12         6.21 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0727 TCGA-13-0751 
       44.55        39.58         2.73        12.39        15.19        55.17 
TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0764 TCGA-13-0765 
        2.50        11.18        11.38        11.54        31.04        28.57 
TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 
       21.40        38.93        36.72        19.59         8.71         7.79 
TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
        8.28        43.86        35.28        35.28        13.61        68.94 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 
       91.40        74.27        66.67        61.84        67.99        69.01 
TCGA-13-0899 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0910 TCGA-13-0911 
       56.15        47.38        48.33        47.84        37.08        27.72 
TCGA-13-0916 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1410 
       21.17         4.64         6.41         6.08        10.88         4.70 
TCGA-13-1482 TCGA-13-1484 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 TCGA-13-1495 
       61.71        98.04        70.82        52.44        73.55        49.25 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1506 TCGA-13-1510 TCGA-13-1511 
        4.24        54.31        37.61         4.41         2.56         3.91 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-20-0987 TCGA-20-0991 
       12.23         8.61        10.78         8.75        23.05        26.20 
TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 
       72.20        27.52        25.38        19.10        16.70         2.93 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1024 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
        2.66        47.54        15.39        49.41         8.81        29.13 
TCGA-23-1032 TCGA-23-1107 TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 TCGA-23-1118 
        2.24         0.30        51.35         3.22        31.20        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-23-2079 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 
       24.95       115.89        91.66        49.84         2.76         4.70 
TCGA-23-2645 TCGA-23-2649 TCGA-24-0966 TCGA-24-0968 TCGA-24-0979 TCGA-24-0982 
        4.50         3.81         7.63        19.66        41.56        22.32 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1419 
       54.12        63.55        47.41         6.31         6.38         7.86 
TCGA-24-1423 TCGA-24-1426 TCGA-24-1428 TCGA-24-1431 TCGA-24-1436 TCGA-24-1464 
        6.25         5.36        17.39        19.17         8.55        12.46 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 
       45.14       105.99         9.11         3.45         1.18        22.22 
TCGA-24-1548 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-24-1565 TCGA-24-1603 
       70.62        39.88        19.53        44.09        10.26        90.15 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 
       88.37        48.33        38.24         3.48         3.72         3.81 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-2019 
        4.37        11.28         5.52         9.80        30.21         4.87 
TCGA-24-2023 TCGA-24-2026 TCGA-24-2030 TCGA-24-2036 TCGA-24-2038 TCGA-24-2260 
       44.84        34.82        53.95        64.01        44.52        36.16 
TCGA-24-2261 TCGA-24-2267 TCGA-24-2281 TCGA-24-2290 TCGA-24-2295 TCGA-24-2297 
        0.79        47.54        44.61        36.23        33.11        55.86 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 
        1.02        26.96        32.02        34.98        65.00        33.96 
TCGA-25-1322 TCGA-25-1324 TCGA-25-1325 TCGA-25-1625 TCGA-25-1627 TCGA-25-1630 
        2.99        34.03        32.09        18.02         0.36         7.86 
TCGA-25-1631 TCGA-25-1870 TCGA-25-1878 TCGA-25-2391 TCGA-25-2392 TCGA-25-2396 
        0.30        14.96        85.05        49.05         1.02         3.02 
TCGA-25-2397 TCGA-25-2399 TCGA-25-2400 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 
       12.00        19.99        42.02        78.90        44.71        47.18 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 
       33.70        31.20         0.53        18.67        59.67        41.98 
TCGA-29-1761 TCGA-29-1763 TCGA-29-1771 TCGA-29-1775 TCGA-29-1778 TCGA-29-1781 
       17.00        66.81        22.55        12.36        14.93         8.38 
TCGA-29-1783 TCGA-29-1784 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2434 
        7.23         5.36        62.47        45.11         4.90        11.47 
TCGA-30-1856 TCGA-30-1860 TCGA-30-1866 TCGA-31-1950 TCGA-31-1955 TCGA-36-1568 
       15.68        44.91        36.62        18.77        42.51        28.77 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1578 TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 
       21.53        22.85        27.85        24.69        33.01        29.49 
TCGA-36-2534 TCGA-36-2542 TCGA-36-2543 TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 
       29.82        21.60         2.24        18.31        20.52         6.05 
TCGA-36-2551 TCGA-42-2582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1992 
       16.18        26.04        11.38        21.14        22.32        29.00 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       25.08        25.02        80.12        22.32       116.12         9.40 
TCGA-59-2355 TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1734 
        2.14         8.09        31.43        18.54        27.88        28.47 
TCGA-61-1736 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 
       48.79        35.80         2.43        33.67        43.69         1.45 
TCGA-61-1899 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        8.42        11.41        13.02         9.07        34.13        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 
       37.05        42.51        48.92        67.76        43.43        15.75 
TCGA-61-1995 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
        2.01        30.64         1.18        45.96        45.40         4.80 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2104 
       51.72        71.74        61.64        58.39        60.62        76.87 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       20.68        44.52       125.75 

$subtype2
TCGA-04-1332 TCGA-04-1337 TCGA-04-1338 TCGA-04-1530 TCGA-09-1667 TCGA-09-1668 
       41.00         2.01        46.62       119.08        61.87        55.36 
TCGA-10-0930 TCGA-13-0726 TCGA-13-0761 TCGA-13-0768 TCGA-13-0793 TCGA-13-0884 
       33.24        31.10        34.06         8.45        28.70       107.18 
TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 TCGA-13-0908 
       43.36        49.61        57.47        57.07        19.36        44.84 
TCGA-13-0919 TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1411 TCGA-13-1412 
       14.89         6.61         7.36         5.92         4.21         5.33 
TCGA-13-1481 TCGA-13-1483 TCGA-13-1485 TCGA-13-1494 TCGA-13-1499 TCGA-13-1500 
       87.06        29.42        20.68        38.20        38.40        13.97 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1507 TCGA-13-1509 TCGA-13-1512 
       32.84        16.57         4.21         4.77         4.18         3.09 
TCGA-13-2071 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1116 TCGA-23-1117 
        6.28        40.54        26.83        31.76         4.57        33.30 
TCGA-23-2078 TCGA-23-2081 TCGA-23-2647 TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 
       87.48        77.00         4.44        11.64        21.80         7.66 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1422 TCGA-24-1425 TCGA-24-1427 TCGA-24-1434 
        7.82         7.99         0.76         5.95         4.83        18.67 
TCGA-24-1435 TCGA-24-1463 TCGA-24-1545 TCGA-24-1546 TCGA-24-1562 TCGA-24-1563 
       43.53        72.92        57.40        64.27        45.50        47.70 
TCGA-24-1564 TCGA-24-1842 TCGA-24-1849 TCGA-24-1923 TCGA-24-1927 TCGA-24-1928 
       25.87         8.32         5.79        22.68        16.44        11.05 
TCGA-24-1930 TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2254 TCGA-24-2262 
       81.11        14.43        18.48        28.18        57.07         0.36 
TCGA-24-2271 TCGA-24-2280 TCGA-24-2288 TCGA-24-2289 TCGA-24-2293 TCGA-24-2298 
       31.63        70.45         0.82        67.36        16.64        53.26 
TCGA-25-1320 TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 
       36.95        31.07        65.06         2.96        18.58        15.81 
TCGA-25-1628 TCGA-25-1633 TCGA-25-1635 TCGA-25-2042 TCGA-25-2398 TCGA-25-2401 
       20.61        60.59        51.22        13.02        45.01         2.96 
TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 
       29.03        31.00        26.99       101.79        38.53         0.79 
TCGA-29-1698 TCGA-29-1701 TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 TCGA-29-1764 
       68.32        16.90        18.25        29.23        34.62        62.93 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1776 TCGA-29-1777 
       39.12        31.23        22.98        24.36        11.84        12.30 
TCGA-29-1785 TCGA-29-2432 TCGA-29-2436 TCGA-30-1718 TCGA-30-1855 TCGA-30-1857 
       34.62        11.84         9.76        51.91         2.47         0.26 
TCGA-30-1861 TCGA-30-1862 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 
       34.78         6.12         1.22        57.57        24.26        30.05 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 TCGA-31-1956 
       48.79        45.57        30.18        22.49         6.71        44.12 
TCGA-31-1959 TCGA-36-1569 TCGA-36-1574 TCGA-36-1576 TCGA-36-1580 TCGA-36-2529 
        2.20        29.10        22.55        30.08        24.23        35.05 
TCGA-36-2538 TCGA-36-2540 TCGA-36-2544 TCGA-36-2548 TCGA-42-2587 TCGA-42-2588 
       25.08        23.80        20.98        14.17        23.74         9.44 
TCGA-42-2589 TCGA-42-2590 TCGA-57-1582 TCGA-57-1585 TCGA-59-2348 TCGA-59-2354 
       42.02         7.46        24.03         1.74       180.20        34.39 
TCGA-61-1721 TCGA-61-1724 TCGA-61-1733 TCGA-61-1737 TCGA-61-1914 TCGA-61-1919 
       11.11        20.94        31.79        44.84        56.61        38.17 
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-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       22.22         6.35        31.07         8.61 

$subtype3
TCGA-04-1347 TCGA-04-1350 TCGA-04-1351 TCGA-04-1364 TCGA-04-1371 TCGA-04-1514 
       63.09        63.98        65.46        33.67        82.39        56.55 
TCGA-04-1542 TCGA-04-1644 TCGA-04-1646 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 
       84.20        48.89        27.88        31.86        45.37        29.16 
TCGA-09-0365 TCGA-09-0369 TCGA-09-1661 TCGA-09-1669 TCGA-09-1674 TCGA-09-2048 
        9.47        35.57        38.43        30.51         8.55         4.54 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2054 TCGA-10-0927 TCGA-10-0928 TCGA-10-0933 
      112.41        71.11        20.94        81.47        18.51        11.70 
TCGA-10-0935 TCGA-10-0938 TCGA-13-0717 TCGA-13-0730 TCGA-13-0762 TCGA-13-0794 
       35.44        19.86        24.59        17.82        32.25        30.35 
TCGA-13-0800 TCGA-13-0802 TCGA-13-0888 TCGA-13-0906 TCGA-13-0912 TCGA-13-0913 
        8.12         8.19        70.39        44.94        34.06        29.98 
TCGA-13-0920 TCGA-13-1407 TCGA-13-1409 TCGA-13-1477 TCGA-13-1487 TCGA-13-1489 
       13.81         6.05         6.84        54.64        22.39        82.88 
TCGA-13-2057 TCGA-13-2066 TCGA-20-0990 TCGA-23-1022 TCGA-23-1031 TCGA-23-1110 
       14.24         9.70        25.94        42.54        18.90        54.51 
TCGA-23-1114 TCGA-23-1121 TCGA-24-1424 TCGA-24-1430 TCGA-24-1544 TCGA-24-1550 
       68.68         6.38         6.02        28.37        26.96        41.06 
TCGA-24-1567 TCGA-24-2020 TCGA-24-2024 TCGA-24-2027 TCGA-25-1315 TCGA-25-1316 
       17.23       152.02        58.16       109.71        51.06        37.02 
TCGA-25-1317 TCGA-25-1323 TCGA-25-1632 TCGA-25-1634 TCGA-25-1871 TCGA-25-1877 
        1.02        12.00        56.94        35.54        24.99        18.05 
TCGA-25-2393 TCGA-29-1762 TCGA-29-1774 TCGA-29-2414 TCGA-29-2425 TCGA-29-2431 
       38.04        85.68        17.33        86.17        65.00        42.25 
TCGA-30-1714 TCGA-30-1853 TCGA-30-1859 TCGA-36-1575 TCGA-36-1577 TCGA-36-2537 
       38.07        36.26        48.10         8.55        25.74        25.91 
TCGA-36-2552 TCGA-42-2591 TCGA-59-2363 TCGA-59-2372 TCGA-61-1730 TCGA-61-1900 
       11.47        40.77         5.42        44.81         4.34         5.79 
TCGA-61-2088 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 
        4.77        65.52        55.50         6.48 

subtype1 subtype2 subtype3 
    0.30     0.26     1.02 
subtype1 subtype2 subtype3 
  129.96   180.20   152.02 
subtype1 subtype2 subtype3 
  28.570   24.720   32.055 
[1] "0.3 - 130.0 (28.6)" "0.3 - 180.2 (24.7)" "1.0 - 152.0 (32.1)"
D2V2, continuous
          vv
clus       OMENTUM OVARY PERITONEUM OVARY
  subtype1       1   312                0
  subtype2       1   157                2
  subtype3       0    89                0
D2V3, multiclass
                  clus
vv                 subtype1 subtype2 subtype3
  OMENTUM                 1        1        0
  OVARY                 312      157       89
  PERITONEUM OVARY        0        2        0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V4, continuous
D2V5, binary
          cls
clus         0   1
  subtype1   1 312
  subtype2   0 160
  subtype3   2  87
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  312
  subtype2    0  160
  subtype3    2   87
     clus
vv    subtype1 subtype2 subtype3
  NO         1        0        2
  YES      312      160       87
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2
  subtype1  8 11  0
  subtype2  2 12  1
  subtype3  4  4  0
D2V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0        8        2        4
  R1       11       12        4
  R2        0        1        0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    10                        14
  subtype2                                2     6                         6
  subtype3                                0     3                         4
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         1   273
  subtype2                                         0   136
  subtype3                                         0    76
D2V7, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 0        2        0
  ASIAN                                           10        6        3
  BLACK OR AFRICAN AMERICAN                       14        6        4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1        0        0
  WHITE                                          273      136       76
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
          cls
clus         0   1
  subtype1   8 178
  subtype2   0  93
  subtype3   3  57
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8  178
  subtype2    0   93
  subtype3    3   57
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            8        0        3
  NOT HISPANIC OR LATINO      178       93       57
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = MIR_CNMF
D3V1, survival
          sevent
clus2        0   1
  subtype1  68  88
  subtype2  70  92
  subtype3 124 113
subtype1 subtype2 subtype3 
     156      162      237 
subtype1 subtype2 subtype3 
      88       92      113 
$subtype1
TCGA-04-1331 TCGA-04-1338 TCGA-04-1343 TCGA-04-1348 TCGA-04-1351 TCGA-04-1362 
       40.24        46.62        11.87        48.76        65.46        44.32 
TCGA-04-1516 TCGA-04-1530 TCGA-04-1542 TCGA-04-1644 TCGA-04-1649 TCGA-04-1651 
       41.59       119.08        84.20        48.89        64.64        36.23 
TCGA-09-1664 TCGA-09-1665 TCGA-09-1670 TCGA-09-1672 TCGA-09-1675 TCGA-09-2044 
       74.93        41.62        17.98         5.85        97.55         6.12 
TCGA-09-2056 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0936 TCGA-10-0938 
       12.46        33.24        32.28        11.70        35.80        19.86 
TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0758 TCGA-13-0760 TCGA-13-0791 
        2.73        12.39        31.10        11.38        11.54        38.93 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0801 TCGA-13-0803 TCGA-13-0884 
       36.72        28.70        19.59         8.28        43.86       107.18 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0893 TCGA-13-0903 TCGA-13-0911 TCGA-13-0919 
       91.40        74.27        43.36        47.38        27.72        14.89 
TCGA-13-0924 TCGA-13-1404 TCGA-13-1484 TCGA-13-1485 TCGA-13-1488 TCGA-13-1494 
        6.08         6.61        98.04        20.68        70.82        38.20 
TCGA-13-1500 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2060 TCGA-13-2071 
       13.97         4.18         3.91         3.09         8.61         6.28 
TCGA-20-0987 TCGA-20-1686 TCGA-23-1024 TCGA-23-1028 TCGA-23-1032 TCGA-23-1116 
       23.05         2.93        15.39        49.41         2.24         4.57 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-2072 TCGA-23-2643 TCGA-24-0966 
       33.30        86.01       129.96        24.95         4.70         7.63 
TCGA-24-0970 TCGA-24-0979 TCGA-24-0980 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 
       11.64        41.56         7.66         6.31         6.38         7.82 
TCGA-24-1434 TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 TCGA-24-1550 TCGA-24-1551 
       18.67         8.55        12.46        45.14        41.06        51.91 
TCGA-24-1552 TCGA-24-1557 TCGA-24-1563 TCGA-24-1565 TCGA-24-1842 TCGA-24-1844 
       41.39        39.88        47.70        10.26         8.32         3.72 
TCGA-24-1846 TCGA-24-1850 TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 TCGA-24-2023 
        4.37         5.52        30.21        16.44        81.11        44.84 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2038 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 
       18.48        28.18        44.52         0.79         0.36        47.54 
TCGA-24-2281 TCGA-24-2289 TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 
       44.61        67.36        55.86        53.26        26.96        51.06 
TCGA-25-1320 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1627 TCGA-25-1628 
       36.95         2.99         2.96        18.58         0.36        20.61 
TCGA-25-1633 TCGA-25-1634 TCGA-25-2391 TCGA-25-2400 TCGA-25-2401 TCGA-25-2408 
       60.59        35.54        49.05        42.02         2.96        31.00 
TCGA-29-1688 TCGA-29-1694 TCGA-29-1695 TCGA-29-1698 TCGA-29-1702 TCGA-29-1711 
       78.90        38.53         0.79        68.32        18.67        34.62 
TCGA-29-1766 TCGA-29-1768 TCGA-29-2425 TCGA-29-2428 TCGA-30-1856 TCGA-30-1857 
       39.12        31.23        65.00        45.11        15.68         0.26 
TCGA-30-1869 TCGA-31-1946 TCGA-31-1959 TCGA-36-2529 TCGA-36-2534 TCGA-36-2537 
       51.39        30.18         2.20        35.05        29.82        25.91 
TCGA-36-2540 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-42-2582 TCGA-42-2587 
       23.80        20.52        14.17         6.05        26.04        23.74 
TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 TCGA-57-1584 TCGA-57-1586 TCGA-57-1994 
        7.46        40.77        24.03        21.14        22.32        25.02 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2354 TCGA-61-1724 TCGA-61-1895 TCGA-61-1903 
       22.32       116.12        34.39        20.94         1.45        13.02 
TCGA-61-1907 TCGA-61-1914 TCGA-61-1919 TCGA-61-2009 TCGA-61-2109 TCGA-61-2113 
       31.30        56.61        38.17        39.85        20.68        22.22 

$subtype2
TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1346 TCGA-04-1361 TCGA-04-1514 
       41.00         1.81         2.01        65.52        32.52        56.55 
TCGA-04-1525 TCGA-04-1648 TCGA-04-1655 TCGA-09-0364 TCGA-09-0369 TCGA-09-1661 
       38.37        28.64        45.37        29.16        35.57        38.43 
TCGA-09-1669 TCGA-09-2043 TCGA-09-2055 TCGA-10-0925 TCGA-10-0927 TCGA-10-0937 
       30.51         6.18        26.93        54.31        81.47        15.12 
TCGA-13-0714 TCGA-13-0727 TCGA-13-0755 TCGA-13-0757 TCGA-13-0766 TCGA-13-0768 
        6.21        15.19         2.50        11.18        21.40         8.45 
TCGA-13-0800 TCGA-13-0805 TCGA-13-0807 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 
        8.12        35.28        13.61        70.39        61.84        67.99 
TCGA-13-0894 TCGA-13-0897 TCGA-13-0900 TCGA-13-0906 TCGA-13-0913 TCGA-13-1405 
       49.61        57.47        57.07        44.94        29.98         7.36 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 TCGA-13-1483 TCGA-13-1487 TCGA-13-1495 
        4.21         5.33        87.06        29.42        22.39        49.25 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1510 TCGA-13-2057 TCGA-13-2059 
       32.84        16.57         4.21         2.56        14.24        12.23 
TCGA-20-1682 TCGA-20-1687 TCGA-23-1023 TCGA-23-1027 TCGA-23-1029 TCGA-23-1114 
       27.52         2.66        40.54        31.76         8.81        68.68 
TCGA-23-1120 TCGA-23-1809 TCGA-23-2077 TCGA-23-2647 TCGA-24-0968 TCGA-24-0975 
        4.27         0.53       115.89         4.44        19.66        21.80 
TCGA-24-0982 TCGA-24-1104 TCGA-24-1105 TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 
       22.32        63.55        47.41         0.76         6.25         5.95 
TCGA-24-1427 TCGA-24-1467 TCGA-24-1545 TCGA-24-1546 TCGA-24-1549 TCGA-24-1553 
        4.83       105.99        57.40        64.27        56.58        58.09 
TCGA-24-1562 TCGA-24-1567 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1847 
       45.50        17.23        88.37        48.33        38.24        11.28 
TCGA-24-1849 TCGA-24-1923 TCGA-24-2019 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 
        5.79        22.68         4.87        58.16       109.71        14.43 
TCGA-24-2254 TCGA-24-2271 TCGA-24-2293 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
       57.07        31.63        16.64        37.02         1.02        34.98 
TCGA-25-1321 TCGA-25-1323 TCGA-25-1326 TCGA-25-1328 TCGA-25-1625 TCGA-25-1626 
       33.96        12.00        31.07        65.06        18.02        15.81 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1635 TCGA-25-2042 TCGA-25-2396 TCGA-25-2398 
        7.86         0.30        51.22        13.02         3.02        45.01 
TCGA-25-2404 TCGA-29-1691 TCGA-29-1693 TCGA-29-1696 TCGA-29-1705 TCGA-29-1710 
       29.03        47.18       101.79        33.70        18.25        29.23 
TCGA-29-1763 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 TCGA-29-1778 
       66.81        24.36        22.55        17.33        11.84        14.93 
TCGA-29-1783 TCGA-29-2414 TCGA-29-2427 TCGA-29-2432 TCGA-29-2436 TCGA-30-1855 
        7.23        86.17        62.47        11.84         9.76         2.47 
TCGA-30-1861 TCGA-30-1862 TCGA-30-1867 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 
       34.78         6.12         1.22        24.26        30.05        48.79 
TCGA-31-1944 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1574 
       45.57        42.51        44.12        28.77        29.10        22.55 
TCGA-36-1580 TCGA-36-2538 TCGA-36-2542 TCGA-42-2588 TCGA-57-1585 TCGA-57-1993 
       24.23        25.08        21.60         9.44         1.74        25.08 
TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 TCGA-61-1721 TCGA-61-1722 TCGA-61-1730 
        9.40         2.14         5.42        11.11         8.09         4.34 
TCGA-61-1736 TCGA-61-1899 TCGA-61-1901 TCGA-61-1904 TCGA-61-1906 TCGA-61-1998 
       48.79         8.42        11.41         9.07        34.13         5.52 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
       17.98         4.01        30.64         1.18        45.96        45.40 
TCGA-61-2095 TCGA-61-2097 TCGA-61-2101 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       61.64        60.62        55.50         6.35        31.07         8.61 

