[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/22507289/OV-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/OV-TP/22555032/OV-TP.mergedcluster.txt"

nPatients in clinical file=590, in cluster file=596, common to both=589
[1]  14 589
[1] "MRNA_CNMF"
[1] 3
  1   2   3   4 
181 113 120 149 
  1   2   3   4 
181 113 120 149 
[1] "MRNA_CHIERARCHICAL"
[1] 3
  1   2   3 
313 161  89 
  1   2   3 
313 161  89 
[1] "MIR_CNMF"
[1] 3
  1   2   3 
181 133 247 
  1   2   3 
181 133 247 
[1] "MIR_CHIERARCHICAL"
[1] 3
 1 10  2  3  4  5  6  7  8  9 
83 57 58 86 35 75 36 36 51 44 
 1 10  2  3  4  5  6  7  8  9 
83 57 58 86 35 75 36 36 51 44 
[1] "CN_CNMF"
[1] 3
  1   2   3 
241 129 203 
  1   2   3 
241 129 203 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3   4 
118 100 188 169 
  1   2   3   4 
118 100 188 169 
[1] "RPPA_CNMF"
[1] 3
  1   2   3 
150 192  78 
  1   2   3 
150 192  78 
[1] "RPPA_CHIERARCHICAL"
[1] 3
  1   2   3   4 
146  57  61 156 
  1   2   3   4 
146  57  61 156 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3 
 79 110 114 
  1   2   3 
 79 110 114 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
147  60  96 
  1   2   3 
147  60  96 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3   4 
 74 135 141 103 
  1   2   3   4 
 74 135 141 103 
[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 4 
6 6 5 5 
1 2 3 4 
6 6 5 5 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
1 2 3 4 5 6 
5 2 2 4 5 4 
1 4 5 6 
5 4 5 4 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "KARNOFSKY_PERFORMANCE_SCORE"         
[14] "HISTOLOGICAL_TYPE"                   
[15] "TUMOR_GRADE"                         
[16] "TUMOR_STAGE"                         
[17] "DAYS_TO_TUMOR_RECURRENCE"            
[18] "CHEMO_THERAPY"                       
[19] "RESIDUAL_TUMOR"                      
[20] "ETHNICITY"                           

Input Data has 20 rows and 589 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=309,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=214,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGIC_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_T_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_N_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "GENDER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HISTOLOGICAL_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'TUMOR_GRADE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_GRADE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 16:'TUMOR_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 17:'DAYS_TO_TUMOR_RECURRENCE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DAYS_TO_TUMOR_RECURRENCE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 18:'CHEMO_THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "CHEMO_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 19:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 589 columns, 1 survival variables, and 6 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"              "TUMOR_TISSUE_SITE"          
[3] "RADIATION_THERAPY"           "KARNOFSKY_PERFORMANCE_SCORE"
[5] "RESIDUAL_TUMOR"              "ETHNICITY"                  
YEARS_TO_BIRTH, nv=55, binary=FALSE, numeric=TRUE
TUMOR_TISSUE_SITE, nv=3, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=6, binary=FALSE, numeric=TRUE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
          sevent
clus2        0   1
  subtype1  72 108
  subtype2  36  77
  subtype3  37  83
  subtype4  80  66
subtype1 subtype2 subtype3 subtype4 
     180      113      120      146 
subtype1 subtype2 subtype3 subtype4 
     108       77       83       66 
$subtype1
TCGA-04-1331 TCGA-04-1341 TCGA-04-1342 TCGA-04-1347 TCGA-04-1350 TCGA-04-1351 
       43.92         1.08        18.51        63.09        63.98        65.46 
TCGA-04-1353 TCGA-04-1356 TCGA-04-1364 TCGA-04-1369 TCGA-04-1371 TCGA-04-1514 
        0.53        49.28        33.67        21.11        82.39        56.55 
TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1542 TCGA-04-1644 TCGA-04-1655 
       19.99         0.79        38.37        84.20        48.89        45.37 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1665 TCGA-09-1669 TCGA-09-1673 TCGA-09-1674 
        9.99        38.43        41.62        30.51         3.02         8.55 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 
        4.54       112.41        71.11        39.75        20.94        26.93 
TCGA-13-1404 TCGA-13-1407 TCGA-13-1409 TCGA-13-1477 TCGA-13-1487 TCGA-13-1489 
       81.17        83.31        57.27        54.64        22.39        83.93 