$subtype3
TCGA-04-1336 TCGA-04-1342 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 
       49.15        18.51        63.09        21.57        63.98        49.28 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1369 TCGA-04-1371 TCGA-04-1517 
       33.67        76.57        71.47        21.11        82.39        19.99 
TCGA-04-1638 TCGA-04-1646 TCGA-04-1652 TCGA-04-1654 TCGA-09-0365 TCGA-09-0366 
       55.43        27.88        31.86        47.70         9.47        57.76 
TCGA-09-0367 TCGA-09-1659 TCGA-09-1662 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 
       17.98         9.99        89.33        57.60        61.87        55.36 
TCGA-09-1673 TCGA-09-1674 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 
        3.02         8.55        35.15         4.54       112.41        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-10-0926 TCGA-10-0928 TCGA-10-0934 
       63.09        39.75        20.94        25.91        18.51         3.91 
TCGA-10-0935 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0730 TCGA-13-0751 
       35.44        24.59        44.55        39.58        17.82        55.17 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0765 TCGA-13-0794 TCGA-13-0797 
       34.06        32.25        31.04        28.57        30.35         8.71 
TCGA-13-0799 TCGA-13-0802 TCGA-13-0804 TCGA-13-0883 TCGA-13-0887 TCGA-13-0891 
        7.79         8.19        35.28        68.94        66.67        69.01 
TCGA-13-0899 TCGA-13-0901 TCGA-13-0904 TCGA-13-0905 TCGA-13-0908 TCGA-13-0910 
       56.15        19.36        48.33        47.84        44.84        37.08 
TCGA-13-0912 TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-1403 
       34.06        21.17        13.81         4.64         6.41        10.88 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1477 TCGA-13-1482 
        6.05         5.92         6.84         4.70        54.64        61.71 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
       82.88        52.44        73.55         4.24        54.31        37.61 
TCGA-13-1499 TCGA-13-1506 TCGA-13-1507 TCGA-13-2061 TCGA-13-2065 TCGA-13-2066 
       38.40         4.41         4.77        10.78         8.75         9.70 
TCGA-20-0990 TCGA-20-0991 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-23-1021 
       25.94        26.20        25.38        19.10        16.70        47.54 
TCGA-23-1022 TCGA-23-1026 TCGA-23-1030 TCGA-23-1031 TCGA-23-1107 TCGA-23-1109 
       42.54        26.83        29.13        18.90         0.30        51.35 
TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 
       54.51         3.22        31.20         6.38        39.09        33.47 
TCGA-23-1124 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
       58.13        87.48        91.66        77.00        49.84         2.76 
TCGA-23-2645 TCGA-23-2649 TCGA-24-1103 TCGA-24-1418 TCGA-24-1419 TCGA-24-1424 
        4.50         3.81        54.12         7.99         7.86         6.02 
TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 TCGA-24-1463 
        5.36        17.39        28.37        19.17        43.53        72.92 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1548 
        9.11         3.45         1.18        22.22        26.96        16.21 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1558 TCGA-24-1560 TCGA-24-1564 TCGA-24-1603 
       88.50        70.62        19.53        44.09        25.87        90.15 
TCGA-24-1843 TCGA-24-1845 TCGA-24-1920 TCGA-24-1928 TCGA-24-2020 TCGA-24-2026 
        3.48         3.81         9.80        11.05       152.02        34.82 
TCGA-24-2030 TCGA-24-2036 TCGA-24-2260 TCGA-24-2280 TCGA-24-2288 TCGA-24-2290 
       53.95        64.01        36.16        70.45         0.82        36.23 
TCGA-24-2295 TCGA-25-1312 TCGA-25-1314 TCGA-25-1319 TCGA-25-1324 TCGA-25-1325 
       33.11         1.02        32.02        65.00        34.03        32.09 
TCGA-25-1632 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2392 
       56.94        14.96        24.99        18.05        85.05         1.02 
TCGA-25-2393 TCGA-25-2397 TCGA-25-2399 TCGA-25-2409 TCGA-29-1690 TCGA-29-1697 
       38.04        12.00        19.99        26.99        44.71        31.20 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 TCGA-29-1707 TCGA-29-1761 TCGA-29-1762 
        0.53        16.90        59.67        41.98        17.00        85.68 
TCGA-29-1764 TCGA-29-1769 TCGA-29-1775 TCGA-29-1777 TCGA-29-1781 TCGA-29-1784 
       62.93        22.98        12.36        12.30         8.38         5.36 
TCGA-29-1785 TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 TCGA-30-1714 TCGA-30-1718 
       34.62         4.90        42.25        11.47        38.07        51.91 
TCGA-30-1853 TCGA-30-1859 TCGA-30-1860 TCGA-30-1866 TCGA-30-1880 TCGA-31-1950 
       36.26        48.10        44.91        36.62        57.57        18.77 
TCGA-31-1951 TCGA-31-1953 TCGA-36-1570 TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 
       22.49         6.71        21.53        22.85         8.55        30.08 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 TCGA-36-2543 
       25.74        27.85        24.69        33.01        29.49         2.24 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2551 TCGA-36-2552 TCGA-42-2589 TCGA-57-1583 
       20.98        18.31        16.18        11.47        42.02        11.38 
TCGA-57-1992 TCGA-59-2348 TCGA-59-2349 TCGA-59-2372 TCGA-61-1725 TCGA-61-1727 
       29.00       180.20        80.12        44.81        31.43        18.54 
TCGA-61-1728 TCGA-61-1733 TCGA-61-1734 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 
       27.88        31.79        28.47        44.84        35.80         2.43 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1900 TCGA-61-1910 TCGA-61-1913 TCGA-61-1915 
       33.67        43.69         5.79        37.05        48.92        67.76 
TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 TCGA-61-2000 TCGA-61-2012 TCGA-61-2087 
       43.43        15.75         2.01        14.50        30.64         4.80 
TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2096 TCGA-61-2098 TCGA-61-2102 
        4.77        51.72        71.74        58.39        65.52         6.48 
TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 
       76.87        44.52       125.75 

subtype1 subtype2 subtype3 
    0.26     0.30     0.30 
subtype1 subtype2 subtype3 
  129.96   115.89   180.20 
subtype1 subtype2 subtype3 
   27.34    24.72    30.35 
[1] "0.3 - 130.0 (27.3)" "0.3 - 115.9 (24.7)" "0.3 - 180.2 (30.4)"
D3V2, continuous
          vv
clus       OMENTUM OVARY PERITONEUM OVARY
  subtype1       0   155                2
  subtype2       1   164                0
  subtype3       1   237                0
D3V3, multiclass
                  clus
vv                 subtype1 subtype2 subtype3
  OMENTUM                 0        1        1
  OVARY                 155      164      237
  PERITONEUM OVARY        2        0        0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V4, continuous
D3V5, binary
          cls
clus         0   1
  subtype1   0 157
  subtype2   0 165
  subtype3   3 235
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0  157
  subtype2    0  165
  subtype3    3  235
     clus
vv    subtype1 subtype2 subtype3
  NO         0        0        3
  YES      157      165      235
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2
  subtype1  4 12  0
  subtype2  3  9  1
  subtype3  7  6  0
D3V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0        4        3        7
  R1       12        9        6
  R2        0        1        0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     2                         8
  subtype2                                2     6                         5
  subtype3                                0    11                        10
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0   136
  subtype2                                         0   143
  subtype3                                         1   205
D3V7, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 0        2        0
  ASIAN                                            2        6       11
  BLACK OR AFRICAN AMERICAN                        8        5       10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        1
  WHITE                                          136      143      205
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
          cls
clus         0   1
  subtype1   5  86
  subtype2   1  97
  subtype3   5 144
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   86
  subtype2    1   97
  subtype3    5  144
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            5        1        5
  NOT HISPANIC OR LATINO       86       97      144
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = MIR_CHIERARCHICAL
D4V1, survival
           sevent
clus2        0  1
  subtype1  36 46
  subtype10 28 28
  subtype2  21 35
  subtype3  44 42
  subtype4  10 25
  subtype5  38 36
  subtype6  17 19
  subtype7  23 13
  subtype8  25 25
  subtype9  20 24
 subtype1 subtype10  subtype2  subtype3  subtype4  subtype5  subtype6  subtype7 
       82        56        56        86        35        74        36        36 
 subtype8  subtype9 
       50        44 
 subtype1 subtype10  subtype2  subtype3  subtype4  subtype5  subtype6  subtype7 
       46        28        35        42        25        36        19        13 
 subtype8  subtype9 
       25        24 
$subtype1
TCGA-04-1331 TCGA-04-1362 TCGA-04-1516 TCGA-04-1530 TCGA-04-1644 TCGA-04-1651 
       40.24        44.32        41.59       119.08        48.89        36.23 
TCGA-09-1672 TCGA-09-2056 TCGA-10-0931 TCGA-13-0724 TCGA-13-0726 TCGA-13-0760 
        5.85        12.46        32.28         2.73        31.10        11.54 
TCGA-13-0791 TCGA-13-0801 TCGA-13-0886 TCGA-13-0919 TCGA-13-1404 TCGA-13-1485 
       38.93         8.28        74.27        14.89         6.61        20.68 
TCGA-13-1494 TCGA-13-1500 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2071 
       38.20        13.97         4.18         3.91         3.09         6.28 
TCGA-20-0987 TCGA-20-1686 TCGA-23-1024 TCGA-23-1028 TCGA-23-1116 TCGA-23-1117 
       23.05         2.93        15.39        49.41         4.57        33.30 
TCGA-23-1119 TCGA-23-1120 TCGA-23-2072 TCGA-23-2643 TCGA-24-0970 TCGA-24-0980 
      129.96         4.27        24.95         4.70        11.64         7.66 
TCGA-24-1416 TCGA-24-1464 TCGA-24-1550 TCGA-24-1551 TCGA-24-1557 TCGA-24-1563 
        6.38        12.46        41.06        51.91        39.88        47.70 
TCGA-24-1565 TCGA-24-1846 TCGA-24-1850 TCGA-24-1930 TCGA-24-2023 TCGA-24-2038 
       10.26         4.37         5.52        81.11        44.84        44.52 
TCGA-24-2254 TCGA-24-2261 TCGA-24-2262 TCGA-24-2281 TCGA-24-2297 TCGA-24-2298 
       57.07         0.79         0.36        44.61        55.86        53.26 
TCGA-25-1313 TCGA-25-1320 TCGA-25-1322 TCGA-25-1329 TCGA-25-1627 TCGA-25-1628 
       26.96        36.95         2.99         2.96         0.36        20.61 
TCGA-25-1633 TCGA-25-2391 TCGA-25-2408 TCGA-29-1694 TCGA-29-1711 TCGA-29-1768 
       60.59        49.05        31.00        38.53        34.62        31.23 
TCGA-29-2428 TCGA-30-1857 TCGA-31-1946 TCGA-31-1959 TCGA-36-1580 TCGA-36-2529 
       45.11         0.26        30.18         2.20        24.23        35.05 
TCGA-36-2537 TCGA-36-2540 TCGA-36-2547 TCGA-42-2587 TCGA-42-2590 TCGA-57-1582 
       25.91        23.80        20.52        23.74         7.46        24.03 
TCGA-59-2351 TCGA-59-2354 TCGA-61-1914 TCGA-61-2009 
      116.12        34.39        56.61        39.85 

$subtype10
TCGA-04-1525 TCGA-09-1664 TCGA-09-1675 TCGA-09-2043 TCGA-09-2045 TCGA-09-2055 
       38.37        74.93        97.55         6.18        35.15        26.93 
TCGA-10-0925 TCGA-10-0936 TCGA-10-0938 TCGA-13-0751 TCGA-13-0755 TCGA-13-0912 
       54.31        35.80        19.86        55.17         2.50        34.06 
TCGA-13-0913 TCGA-13-1477 TCGA-13-1489 TCGA-13-2059 TCGA-20-1685 TCGA-23-2077 
       29.98        54.64        82.88        12.23        16.70       115.89 
TCGA-24-0966 TCGA-24-0979 TCGA-24-1103 TCGA-24-1413 TCGA-24-1426 TCGA-24-1844 
        7.63        41.56        54.12         6.31         5.36         3.72 
TCGA-24-1923 TCGA-24-2019 TCGA-24-2036 TCGA-25-1317 TCGA-25-1321 TCGA-25-1625 
       22.68         4.87        64.01         1.02        33.96        18.02 
TCGA-25-1870 TCGA-25-2404 TCGA-29-1695 TCGA-29-1703 TCGA-29-1771 TCGA-29-1783 
       14.96        29.03         0.79        59.67        22.55         7.23 
TCGA-36-1570 TCGA-36-1571 TCGA-36-2538 TCGA-42-2582 TCGA-42-2591 TCGA-57-1993 
       21.53        22.85        25.08        26.04        40.77        25.08 
TCGA-59-2352 TCGA-61-1721 TCGA-61-1728 TCGA-61-1734 TCGA-61-1736 TCGA-61-1899 
        9.40        11.11        27.88        28.47        48.79         8.42 
TCGA-61-1901 TCGA-61-1904 TCGA-61-1906 TCGA-61-1918 TCGA-61-2008 TCGA-61-2018 
       11.41         9.07        34.13        15.75        30.64        45.40 
TCGA-61-2096 TCGA-61-2102 
       58.39         6.48 

$subtype2
TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 TCGA-04-1517 
       41.00         1.81         2.01        18.51        11.87        19.99 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1652 
       84.20        55.43        27.88        28.64        64.64        31.86 
TCGA-09-1661 TCGA-09-1670 TCGA-10-0928 TCGA-13-0921 TCGA-13-1482 TCGA-13-1487 
       38.43        17.98        18.51         4.64        61.71        22.39 
TCGA-13-1488 TCGA-13-1491 TCGA-13-1506 TCGA-20-1684 TCGA-23-1031 TCGA-23-1111 
       70.82        52.44         4.41        19.10        18.90         3.22 
TCGA-23-2641 TCGA-24-0982 TCGA-24-1435 TCGA-24-1467 TCGA-24-1544 TCGA-24-1552 
        2.76        22.32        43.53       105.99        26.96        41.39 
TCGA-24-1556 TCGA-24-1603 TCGA-24-1616 TCGA-24-1842 TCGA-24-1845 TCGA-24-2024 
       70.62        90.15        38.24         8.32         3.81        58.16 
TCGA-25-1315 TCGA-25-1319 TCGA-25-1630 TCGA-25-1631 TCGA-25-2400 TCGA-29-1707 
       51.06        65.00         7.86         0.30        42.02        41.98 
TCGA-29-1778 TCGA-29-2425 TCGA-31-1955 TCGA-36-1574 TCGA-36-2548 TCGA-36-2549 
       14.93        65.00        42.51        22.55        14.17         6.05 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1994 TCGA-61-1724 TCGA-61-1915 TCGA-61-1995 
       11.38        21.14        25.02        20.94        67.76         2.01 
TCGA-61-2095 TCGA-61-2097 
       61.64        60.62 

$subtype3
TCGA-04-1336 TCGA-04-1349 TCGA-04-1351 TCGA-04-1356 TCGA-04-1365 TCGA-04-1367 
       49.15        21.57        65.46        49.28        76.57        71.47 
TCGA-04-1369 TCGA-04-1371 TCGA-04-1654 TCGA-09-0367 TCGA-09-1659 TCGA-09-1666 
       21.11        82.39        47.70        17.98         9.99        57.60 
TCGA-09-2051 TCGA-10-0930 TCGA-10-0934 TCGA-13-0720 TCGA-13-0723 TCGA-13-0764 
       63.09        33.24         3.91        44.55        39.58        31.04 
TCGA-13-0765 TCGA-13-0797 TCGA-13-0804 TCGA-13-0887 TCGA-13-0901 TCGA-13-0905 
       28.57         8.71        35.28        66.67        19.36        47.84 
TCGA-13-0908 TCGA-13-0916 TCGA-13-0923 TCGA-13-1403 TCGA-13-1408 TCGA-13-1410 
       44.84        21.17         6.41        10.88         5.92         4.70 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-2061 TCGA-23-1021 TCGA-23-1026 
        4.24        54.31        37.61        10.78        47.54        26.83 
TCGA-23-1032 TCGA-23-1107 TCGA-23-1118 TCGA-23-1123 TCGA-23-1124 TCGA-23-2079 
        2.24         0.30        86.01        33.47        58.13        91.66 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2649 TCGA-24-1422 TCGA-24-1430 TCGA-24-1436 
       77.00        49.84         3.81         0.76        28.37         8.55 
TCGA-24-1466 TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 TCGA-24-1548 TCGA-24-1555 
       45.14         9.11         1.18        22.22        16.21        88.50 
TCGA-24-1560 TCGA-24-1843 TCGA-24-2030 TCGA-24-2288 TCGA-24-2290 TCGA-25-1314 
       44.09         3.48        53.95         0.82        36.23        32.02 
TCGA-25-1632 TCGA-25-1878 TCGA-25-2397 TCGA-25-2409 TCGA-29-1781 TCGA-29-1784 
       56.94        85.05        12.00        26.99         8.38         5.36 
TCGA-29-2434 TCGA-30-1860 TCGA-30-1866 TCGA-31-1950 TCGA-31-1953 TCGA-36-1576 
       11.47        44.91        36.62        18.77         6.71        30.08 
TCGA-36-1578 TCGA-36-2530 TCGA-36-2532 TCGA-36-2543 TCGA-36-2551 TCGA-59-2349 
       27.85        33.01        29.49         2.24        16.18        80.12 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1910 TCGA-61-2000 TCGA-61-2087 
       44.84        35.80         2.43        37.05        14.50         4.80 
TCGA-61-2092 TCGA-61-2111 
       51.72       125.75 

$subtype4
TCGA-04-1338 TCGA-09-1665 TCGA-13-0725 TCGA-13-0766 TCGA-13-0793 TCGA-13-0807 
       46.62        41.62        12.39        21.40        28.70        13.61 
TCGA-13-0900 TCGA-13-0911 TCGA-13-0924 TCGA-24-0968 TCGA-24-1434 TCGA-24-1545 
       57.07        27.72         6.08        19.66        18.67        57.40 
TCGA-24-1546 TCGA-24-1928 TCGA-24-2033 TCGA-24-2035 TCGA-24-2260 TCGA-24-2289 
       64.27        11.05        18.48        28.18        36.16        67.36 
TCGA-25-1326 TCGA-25-1623 TCGA-25-1626 TCGA-25-2401 TCGA-29-1693 TCGA-29-1698 
       31.07        18.58        15.81         2.96       101.79        68.32 
TCGA-29-1701 TCGA-29-1766 TCGA-30-1856 TCGA-30-1867 TCGA-30-1869 TCGA-61-1895 
       16.90        39.12        15.68         1.22        51.39         1.45 
TCGA-61-1919 TCGA-61-1998 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 
       38.17         5.52        22.22         6.35        31.07 

$subtype5
TCGA-04-1346 TCGA-09-1662 TCGA-09-1673 TCGA-09-2053 TCGA-09-2054 TCGA-10-0927 
       65.52        89.33         3.02        39.75        20.94        81.47 
TCGA-13-0727 TCGA-13-0757 TCGA-13-0761 TCGA-13-0768 TCGA-13-0799 TCGA-13-0805 
       15.19        11.18        34.06         8.45         7.79        35.28 
TCGA-13-0883 TCGA-13-0889 TCGA-13-0890 TCGA-13-0910 TCGA-13-1405 TCGA-13-1411 
       68.94        61.84        67.99        37.08         7.36         4.21 
TCGA-13-1481 TCGA-13-1495 TCGA-13-1499 TCGA-13-1505 TCGA-13-1507 TCGA-20-1683 
       87.06        49.25        38.40         4.21         4.77        25.38 
TCGA-23-1023 TCGA-23-1109 TCGA-23-1122 TCGA-24-0975 TCGA-24-1423 TCGA-24-1425 
       40.54        51.35        39.09        21.80         6.25         5.95 
TCGA-24-1428 TCGA-24-1463 TCGA-24-1470 TCGA-24-1553 TCGA-24-1564 TCGA-24-1604 
       17.39        72.92         3.45        58.09        25.87        88.37 
TCGA-24-1614 TCGA-24-1849 TCGA-24-2026 TCGA-24-2271 TCGA-24-2280 TCGA-24-2293 
       48.33         5.79        34.82        31.63        70.45        16.64 
TCGA-25-1328 TCGA-25-2042 TCGA-25-2396 TCGA-25-2398 TCGA-29-1710 TCGA-29-1763 
       65.06        13.02         3.02        45.01        29.23        66.81 
TCGA-29-1764 TCGA-29-1769 TCGA-29-1770 TCGA-29-1777 TCGA-29-1785 TCGA-29-2414 
       62.93        22.98        24.36        12.30        34.62        86.17 
TCGA-29-2427 TCGA-29-2431 TCGA-29-2432 TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 
       62.47        42.25        11.84        38.07        51.91         2.47 
TCGA-30-1862 TCGA-30-1892 TCGA-31-1951 TCGA-31-1956 TCGA-36-2542 TCGA-36-2544 
        6.12        48.79        22.49        44.12        21.60        20.98 
TCGA-57-1585 TCGA-57-1586 TCGA-59-2348 TCGA-61-2003 TCGA-61-2101 TCGA-61-2104 
        1.74        22.32       180.20         4.01        55.50        76.87 
TCGA-61-2110 TCGA-61-2614 
       44.52         8.61 

$subtype6
TCGA-04-1347 TCGA-04-1350 TCGA-09-0365 TCGA-09-2050 TCGA-10-0935 TCGA-13-0762 
       63.09        63.98         9.47        71.11        35.44        32.25 
TCGA-13-0794 TCGA-13-0899 TCGA-13-0904 TCGA-13-1407 TCGA-13-1409 TCGA-13-1492 
       30.35        56.15        48.33         6.05         6.84        73.55 
TCGA-13-2066 TCGA-20-0990 TCGA-23-1030 TCGA-23-1110 TCGA-23-1113 TCGA-24-1424 
        9.70        25.94        29.13        54.51        31.20         6.02 
TCGA-24-1431 TCGA-24-1558 TCGA-24-2295 TCGA-25-1312 TCGA-25-1324 TCGA-29-1696 
       19.17        19.53        33.11         1.02        34.03        33.70 
TCGA-29-1697 TCGA-29-1761 TCGA-29-2429 TCGA-30-1853 TCGA-30-1859 TCGA-30-1880 
       31.20        17.00         4.90        36.26        48.10        57.57 
TCGA-36-1575 TCGA-59-2372 TCGA-61-1733 TCGA-61-1743 TCGA-61-1917 TCGA-61-2088 
        8.55        44.81        31.79        43.69        43.43         4.77 

$subtype7
TCGA-04-1348 TCGA-09-1667 TCGA-09-1668 TCGA-09-2044 TCGA-13-0758 TCGA-13-0795 
       48.76        61.87        55.36         6.12        11.38        19.59 
TCGA-13-0885 TCGA-13-0891 TCGA-13-1484 TCGA-13-2060 TCGA-13-2065 TCGA-20-0991 
       91.40        69.01        98.04         8.61         8.75        26.20 
TCGA-23-2078 TCGA-24-1417 TCGA-24-1924 TCGA-24-1927 TCGA-24-2029 TCGA-24-2267 
       87.48         7.82        30.21        16.44        14.43        47.54 
TCGA-25-1325 TCGA-25-1635 TCGA-29-1688 TCGA-29-1690 TCGA-29-1699 TCGA-36-1581 
       32.09        51.22        78.90        44.71         0.53        24.69 
TCGA-36-2534 TCGA-36-2545 TCGA-42-2589 TCGA-59-2350 TCGA-61-1722 TCGA-61-1727 
       29.82        18.31        42.02        22.32         8.09        18.54 
TCGA-61-1903 TCGA-61-1907 TCGA-61-1913 TCGA-61-2012 TCGA-61-2094 TCGA-61-2109 
       13.02        31.30        48.92        30.64        71.74        20.68 

$subtype8
TCGA-04-1364 TCGA-04-1514 TCGA-04-1655 TCGA-09-0364 TCGA-09-0369 TCGA-09-1669 
       33.67        56.55        45.37        29.16        35.57        30.51 
TCGA-09-1674 TCGA-09-2048 TCGA-09-2049 TCGA-10-0926 TCGA-10-0933 TCGA-13-0717 
        8.55         4.54       112.41        25.91        11.70        24.59 
TCGA-13-0730 TCGA-13-0800 TCGA-13-0802 TCGA-13-0888 TCGA-13-0906 TCGA-13-0920 
       17.82         8.12         8.19        70.39        44.94        13.81 
TCGA-13-2057 TCGA-20-1682 TCGA-23-1022 TCGA-23-1029 TCGA-23-1114 TCGA-23-1121 
       14.24        27.52        42.54         8.81        68.68         6.38 
TCGA-23-1809 TCGA-23-2645 TCGA-24-1418 TCGA-24-1419 TCGA-24-1567 TCGA-24-1920 
        0.53         4.50         7.99         7.86        17.23         9.80 
TCGA-24-2020 TCGA-24-2027 TCGA-25-1316 TCGA-25-1323 TCGA-25-1634 TCGA-25-1871 
      152.02       109.71        37.02        12.00        35.54        24.99 
TCGA-25-1877 TCGA-25-2393 TCGA-29-1702 TCGA-29-1762 TCGA-29-1774 TCGA-29-1775 
       18.05        38.04        18.67        85.68        17.33        12.36 
TCGA-36-1577 TCGA-36-2552 TCGA-57-1992 TCGA-59-2363 TCGA-61-1730 TCGA-61-1741 
       25.74        11.47        29.00         5.42         4.34        33.67 
TCGA-61-1900 TCGA-61-2098 
        5.79        65.52 

$subtype9
TCGA-04-1361 TCGA-09-0366 TCGA-10-0937 TCGA-13-0714 TCGA-13-0792 TCGA-13-0803 
       32.52        57.76        15.12         6.21        36.72        43.86 
TCGA-13-0884 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0903 TCGA-13-1412 
      107.18        43.36        49.61        57.47        47.38         5.33 
TCGA-13-1483 TCGA-13-1501 TCGA-13-1504 TCGA-13-1510 TCGA-20-1687 TCGA-23-1027 
       29.42        32.84        16.57         2.56         2.66        31.76 
TCGA-23-2647 TCGA-24-1104 TCGA-24-1105 TCGA-24-1427 TCGA-24-1549 TCGA-24-1562 
        4.44        63.55        47.41         4.83        56.58        45.50 
TCGA-24-1847 TCGA-25-1318 TCGA-25-2392 TCGA-25-2399 TCGA-29-1691 TCGA-29-1705 
       11.28        34.98         1.02        19.99        47.18        18.25 
TCGA-29-1776 TCGA-29-2436 TCGA-30-1861 TCGA-30-1887 TCGA-30-1891 TCGA-31-1944 
       11.84         9.76        34.78        24.26        30.05        45.57 
TCGA-36-1568 TCGA-36-1569 TCGA-42-2588 TCGA-59-2355 TCGA-61-1725 TCGA-61-2002 
       28.77        29.10         9.44         2.14        31.43        17.98 
TCGA-61-2016 TCGA-61-2017 
        1.18        45.96 

 subtype1 subtype10  subtype2  subtype3  subtype4  subtype5  subtype6  subtype7 
     0.26      0.79      0.30      0.30      1.22      1.74      1.02      0.53 
 subtype8  subtype9 
     0.53      1.02 
 subtype1 subtype10  subtype2  subtype3  subtype4  subtype5  subtype6  subtype7 
   129.96    115.89    105.99    125.75    101.79    180.20     73.55     98.04 
 subtype8  subtype9 
   152.02    107.18 
 subtype1 subtype10  subtype2  subtype3  subtype4  subtype5  subtype6  subtype7 
   25.430    25.560    25.990    30.560    22.220    34.340    32.020    30.015 
 subtype8  subtype9 
   21.630    29.735 
 [1] "0.3 - 130.0 (25.4)" "0.8 - 115.9 (25.6)" "0.3 - 106.0 (26.0)"
 [4] "0.3 - 125.8 (30.6)" "1.2 - 101.8 (22.2)" "1.7 - 180.2 (34.3)"
 [7] "1.0 - 73.5 (32.0)"  "0.5 - 98.0 (30.0)"  "0.5 - 152.0 (21.6)"
[10] "1.0 - 107.2 (29.7)"
D4V2, continuous
           vv
clus        OMENTUM OVARY PERITONEUM OVARY
  subtype1        0    81                1
  subtype10       0    57                0
  subtype2        0    58                0
  subtype3        1    85                0
  subtype4        0    34                1
  subtype5        1    74                0
  subtype6        0    36                0
  subtype7        0    36                0
  subtype8        0    51                0
  subtype9        0    44                0
D4V3, multiclass
                  clus
vv                 subtype1 subtype10 subtype2 subtype3 subtype4 subtype5
  OMENTUM                 0         0        0        1        0        1
  OVARY                  81        57       58       85       34       74
  PERITONEUM OVARY        1         0        0        0        1        0
                  clus
vv                 subtype6 subtype7 subtype8 subtype9
  OMENTUM                 0        0        0        0
  OVARY                  36       36       51       44
  PERITONEUM OVARY        0        0        0        0
[1]  3 10
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V4, continuous
D4V5, binary
           cls
clus         0  1
  subtype1   0 82
  subtype10  0 57
  subtype2   0 58
  subtype3   0 86
  subtype4   0 35
  subtype5   1 74
  subtype6   0 36
  subtype7   1 35
  subtype8   1 50
  subtype9   0 44
[1] "tbl2"
           cls
clus        [,1] [,2]
  subtype1     0   82
  subtype10    0   57
  subtype2     0   58
  subtype3     0   86
  subtype4     0   35
  subtype5     1   74
  subtype6     0   36
  subtype7     1   35
  subtype8     1   50
  subtype9     0   44
     clus
vv    subtype1 subtype10 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO         0         0        0        0        0        1        0        1
  YES       82        57       58       86       35       74       36       35
     clus
vv    subtype8 subtype9
  NO         1        0
  YES       50       44
[1]  2 10
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
           vv
clus        R0 R1 R2
  subtype1   2  7  0
  subtype10  2  1  0
  subtype2   1  2  0
  subtype3   2  4  0
  subtype4   0  5  0
  subtype5   1  6  0
  subtype6   1  1  0
  subtype7   2  1  0
  subtype8   2  0  0
  subtype9   1  0  1
D4V6, multiclass
[1] "Remove cluster labels:" "subtype6"               "subtype8"              
[4] "subtype9"              
clus
 subtype1 subtype10  subtype2  subtype3  subtype4  subtype5  subtype6  subtype7 
        9         3         3         6         5         7         2         3 
 subtype8  subtype9 
        2         2 
 [1] "subtype3"  "subtype1"  "subtype1"  "subtype4"  "subtype4"  "subtype4" 
 [7] "subtype5"  "subtype2"  "subtype5"  "subtype1"  "subtype5"  "subtype5" 
[13] "subtype3"  "subtype1"  "subtype3"  "subtype3"  "subtype7"  "subtype1" 
[19] "subtype10" "subtype1"  "subtype5"  "subtype3"  "subtype5"  "subtype7" 
[25] "subtype1"  "subtype2"  "subtype2"  "subtype3"  "subtype10" "subtype1" 
[31] "subtype7"  "subtype1"  "subtype10" "subtype4"  "subtype4"  "subtype5" 
    clus
vv   subtype1 subtype10 subtype2 subtype3 subtype4 subtype5 subtype7
  R0        2         2        1        2        0        1        2
  R1        7         1        2        4        5        6        1
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
           vv
clus        AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                 0     1                         3
  subtype10                                1     2                         4
  subtype2                                 0     2                         5
  subtype3                                 0     4                         4
  subtype4                                 0     0                         1
  subtype5                                 1     3                         2
  subtype6                                 0     1                         0
  subtype7                                 0     1                         1
  subtype8                                 0     4                         1
  subtype9                                 0     1                         2
           vv
clus        NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                          0    71
  subtype10                                         0    47
  subtype2                                          0    47
  subtype3                                          1    73
  subtype4                                          0    33
  subtype5                                          0    66
  subtype6                                          0    34
  subtype7                                          0    32
  subtype8                                          0    42
  subtype9                                          0    39
D4V7, multiclass
                                           clus
vv                                          subtype1 subtype10 subtype2
  AMERICAN INDIAN OR ALASKA NATIVE                 0         1        0
  ASIAN                                            1         2        2
  BLACK OR AFRICAN AMERICAN                        3         4        5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0         0        0
  WHITE                                           71        47       47
                                           clus
vv                                          subtype3 subtype4 subtype5 subtype6
  AMERICAN INDIAN OR ALASKA NATIVE                 0        0        1        0
  ASIAN                                            4        0        3        1
  BLACK OR AFRICAN AMERICAN                        4        1        2        0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1        0        0        0
  WHITE                                           73       33       66       34
                                           clus
vv                                          subtype7 subtype8 subtype9
  AMERICAN INDIAN OR ALASKA NATIVE                 0        0        0
  ASIAN                                            1        4        1
  BLACK OR AFRICAN AMERICAN                        1        1        2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        0
  WHITE                                           32       42       39
[1]  5 10
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
           cls
clus         0  1
  subtype1   3 45
  subtype10  0 36
  subtype2   0 24
  subtype3   3 56
  subtype4   1 18
  subtype5   1 44
  subtype6   2 23
  subtype7   1 19
  subtype8   0 34
  subtype9   0 28
[1] "tbl2"
           cls
clus        [,1] [,2]
  subtype1     3   45
  subtype10    0   36
  subtype2     0   24
  subtype3     3   56
  subtype4     1   18
  subtype5     1   44
  subtype6     2   23
  subtype7     1   19
  subtype8     0   34
  subtype9     0   28
                        clus
vv                       subtype1 subtype10 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            3         0        0        3        1        1
  NOT HISPANIC OR LATINO       45        36       24       56       18       44
                        clus
vv                       subtype6 subtype7 subtype8 subtype9
  HISPANIC OR LATINO            2        1        0        0
  NOT HISPANIC OR LATINO       23       19       34       28
[1]  2 10
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = CN_CNMF
D5V1, survival
          sevent
clus2        0   1
  subtype1  71  97
  subtype2 104  92
  subtype3  85  98
subtype1 subtype2 subtype3 
     168      196      183 
subtype1 subtype2 subtype3 
      97       92       98 
$subtype1
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1350 TCGA-04-1351 
       40.24        41.00         1.81         2.01        63.98        65.46 
TCGA-04-1514 TCGA-04-1530 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-09-0364 
       56.55       119.08        55.43        48.89        28.64        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0369 TCGA-09-1659 TCGA-09-1664 TCGA-09-1666 
        9.47        57.76        35.57         9.99        74.93        57.60 
TCGA-09-1672 TCGA-09-2045 TCGA-09-2048 TCGA-09-2055 TCGA-09-2056 TCGA-10-0926 
        5.85        35.15         4.54        26.93        12.46        25.91 
TCGA-10-0930 TCGA-10-0934 TCGA-10-0935 TCGA-13-0714 TCGA-13-0720 TCGA-13-0762 
       33.24         3.91        35.44         6.21        44.55        32.25 
TCGA-13-0768 TCGA-13-0793 TCGA-13-0799 TCGA-13-0800 TCGA-13-0803 TCGA-13-0804 
        8.45        28.70         7.79         8.12        43.86        35.28 
TCGA-13-0805 TCGA-13-0886 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0899 
       35.28        74.27        61.84        67.99        69.01        56.15 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0919 TCGA-13-0921 TCGA-13-1405 
       37.08        27.72        34.06        14.89         4.64         7.36 
TCGA-13-1411 TCGA-13-1477 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 
        4.21        54.64        29.42        98.04        20.68        22.39 
TCGA-13-1494 TCGA-13-1499 TCGA-13-1500 TCGA-13-1507 TCGA-13-1510 TCGA-20-0987 
       38.20        38.40        13.97         4.77         2.56        23.05 
TCGA-20-0991 TCGA-20-0996 TCGA-23-1023 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       26.20        72.20        40.54        29.13        18.90         2.24 
TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-2072 TCGA-23-2078 
       31.20         4.57        33.30        86.01        24.95        87.48 
TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-1105 TCGA-24-1416 
        7.63        11.64        21.80         7.66        47.41         6.38 
TCGA-24-1422 TCGA-24-1430 TCGA-24-1463 TCGA-24-1467 TCGA-24-1471 TCGA-24-1545 
        0.76        28.37        72.92       105.99         1.18        57.40 
TCGA-24-1546 TCGA-24-1551 TCGA-24-1555 TCGA-24-1560 TCGA-24-1562 TCGA-24-1564 
       64.27        51.91        88.50        44.09        45.50        25.87 
TCGA-24-1565 TCGA-24-1603 TCGA-24-1844 TCGA-24-1849 TCGA-24-1923 TCGA-24-2024 
       10.26        90.15         3.72         5.79        22.68        58.16 
TCGA-24-2029 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2271 
       14.43        28.18        64.01        44.52        57.07        31.63 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2293 TCGA-24-2298 TCGA-25-1316 TCGA-25-1623 
       70.45        44.61        16.64        53.26        37.02        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1628 TCGA-25-1630 TCGA-25-1633 TCGA-25-2042 
       18.02        15.81        20.61         7.86        60.59        13.02 
TCGA-25-2399 TCGA-25-2408 TCGA-29-1690 TCGA-29-1707 TCGA-29-1762 TCGA-29-1771 
       19.99        31.00        44.71        41.98        85.68        22.55 
TCGA-29-1785 TCGA-29-2427 TCGA-29-2436 TCGA-30-1853 TCGA-30-1855 TCGA-30-1880 
       34.62        62.47         9.76        36.26         2.47        57.57 
TCGA-30-1892 TCGA-31-1950 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1576 
       48.79        18.77        44.12        28.77        29.10        30.08 
TCGA-36-1577 TCGA-36-1580 TCGA-36-2532 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       25.74        24.23        29.49        25.91        25.08        23.80 
TCGA-36-2543 TCGA-42-2587 TCGA-42-2590 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 
        2.24        23.74         7.46        80.12        22.32       116.12 
TCGA-59-2354 TCGA-59-2355 TCGA-61-1721 TCGA-61-1727 TCGA-61-1734 TCGA-61-1736 
       34.39         2.14        11.11        18.54        28.47        48.79 
TCGA-61-1743 TCGA-61-1901 TCGA-61-1911 TCGA-61-1995 TCGA-61-1998 TCGA-61-2002 
       43.69        11.41        42.51         2.01         5.52        17.98 
TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2092 TCGA-61-2094 
       39.85         1.18        45.96        45.40        51.72        71.74 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2110 TCGA-61-2612 TCGA-61-2613 
       61.64        58.39        60.62        44.52         6.35        31.07 

$subtype2
TCGA-04-1336 TCGA-04-1338 TCGA-04-1349 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 
       49.15        46.62        21.57        49.28        32.52        44.32 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1536 TCGA-04-1651 TCGA-04-1654 TCGA-09-0367 
       76.57        71.47        29.10        36.23        47.70        17.98 
TCGA-09-1662 TCGA-09-1665 TCGA-09-1668 TCGA-09-1669 TCGA-09-1673 TCGA-09-1675 
       89.33        41.62        55.36        30.51         3.02        97.55 
TCGA-09-2051 TCGA-10-0925 TCGA-10-0928 TCGA-10-0931 TCGA-10-0937 TCGA-13-0725 
       63.09        54.31        18.51        32.28        15.12        12.39 
TCGA-13-0726 TCGA-13-0755 TCGA-13-0758 TCGA-13-0761 TCGA-13-0766 TCGA-13-0792 
       31.10         2.50        11.38        34.06        21.40        36.72 
TCGA-13-0797 TCGA-13-0801 TCGA-13-0802 TCGA-13-0883 TCGA-13-0884 TCGA-13-0887 
        8.71         8.28         8.19        68.94       107.18        66.67 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 
       43.36        57.47        57.07        19.36        47.38        48.33 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 
       47.84        44.94        44.84        29.98        21.17        13.81 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1412 TCGA-13-1481 TCGA-13-1482 
        6.08        10.88         6.61         5.33        87.06        61.71 
TCGA-13-1488 TCGA-13-1497 TCGA-13-1501 TCGA-13-1505 TCGA-13-1509 TCGA-13-1512 
       70.82        54.31        32.84         4.21         4.18         3.09 
TCGA-13-2059 TCGA-13-2065 TCGA-13-2071 TCGA-20-1682 TCGA-20-1685 TCGA-20-1686 
       12.23         8.75         6.28        27.52        16.70         2.93 
TCGA-20-1687 TCGA-23-1022 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 
        2.66        42.54        26.83        31.76        49.41         8.81 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 TCGA-23-1124 
       51.35        54.51       129.96         4.27        39.09        58.13 
TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2645 
      115.89        91.66        77.00        49.84         2.76         4.50 
TCGA-24-0979 TCGA-24-1103 TCGA-24-1104 TCGA-24-1417 TCGA-24-1419 TCGA-24-1423 
       41.56        54.12        63.55         7.82         7.86         6.25 
TCGA-24-1425 TCGA-24-1427 TCGA-24-1428 TCGA-24-1435 TCGA-24-1436 TCGA-24-1464 
        5.95         4.83        17.39        43.53         8.55        12.46 
TCGA-24-1466 TCGA-24-1470 TCGA-24-1474 TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 
       45.14         3.45        22.22        58.09        70.62        39.88 
TCGA-24-1563 TCGA-24-1567 TCGA-24-1604 TCGA-24-1842 TCGA-24-1846 TCGA-24-1847 
       47.70        17.23        88.37         8.32         4.37        11.28 
TCGA-24-1920 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-2026 TCGA-24-2030 
        9.80        30.21        16.44        11.05        34.82        53.95 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2289 TCGA-24-2290 TCGA-24-2297 TCGA-25-1313 
        0.36        47.54        67.36        36.23        55.86        26.96 
TCGA-25-1314 TCGA-25-1318 TCGA-25-1319 TCGA-25-1322 TCGA-25-1632 TCGA-25-1878 
       32.02        34.98        65.00         2.99        56.94        85.05 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2397 TCGA-25-2401 TCGA-25-2409 TCGA-29-1688 
       49.05         1.02        12.00         2.96        26.99        78.90 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1701 TCGA-29-1702 
      101.79        38.53        33.70        31.20        16.90        18.67 
TCGA-29-1705 TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1775 
       18.25        62.93        31.23        22.98        24.36        12.36 
TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1784 TCGA-29-2425 TCGA-29-2432 
       11.84        12.30         8.38         5.36        65.00        11.84 
TCGA-30-1718 TCGA-30-1857 TCGA-30-1860 TCGA-30-1861 TCGA-30-1891 TCGA-31-1944 
       51.91         0.26        44.91        34.78        30.05        45.57 
TCGA-31-1946 TCGA-31-1955 TCGA-31-1959 TCGA-36-1570 TCGA-36-1574 TCGA-36-1578 
       30.18        42.51         2.20        21.53        22.55        27.85 
TCGA-36-2530 TCGA-36-2534 TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 
       33.01        29.82        21.60        20.98        18.31        20.52 
TCGA-36-2549 TCGA-42-2582 TCGA-42-2588 TCGA-42-2591 TCGA-57-1582 TCGA-57-1583 
        6.05        26.04         9.44        40.77        24.03        11.38 
TCGA-57-1584 TCGA-57-1585 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1728 
       21.14         1.74         8.09        20.94        31.43        27.88 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1895 TCGA-61-1900 TCGA-61-1903 
       44.84        35.80         2.43         1.45         5.79        13.02 
TCGA-61-1907 TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 
       31.30        37.05        48.92        56.61        67.76        15.75 
TCGA-61-1919 TCGA-61-2008 TCGA-61-2104 TCGA-61-2109 
       38.17        30.64        76.87        20.68 