TCGA-13-1492 TCGA-13-1497 TCGA-13-1505 TCGA-13-1506 TCGA-13-2057 TCGA-13-2066 
      125.56       127.27        65.69        34.16        80.02        70.13 
TCGA-20-0990 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-23-1022 
       25.94        25.38        19.10        16.70         2.93        49.68 
TCGA-23-1024 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1107 
       15.39         8.81        29.13        18.90         2.76         0.30 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 TCGA-23-1119 TCGA-23-1121 
       51.35        54.51        31.20        68.68       129.96         6.38 
TCGA-23-1122 TCGA-23-1809 TCGA-23-2645 TCGA-23-2647 TCGA-24-0982 TCGA-24-1419 
       39.09         0.53         4.50         4.44        22.32         7.86 
TCGA-24-1424 TCGA-24-1426 TCGA-24-1430 TCGA-24-1469 TCGA-24-1474 TCGA-24-1544 
        6.02         5.36        28.37         9.11        22.22        26.96 
TCGA-24-1548 TCGA-24-1552 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1567 
       16.21        41.39        39.88        19.53        44.09        17.23 
TCGA-24-1603 TCGA-24-1614 TCGA-24-1844 TCGA-24-1850 TCGA-24-1920 TCGA-24-2019 
       90.15        48.33         3.72         5.52         9.80         4.87 
TCGA-24-2020 TCGA-24-2027 TCGA-24-2030 TCGA-24-2033 TCGA-24-2036 TCGA-24-2260 
      152.02       109.71        55.92        18.48        64.01        36.16 
TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 
       33.11        55.86         1.02        33.01        52.04        42.05 
TCGA-25-1317 TCGA-25-1319 TCGA-25-1323 TCGA-25-1324 TCGA-25-1325 TCGA-25-1627 
        2.01        65.00        12.99        34.03        32.09        12.95 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
        0.30        59.15        35.87        14.96        24.99        24.00 
TCGA-25-2393 TCGA-25-2400 TCGA-29-1691 TCGA-29-1697 TCGA-29-1698 TCGA-29-1702 
       38.04        42.02        48.33        31.20        68.32        23.93 
TCGA-29-1703 TCGA-29-1762 TCGA-29-1763 TCGA-29-1774 TCGA-29-1775 TCGA-29-2414 
       59.67        86.60        66.81        17.33        12.36        86.17 
TCGA-29-2425 TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 TCGA-30-1853 TCGA-30-1859 
       65.00        13.84        42.25        11.47        36.26        48.10 
TCGA-30-1866 TCGA-31-1955 TCGA-36-1570 TCGA-36-1571 TCGA-36-1575 TCGA-36-1577 
       36.62        42.51        21.53        22.85         8.55        25.74 
TCGA-36-2544 TCGA-36-2547 TCGA-36-2552 TCGA-42-2591 TCGA-57-1582 TCGA-57-1583 
       20.98        20.52        11.47        40.77        24.03        11.38 
TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-59-2350 TCGA-59-2352 TCGA-59-2363 
       22.32        29.00        25.08        22.32         9.40         5.42 
TCGA-59-2372 TCGA-61-1730 TCGA-61-1741 TCGA-61-1743 TCGA-61-1900 TCGA-61-1910 
       44.81         4.34        33.67        43.69         5.79        37.05 
TCGA-61-1917 TCGA-61-2088 TCGA-61-2092 TCGA-61-2096 TCGA-61-2098 TCGA-61-2102 
       43.43         4.77        51.72        58.39        65.52         6.48 
TCGA-61-2111 TCGA-09-0364 TCGA-09-0365 TCGA-09-0369 TCGA-10-0927 TCGA-10-0928 
      125.75        29.16         9.47        35.57        81.86        18.51 
TCGA-10-0933 TCGA-10-0935 TCGA-10-0938 TCGA-13-0717 TCGA-13-0730 TCGA-13-0757 
       14.66        35.44        20.91        24.59        17.82        11.18 
TCGA-13-0766 TCGA-13-0794 TCGA-13-0799 TCGA-13-0800 TCGA-13-0802 TCGA-13-0888 
       56.71        63.09        83.34        87.48        51.02        92.42 
TCGA-13-0891 TCGA-13-0901 TCGA-13-0906 TCGA-13-0910 TCGA-13-0916 TCGA-13-0920 
      102.84        19.36       118.98       116.65        58.68        48.79 

$subtype2
TCGA-04-1332 TCGA-04-1337 TCGA-04-1338 TCGA-04-1343 TCGA-04-1530 TCGA-13-1405 
       41.00         2.01        46.62        11.87       119.08        28.54 
TCGA-13-1408 TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 TCGA-13-1483 TCGA-13-1485 
       55.23        17.46        32.35        87.06        29.42        20.68 
TCGA-13-1494 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1509 TCGA-13-1512 
       93.90       115.07        43.20        34.82        80.15        14.53 
TCGA-20-1682 TCGA-23-1023 TCGA-23-1027 TCGA-23-1116 TCGA-23-1117 TCGA-23-2078 
       27.52        40.54        32.09        19.46        33.30        87.48 
TCGA-24-0970 TCGA-24-0975 TCGA-24-1105 TCGA-24-1418 TCGA-24-1422 TCGA-24-1425 