$subtype3
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1364 
       18.51        11.87        65.52        63.09        48.76        33.67 
TCGA-04-1371 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1542 TCGA-04-1646 
       82.39        41.59        19.99        38.37        84.20        27.88 
TCGA-04-1649 TCGA-04-1652 TCGA-04-1655 TCGA-09-1661 TCGA-09-1667 TCGA-09-1670 
       64.64        31.86        45.37        38.43        61.87        17.98 
TCGA-09-1674 TCGA-09-2043 TCGA-09-2044 TCGA-09-2049 TCGA-09-2050 TCGA-09-2053 
        8.55         6.18         6.12       112.41        71.11        39.75 
TCGA-09-2054 TCGA-10-0927 TCGA-10-0933 TCGA-10-0936 TCGA-10-0938 TCGA-13-0717 
       20.94        81.47        11.70        35.80        19.86        24.59 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 
       39.58         2.73        15.19        17.82        55.17        11.18 
TCGA-13-0760 TCGA-13-0764 TCGA-13-0791 TCGA-13-0794 TCGA-13-0795 TCGA-13-0807 
       11.54        31.04        38.93        30.35        19.59        13.61 
TCGA-13-0885 TCGA-13-0888 TCGA-13-0923 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
       91.40        70.39         6.41         6.05         5.92         6.84 
TCGA-13-1410 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1495 TCGA-13-1496 
        4.70        82.88        52.44        73.55        49.25         4.24 
TCGA-13-1498 TCGA-13-1504 TCGA-13-1506 TCGA-13-1511 TCGA-13-2057 TCGA-13-2060 
       37.61        16.57         4.41         3.91        14.24         8.61 
TCGA-13-2061 TCGA-20-0990 TCGA-20-1683 TCGA-20-1684 TCGA-23-1021 TCGA-23-1024 
       10.78        25.94        25.38        19.10        47.54        15.39 
TCGA-23-1111 TCGA-23-1114 TCGA-23-1121 TCGA-23-1123 TCGA-23-1809 TCGA-23-2643 
        3.22        68.68         6.38        33.47         0.53         4.70 
TCGA-24-0968 TCGA-24-0982 TCGA-24-1413 TCGA-24-1418 TCGA-24-1424 TCGA-24-1426 
       19.66        22.32         6.31         7.99         6.02         5.36 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1469 TCGA-24-1544 TCGA-24-1548 TCGA-24-1549 
       19.17        18.67         9.11        26.96        16.21        56.58 
TCGA-24-1550 TCGA-24-1552 TCGA-24-1558 TCGA-24-1614 TCGA-24-1616 TCGA-24-1843 
       41.06        41.39        19.53        48.33        38.24         3.48 
TCGA-24-1845 TCGA-24-1850 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 
        3.81         5.52        81.11         4.87       152.02        44.84 
TCGA-24-2027 TCGA-24-2033 TCGA-24-2260 TCGA-24-2261 TCGA-24-2288 TCGA-24-2295 
      109.71        18.48        36.16         0.79         0.82        33.11 
TCGA-25-1312 TCGA-25-1315 TCGA-25-1317 TCGA-25-1320 TCGA-25-1321 TCGA-25-1323 
        1.02        51.06         1.02        36.95        33.96        12.00 
TCGA-25-1329 TCGA-25-1627 TCGA-25-1631 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 
        2.96         0.36         0.30        35.54        51.22        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 TCGA-25-2400 
       24.99        18.05        38.04         3.02        45.01        42.02 
TCGA-25-2404 TCGA-29-1691 TCGA-29-1695 TCGA-29-1698 TCGA-29-1699 TCGA-29-1703 
       29.03        47.18         0.79        68.32         0.53        59.67 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1763 TCGA-29-1766 TCGA-29-1774 
       29.23        34.62        17.00        66.81        39.12        17.33 
TCGA-29-1778 TCGA-29-1783 TCGA-29-2414 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 
       14.93         7.23        86.17        45.11         4.90        42.25 
TCGA-29-2434 TCGA-30-1714 TCGA-30-1856 TCGA-30-1859 TCGA-30-1862 TCGA-30-1866 
       11.47        38.07        15.68        48.10         6.12        36.62 
TCGA-30-1867 TCGA-30-1887 TCGA-31-1951 TCGA-31-1953 TCGA-36-1571 TCGA-36-1575 
        1.22        24.26        22.49         6.71        22.85         8.55 
TCGA-36-1581 TCGA-36-2529 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2589 
       24.69        35.05        14.17        16.18        11.47        42.02 
TCGA-42-2593 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 
        1.48        22.32        29.00        25.08        25.02       180.20 
TCGA-59-2352 TCGA-59-2363 TCGA-59-2372 TCGA-61-1730 TCGA-61-1733 TCGA-61-1741 
        9.40         5.42        44.81         4.34        31.79        33.67 
TCGA-61-1899 TCGA-61-1904 TCGA-61-1906 TCGA-61-1917 TCGA-61-2000 TCGA-61-2003 
        8.42         9.07        34.13        43.43        14.50         4.01 
TCGA-61-2012 TCGA-61-2087 TCGA-61-2088 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 
       30.64         4.80         4.77        65.52        55.50         6.48 
TCGA-61-2111 TCGA-61-2113 TCGA-61-2614 
      125.75        22.22         8.61 

subtype1 subtype2 subtype3 
    0.76     0.26     0.30 
subtype1 subtype2 subtype3 
  119.08   129.96   180.20 
subtype1 subtype2 subtype3 
  29.785   30.115   22.320 
[1] "0.8 - 119.1 (29.8)" "0.3 - 130.0 (30.1)" "0.3 - 180.2 (22.3)"
D5V2, continuous
          vv
clus       OMENTUM OVARY PERITONEUM OVARY
  subtype1       1   169                0
  subtype2       1   197                0
  subtype3       0   182                2
D5V3, multiclass
                  clus
vv                 subtype1 subtype2 subtype3
  OMENTUM                 1        1        0
  OVARY                 169      197      182
  PERITONEUM OVARY        0        0        2
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V4, continuous
D5V5, binary
          cls
clus         0   1
  subtype1   1 172
  subtype2   0 201
  subtype3   2 186
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  172
  subtype2    0  201
  subtype3    2  186
     clus
vv    subtype1 subtype2 subtype3
  NO         1        0        2
  YES      172      201      186
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2
  subtype1  2 11  0
  subtype2  4  6  1
  subtype3  8  9  1
D5V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0        2        4        8
  R1       11        6        9
  R2        0        1        1
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     4                         6
  subtype2                                0     8                        11
  subtype3                                2     6                         7
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0   148
  subtype2                                         1   167
  subtype3                                         0   160
D5V7, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 1        0        2
  ASIAN                                            4        8        6
  BLACK OR AFRICAN AMERICAN                        6       11        7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        1        0
  WHITE                                          148      167      160
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
          cls
clus         0   1
  subtype1   1 105
  subtype2   5 109
  subtype3   4 105
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  105
  subtype2    5  109
  subtype3    4  105
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        5        4
  NOT HISPANIC OR LATINO      105      109      105
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = RPPA_CNMF
D6V1, survival
          sevent
clus2        0   1
  subtype1  54  66
  subtype2 105  92
  subtype3  29  55
subtype1 subtype2 subtype3 
     120      197       84 
subtype1 subtype2 subtype3 
      66       92       55 
$subtype1
TCGA-04-1335 TCGA-04-1338 TCGA-04-1342 TCGA-04-1525 TCGA-04-1542 TCGA-04-1638 
        1.81        46.62        18.51        38.37        84.20        55.43 
TCGA-09-1664 TCGA-09-1665 TCGA-09-2049 TCGA-09-2056 TCGA-10-0925 TCGA-10-0933 
       74.93        41.62       112.41        12.46        54.31        11.70 
TCGA-13-0725 TCGA-13-0793 TCGA-13-0894 TCGA-13-0901 TCGA-13-0903 TCGA-13-0906 
       12.39        28.70        49.61        19.36        47.38        44.94 
TCGA-13-0910 TCGA-13-0913 TCGA-13-1408 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 
       37.08        29.98         5.92         4.21         5.33        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1488 TCGA-13-1489 
       87.06        61.71        29.42        98.04        70.82        82.88 
TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 
       52.44        38.20        49.25        37.61        38.40        13.97 
TCGA-13-1501 TCGA-13-2065 TCGA-20-1683 TCGA-20-1686 TCGA-23-1122 TCGA-23-2078 
       32.84         8.75        25.38         2.93        39.09        87.48 
TCGA-24-0970 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1104 TCGA-24-1105 
       11.64        41.56         7.66        22.32        63.55        47.41 
TCGA-24-1427 TCGA-24-1545 TCGA-24-1546 TCGA-24-1553 TCGA-24-1563 TCGA-24-1842 
        4.83        57.40        64.27        58.09        47.70         8.32 
TCGA-24-1850 TCGA-24-1923 TCGA-24-1924 TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 
        5.52        22.68        30.21       109.71        14.43        18.48 
TCGA-24-2038 TCGA-24-2260 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 
       44.52        36.16         0.36        47.54        31.63        44.61 
TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 TCGA-25-1319 TCGA-25-1322 TCGA-25-1323 
       16.64        55.86        53.26        65.00         2.99        12.00 
TCGA-25-1326 TCGA-25-1623 TCGA-25-1630 TCGA-25-2042 TCGA-25-2398 TCGA-25-2404 
       31.07        18.58         7.86        13.02        45.01        29.03 
TCGA-25-2408 TCGA-29-1690 TCGA-29-1768 TCGA-29-1771 TCGA-29-1776 TCGA-29-2425 
       31.00        44.71        31.23        22.55        11.84        65.00 
TCGA-29-2427 TCGA-29-2429 TCGA-30-1856 TCGA-30-1892 TCGA-31-1944 TCGA-31-1950 
       62.47         4.90        15.68        48.79        45.57        18.77 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1575 TCGA-36-1577 TCGA-36-1580 TCGA-36-1581 
       28.77        29.10         8.55        25.74        24.23        24.69 
TCGA-36-2537 TCGA-36-2540 TCGA-36-2543 TCGA-36-2549 TCGA-42-2587 TCGA-42-2591 
       25.91        23.80         2.24         6.05        23.74        40.77 
TCGA-59-2351 TCGA-59-2363 TCGA-61-1722 TCGA-61-1900 TCGA-61-1903 TCGA-61-1906 
      116.12         5.42         8.09         5.79        13.02        34.13 
TCGA-61-1907 TCGA-61-1919 TCGA-61-2003 TCGA-61-2012 TCGA-61-2094 TCGA-61-2095 
       31.30        38.17         4.01        30.64        71.74        61.64 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2111 TCGA-61-2113 TCGA-61-2610 TCGA-61-2613 
       65.52        55.50       125.75        22.22        51.91        31.07 

$subtype2
TCGA-04-1336 TCGA-04-1348 TCGA-04-1349 TCGA-04-1356 TCGA-04-1361 TCGA-04-1369 
       49.15        48.76        21.57        49.28        32.52        21.11 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1646 TCGA-04-1649 TCGA-04-1651 
       56.55        41.59        19.99        27.88        64.64        36.23 
TCGA-09-1666 TCGA-09-1670 TCGA-09-1673 TCGA-09-2043 TCGA-09-2044 TCGA-09-2051 
       57.60        17.98         3.02         6.18         6.12        63.09 
TCGA-09-2054 TCGA-09-2055 TCGA-10-0931 TCGA-10-0936 TCGA-13-0720 TCGA-13-0794 
       20.94        26.93        32.28        35.80        44.55        30.35 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 
        8.71         7.79         8.12         8.28         8.19        35.28 
TCGA-13-0884 TCGA-13-0887 TCGA-13-0888 TCGA-13-0891 TCGA-13-0899 TCGA-13-0916 
      107.18        66.67        70.39        69.01        56.15        21.17 
TCGA-13-0920 TCGA-13-0921 TCGA-13-1404 TCGA-13-1409 TCGA-13-1410 TCGA-13-1487 
       13.81         4.64         6.61         6.84         4.70        22.39 
TCGA-13-1492 TCGA-13-1496 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1511 
       73.55         4.24        16.57         4.21         4.41         3.91 
TCGA-13-1512 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2066 TCGA-20-1684 
        3.09        12.23         8.61        10.78         9.70        19.10 
TCGA-20-1685 TCGA-20-1687 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1121 
       16.70         2.66        51.35        54.51         3.22         6.38 
TCGA-23-1123 TCGA-23-1809 TCGA-23-2077 TCGA-23-2079 TCGA-23-2641 TCGA-23-2643 
       33.47         0.53       115.89        91.66         2.76         4.70 
TCGA-23-2645 TCGA-23-2649 TCGA-24-0966 TCGA-24-1103 TCGA-24-1416 TCGA-24-1417 
        4.50         3.81         7.63        54.12         6.38         7.82 
TCGA-24-1419 TCGA-24-1424 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 
        7.86         6.02        17.39        28.37        19.17        43.53 
TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1471 
        8.55        12.46        45.14       105.99         9.11         1.18 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 
       22.22        26.96        16.21        56.58        51.91        41.39 
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-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1614 TCGA-24-1616 TCGA-24-1844 
       10.26        17.23        90.15        48.33        38.24         3.72 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1930 TCGA-24-2020 TCGA-24-2023 TCGA-24-2026 
        3.81         4.37        81.11       152.02        44.84        34.82 
TCGA-24-2030 TCGA-24-2036 TCGA-24-2254 TCGA-24-2261 TCGA-24-2288 TCGA-24-2290 
       53.95        64.01        57.07         0.79         0.82        36.23 
TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 TCGA-25-1318 TCGA-25-1321 TCGA-25-1329 
        1.02        32.02        51.06        34.98        33.96         2.96 
TCGA-25-1627 TCGA-25-1631 TCGA-25-1635 TCGA-25-1878 TCGA-25-2393 TCGA-25-2396 
        0.36         0.30        51.22        85.05        38.04         3.02 
TCGA-25-2397 TCGA-25-2400 TCGA-25-2409 TCGA-29-1688 TCGA-29-1691 TCGA-29-1693 
       12.00        42.02        26.99        78.90        47.18       101.79 
TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 
        0.79        31.20        68.32        18.67        59.67        18.25 
TCGA-29-1707 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 TCGA-29-1774 
       41.98        34.62        17.00        85.68        62.93        17.33 
TCGA-29-1775 TCGA-29-1778 TCGA-29-1781 TCGA-29-2428 TCGA-29-2431 TCGA-29-2434 
       12.36        14.93         8.38        45.11        42.25        11.47 
TCGA-29-2435 TCGA-30-1859 TCGA-30-1869 TCGA-31-1951 TCGA-31-1955 TCGA-36-1570 
        1.12        48.10        51.39        22.49        42.51        21.53 
TCGA-36-1571 TCGA-36-1578 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       22.85        27.85        35.05        33.01        29.49        29.82 
TCGA-36-2538 TCGA-36-2542 TCGA-36-2547 TCGA-36-2548 TCGA-36-2552 TCGA-42-2589 
       25.08        21.60        20.52        14.17        11.47        42.02 
TCGA-42-2593 TCGA-57-1586 TCGA-59-2348 TCGA-59-2352 TCGA-59-2372 TCGA-61-1724 
        1.48        22.32       180.20         9.40        44.81        20.94 
TCGA-61-1727 TCGA-61-1730 TCGA-61-1734 TCGA-61-1736 TCGA-61-1740 TCGA-61-1741 
       18.54         4.34        28.47        48.79         2.43        33.67 
TCGA-61-1743 TCGA-61-1899 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1915 
       43.69         8.42        37.05        42.51        48.92        67.76 
TCGA-61-1918 TCGA-61-1995 TCGA-61-2000 TCGA-61-2009 TCGA-61-2018 TCGA-61-2087 
       15.75         2.01        14.50        39.85        45.40         4.80 
TCGA-61-2088 TCGA-61-2092 TCGA-61-2096 TCGA-61-2104 TCGA-61-2109 
        4.77        51.72        58.39        76.87        20.68 

$subtype3
TCGA-04-1343 TCGA-04-1362 TCGA-04-1370 TCGA-04-1644 TCGA-04-1648 TCGA-04-1654 
       11.87        44.32        59.97        48.89        28.64        47.70 
TCGA-09-1662 TCGA-09-1674 TCGA-09-2045 TCGA-10-0926 TCGA-13-0886 TCGA-13-0897 
       89.33         8.55        35.15        25.91        74.27        57.47 
TCGA-13-0911 TCGA-13-1405 TCGA-13-1507 TCGA-13-1509 TCGA-20-1682 TCGA-23-1124 
       27.72         7.36         4.77         4.18        27.52        58.13 
TCGA-23-2081 TCGA-23-2647 TCGA-24-1422 TCGA-24-1423 TCGA-24-1434 TCGA-24-1463 
       77.00         4.44         0.76         6.25        18.67        72.92 
TCGA-24-1470 TCGA-24-1550 TCGA-24-1564 TCGA-24-1604 TCGA-24-1849 TCGA-24-1920 
        3.45        41.06        25.87        88.37         5.79         9.80 
TCGA-24-1927 TCGA-24-2024 TCGA-24-2289 TCGA-24-2295 TCGA-25-1313 TCGA-25-1316 
       16.44        58.16        67.36        33.11        26.96        37.02 
TCGA-25-1320 TCGA-25-1325 TCGA-25-1328 TCGA-25-1625 TCGA-25-1626 TCGA-25-1628 
       36.95        32.09        65.06        18.02        15.81        20.61 
TCGA-25-1632 TCGA-25-1633 TCGA-25-2391 TCGA-25-2399 TCGA-25-2401 TCGA-29-1694 
       56.94        60.59        49.05        19.99         2.96        38.53 
TCGA-29-1696 TCGA-29-1699 TCGA-29-1701 TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 
       33.70         0.53        16.90        39.12        22.98        24.36 
TCGA-29-1777 TCGA-29-1783 TCGA-29-1785 TCGA-29-2432 TCGA-29-2436 TCGA-30-1718 
       12.30         7.23        34.62        11.84         9.76        51.91 
TCGA-30-1855 TCGA-30-1860 TCGA-30-1861 TCGA-30-1887 TCGA-30-1891 TCGA-31-1946 
        2.47        44.91        34.78        24.26        30.05        30.18 
TCGA-36-1576 TCGA-36-2544 TCGA-36-2545 TCGA-36-2551 TCGA-42-2582 TCGA-42-2588 
       30.08        20.98        18.31        16.18        26.04         9.44 
TCGA-42-2590 TCGA-59-2349 TCGA-59-2354 TCGA-61-1721 TCGA-61-1733 TCGA-61-1738 
        7.46        80.12        34.39        11.11        31.79        35.80 
TCGA-61-1895 TCGA-61-1914 TCGA-61-2017 TCGA-61-2102 TCGA-61-2612 TCGA-61-2614 
        1.45        56.61        45.96         6.48         6.35         8.61 

subtype1 subtype2 subtype3 
    0.36     0.30     0.53 
subtype1 subtype2 subtype3 
  125.75   180.20    89.33 
subtype1 subtype2 subtype3 
   31.15    25.08    27.24 
[1] "0.4 - 125.8 (31.1)" "0.3 - 180.2 (25.1)" "0.5 - 89.3 (27.2)" 
D6V2, continuous
          vv
clus       OMENTUM OVARY PERITONEUM OVARY
  subtype1       1   122                0
  subtype2       1   197                1
  subtype3       0    84                1
D6V3, multiclass
                  clus
vv                 subtype1 subtype2 subtype3
  OMENTUM                 1        1        0
  OVARY                 122      197       84
  PERITONEUM OVARY        0        1        1
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V4, continuous
D6V5, binary
          cls
clus         0   1
  subtype1   2 121
  subtype2   0 199
  subtype3   0  85
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  121
  subtype2    0  199
  subtype3    0   85
     clus
vv    subtype1 subtype2 subtype3
  NO         2        0        0
  YES      121      199       85
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2
  subtype1  2 10  0
  subtype2  8  9  1
  subtype3  3  9  1
D6V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0        2        8        3
  R1       10        9        9
  R2        0        1        1
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                2     5                         6
  subtype2                                1     9                        10
  subtype3                                0     2                         3
          vv
clus       WHITE
  subtype1   100
  subtype2   169
  subtype3    73
D6V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        2        1        0
  ASIAN                                   5        9        2
  BLACK OR AFRICAN AMERICAN               6       10        3
  WHITE                                 100      169       73
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
          cls
clus         0   1
  subtype1   2  65
  subtype2   5 102
  subtype3   1  40
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   65
  subtype2    5  102
  subtype3    1   40
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        5        1
  NOT HISPANIC OR LATINO       65      102       40
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = RPPA_CHIERARCHICAL
D7V1, survival
          sevent
clus2       0  1
  subtype1 42 77
  subtype2 52 43
  subtype3 69 59
  subtype4 25 34
subtype1 subtype2 subtype3 subtype4 
     119       95      128       59 
subtype1 subtype2 subtype3 subtype4 
      77       43       59       34 
$subtype1
TCGA-04-1335 TCGA-04-1338 TCGA-04-1342 TCGA-04-1343 TCGA-04-1349 TCGA-04-1638 
        1.81        46.62        18.51        11.87        21.57        55.43 
TCGA-09-1662 TCGA-09-1665 TCGA-13-0886 TCGA-13-0894 TCGA-13-0911 TCGA-13-1405 
       89.33        41.62        74.27        49.61        27.72         7.36 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
        5.92         6.84         4.21         5.33        54.64        87.06 
TCGA-13-1483 TCGA-13-1488 TCGA-13-1494 TCGA-13-1500 TCGA-13-1501 TCGA-13-1505 
       29.42        70.82        38.20        13.97        32.84         4.21 
TCGA-13-2065 TCGA-20-1682 TCGA-23-1122 TCGA-23-2078 TCGA-23-2647 TCGA-24-0980 
        8.75        27.52        39.09        87.48         4.44         7.66 
TCGA-24-0982 TCGA-24-1423 TCGA-24-1427 TCGA-24-1434 TCGA-24-1463 TCGA-24-1545 
       22.32         6.25         4.83        18.67        72.92        57.40 
TCGA-24-1546 TCGA-24-1550 TCGA-24-1553 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
       64.27        41.06        58.09        45.50        47.70        25.87 
TCGA-24-1849 TCGA-24-1850 TCGA-24-1923 TCGA-24-1924 TCGA-24-2029 TCGA-24-2038 
        5.79         5.52        22.68        30.21        14.43        44.52 
TCGA-24-2262 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 TCGA-24-2293 TCGA-24-2297 
        0.36        31.63        44.61         0.82        16.64        55.86 
TCGA-24-2298 TCGA-25-1313 TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 TCGA-25-1325 
       53.26        26.96        65.00        36.95         2.99        32.09 
TCGA-25-1328 TCGA-25-1623 TCGA-25-1626 TCGA-25-1628 TCGA-25-1630 TCGA-25-1633 
       65.06        18.58        15.81        20.61         7.86        60.59 
TCGA-25-2042 TCGA-25-2398 TCGA-25-2401 TCGA-25-2408 TCGA-29-1690 TCGA-29-1699 
       13.02        45.01         2.96        31.00        44.71         0.53 
TCGA-29-1701 TCGA-29-1707 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 
       16.90        41.98        39.12        31.23        22.98        24.36 
TCGA-29-1771 TCGA-29-1776 TCGA-29-1777 TCGA-29-1785 TCGA-29-2425 TCGA-29-2431 
       22.55        11.84        12.30        34.62        65.00        42.25 
TCGA-29-2432 TCGA-29-2436 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1887 
       11.84         9.76        51.91         2.47        15.68        24.26 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1946 TCGA-31-1950 TCGA-36-1568 TCGA-36-1569 
       30.05        48.79        30.18        18.77        28.77        29.10 
TCGA-36-1576 TCGA-36-1580 TCGA-36-1581 TCGA-36-2540 TCGA-36-2543 TCGA-42-2582 
       30.08        24.23        24.69        23.80         2.24        26.04 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 TCGA-59-2354 TCGA-61-1721 TCGA-61-1895 
       23.74         9.44         7.46        34.39        11.11         1.45 
TCGA-61-1906 TCGA-61-1918 TCGA-61-1919 TCGA-61-2003 TCGA-61-2012 TCGA-61-2111 
       34.13        15.75        38.17         4.01        30.64       125.75 
TCGA-61-2113 TCGA-61-2610 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       22.22        51.91         6.35        31.07         8.61 

$subtype2
TCGA-04-1336 TCGA-04-1361 TCGA-04-1514 TCGA-04-1517 TCGA-04-1646 TCGA-04-1649 
       49.15        32.52        56.55        19.99        27.88        64.64 
TCGA-09-1664 TCGA-09-1666 TCGA-09-1670 TCGA-09-1673 TCGA-09-2043 TCGA-09-2051 
       74.93        57.60        17.98         3.02         6.18        63.09 
TCGA-10-0931 TCGA-13-0799 TCGA-13-0801 TCGA-13-0888 TCGA-13-0913 TCGA-13-0916 
       32.28         7.79         8.28        70.39        29.98        21.17 
TCGA-13-0921 TCGA-13-2059 TCGA-20-1687 TCGA-23-1109 TCGA-23-1110 TCGA-23-1123 
        4.64        12.23         2.66        51.35        54.51        33.47 
TCGA-23-2077 TCGA-23-2079 TCGA-23-2649 TCGA-24-1416 TCGA-24-1419 TCGA-24-1424 
      115.89        91.66         3.81         6.38         7.86         6.02 
TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1471 TCGA-24-1548 TCGA-24-1549 
       17.39        28.37        19.17         1.18        16.21        56.58 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 TCGA-24-1557 TCGA-24-1560 TCGA-24-1565 
       51.91        41.39        88.50        39.88        44.09        10.26 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-1844 TCGA-24-1846 TCGA-24-2033 
       90.15        88.37        38.24         3.72         4.37        18.48 
TCGA-24-2036 TCGA-24-2254 TCGA-24-2267 TCGA-25-1312 TCGA-25-1314 TCGA-25-1321 
       64.01        57.07        47.54         1.02        32.02        33.96 
TCGA-25-1627 TCGA-25-1631 TCGA-25-2396 TCGA-25-2397 TCGA-25-2400 TCGA-29-1696 
        0.36         0.30         3.02        12.00        42.02        33.70 
TCGA-29-1702 TCGA-29-1761 TCGA-29-1775 TCGA-29-1778 TCGA-29-1783 TCGA-30-1859 
       18.67        17.00        12.36        14.93         7.23        48.10 
TCGA-31-1955 TCGA-36-1570 TCGA-36-1578 TCGA-36-2530 TCGA-36-2532 TCGA-36-2538 
       42.51        21.53        27.85        33.01        29.49        25.08 
TCGA-36-2547 TCGA-36-2549 TCGA-36-2551 TCGA-59-2352 TCGA-59-2372 TCGA-61-1722 
       20.52         6.05        16.18         9.40        44.81         8.09 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 TCGA-61-1741 TCGA-61-1899 TCGA-61-1907 
        4.34        31.79        48.79        33.67         8.42        31.30 
TCGA-61-1913 TCGA-61-1915 TCGA-61-1995 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
       48.92        67.76         2.01        45.40         4.80         4.77 
TCGA-61-2092 TCGA-61-2096 TCGA-61-2101 TCGA-61-2104 TCGA-61-2109 
       51.72        58.39        55.50        76.87        20.68 

$subtype3
TCGA-04-1348 TCGA-04-1369 TCGA-04-1516 TCGA-04-1525 TCGA-04-1542 TCGA-04-1644 
       48.76        21.11        41.59        38.37        84.20        48.89 
TCGA-04-1651 TCGA-09-1674 TCGA-09-2044 TCGA-09-2049 TCGA-09-2054 TCGA-09-2056 
       36.23         8.55         6.12       112.41        20.94        12.46 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0933 TCGA-10-0936 TCGA-13-0725 TCGA-13-0793 
       54.31        25.91        11.70        35.80        12.39        28.70 
TCGA-13-0794 TCGA-13-0797 TCGA-13-0800 TCGA-13-0802 TCGA-13-0804 TCGA-13-0884 
       30.35         8.71         8.12         8.19        35.28       107.18 
TCGA-13-0887 TCGA-13-0901 TCGA-13-0903 TCGA-13-0906 TCGA-13-0910 TCGA-13-0920 
       66.67        19.36        47.38        44.94        37.08        13.81 
TCGA-13-1404 TCGA-13-1410 TCGA-13-1482 TCGA-13-1484 TCGA-13-1487 TCGA-13-1489 
        6.61         4.70        61.71        98.04        22.39        82.88 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1499 TCGA-13-1504 TCGA-13-1506 TCGA-13-1511 
       52.44        73.55        38.40        16.57         4.41         3.91 
TCGA-13-1512 TCGA-13-2060 TCGA-13-2061 TCGA-13-2066 TCGA-20-1683 TCGA-20-1684 
        3.09         8.61        10.78         9.70        25.38        19.10 
TCGA-20-1685 TCGA-20-1686 TCGA-23-1121 TCGA-23-1809 TCGA-23-2643 TCGA-23-2645 
       16.70         2.93         6.38         0.53         4.70         4.50 
TCGA-24-0966 TCGA-24-0970 TCGA-24-0979 TCGA-24-1104 TCGA-24-1105 TCGA-24-1417 
        7.63        11.64        41.56        63.55        47.41         7.82 
TCGA-24-1436 TCGA-24-1464 TCGA-24-1467 TCGA-24-1474 TCGA-24-1544 TCGA-24-1556 
        8.55        12.46       105.99        22.22        26.96        70.62 
TCGA-24-1558 TCGA-24-1567 TCGA-24-1614 TCGA-24-1842 TCGA-24-1845 TCGA-24-1930 
       19.53        17.23        48.33         8.32         3.81        81.11 
TCGA-24-2020 TCGA-24-2023 TCGA-24-2027 TCGA-24-2260 TCGA-25-1315 TCGA-25-1316 
      152.02        44.84       109.71        36.16        51.06        37.02 
TCGA-25-1318 TCGA-25-1323 TCGA-25-1326 TCGA-25-1329 TCGA-25-1635 TCGA-25-1878 
       34.98        12.00        31.07         2.96        51.22        85.05 
TCGA-25-2393 TCGA-25-2404 TCGA-29-1691 TCGA-29-1693 TCGA-29-1697 TCGA-29-1703 
       38.04        29.03        47.18       101.79        31.20        59.67 
TCGA-29-1762 TCGA-29-1764 TCGA-29-1774 TCGA-29-1781 TCGA-29-2427 TCGA-29-2428 
       85.68        62.93        17.33         8.38        62.47        45.11 
TCGA-29-2429 TCGA-29-2434 TCGA-29-2435 TCGA-30-1869 TCGA-31-1944 TCGA-36-1571 
        4.90        11.47         1.12        51.39        45.57        22.85 
TCGA-36-1575 TCGA-36-1577 TCGA-36-2529 TCGA-36-2537 TCGA-36-2542 TCGA-36-2548 
        8.55        25.74        35.05        25.91        21.60        14.17 
TCGA-36-2552 TCGA-42-2589 TCGA-42-2591 TCGA-42-2593 TCGA-57-1586 TCGA-59-2349 
       11.47        42.02        40.77         1.48        22.32        80.12 
TCGA-59-2351 TCGA-59-2363 TCGA-61-1724 TCGA-61-1734 TCGA-61-1740 TCGA-61-1900 
      116.12         5.42        20.94        28.47         2.43         5.79 
TCGA-61-1903 TCGA-61-1911 TCGA-61-2000 TCGA-61-2009 TCGA-61-2094 TCGA-61-2095 
       13.02        42.51        14.50        39.85        71.74        61.64 
TCGA-61-2098 TCGA-61-2102 
       65.52         6.48 

$subtype4
TCGA-04-1356 TCGA-04-1362 TCGA-04-1370 TCGA-04-1648 TCGA-04-1654 TCGA-09-2045 
       49.28        44.32        59.97        28.64        47.70        35.15 
TCGA-09-2055 TCGA-13-0720 TCGA-13-0891 TCGA-13-0897 TCGA-13-0899 TCGA-13-1495 
       26.93        44.55        69.01        57.47        56.15        49.25 
TCGA-13-1496 TCGA-13-1498 TCGA-13-1507 TCGA-13-1509 TCGA-23-1111 TCGA-23-1124 
        4.24        37.61         4.77         4.18         3.22        58.13 
TCGA-23-2081 TCGA-23-2641 TCGA-24-1103 TCGA-24-1422 TCGA-24-1435 TCGA-24-1466 
       77.00         2.76        54.12         0.76        43.53        45.14 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1920 TCGA-24-1927 TCGA-24-2024 TCGA-24-2026 
        9.11         3.45         9.80        16.44        58.16        34.82 
TCGA-24-2030 TCGA-24-2261 TCGA-24-2289 TCGA-24-2290 TCGA-24-2295 TCGA-25-1625 
       53.95         0.79        67.36        36.23        33.11        18.02 
TCGA-25-1632 TCGA-25-2391 TCGA-25-2399 TCGA-25-2409 TCGA-29-1688 TCGA-29-1694 
       56.94        49.05        19.99        26.99        78.90        38.53 
TCGA-29-1695 TCGA-29-1698 TCGA-29-1705 TCGA-29-1711 TCGA-30-1860 TCGA-30-1861 
        0.79        68.32        18.25        34.62        44.91        34.78 
TCGA-31-1951 TCGA-36-2534 TCGA-36-2544 TCGA-36-2545 TCGA-59-2348 TCGA-61-1727 
       22.49        29.82        20.98        18.31       180.20        18.54 
TCGA-61-1738 TCGA-61-1743 TCGA-61-1910 TCGA-61-1914 TCGA-61-2017 
       35.80        43.69        37.05        56.61        45.96 

subtype1 subtype2 subtype3 subtype4 
    0.36     0.30     0.53     0.76 
subtype1 subtype2 subtype3 subtype4 
  125.75   115.89   152.02   180.20 
subtype1 subtype2 subtype3 subtype4 
  25.870   28.370   26.435   36.230 
[1] "0.4 - 125.8 (25.9)" "0.3 - 115.9 (28.4)" "0.5 - 152.0 (26.4)"
[4] "0.8 - 180.2 (36.2)"
D7V2, continuous
          vv
clus       OMENTUM OVARY PERITONEUM OVARY
  subtype1       1   118                1
  subtype2       0    98                0
  subtype3       0   129                1
  subtype4       1    58                0
D7V3, multiclass
                  clus
vv                 subtype1 subtype2 subtype3 subtype4
  OMENTUM                 1        0        0        1
  OVARY                 118       98      129       58
  PERITONEUM OVARY        1        0        1        0
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V4, continuous
D7V5, binary
          cls
clus         0   1
  subtype1   1 119
  subtype2   0  98
  subtype3   1 129
  subtype4   0  59
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  119
  subtype2    0   98
  subtype3    1  129
  subtype4    0   59
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         1        0        1        0
  YES      119       98      129       59
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2
  subtype1  3 11  1
  subtype2  4  4  0
  subtype3  5 10  1
  subtype4  1  3  0
D7V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0        3        4        5        1
  R1       11        4       10        3
  R2        1        0        1        0
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     2                         5
  subtype2                                0     4                         1
  subtype3                                2     9                         7
  subtype4                                0     1                         6
          vv
clus       WHITE
  subtype1   105
  subtype2    85
  subtype3   103
  subtype4    49
D7V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        2        0
  ASIAN                                   2        4        9        1
  BLACK OR AFRICAN AMERICAN               5        1        7        6
  WHITE                                 105       85      103       49
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
          cls
clus        0  1
  subtype1  0 64
  subtype2  1 44
  subtype3  5 75
  subtype4  2 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   64
  subtype2    1   44
  subtype3    5   75
  subtype4    2   24
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            0        1        5        2
  NOT HISPANIC OR LATINO       64       44       75       24
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MRNASEQ_CNMF
D8V1, survival
          sevent
clus2       0  1
  subtype1 47 55
  subtype2 30 36
  subtype3 35 56
subtype1 subtype2 subtype3 
     102       66       91 
subtype1 subtype2 subtype3 
      55       36       56 
$subtype1
TCGA-04-1348 TCGA-09-1662 TCGA-09-1667 TCGA-09-1668 TCGA-09-2044 TCGA-13-0890 
       48.76        89.33        61.87        55.36         6.12        67.99 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0924 TCGA-13-1403 TCGA-13-1405 TCGA-13-1410 
       43.36        57.47         6.08        10.88         7.36         4.70 
TCGA-13-1481 TCGA-13-1497 TCGA-13-1498 TCGA-13-1507 TCGA-13-1511 TCGA-13-1512 
       87.06        54.31        37.61         4.77         3.91         3.09 
TCGA-13-2060 TCGA-20-1682 TCGA-20-1687 TCGA-23-1026 TCGA-23-1027 TCGA-23-1109 
        8.61        27.52         2.66        26.83        31.76        51.35 
TCGA-23-1120 TCGA-24-0975 TCGA-24-1417 TCGA-24-1418 TCGA-24-1427 TCGA-24-1428 
        4.27        21.80         7.82         7.99         4.83        17.39 
TCGA-24-1436 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1562 TCGA-24-1563 
        8.55        51.91        41.39        58.09        45.50        47.70 
TCGA-24-1564 TCGA-24-1604 TCGA-24-1842 TCGA-24-1846 TCGA-24-1924 TCGA-24-1930 
       25.87        88.37         8.32         4.37        30.21        81.11 
TCGA-24-2024 TCGA-24-2026 TCGA-24-2035 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 
       58.16        34.82        28.18         0.79         0.36        47.54 
TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 TCGA-24-2290 TCGA-24-2298 TCGA-25-1314 
       31.63        44.61         0.82        36.23        53.26        32.02 
TCGA-25-1318 TCGA-25-1322 TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 
       34.98         2.99        31.07        65.06         2.96        18.58 
TCGA-25-1625 TCGA-25-1635 TCGA-25-2399 TCGA-25-2404 TCGA-25-2409 TCGA-29-1693 
       18.02        51.22        19.99        29.03        26.99       101.79 
TCGA-29-1695 TCGA-29-1699 TCGA-29-1701 TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 
        0.79         0.53        16.90        18.25        29.23        34.62 
TCGA-29-1770 TCGA-29-1776 TCGA-29-1781 TCGA-29-1785 TCGA-29-2427 TCGA-29-2428 
       24.36        11.84         8.38        34.62        62.47        45.11 
TCGA-30-1718 TCGA-30-1855 TCGA-30-1860 TCGA-30-1862 TCGA-30-1891 TCGA-31-1951 
       51.91         2.47        44.91         6.12        30.05        22.49 
TCGA-31-1953 TCGA-31-1956 TCGA-36-1568 TCGA-36-1574 TCGA-36-1578 TCGA-36-1580 
        6.71        44.12        28.77        22.55        27.85        24.23 
TCGA-36-1581 TCGA-57-1582 TCGA-59-2348 TCGA-59-2351 TCGA-61-1725 TCGA-61-1740 
       24.69        24.03       180.20       116.12        31.43         2.43 
TCGA-61-1919 TCGA-61-2000 TCGA-61-2009 TCGA-61-2012 TCGA-61-2094 TCGA-61-2113 
       38.17        14.50        39.85        30.64        71.74        22.22 

$subtype2
TCGA-04-1362 TCGA-04-1365 TCGA-09-0366 TCGA-09-0367 TCGA-09-1666 TCGA-09-1670 
       44.32        76.57        57.76        17.98        57.60        17.98 
TCGA-09-2045 TCGA-09-2051 TCGA-09-2056 TCGA-10-0936 TCGA-13-0799 TCGA-13-0801 
       35.15        63.09        12.46        35.80         7.79         8.28 
TCGA-20-1685 TCGA-23-1023 TCGA-23-1029 TCGA-23-2081 TCGA-23-2084 TCGA-24-1103 
       16.70        40.54         8.81        77.00        49.84        54.12 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1423 TCGA-24-1467 TCGA-24-1549 TCGA-24-1555 
        6.31         6.38         6.25       105.99        56.58        88.50 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1616 TCGA-24-1844 TCGA-24-1847 TCGA-24-2019 
       70.62        39.88        38.24         3.72        11.28         4.87 
TCGA-24-2023 TCGA-24-2036 TCGA-24-2038 TCGA-24-2297 TCGA-25-1313 TCGA-25-1319 
       44.84        64.01        44.52        55.86        26.96        65.00 
TCGA-25-1321 TCGA-25-1630 TCGA-25-2391 TCGA-25-2392 TCGA-25-2396 TCGA-25-2397 
       33.96         7.86        49.05         1.02         3.02        12.00 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1694 TCGA-29-1696 TCGA-29-1778 TCGA-29-1784 
       78.90        44.71        38.53        33.70        14.93         5.36 
TCGA-31-1944 TCGA-36-1570 TCGA-57-1584 TCGA-57-1993 TCGA-59-2355 TCGA-61-1724 
       45.57        21.53        21.14        25.08         2.14        20.94 
TCGA-61-1728 TCGA-61-1736 TCGA-61-1907 TCGA-61-1910 TCGA-61-1914 TCGA-61-1918 
       27.88        48.79        31.30        37.05        56.61        15.75 
TCGA-61-2008 TCGA-61-2016 TCGA-61-2092 TCGA-61-2097 TCGA-61-2104 TCGA-61-2109 
       30.64         1.18        51.72        60.62        76.87        20.68 

$subtype3
TCGA-04-1364 TCGA-04-1514 TCGA-09-0364 TCGA-09-0369 TCGA-09-1669 TCGA-09-1673 
       33.67        56.55        29.16        35.57        30.51         3.02 
TCGA-09-1674 TCGA-09-2048 TCGA-09-2054 TCGA-10-0928 TCGA-13-0730 TCGA-13-0800 
        8.55         4.54        20.94        18.51        17.82         8.12 
TCGA-13-0899 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-1505 TCGA-13-1506 
       56.15        29.98        21.17        13.81         4.21         4.41 
TCGA-20-1683 TCGA-20-1684 TCGA-23-1111 TCGA-23-1114 TCGA-23-1122 TCGA-23-1123 
       25.38        19.10         3.22        68.68        39.09        33.47 
TCGA-23-1809 TCGA-23-2077 TCGA-24-1419 TCGA-24-1424 TCGA-24-1430 TCGA-24-1469 
        0.53       115.89         7.86         6.02        28.37         9.11 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1548 TCGA-24-1550 TCGA-24-1558 TCGA-24-1560 
       22.22        26.96        16.21        41.06        19.53        44.09 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1843 TCGA-24-1850 TCGA-24-2020 TCGA-24-2027 
       17.23        90.15         3.48         5.52       152.02       109.71 
TCGA-24-2033 TCGA-24-2254 TCGA-25-1312 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
       18.48        57.07         1.02        51.06        37.02         1.02 
TCGA-25-1323 TCGA-25-1324 TCGA-25-1627 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
       12.00        34.03         0.36         0.30        56.94        60.59 
TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-2393 TCGA-25-2400 TCGA-29-1691 
       35.54        14.96        24.99        38.04        42.02        47.18 
TCGA-29-1697 TCGA-29-1702 TCGA-29-1703 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
       31.20        18.67        59.67        17.00        85.68        66.81 
TCGA-29-1783 TCGA-29-2414 TCGA-29-2425 TCGA-36-1571 TCGA-36-1575 TCGA-36-1577 
        7.23        86.17        65.00        22.85         8.55        25.74 
TCGA-57-1583 TCGA-57-1994 TCGA-59-2350 TCGA-59-2352 TCGA-59-2363 TCGA-61-1721 
       11.38        25.02        22.32         9.40         5.42        11.11 
TCGA-61-1733 TCGA-61-1738 TCGA-61-1741 TCGA-61-1743 TCGA-61-1900 TCGA-61-1917 
       31.79        35.80        33.67        43.69         5.79        43.43 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2088 TCGA-61-2098 TCGA-61-2102 TCGA-61-2110 
        2.01         5.52         4.77        65.52         6.48        44.52 
TCGA-61-2111 
      125.75 

subtype1 subtype2 subtype3 
    0.36     1.02     0.30 
subtype1 subtype2 subtype3 
  180.20   105.99   152.02 
subtype1 subtype2 subtype3 
  28.475   34.555   24.990 
[1] "0.4 - 180.2 (28.5)" "1.0 - 106.0 (34.6)" "0.3 - 152.0 (25.0)"
D8V2, continuous
          vv
clus       OMENTUM OVARY
  subtype1       1   101
  subtype2       0    67
  subtype3       0    92
D8V3, multiclass
         clus
vv        subtype1 subtype2 subtype3
  OMENTUM        1        0        0
  OVARY        101       67       92
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V4, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
clus
subtype1 subtype2 subtype3 
      10        2        2 
 [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [7] "subtype1" "subtype1" "subtype1" "subtype1"
D8V5, binary
          cls
clus         0   1
  subtype1   1 101
  subtype2   0  67
  subtype3   1  91
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  101
  subtype2    0   67
  subtype3    1   91
     clus
vv    subtype1 subtype2 subtype3
  NO         1        0        1
  YES      101       67       91
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1
  subtype1  0  2
  subtype2  1  0
  subtype3  1  3
D8V6, multiclass
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
clus
subtype1 subtype2 subtype3 
       2        1        4 
[1] "subtype3" "subtype3" "subtype3" "subtype3"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     6                         5
  subtype2                                0     3                         3
  subtype3                                0     3                         8
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    86
  subtype2                                         1    58
  subtype3                                         0    78
D8V7, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 1        0        0
  ASIAN                                            6        3        3
  BLACK OR AFRICAN AMERICAN                        5        3        8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        1        0
  WHITE                                           86       58       78
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
          cls
clus        0  1
  subtype1  2 53
  subtype2  1 34
  subtype3  0 50
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   53
  subtype2    1   34
  subtype3    0   50
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        1        0
  NOT HISPANIC OR LATINO       53       34       50
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MRNASEQ_CHIERARCHICAL
D9V1, survival
          sevent
clus2       0  1
  subtype1 51 55
  subtype2 48 68
  subtype3 13 24
subtype1 subtype2 subtype3 
     106      116       37 
subtype1 subtype2 subtype3 
      55       68       24 
$subtype1
TCGA-04-1348 TCGA-04-1365 TCGA-09-1667 TCGA-09-1668 TCGA-09-2044 TCGA-13-0801 
       48.76        76.57        61.87        55.36         6.12         8.28 
TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0924 TCGA-13-1403 TCGA-13-1405 
       67.99        43.36        57.47         6.08        10.88         7.36 
TCGA-13-1410 TCGA-13-1481 TCGA-13-1497 TCGA-13-1498 TCGA-13-1507 TCGA-13-1511 
        4.70        87.06        54.31        37.61         4.77         3.91 
TCGA-13-1512 TCGA-13-2060 TCGA-20-1682 TCGA-20-1687 TCGA-23-1026 TCGA-23-1027 
        3.09         8.61        27.52         2.66        26.83        31.76 
TCGA-23-1109 TCGA-23-1120 TCGA-23-1122 TCGA-23-2081 TCGA-24-0975 TCGA-24-1417 
       51.35         4.27        39.09        77.00        21.80         7.82 
TCGA-24-1418 TCGA-24-1427 TCGA-24-1428 TCGA-24-1436 TCGA-24-1551 TCGA-24-1552 
        7.99         4.83        17.39         8.55        51.91        41.39 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1842 TCGA-24-1846 TCGA-24-1850 
       45.50        47.70        25.87         8.32         4.37         5.52 
TCGA-24-1924 TCGA-24-1930 TCGA-24-2026 TCGA-24-2035 TCGA-24-2261 TCGA-24-2262 
       30.21        81.11        34.82        28.18         0.79         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 TCGA-24-2290 TCGA-24-2298 
       47.54        31.63        44.61         0.82        36.23        53.26 
TCGA-25-1314 TCGA-25-1322 TCGA-25-1326 TCGA-25-1329 TCGA-25-1623 TCGA-25-1633 
       32.02         2.99        31.07         2.96        18.58        60.59 
TCGA-25-1635 TCGA-25-2396 TCGA-25-2399 TCGA-25-2404 TCGA-25-2409 TCGA-29-1688 
       51.22         3.02        19.99        29.03        26.99        78.90 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1699 TCGA-29-1701 TCGA-29-1705 
      101.79        38.53         0.79         0.53        16.90        18.25 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1770 TCGA-29-1776 TCGA-29-1781 TCGA-29-1784 
       29.23        34.62        24.36        11.84         8.38         5.36 
TCGA-29-1785 TCGA-29-2427 TCGA-29-2428 TCGA-30-1718 TCGA-30-1855 TCGA-30-1860 
       34.62        62.47        45.11        51.91         2.47        44.91 
TCGA-30-1862 TCGA-30-1891 TCGA-31-1951 TCGA-31-1953 TCGA-31-1956 TCGA-36-1574 
        6.12        30.05        22.49         6.71        44.12        22.55 
TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-57-1582 TCGA-59-2348 TCGA-61-1724 
       27.85        24.23        24.69        24.03       180.20        20.94 
TCGA-61-1725 TCGA-61-1733 TCGA-61-1740 TCGA-61-1907 TCGA-61-1914 TCGA-61-1919 
       31.43        31.79         2.43        31.30        56.61        38.17 
TCGA-61-2000 TCGA-61-2009 TCGA-61-2094 TCGA-61-2113 
       14.50        39.85        71.74        22.22 

$subtype2
TCGA-04-1362 TCGA-09-0366 TCGA-09-0367 TCGA-09-1662 TCGA-09-1666 TCGA-09-1670 
       44.32        57.76        17.98        89.33        57.60        17.98 
TCGA-09-2045 TCGA-09-2051 TCGA-09-2056 TCGA-10-0928 TCGA-10-0936 TCGA-13-0799 
       35.15        63.09        12.46        18.51        35.80         7.79 
TCGA-13-0899 TCGA-13-0913 TCGA-13-0916 TCGA-13-1505 TCGA-13-1506 TCGA-20-1683 
       56.15        29.98        21.17         4.21         4.41        25.38 
TCGA-20-1684 TCGA-20-1685 TCGA-23-1023 TCGA-23-1029 TCGA-23-1111 TCGA-23-1123 
       19.10        16.70        40.54         8.81         3.22        33.47 
TCGA-23-1809 TCGA-23-2077 TCGA-23-2084 TCGA-24-1103 TCGA-24-1413 TCGA-24-1416 
        0.53       115.89        49.84        54.12         6.31         6.38 
TCGA-24-1419 TCGA-24-1423 TCGA-24-1424 TCGA-24-1430 TCGA-24-1467 TCGA-24-1469 
        7.86         6.25         6.02        28.37       105.99         9.11 
TCGA-24-1474 TCGA-24-1548 TCGA-24-1549 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 
       22.22        16.21        56.58        58.09        88.50        70.62 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 
       39.88        19.53        44.09        90.15        88.37        38.24 
TCGA-24-1843 TCGA-24-1844 TCGA-24-1847 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 
        3.48         3.72        11.28         4.87        44.84        58.16 
TCGA-24-2033 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2297 TCGA-25-1312 
       18.48        64.01        44.52        57.07        55.86         1.02 
TCGA-25-1313 TCGA-25-1315 TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 TCGA-25-1328 
       26.96        51.06        34.98        65.00        33.96        65.06 
TCGA-25-1625 TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1870 
       18.02         0.36         7.86         0.30        56.94        14.96 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2397 TCGA-25-2400 TCGA-29-1690 TCGA-29-1691 
       49.05         1.02        12.00        42.02        44.71        47.18 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1703 TCGA-29-1761 TCGA-29-1778 TCGA-29-1783 
       33.70        31.20        59.67        17.00        14.93         7.23 
TCGA-29-2414 TCGA-29-2425 TCGA-31-1944 TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 
       86.17        65.00        45.57        28.77        21.53        22.85 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1993 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       11.38        21.14        25.08        22.32       116.12         9.40 
TCGA-59-2355 TCGA-61-1721 TCGA-61-1728 TCGA-61-1736 TCGA-61-1738 TCGA-61-1743 
        2.14        11.11        27.88        48.79        35.80        43.69 
TCGA-61-1910 TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 TCGA-61-2008 
       37.05        43.43        15.75         2.01         5.52        30.64 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2092 TCGA-61-2097 TCGA-61-2104 TCGA-61-2109 
       30.64         1.18        51.72        60.62        76.87        20.68 
TCGA-61-2110 TCGA-61-2111 
       44.52       125.75 

$subtype3
TCGA-04-1364 TCGA-04-1514 TCGA-09-0364 TCGA-09-0369 TCGA-09-1669 TCGA-09-1673 
       33.67        56.55        29.16        35.57        30.51         3.02 
TCGA-09-1674 TCGA-09-2048 TCGA-09-2054 TCGA-13-0730 TCGA-13-0800 TCGA-13-0920 
        8.55         4.54        20.94        17.82         8.12        13.81 
TCGA-23-1114 TCGA-24-1544 TCGA-24-1550 TCGA-24-1567 TCGA-24-2020 TCGA-24-2027 
       68.68        26.96        41.06        17.23       152.02       109.71 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1323 TCGA-25-1324 TCGA-25-1634 TCGA-25-1871 
       37.02         1.02        12.00        34.03        35.54        24.99 
TCGA-25-2393 TCGA-29-1702 TCGA-29-1762 TCGA-29-1763 TCGA-36-1575 TCGA-36-1577 
       38.04        18.67        85.68        66.81         8.55        25.74 
TCGA-57-1994 TCGA-59-2363 TCGA-61-1741 TCGA-61-1900 TCGA-61-2088 TCGA-61-2098 
       25.02         5.42        33.67         5.79         4.77        65.52 
TCGA-61-2102 
        6.48 

subtype1 subtype2 subtype3 
    0.36     0.30     1.02 
subtype1 subtype2 subtype3 
  180.20   125.75   152.02 
subtype1 subtype2 subtype3 
  27.685   30.310   25.740 
[1] "0.4 - 180.2 (27.7)" "0.3 - 125.8 (30.3)" "1.0 - 152.0 (25.7)"
D9V2, continuous
          vv
clus       OMENTUM OVARY
  subtype1       1   106
  subtype2       0   117
  subtype3       0    37
D9V3, multiclass
         clus
vv        subtype1 subtype2 subtype3
  OMENTUM        1        0        0
  OVARY        106      117       37
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V4, continuous
D9V5, binary
          cls
clus         0   1
  subtype1   0 107
  subtype2   1 116
  subtype3   1  36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0  107
  subtype2    1  116
  subtype3    1   36
     clus
vv    subtype1 subtype2 subtype3
  NO         0        1        1
  YES      107      116       36
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1
  subtype1  0  2
  subtype2  1  3
  subtype3  1  0
D9V6, multiclass
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
clus
subtype1 subtype2 subtype3 
       2        4        1 
[1] "subtype2" "subtype2" "subtype2" "subtype2"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     6                         5
  subtype2                                0     4                         7
  subtype3                                0     2                         4
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    90
  subtype2                                         1   102
  subtype3                                         0    30
D9V7, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 1        0        0
  ASIAN                                            6        4        2
  BLACK OR AFRICAN AMERICAN                        5        7        4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        1        0
  WHITE                                           90      102       30
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
          cls
clus        0  1
  subtype1  2 54
  subtype2  1 59
  subtype3  0 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   54
  subtype2    1   59
  subtype3    0   24
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        1        0
  NOT HISPANIC OR LATINO       54       59       24
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_CNMF
D10V1, survival
          sevent
clus2       0  1
  subtype1 46 78
  subtype2 86 98
  subtype3 66 76
subtype1 subtype2 subtype3 
     124      184      142 
subtype1 subtype2 subtype3 
      78       98       76 
$subtype1
TCGA-04-1331 TCGA-04-1332 TCGA-04-1346 TCGA-04-1349 TCGA-04-1530 TCGA-09-1662 
       40.24        41.00        65.52        21.57       119.08        89.33 
TCGA-09-2054 TCGA-13-0768 TCGA-13-0890 TCGA-13-0894 TCGA-13-0900 TCGA-13-0908 
       20.94         8.45        67.99        49.61        57.07        44.84 
TCGA-13-1405 TCGA-13-1408 TCGA-13-1411 TCGA-13-1477 TCGA-13-1481 TCGA-13-1485 
        7.36         5.92         4.21        54.64        87.06        20.68 
TCGA-13-1487 TCGA-13-1499 TCGA-13-1501 TCGA-13-1505 TCGA-13-2060 TCGA-23-1026 
       22.39        38.40        32.84         4.21         8.61        26.83 
TCGA-23-1121 TCGA-23-2078 TCGA-23-2081 TCGA-24-0968 TCGA-24-0970 TCGA-24-1418 
        6.38        87.48        77.00        19.66        11.64         7.99 
TCGA-24-1422 TCGA-24-1425 TCGA-24-1427 TCGA-24-1434 TCGA-24-1546 TCGA-24-1550 
        0.76         5.95         4.83        18.67        64.27        41.06 
TCGA-24-1556 TCGA-24-1563 TCGA-24-1842 TCGA-24-1843 TCGA-24-1846 TCGA-24-1849 
       70.62        47.70         8.32         3.48         4.37         5.79 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1928 TCGA-24-1930 TCGA-24-2020 
        5.52         9.80        22.68        11.05        81.11       152.02 
TCGA-24-2024 TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2260 TCGA-24-2261 
       58.16        14.43        18.48        28.18        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-25-1316 TCGA-25-1320 
       67.36        36.23        16.64        53.26        37.02        36.95 
TCGA-25-1326 TCGA-25-1328 TCGA-25-1626 TCGA-25-1628 TCGA-25-1633 TCGA-25-1635 
       31.07        65.06        15.81        20.61        60.59        51.22 
TCGA-25-1877 TCGA-25-2042 TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2401 
       18.05        13.02         3.02        45.01        19.99         2.96 
TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1695 TCGA-29-1698 TCGA-29-1702 
       29.03        31.00        26.99         0.79        68.32        18.67 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1710 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 
       59.67        18.25        29.23        62.93        39.12        31.23 
TCGA-29-1770 TCGA-29-2414 TCGA-29-2427 TCGA-30-1857 TCGA-30-1861 TCGA-30-1862 
       24.36        86.17        62.47         0.26        34.78         6.12 
TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 
        1.22        57.57        24.26        30.05        48.79        45.57 
TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 TCGA-31-1956 TCGA-31-1959 TCGA-36-1574 
       30.18        22.49         6.71        44.12         2.20        22.55 
TCGA-36-1575 TCGA-36-1576 TCGA-57-1585 TCGA-59-2354 TCGA-61-1721 TCGA-61-1724 
        8.55        30.08         1.74        34.39        11.11        20.94 
TCGA-61-1733 TCGA-61-1919 TCGA-61-2002 TCGA-61-2003 TCGA-61-2009 TCGA-61-2101 
       31.79        38.17        17.98         4.01        39.85        55.50 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2111 TCGA-61-2113 
        6.48        76.87       125.75        22.22 

$subtype2
TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 TCGA-04-1347 TCGA-04-1348 TCGA-04-1350 
       49.15         2.01        18.51        63.09        48.76        63.98 
TCGA-04-1356 TCGA-04-1365 TCGA-04-1367 TCGA-04-1536 TCGA-04-1646 TCGA-04-1654 
       49.28        76.57        71.47        29.10        27.88        47.70 
TCGA-09-0366 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1673 
       57.76        41.62        57.60        61.87        55.36         3.02 
TCGA-09-1674 TCGA-10-0926 TCGA-10-0927 TCGA-13-0714 TCGA-13-0720 TCGA-13-0723 
        8.55        25.91        81.47         6.21        44.55        39.58 
TCGA-13-0724 TCGA-13-0751 TCGA-13-0757 TCGA-13-0760 TCGA-13-0766 TCGA-13-0797 
        2.73        55.17        11.18        11.54        21.40         8.71 
TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0805 TCGA-13-0883 
        7.79         8.28         8.19        43.86        35.28        68.94 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0891 
      107.18        91.40        74.27        66.67        61.84        69.01 
TCGA-13-0893 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0910 
       43.36        19.36        47.38        48.33        47.84        37.08 
TCGA-13-0911 TCGA-13-0916 TCGA-13-0919 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 
       27.72        21.17        14.89         6.41         6.08        10.88 
TCGA-13-1404 TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 TCGA-13-1412 TCGA-13-1482 
        6.61         6.05         6.84         4.70         5.33        61.71 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       29.42        98.04        70.82        52.44        73.55        38.20 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 TCGA-13-1504 
       49.25         4.24        54.31        37.61        13.97        16.57 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
        4.41         4.77         4.18         2.56         3.91         3.09 
TCGA-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-20-1687 TCGA-23-1021 TCGA-23-1023 TCGA-23-1027 TCGA-23-1028 TCGA-23-1030 
        2.66        47.54        40.54        31.76        49.41        29.13 
TCGA-23-1032 TCGA-23-1107 TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 
        2.24         0.30        51.35        54.51        31.20        68.68 
TCGA-23-1118 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2079 TCGA-24-0975 
       86.01        39.09        33.47        58.13        91.66        21.80 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1417 TCGA-24-1423 TCGA-24-1428 TCGA-24-1430 
       63.55        47.41         7.82         6.25        17.39        28.37 
TCGA-24-1431 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 TCGA-24-1469 
       19.17        43.53         8.55        72.92        45.14         9.11 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 
        3.45         1.18        22.22        26.96        57.40        16.21 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1558 TCGA-24-1562 
       51.91        41.39        58.09        88.50        19.53        45.50 
TCGA-24-1564 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1845 TCGA-24-1924 
       25.87        90.15        88.37        48.33         3.81        30.21 
TCGA-24-2026 TCGA-24-2030 TCGA-25-1312 TCGA-25-1314 TCGA-25-1318 TCGA-25-1319 
       34.82        53.95         1.02        32.02        34.98        65.00 
TCGA-25-1324 TCGA-25-1325 TCGA-25-1329 TCGA-25-1623 TCGA-25-1632 TCGA-25-2397 
       34.03        32.09         2.96        18.58        56.94        12.00 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1697 TCGA-29-1699 
       78.90        44.71        47.18       101.79        31.20         0.53 
TCGA-29-1701 TCGA-29-1707 TCGA-29-1711 TCGA-29-1769 TCGA-29-1776 TCGA-29-1777 
       16.90        41.98        34.62        22.98        11.84        12.30 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2425 TCGA-29-2428 TCGA-30-1718 TCGA-30-1853 
        5.36        34.62        65.00        45.11        51.91        36.26 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 TCGA-30-1860 TCGA-30-1866 TCGA-36-1569 
        2.47        15.68        48.10        44.91        36.62        29.10 
TCGA-36-1578 TCGA-36-1581 TCGA-57-1582 TCGA-57-1583 TCGA-59-2348 TCGA-59-2350 
       27.85        24.69        24.03        11.38       180.20        22.32 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 TCGA-61-1907 TCGA-61-1910 
       35.80         2.43        33.67         1.45        31.30        37.05 
TCGA-61-1911 TCGA-61-1913 TCGA-61-2000 TCGA-61-2012 
       42.51        48.92        14.50        30.64 

$subtype3
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1514 TCGA-04-1517 TCGA-04-1525 
       32.52        44.32        33.67        56.55        19.99        38.37 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 
       84.20        55.43        28.64        64.64        36.23        31.86 
TCGA-04-1655 TCGA-09-0364 TCGA-09-1661 TCGA-09-1669 TCGA-09-1670 TCGA-09-2044 
       45.37        29.16        38.43        30.51        17.98         6.12 
TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 
       35.15         4.54        71.11        63.09        39.75        12.46 
TCGA-10-0928 TCGA-10-0933 TCGA-10-0934 TCGA-13-0755 TCGA-13-0791 TCGA-13-0792 
       18.51        11.70         3.91         2.50        38.93        36.72 
TCGA-13-0800 TCGA-13-0888 TCGA-13-0906 TCGA-13-0912 TCGA-13-0913 TCGA-13-0920 
        8.12        70.39        44.94        34.06        29.98        13.81 
TCGA-13-0921 TCGA-13-1489 TCGA-20-1685 TCGA-20-1686 TCGA-23-1022 TCGA-23-1029 
        4.64        82.88        16.70         2.93        42.54         8.81 
TCGA-23-1111 TCGA-23-1119 TCGA-23-1120 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 
        3.22       129.96         4.27         0.53        24.95       115.89 
TCGA-23-2084 TCGA-24-0966 TCGA-24-0979 TCGA-24-0982 TCGA-24-1103 TCGA-24-1413 
       49.84         7.63        41.56        22.32        54.12         6.31 
TCGA-24-1416 TCGA-24-1419 TCGA-24-1424 TCGA-24-1426 TCGA-24-1464 TCGA-24-1467 
        6.38         7.86         6.02         5.36        12.46       105.99 
TCGA-24-1549 TCGA-24-1557 TCGA-24-1560 TCGA-24-1565 TCGA-24-1567 TCGA-24-1616 
       56.58        39.88        44.09        10.26        17.23        38.24 
TCGA-24-1844 TCGA-24-1847 TCGA-24-2019 TCGA-24-2023 TCGA-24-2027 TCGA-24-2036 
        3.72        11.28         4.87        44.84       109.71        64.01 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2297 TCGA-25-1313 TCGA-25-1315 TCGA-25-1317 
       44.52        57.07        55.86        26.96        51.06         1.02 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1625 TCGA-25-1627 TCGA-25-1630 
       33.96         2.99        12.00        18.02         0.36         7.86 
TCGA-25-1631 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 TCGA-25-2391 
        0.30        35.54        14.96        24.99        85.05        49.05 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2400 TCGA-29-1694 TCGA-29-1696 TCGA-29-1761 
        1.02        38.04        42.02        38.53        33.70        17.00 
TCGA-29-1762 TCGA-29-1763 TCGA-29-1771 TCGA-29-1774 TCGA-29-1778 TCGA-29-1781 
       85.68        66.81        22.55        17.33        14.93         8.38 
TCGA-29-1783 TCGA-30-1714 TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 TCGA-36-1577 
        7.23        38.07        28.77        21.53        22.85        25.74 
TCGA-36-1580 TCGA-57-1584 TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2351 
       24.23        21.14        22.32        25.08        25.02       116.12 
TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 TCGA-61-1725 TCGA-61-1728 TCGA-61-1736 
        9.40         2.14         5.42        31.43        27.88        48.79 
TCGA-61-1737 TCGA-61-1743 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1906 
       44.84        43.69         8.42         5.79        11.41        34.13 
TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 
       56.61        67.76        43.43        15.75         2.01         5.52 
TCGA-61-2008 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-61-2098 TCGA-61-2109 TCGA-61-2110 
       60.62        65.52        20.68        44.52 

subtype1 subtype2 subtype3 
    0.26     0.30     0.30 
subtype1 subtype2 subtype3 
  152.02   180.20   129.96 
subtype1 subtype2 subtype3 
  28.605   32.055   28.705 
[1] "0.3 - 152.0 (28.6)" "0.3 - 180.2 (32.1)" "0.3 - 130.0 (28.7)"
D10V2, continuous
          vv
clus       OMENTUM OVARY PERITONEUM OVARY
  subtype1       2   121                1
  subtype2       0   185                0
  subtype3       0   144                0
D10V3, multiclass
                  clus
vv                 subtype1 subtype2 subtype3
  OMENTUM                 2        0        0
  OVARY                 121      185      144
  PERITONEUM OVARY        1        0        0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V4, continuous
D10V5, binary
          cls
clus         0   1
  subtype1   0 124
  subtype2   1 184
  subtype3   2 142
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0  124
  subtype2    1  184
  subtype3    2  142
     clus
vv    subtype1 subtype2 subtype3
  NO         0        1        2
  YES      124      184      142
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1
  subtype1  0  3
  subtype2  0  3
  subtype3  2  0
D10V6, multiclass
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 
       3        3        2 
[1] "subtype2" "subtype1" "subtype1" "subtype2" "subtype1" "subtype2"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                2     3                         6
  subtype2                                0     6                        10
  subtype3                                0     6                         5
          vv
clus       WHITE
  subtype1   106
  subtype2   166
  subtype3   128
D10V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        2        0        0
  ASIAN                                   3        6        6
  BLACK OR AFRICAN AMERICAN               6       10        5
  WHITE                                 106      166      128
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
          cls
clus         0   1
  subtype1   0  66
  subtype2   7 113
  subtype3   1  83
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   66
  subtype2    7  113
  subtype3    1   83
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        7        1
  NOT HISPANIC OR LATINO       66      113       83
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = MIRSEQ_CHIERARCHICAL
D11V1, survival
          sevent
clus2       0  1
  subtype1 52 53
  subtype2 27 45
  subtype3 69 99
  subtype4 50 55
subtype1 subtype2 subtype3 subtype4 
     105       72      168      105 
subtype1 subtype2 subtype3 subtype4 
      53       45       99       55 
$subtype1
TCGA-04-1331 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 TCGA-04-1347 TCGA-09-0366 
       40.24        49.15         2.01        18.51        63.09        57.76 
TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 TCGA-13-0714 TCGA-13-0720 TCGA-13-0724 
       41.62        61.87        55.36         6.21        44.55         2.73 
TCGA-13-0751 TCGA-13-0760 TCGA-13-0766 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 
       55.17        11.54        21.40         8.71         7.79         8.28 
TCGA-13-0803 TCGA-13-0805 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
       43.86        35.28       107.18        91.40        74.27        66.67 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0900 TCGA-13-0903 
       61.84        67.99        69.01        43.36        57.07        47.38 
TCGA-13-0905 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0916 TCGA-13-0919 
       47.84        44.84        37.08        27.72        21.17        14.89 
TCGA-13-0924 TCGA-13-1404 TCGA-13-1411 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
        6.08         6.61         4.21        61.71        29.42        98.04 
TCGA-13-1485 TCGA-13-1500 TCGA-13-1501 TCGA-13-1511 TCGA-13-1512 TCGA-20-0990 
       20.68        13.97        32.84         3.91         3.09        25.94 
TCGA-20-0991 TCGA-20-1687 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       26.20         2.66        40.54        26.83        31.76        49.41 
TCGA-23-1109 TCGA-23-1113 TCGA-23-1118 TCGA-23-2079 TCGA-23-2081 TCGA-24-0970 
       51.35        31.20        86.01        91.66        77.00        11.64 
TCGA-24-0975 TCGA-24-1105 TCGA-24-1417 TCGA-24-1425 TCGA-24-1428 TCGA-24-1435 
       21.80        47.41         7.82         5.95        17.39        43.53 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 TCGA-24-1470 TCGA-24-1545 TCGA-24-1546 
        8.55        72.92        45.14         3.45        57.40        64.27 
TCGA-24-1551 TCGA-24-1555 TCGA-24-1563 TCGA-24-1614 TCGA-24-1845 TCGA-24-1846 
       51.91        88.50        47.70        48.33         3.81         4.37 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2271 TCGA-24-2298 TCGA-25-1314 TCGA-25-1623 
       36.16         0.79        31.63        53.26        32.02        18.58 
TCGA-25-1626 TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1711 
       15.81         2.96        31.00        26.99        78.90        34.62 
TCGA-29-1764 TCGA-29-1768 TCGA-29-1770 TCGA-29-2427 TCGA-30-1856 TCGA-30-1857 
       62.93        31.23        24.36        62.47        15.68         0.26 
TCGA-30-1860 TCGA-31-1953 TCGA-31-1956 TCGA-36-1574 TCGA-36-1578 TCGA-59-2354 
       44.91         6.71        44.12        22.55        27.85        34.39 
TCGA-61-1740 TCGA-61-1907 TCGA-61-1913 
        2.43        31.30        48.92 

$subtype2
TCGA-04-1332 TCGA-04-1346 TCGA-04-1349 TCGA-04-1364 TCGA-04-1514 TCGA-04-1517 
       41.00        65.52        21.57        33.67        56.55        19.99 
TCGA-04-1536 TCGA-04-1655 TCGA-09-0364 TCGA-09-1662 TCGA-09-2044 TCGA-09-2048 
       29.10        45.37        29.16        89.33         6.12         4.54 
TCGA-09-2050 TCGA-10-0927 TCGA-13-0755 TCGA-13-0791 TCGA-13-0800 TCGA-13-0883 
       71.11        81.47         2.50        38.93         8.12        68.94 
TCGA-13-0888 TCGA-13-0906 TCGA-13-1409 TCGA-13-1477 TCGA-20-1686 TCGA-23-1022 
       70.39        44.94         6.84        54.64         2.93        42.54 
TCGA-23-1032 TCGA-23-1110 TCGA-23-1114 TCGA-23-1120 TCGA-23-1121 TCGA-23-1123 
        2.24        54.51        68.68         4.27         6.38        33.47 
TCGA-23-2084 TCGA-24-0982 TCGA-24-1104 TCGA-24-1423 TCGA-24-1424 TCGA-24-1544 
       49.84        22.32        63.55         6.25         6.02        26.96 
TCGA-24-1549 TCGA-24-1558 TCGA-24-1567 TCGA-24-1604 TCGA-24-1923 TCGA-25-1312 
       56.58        19.53        17.23        88.37        22.68         1.02 
TCGA-25-1313 TCGA-25-1315 TCGA-25-1322 TCGA-25-1324 TCGA-25-1328 TCGA-25-1633 
       26.96        51.06         2.99        34.03        65.06        60.59 
TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-2392 TCGA-25-2393 TCGA-29-1690 
       35.54        14.96        24.99         1.02        38.04        44.71 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1774 TCGA-29-1776 TCGA-29-1778 TCGA-29-1781 
       17.00        85.68        17.33        11.84        14.93         8.38 
TCGA-29-1784 TCGA-31-1944 TCGA-36-1575 TCGA-36-1577 TCGA-36-1580 TCGA-61-1721 
        5.36        45.57         8.55        25.74        24.23        11.11 
TCGA-61-1743 TCGA-61-1915 TCGA-61-1917 TCGA-61-1998 TCGA-61-2003 TCGA-61-2104 
       43.69        67.76        43.43         5.52         4.01        76.87 

$subtype3
TCGA-04-1348 TCGA-04-1350 TCGA-04-1356 TCGA-04-1365 TCGA-04-1367 TCGA-04-1530 
       48.76        63.98        49.28        76.57        71.47       119.08 
TCGA-04-1646 TCGA-04-1654 TCGA-09-1666 TCGA-09-1673 TCGA-09-1674 TCGA-09-2054 
       27.88        47.70        57.60         3.02         8.55        20.94 
TCGA-10-0926 TCGA-13-0723 TCGA-13-0757 TCGA-13-0768 TCGA-13-0802 TCGA-13-0894 
       25.91        39.58        11.18         8.45         8.19        49.61 
TCGA-13-0901 TCGA-13-0904 TCGA-13-0923 TCGA-13-1403 TCGA-13-1405 TCGA-13-1407 
       19.36        48.33         6.41        10.88         7.36         6.05 
TCGA-13-1408 TCGA-13-1410 TCGA-13-1412 TCGA-13-1481 TCGA-13-1487 TCGA-13-1488 
        5.92         4.70         5.33        87.06        22.39        70.82 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 
       52.44        73.55        38.20        49.25         4.24        54.31 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
       37.61        38.40        16.57         4.21         4.41         4.77 
TCGA-13-1509 TCGA-13-1510 TCGA-13-2060 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 
        4.18         2.56         8.61        27.52        25.38        19.10 
TCGA-23-1021 TCGA-23-1030 TCGA-23-1107 TCGA-23-1122 TCGA-23-1124 TCGA-23-2078 
       47.54        29.13         0.30        39.09        58.13        87.48 
TCGA-24-0968 TCGA-24-1418 TCGA-24-1422 TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 
       19.66         7.99         0.76         4.83        28.37        19.17 
TCGA-24-1434 TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 TCGA-24-1548 TCGA-24-1550 
       18.67         9.11         1.18        22.22        16.21        41.06 
TCGA-24-1552 TCGA-24-1556 TCGA-24-1562 TCGA-24-1564 TCGA-24-1603 TCGA-24-1842 
       41.39        70.62        45.50        25.87        90.15         8.32 
TCGA-24-1843 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-1928 
        3.48         5.79         5.52         9.80        30.21        11.05 
TCGA-24-1930 TCGA-24-2020 TCGA-24-2024 TCGA-24-2026 TCGA-24-2029 TCGA-24-2030 
       81.11       152.02        58.16        34.82        14.43        53.95 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2262 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
       18.48        28.18         0.36        70.45        44.61         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-25-1316 TCGA-25-1318 TCGA-25-1319 
       67.36        36.23        16.64        37.02        34.98        65.00 
TCGA-25-1320 TCGA-25-1325 TCGA-25-1326 TCGA-25-1329 TCGA-25-1628 TCGA-25-1632 
       36.95        32.09        31.07         2.96        20.61        56.94 
TCGA-25-1635 TCGA-25-1877 TCGA-25-2042 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 
       51.22        18.05        13.02         3.02        12.00        45.01 
TCGA-25-2399 TCGA-29-1691 TCGA-29-1693 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 
       19.99        47.18       101.79         0.79        31.20        68.32 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
        0.53        16.90        18.67        59.67        18.25        41.98 
TCGA-29-1710 TCGA-29-1766 TCGA-29-1769 TCGA-29-1777 TCGA-29-1785 TCGA-29-2414 
       29.23        39.12        22.98        12.30        34.62        86.17 
TCGA-29-2425 TCGA-29-2428 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1859 
       65.00        45.11        51.91        36.26         2.47        48.10 
TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 
       34.78         6.12        36.62         1.22        57.57        24.26 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1946 TCGA-31-1951 TCGA-31-1959 TCGA-36-1569 
       30.05        48.79        30.18        22.49         2.20        29.10 
TCGA-36-1576 TCGA-36-1581 TCGA-57-1582 TCGA-57-1583 TCGA-57-1585 TCGA-59-2348 
       30.08        24.69        24.03        11.38         1.74       180.20 
TCGA-59-2350 TCGA-61-1724 TCGA-61-1733 TCGA-61-1738 TCGA-61-1741 TCGA-61-1895 
       22.32        20.94        31.79        35.80        33.67         1.45 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1919 TCGA-61-2000 TCGA-61-2002 TCGA-61-2009 
       37.05        42.51        38.17        14.50        17.98        39.85 
TCGA-61-2012 TCGA-61-2088 TCGA-61-2101 TCGA-61-2102 TCGA-61-2111 TCGA-61-2113 
       30.64         4.77        55.50         6.48       125.75        22.22 

$subtype4
TCGA-04-1361 TCGA-04-1362 TCGA-04-1525 TCGA-04-1542 TCGA-04-1638 TCGA-04-1648 
       32.52        44.32        38.37        84.20        55.43        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-09-1661 TCGA-09-1669 TCGA-09-1670 
       64.64        36.23        31.86        38.43        30.51        17.98 
TCGA-09-2045 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-10-0928 TCGA-10-0933 
       35.15        63.09        39.75        12.46        18.51        11.70 
TCGA-10-0934 TCGA-13-0792 TCGA-13-0912 TCGA-13-0913 TCGA-13-0920 TCGA-13-0921 
        3.91        36.72        34.06        29.98        13.81         4.64 
TCGA-13-1489 TCGA-20-0987 TCGA-20-1685 TCGA-23-1029 TCGA-23-1111 TCGA-23-1119 
       82.88        23.05        16.70         8.81         3.22       129.96 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-24-0966 TCGA-24-0979 TCGA-24-1103 
        0.53        24.95       115.89         7.63        41.56        54.12 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1419 TCGA-24-1426 TCGA-24-1464 TCGA-24-1467 
        6.31         6.38         7.86         5.36        12.46       105.99 
TCGA-24-1553 TCGA-24-1557 TCGA-24-1560 TCGA-24-1565 TCGA-24-1616 TCGA-24-1844 
       58.09        39.88        44.09        10.26        38.24         3.72 
TCGA-24-1847 TCGA-24-2019 TCGA-24-2023 TCGA-24-2027 TCGA-24-2036 TCGA-24-2038 
       11.28         4.87        44.84       109.71        64.01        44.52 
TCGA-24-2254 TCGA-24-2267 TCGA-24-2297 TCGA-25-1317 TCGA-25-1321 TCGA-25-1323 
       57.07        47.54        55.86         1.02        33.96        12.00 
TCGA-25-1625 TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 TCGA-25-1878 TCGA-25-2391 
       18.02         0.36         7.86         0.30        85.05        49.05 
TCGA-25-2400 TCGA-25-2404 TCGA-29-1694 TCGA-29-1696 TCGA-29-1763 TCGA-29-1771 
       42.02        29.03        38.53        33.70        66.81        22.55 
TCGA-29-1783 TCGA-30-1714 TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 TCGA-57-1584 
        7.23        38.07        28.77        21.53        22.85        21.14 
TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 
       22.32        25.08        25.02       116.12         9.40         2.14 
TCGA-59-2363 TCGA-61-1725 TCGA-61-1728 TCGA-61-1736 TCGA-61-1737 TCGA-61-1899 
        5.42        31.43        27.88        48.79        44.84         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1906 TCGA-61-1914 TCGA-61-1918 TCGA-61-1995 
        5.79        11.41        34.13        56.61        15.75         2.01 
TCGA-61-2008 TCGA-61-2016 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 
       30.64         1.18        51.72        71.74        61.64        60.62 
TCGA-61-2098 TCGA-61-2109 TCGA-61-2110 
       65.52        20.68        44.52 

subtype1 subtype2 subtype3 subtype4 
    0.26     1.02     0.30     0.30 
subtype1 subtype2 subtype3 subtype4 
  107.18    89.33   180.20   129.96 
subtype1 subtype2 subtype3 subtype4 
  32.840   28.030   28.275   30.510 
[1] "0.3 - 107.2 (32.8)" "1.0 - 89.3 (28.0)"  "0.3 - 180.2 (28.3)"
[4] "0.3 - 130.0 (30.5)"
D11V2, continuous
          vv
clus       OMENTUM OVARY PERITONEUM OVARY
  subtype1       0   105                0
  subtype2       0    73                0
  subtype3       2   166                1
  subtype4       0   106                0
D11V3, multiclass
                  clus
vv                 subtype1 subtype2 subtype3 subtype4
  OMENTUM                 0        0        2        0
  OVARY                 105       73      166      106
  PERITONEUM OVARY        0        0        1        0
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V4, continuous
D11V5, binary
          cls
clus         0   1
  subtype1   0 105
  subtype2   1  72
  subtype3   1 168
  subtype4   1 105
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0  105
  subtype2    1   72
  subtype3    1  168
  subtype4    1  105
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         0        1        1        1
  YES      105       72      168      105
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1
  subtype1  0  2
  subtype2  0  0
  subtype3  0  4
  subtype4  2  0
D11V6, multiclass
[1] "Remove cluster labels:" "subtype1"               "subtype4"              
clus
subtype1 subtype3 subtype4 
       2        4        2 
[1] "subtype3" "subtype3" "subtype3" "subtype3"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     6                         4
  subtype2                                0     3                         4
  subtype3                                1     3                         8
  subtype4                                1     3                         5
          vv
clus       WHITE
  subtype1    94
  subtype2    61
  subtype3   151
  subtype4    94
D11V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1        1
  ASIAN                                   6        3        3        3
  BLACK OR AFRICAN AMERICAN               4        4        8        5
  WHITE                                  94       61      151       94
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
          cls
clus        0  1
  subtype1  3 70
  subtype2  2 45
  subtype3  2 90
  subtype4  1 57
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   70
  subtype2    2   45
  subtype3    2   90
  subtype4    1   57
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        2        2        1
  NOT HISPANIC OR LATINO       70       45       90       57
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = MIRSEQ_MATURE_CNMF
D12V1, survival
          sevent
clus2        0   1
  subtype1  29  69
  subtype2  97 100
  subtype3  72  83
subtype1 subtype2 subtype3 
      98      197      155 
subtype1 subtype2 subtype3 
      69      100       83 
$subtype1
TCGA-04-1331 TCGA-04-1346 TCGA-04-1349 TCGA-04-1530 TCGA-09-1662 TCGA-09-2054 
       40.24        65.52        21.57       119.08        89.33        20.94 
TCGA-13-0768 TCGA-13-0886 TCGA-13-0894 TCGA-13-0900 TCGA-13-1405 TCGA-13-1408 
        8.45        74.27        49.61        57.07         7.36         5.92 
TCGA-13-1411 TCGA-13-1477 TCGA-13-1481 TCGA-13-1485 TCGA-13-1487 TCGA-23-1026 
        4.21        54.64        87.06        20.68        22.39        26.83 
TCGA-24-0968 TCGA-24-0970 TCGA-24-1422 TCGA-24-1427 TCGA-24-1434 TCGA-24-1546 
       19.66        11.64         0.76         4.83        18.67        64.27 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1556 TCGA-24-1563 TCGA-24-1842 TCGA-24-1843 
       41.06        51.91        70.62        47.70         8.32         3.48 
TCGA-24-1849 TCGA-24-1850 TCGA-24-1928 TCGA-24-1930 TCGA-24-2020 TCGA-24-2024 
        5.79         5.52        11.05        81.11       152.02        58.16 
TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 
       14.43        18.48        28.18        36.16         0.79         0.36 
TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2289 TCGA-24-2293 TCGA-24-2298 
       31.63        70.45        44.61        67.36        16.64        53.26 
TCGA-25-1316 TCGA-25-1326 TCGA-25-1328 TCGA-25-1623 TCGA-25-1626 TCGA-25-1628 
       37.02        31.07        65.06        18.58        15.81        20.61 
TCGA-25-1635 TCGA-25-1877 TCGA-25-2042 TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 
       51.22        18.05        13.02         3.02        45.01        19.99 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1698 TCGA-29-1702 
        2.96        29.03        31.00        26.99        68.32        18.67 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1710 TCGA-29-1766 TCGA-29-1768 TCGA-29-2427 
       59.67        18.25        29.23        39.12        31.23        62.47 
TCGA-30-1857 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1867 TCGA-30-1887 
        0.26        44.91        34.78         6.12         1.22        24.26 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 
       30.05        48.79        45.57        30.18        22.49         6.71 
TCGA-31-1956 TCGA-31-1959 TCGA-36-1569 TCGA-36-1574 TCGA-57-1585 TCGA-59-2354 
       44.12         2.20        29.10        22.55         1.74        34.39 
TCGA-61-1721 TCGA-61-1919 TCGA-61-2002 TCGA-61-2009 TCGA-61-2101 TCGA-61-2102 
       11.11        38.17        17.98        39.85        55.50         6.48 
TCGA-61-2111 TCGA-61-2113 
      125.75        22.22 

$subtype2
TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 TCGA-04-1347 TCGA-04-1348 
       41.00        49.15         2.01        18.51        63.09        48.76 
TCGA-04-1350 TCGA-04-1356 TCGA-04-1365 TCGA-04-1367 TCGA-04-1536 TCGA-04-1646 
       63.98        49.28        76.57        71.47        29.10        27.88 
TCGA-04-1654 TCGA-09-0366 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 
       47.70        57.76        41.62        57.60        61.87        55.36 
TCGA-09-1673 TCGA-09-1674 TCGA-10-0926 TCGA-10-0927 TCGA-13-0714 TCGA-13-0720 
        3.02         8.55        25.91        81.47         6.21        44.55 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0751 TCGA-13-0757 TCGA-13-0760 TCGA-13-0766 
       39.58         2.73        55.17        11.18        11.54        21.40 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0805 
        8.71         7.79         8.28         8.19        43.86        35.28 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 
       68.94       107.18        91.40        66.67        61.84        67.99 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       69.01        43.36        19.36        47.38        48.33        47.84 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0916 TCGA-13-0919 TCGA-13-0923 
       44.84        37.08        27.72        21.17        14.89         6.41 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 
        6.08        10.88         6.61         6.05         6.84         4.70 
TCGA-13-1412 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1488 TCGA-13-1491 
        5.33        61.71        29.42        98.04        70.82        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
       73.55        38.20        49.25         4.24        54.31        37.61 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       38.40        13.97        32.84        16.57         4.21         4.41 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2060 
        4.77         4.18         2.56         3.91         3.09         8.61 
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-20-1687 TCGA-23-1021 TCGA-23-1023 TCGA-23-1027 TCGA-23-1028 TCGA-23-1030 
        2.66        47.54        40.54        31.76        49.41        29.13 
TCGA-23-1107 TCGA-23-1109 TCGA-23-1113 TCGA-23-1114 TCGA-23-1118 TCGA-23-1122 
        0.30        51.35        31.20        68.68        86.01        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-24-0975 
       33.47        58.13        87.48        91.66        77.00        21.80 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1417 TCGA-24-1418 TCGA-24-1425 TCGA-24-1428 
       63.55        47.41         7.82         7.99         5.95        17.39 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 
       28.37        19.17        43.53         8.55        72.92        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-24-1552 TCGA-24-1555 TCGA-24-1558 TCGA-24-1562 TCGA-24-1564 
       16.21        41.39        88.50        19.53        45.50        25.87 
TCGA-24-1603 TCGA-24-1614 TCGA-24-1845 TCGA-24-1846 TCGA-24-1920 TCGA-24-1924 
       90.15        48.33         3.81         4.37         9.80        30.21 
TCGA-24-2026 TCGA-24-2030 TCGA-24-2288 TCGA-24-2290 TCGA-25-1312 TCGA-25-1314 
       34.82        53.95         0.82        36.23         1.02        32.02 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1324 TCGA-25-1325 TCGA-25-1329 
       34.98        65.00        36.95        34.03        32.09         2.96 
TCGA-25-2397 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1695 
       12.00        78.90        44.71        47.18       101.79         0.79 
TCGA-29-1697 TCGA-29-1699 TCGA-29-1701 TCGA-29-1707 TCGA-29-1711 TCGA-29-1764 
       31.20         0.53        16.90        41.98        34.62        62.93 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1776 TCGA-29-1777 TCGA-29-1784 TCGA-29-1785 
       22.98        24.36        11.84        12.30         5.36        34.62 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 
       86.17        65.00        45.11        51.91        36.26         2.47 
TCGA-30-1856 TCGA-30-1859 TCGA-30-1866 TCGA-30-1880 TCGA-36-1575 TCGA-36-1576 
       15.68        48.10        36.62        57.57         8.55        30.08 
TCGA-36-1578 TCGA-36-1581 TCGA-57-1582 TCGA-57-1583 TCGA-59-2348 TCGA-59-2350 
       27.85        24.69        24.03        11.38       180.20        22.32 
TCGA-61-1724 TCGA-61-1733 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1907 
       20.94        31.79        35.80         2.43        33.67        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-2000 TCGA-61-2088 
       37.05        42.51        48.92        14.50         4.77 

$subtype3
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1514 TCGA-04-1517 TCGA-04-1525 
       32.52        44.32        33.67        56.55        19.99        38.37 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 
       84.20        55.43        28.64        64.64        36.23        31.86 
TCGA-04-1655 TCGA-09-0364 TCGA-09-1661 TCGA-09-1669 TCGA-09-1670 TCGA-09-2044 
       45.37        29.16        38.43        30.51        17.98         6.12 
TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 
       35.15         4.54        71.11        63.09        39.75        12.46 
TCGA-10-0928 TCGA-10-0933 TCGA-10-0934 TCGA-13-0755 TCGA-13-0791 TCGA-13-0792 
       18.51        11.70         3.91         2.50        38.93        36.72 
TCGA-13-0800 TCGA-13-0888 TCGA-13-0906 TCGA-13-0912 TCGA-13-0913 TCGA-13-0920 
        8.12        70.39        44.94        34.06        29.98        13.81 
TCGA-13-0921 TCGA-13-1489 TCGA-20-1685 TCGA-20-1686 TCGA-23-1022 TCGA-23-1029 
        4.64        82.88        16.70         2.93        42.54         8.81 
TCGA-23-1032 TCGA-23-1110 TCGA-23-1111 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 
        2.24        54.51         3.22       129.96         4.27         6.38 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2084 TCGA-24-0966 TCGA-24-0979 
        0.53        24.95       115.89        49.84         7.63        41.56 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1413 TCGA-24-1416 TCGA-24-1419 TCGA-24-1423 
       22.32        54.12         6.31         6.38         7.86         6.25 
TCGA-24-1424 TCGA-24-1426 TCGA-24-1464 TCGA-24-1467 TCGA-24-1549 TCGA-24-1553 
        6.02         5.36        12.46       105.99        56.58        58.09 
TCGA-24-1557 TCGA-24-1560 TCGA-24-1565 TCGA-24-1567 TCGA-24-1604 TCGA-24-1616 
       39.88        44.09        10.26        17.23        88.37        38.24 
TCGA-24-1844 TCGA-24-1847 TCGA-24-1923 TCGA-24-2019 TCGA-24-2023 TCGA-24-2027 
        3.72        11.28        22.68         4.87        44.84       109.71 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2267 TCGA-24-2297 TCGA-25-1313 
       64.01        44.52        57.07        47.54        55.86        26.96 
TCGA-25-1315 TCGA-25-1317 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1625 
       51.06         1.02        33.96         2.99        12.00        18.02 
TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
        0.36         7.86         0.30        56.94        60.59        35.54 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 
       14.96        24.99        85.05        49.05         1.02        38.04 
TCGA-25-2400 TCGA-29-1694 TCGA-29-1696 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
       42.02        38.53        33.70        17.00        85.68        66.81 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-30-1714 
       22.55        17.33        14.93         8.38         7.23        38.07 
TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 TCGA-36-1577 TCGA-36-1580 TCGA-57-1584 
       28.77        21.53        22.85        25.74        24.23        21.14 
TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 
       22.32        25.08        25.02       116.12         9.40         2.14 
TCGA-59-2363 TCGA-61-1725 TCGA-61-1728 TCGA-61-1736 TCGA-61-1737 TCGA-61-1743 
        5.42        31.43        27.88        48.79        44.84        43.69 
TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1906 TCGA-61-1914 
        1.45         8.42         5.79        11.41        34.13        56.61 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 TCGA-61-2003 
       67.76        43.43        15.75         2.01         5.52         4.01 
TCGA-61-2008 TCGA-61-2012 TCGA-61-2016 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       30.64        30.64         1.18        51.72        71.74        61.64 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       60.62        65.52        76.87        20.68        44.52 

subtype1 subtype2 subtype3 
    0.26     0.30     0.30 
subtype1 subtype2 subtype3 
  152.02   180.20   129.96 
subtype1 subtype2 subtype3 
  28.605   31.790   29.160 
[1] "0.3 - 152.0 (28.6)" "0.3 - 180.2 (31.8)" "0.3 - 130.0 (29.2)"
D12V2, continuous
          vv
clus       OMENTUM OVARY PERITONEUM OVARY
  subtype1       1    96                1
  subtype2       1   197                0
  subtype3       0   157                0
D12V3, multiclass
                  clus
vv                 subtype1 subtype2 subtype3
  OMENTUM                 1        1        0
  OVARY                  96      197      157
  PERITONEUM OVARY        1        0        0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V4, continuous
D12V5, binary
          cls
clus         0   1
  subtype1   0  98
  subtype2   0 198
  subtype3   3 154
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   98
  subtype2    0  198
  subtype3    3  154
     clus
vv    subtype1 subtype2 subtype3
  NO         0        0        3
  YES       98      198      154
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1
  subtype1  0  2
  subtype2  0  4
  subtype3  2  0
D12V6, multiclass
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
clus
subtype1 subtype2 subtype3 
       2        4        2 
[1] "subtype2" "subtype2" "subtype2" "subtype2"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                2     3                         6
  subtype2                                0     6                         9
  subtype3                                0     6                         6
          vv
clus       WHITE
  subtype1    84
  subtype2   177
  subtype3   139
D12V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        2        0        0
  ASIAN                                   3        6        6
  BLACK OR AFRICAN AMERICAN               6        9        6
  WHITE                                  84      177      139
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, binary
          cls
clus         0   1
  subtype1   1  54
  subtype2   5 119
  subtype3   2  89
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   54
  subtype2    5  119
  subtype3    2   89
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        5        2
  NOT HISPANIC OR LATINO       54      119       89
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D13V1, survival
          sevent
clus2        0   1
  subtype1  70 102
  subtype2  78  96
  subtype3  50  54
subtype1 subtype2 subtype3 
     172      174      104 
subtype1 subtype2 subtype3 
     102       96       54 
$subtype1
TCGA-04-1331 TCGA-04-1337 TCGA-04-1348 TCGA-04-1349 TCGA-04-1356 TCGA-04-1530 
       40.24         2.01        48.76        21.57        49.28       119.08 
TCGA-04-1536 TCGA-04-1654 TCGA-09-1662 TCGA-09-1667 TCGA-09-1668 TCGA-09-1674 
       29.10        47.70        89.33        61.87        55.36         8.55 
TCGA-09-2054 TCGA-10-0926 TCGA-13-0714 TCGA-13-0757 TCGA-13-0768 TCGA-13-0884 
       20.94        25.91         6.21        11.18         8.45       107.18 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0890 TCGA-13-0893 TCGA-13-0894 TCGA-13-0900 
       91.40        74.27        67.99        43.36        49.61        57.07 
TCGA-13-0908 TCGA-13-0919 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
       44.84        14.89         6.08        10.88         6.61         7.36 
TCGA-13-1408 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 
        5.92         4.21         5.33        54.64        87.06        61.71 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1494 TCGA-13-1495 TCGA-13-1497 
       29.42        98.04        20.68        38.20        49.25        54.31 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1511 TCGA-13-1512 
       38.40        13.97        32.84        16.57         3.91         3.09 
TCGA-13-2060 TCGA-20-1682 TCGA-20-1683 TCGA-20-1687 TCGA-23-1023 TCGA-23-1026 
        8.61        27.52        25.38         2.66        40.54        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1118 TCGA-23-1121 TCGA-23-2078 TCGA-23-2079 
       31.76        49.41        86.01         6.38        87.48        91.66 
TCGA-23-2081 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-1105 TCGA-24-1418 
       77.00        19.66        11.64        21.80        47.41         7.99 
TCGA-24-1422 TCGA-24-1425 TCGA-24-1427 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
        0.76         5.95         4.83        18.67        43.53         8.55 
TCGA-24-1463 TCGA-24-1470 TCGA-24-1545 TCGA-24-1546 TCGA-24-1550 TCGA-24-1551 
       72.92         3.45        57.40        64.27        41.06        51.91 
TCGA-24-1556 TCGA-24-1563 TCGA-24-1564 TCGA-24-1842 TCGA-24-1846 TCGA-24-1849 
       70.62        47.70        25.87         8.32         4.37         5.79 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1928 TCGA-24-1930 TCGA-24-2020 TCGA-24-2024 
        5.52         9.80        11.05        81.11       152.02        58.16 
TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 
       14.43        18.48        28.18        36.16         0.79         0.36 
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-25-1314 TCGA-25-1316 TCGA-25-1318 TCGA-25-1320 
       16.64        53.26        32.02        37.02        34.98        36.95 
TCGA-25-1326 TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1628 TCGA-25-1633 
       31.07         2.96        18.58        15.81        20.61        60.59 
TCGA-25-1635 TCGA-25-1877 TCGA-25-2042 TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 
       51.22        18.05        13.02         3.02        45.01        19.99 
TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1691 TCGA-29-1698 
        2.96        31.00        26.99        78.90        47.18        68.32 
TCGA-29-1702 TCGA-29-1705 TCGA-29-1710 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 
       18.67        18.25        29.23        62.93        39.12        31.23 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1776 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 
       22.98        24.36        11.84        65.00        62.47        45.11 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 
        2.47        15.68         0.26        44.91        34.78         6.12 
TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1946 
        1.22        57.57        24.26        30.05        48.79        30.18 
TCGA-31-1951 TCGA-31-1953 TCGA-31-1956 TCGA-31-1959 TCGA-36-1574 TCGA-36-1575 
       22.49         6.71        44.12         2.20        22.55         8.55 
TCGA-36-1576 TCGA-57-1582 TCGA-57-1585 TCGA-59-2354 TCGA-61-1724 TCGA-61-1733 
       30.08        24.03         1.74        34.39        20.94        31.79 
TCGA-61-1740 TCGA-61-1913 TCGA-61-1919 TCGA-61-2000 TCGA-61-2002 TCGA-61-2009 
        2.43        48.92        38.17        14.50        17.98        39.85 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2111 TCGA-61-2113 
       55.50         6.48       125.75        22.22 

$subtype2
TCGA-04-1332 TCGA-04-1346 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1367 
       41.00        65.52        32.52        44.32        33.67        71.47 
TCGA-04-1514 TCGA-04-1517 TCGA-04-1525 TCGA-04-1542 TCGA-04-1638 TCGA-04-1648 
       56.55        19.99        38.37        84.20        55.43        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 TCGA-09-1661 
       64.64        36.23        31.86        45.37        29.16        38.43 
TCGA-09-1669 TCGA-09-1670 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 
       30.51        17.98         6.12        35.15         4.54        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-10-0928 TCGA-10-0933 TCGA-10-0934 
       63.09        39.75        12.46        18.51        11.70         3.91 
TCGA-13-0755 TCGA-13-0791 TCGA-13-0792 TCGA-13-0800 TCGA-13-0883 TCGA-13-0888 
        2.50        38.93        36.72         8.12        68.94        70.39 
TCGA-13-0906 TCGA-13-0912 TCGA-13-0913 TCGA-13-0920 TCGA-13-0921 TCGA-13-1489 
       44.94        34.06        29.98        13.81         4.64        82.88 
TCGA-13-1506 TCGA-20-0987 TCGA-20-0990 TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 
        4.41        23.05        25.94        16.70         2.93        47.54 
TCGA-23-1022 TCGA-23-1029 TCGA-23-1032 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 
       42.54         8.81         2.24        54.51         3.22        68.68 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1809 TCGA-23-2072 
      129.96         4.27        39.09        33.47         0.53        24.95 
TCGA-23-2077 TCGA-23-2084 TCGA-24-0966 TCGA-24-0979 TCGA-24-0982 TCGA-24-1103 
      115.89        49.84         7.63        41.56        22.32        54.12 
TCGA-24-1104 TCGA-24-1413 TCGA-24-1416 TCGA-24-1419 TCGA-24-1423 TCGA-24-1424 
       63.55         6.31         6.38         7.86         6.25         6.02 
TCGA-24-1426 TCGA-24-1464 TCGA-24-1467 TCGA-24-1544 TCGA-24-1549 TCGA-24-1553 
        5.36        12.46       105.99        26.96        56.58        58.09 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1565 TCGA-24-1567 TCGA-24-1604 
       39.88        19.53        44.09        10.26        17.23        88.37 
TCGA-24-1616 TCGA-24-1843 TCGA-24-1844 TCGA-24-1847 TCGA-24-1923 TCGA-24-2019 
       38.24         3.48         3.72        11.28        22.68         4.87 
TCGA-24-2023 TCGA-24-2027 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2267 
       44.84       109.71        64.01        44.52        57.07        47.54 
TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 TCGA-25-1315 TCGA-25-1317 TCGA-25-1321 
       55.86         1.02        26.96        51.06         1.02        33.96 
TCGA-25-1322 TCGA-25-1323 TCGA-25-1328 TCGA-25-1625 TCGA-25-1627 TCGA-25-1630 
        2.99        12.00        65.06        18.02         0.36         7.86 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 
        0.30        56.94        35.54        14.96        24.99        85.05 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2400 TCGA-25-2404 TCGA-29-1690 
       49.05         1.02        38.04        42.02        29.03        44.71 
TCGA-29-1694 TCGA-29-1696 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1771 
       38.53        33.70        17.00        85.68        66.81        22.55 
TCGA-29-1774 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-30-1714 
       17.33        14.93         8.38         7.23         5.36        38.07 
TCGA-31-1944 TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 TCGA-36-1577 TCGA-36-1580 
       45.57        28.77        21.53        22.85        25.74        24.23 
TCGA-57-1584 TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2351 TCGA-59-2352 
       21.14        22.32        25.08        25.02       116.12         9.40 
TCGA-59-2355 TCGA-59-2363 TCGA-61-1721 TCGA-61-1725 TCGA-61-1728 TCGA-61-1736 
        2.14         5.42        11.11        31.43        27.88        48.79 
TCGA-61-1737 TCGA-61-1743 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1906 
       44.84        43.69         8.42         5.79        11.41        34.13 
TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 
       56.61        67.76        43.43        15.75         2.01         5.52 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 TCGA-61-2016 TCGA-61-2092 TCGA-61-2094 
        4.01        30.64        30.64         1.18        51.72        71.74 
TCGA-61-2095 TCGA-61-2097 TCGA-61-2098 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       61.64        60.62        65.52        76.87        20.68        44.52 

$subtype3
TCGA-04-1336 TCGA-04-1342 TCGA-04-1347 TCGA-04-1350 TCGA-04-1365 TCGA-04-1646 
       49.15        18.51        63.09        63.98        76.57        27.88 
TCGA-09-0366 TCGA-09-1665 TCGA-09-1666 TCGA-09-1673 TCGA-10-0927 TCGA-13-0720 
       57.76        41.62        57.60         3.02        81.47        44.55 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0751 TCGA-13-0760 TCGA-13-0766 TCGA-13-0797 
       39.58         2.73        55.17        11.54        21.40         8.71 
TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0805 TCGA-13-0887 
        7.79         8.28         8.19        43.86        35.28        66.67 
TCGA-13-0889 TCGA-13-0891 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       61.84        69.01        19.36        47.38        48.33        47.84 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0916 TCGA-13-0923 TCGA-13-1407 TCGA-13-1409 
       37.08        27.72        21.17         6.41         6.05         6.84 
TCGA-13-1410 TCGA-13-1487 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 TCGA-13-1496 
        4.70        22.39        70.82        52.44        73.55         4.24 
TCGA-13-1498 TCGA-13-1505 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-20-0991 
       37.61         4.21         4.77         4.18         2.56        26.20 
TCGA-20-1684 TCGA-23-1030 TCGA-23-1107 TCGA-23-1109 TCGA-23-1113 TCGA-23-1124 
       19.10        29.13         0.30        51.35        31.20        58.13 
TCGA-24-1417 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1466 TCGA-24-1469 
        7.82        17.39        28.37        19.17        45.14         9.11 
TCGA-24-1471 TCGA-24-1474 TCGA-24-1548 TCGA-24-1552 TCGA-24-1555 TCGA-24-1562 
        1.18        22.22        16.21        41.39        88.50        45.50 
TCGA-24-1603 TCGA-24-1614 TCGA-24-1845 TCGA-24-1924 TCGA-24-2026 TCGA-24-2030 
       90.15        48.33         3.81        30.21        34.82        53.95 
TCGA-25-1319 TCGA-25-1324 TCGA-25-1325 TCGA-25-2397 TCGA-29-1693 TCGA-29-1695 
       65.00        34.03        32.09        12.00       101.79         0.79 
TCGA-29-1697 TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 TCGA-29-1707 TCGA-29-1711 
       31.20         0.53        16.90        59.67        41.98        34.62 
TCGA-29-1777 TCGA-29-1785 TCGA-29-2414 TCGA-30-1718 TCGA-30-1853 TCGA-30-1859 
       12.30        34.62        86.17        51.91        36.26        48.10 
TCGA-30-1866 TCGA-36-1569 TCGA-36-1578 TCGA-36-1581 TCGA-57-1583 TCGA-59-2348 
       36.62        29.10        27.85        24.69        11.38       180.20 
TCGA-59-2350 TCGA-61-1738 TCGA-61-1741 TCGA-61-1895 TCGA-61-1907 TCGA-61-1910 
       22.32        35.80        33.67         1.45        31.30        37.05 
TCGA-61-1911 TCGA-61-2088 
       42.51         4.77 

subtype1 subtype2 subtype3 
    0.26     0.30     0.30 
subtype1 subtype2 subtype3 
  152.02   129.96   180.20 
subtype1 subtype2 subtype3 
  29.165   30.245   31.695 
[1] "0.3 - 152.0 (29.2)" "0.3 - 130.0 (30.2)" "0.3 - 180.2 (31.7)"
D13V2, continuous
          vv
clus       OMENTUM OVARY PERITONEUM OVARY
  subtype1       2   170                1
  subtype2       0   176                0
  subtype3       0   104                0
D13V3, multiclass
                  clus
vv                 subtype1 subtype2 subtype3
  OMENTUM                 2        0        0
  OVARY                 170      176      104
  PERITONEUM OVARY        1        0        0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V4, continuous
D13V5, binary
          cls
clus         0   1
  subtype1   0 173
  subtype2   3 173
  subtype3   0 104
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0  173
  subtype2    3  173
  subtype3    0  104
     clus
vv    subtype1 subtype2 subtype3
  NO         0        3        0
  YES      173      173      104
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1
  subtype1  0  4
  subtype2  2  0
  subtype3  0  2
D13V6, multiclass
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
clus
subtype1 subtype2 subtype3 
       4        2        2 
[1] "subtype1" "subtype1" "subtype1" "subtype1"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     4                         8
  subtype2                                1     6                         7
  subtype3                                0     5                         6
          vv
clus       WHITE
  subtype1   152
  subtype2   157
  subtype3    91
D13V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        1        0
  ASIAN                                   4        6        5
  BLACK OR AFRICAN AMERICAN               8        7        6
  WHITE                                 152      157       91
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V8, binary
          cls
clus         0   1
  subtype1   4  99
  subtype2   2 101
  subtype3   2  62
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   99
  subtype2    2  101
  subtype3    2   62
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        2        2
  NOT HISPANIC OR LATINO       99      101       62
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