       11.64        21.80        47.41         7.99         0.76         5.95 
TCGA-24-1427 TCGA-24-1434 TCGA-24-1463 TCGA-24-1545 TCGA-24-1546 TCGA-24-1550 
        4.83        18.67        72.92        57.40        64.27        41.06 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1849 TCGA-24-1928 TCGA-24-2029 
       45.50        47.70        25.87         5.79        11.05        14.43 
TCGA-24-2035 TCGA-24-2280 TCGA-24-2289 TCGA-24-2293 TCGA-24-2298 TCGA-25-1320 
       28.18        70.45        67.36        16.64        53.26        37.97 
TCGA-25-1326 TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1628 TCGA-25-1633 
       41.06        15.02        18.58        17.03        20.61        62.17 
TCGA-25-1635 TCGA-25-2042 TCGA-25-2398 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 
       52.04        13.02        45.01         2.96        29.03        31.00 
TCGA-29-1693 TCGA-29-1695 TCGA-29-1705 TCGA-29-1710 TCGA-29-1764 TCGA-29-1766 
      101.79        40.41        18.25        31.27        62.93        39.42 
TCGA-29-1768 TCGA-29-1770 TCGA-29-1783 TCGA-29-2432 TCGA-29-2436 TCGA-30-1855 
       31.30        24.36         7.23        21.47         9.76         2.47 
TCGA-30-1857 TCGA-30-1861 TCGA-30-1862 TCGA-30-1867 TCGA-30-1891 TCGA-30-1892 
        0.26        34.78         6.12         1.22        30.05        48.79 
TCGA-31-1951 TCGA-31-1956 TCGA-31-1959 TCGA-36-1569 TCGA-36-1576 TCGA-36-1580 
       22.49        44.12         2.20        29.10        30.08        24.23 
TCGA-36-2540 TCGA-36-2548 TCGA-42-2587 TCGA-42-2588 TCGA-57-1585 TCGA-59-2354 
       23.80        14.17        23.74        28.93         1.74        34.39 
TCGA-61-1721 TCGA-61-1733 TCGA-61-1737 TCGA-61-1919 TCGA-61-1998 TCGA-61-2003 
       11.11        31.79        44.84        38.17         5.52         4.01 
TCGA-61-2009 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-10-0930 
       39.85        22.22         6.35        31.07         8.61        34.19 
TCGA-13-0768 TCGA-13-0793 TCGA-13-0805 TCGA-13-0886 TCGA-13-0890 TCGA-13-0894 
       58.65       107.28        35.31       153.37       145.45        49.61 
TCGA-13-0900 TCGA-13-0908 TCGA-13-0911 TCGA-13-0919 TCGA-13-2071 
      134.04        60.59        44.55        84.53        25.41 

$subtype3
TCGA-04-1335 TCGA-04-1349 TCGA-04-1361 TCGA-04-1362 TCGA-04-1367 TCGA-04-1638 
        1.81        21.57        32.52        44.32       103.40        55.43 
TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-09-1664 
       27.88        28.64        64.64        36.23        31.86        74.93 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1675 TCGA-09-2043 TCGA-09-2045 TCGA-13-1403 
       17.98         5.85        97.55         6.18        35.15        77.10 
TCGA-13-1482 TCGA-13-1491 TCGA-13-1495 TCGA-13-1498 TCGA-13-1500 TCGA-13-1510 
       61.71        52.44        90.38        66.15        13.97        44.68 
TCGA-13-1511 TCGA-13-2059 TCGA-20-0996 TCGA-20-1687 TCGA-23-1021 TCGA-23-1028 
       54.25        78.48        72.20         2.66        47.54        49.41 
TCGA-23-1111 TCGA-23-1118 TCGA-23-1124 TCGA-23-2072 TCGA-23-2081 TCGA-23-2641 
        3.22        86.01        58.13        24.95        77.00         2.76 
TCGA-23-2643 TCGA-24-0966 TCGA-24-0979 TCGA-24-1103 TCGA-24-1413 TCGA-24-1416 
        4.70         7.63        41.56        54.12         6.31         6.38 
TCGA-24-1423 TCGA-24-1431 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1471 
        6.25        18.64        12.46        45.14       105.99         1.18 
TCGA-24-1555 TCGA-24-1565 TCGA-24-1604 TCGA-24-1616 TCGA-24-1923 TCGA-24-2024 
       88.50        10.26        88.37        38.24        22.68        58.16 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2271 TCGA-25-1318 TCGA-25-1321 TCGA-25-1328 
       44.52        57.07        31.63        34.98        33.96        66.05 
TCGA-25-1625 TCGA-25-2397 TCGA-25-2409 TCGA-29-1690 TCGA-29-1694 TCGA-29-1696 
       27.62        12.00        26.99        47.61        39.02        33.93 
TCGA-29-1771 TCGA-29-1776 TCGA-30-1714 TCGA-30-1880 TCGA-36-1568 TCGA-36-2537 
       22.55        11.84        38.07        57.57        28.77        25.91 
TCGA-36-2538 TCGA-36-2549 TCGA-57-1584 TCGA-59-2355 TCGA-61-1728 TCGA-61-1901 
       25.08         6.05        21.14         2.14        27.88        11.41 
TCGA-61-1904 TCGA-61-2008 TCGA-61-2017 TCGA-61-2095 TCGA-61-2097 TCGA-61-2101 
        9.07        30.64        45.96        61.64        60.62        55.50 
TCGA-61-2109 TCGA-61-2110 TCGA-09-0366 TCGA-09-0367 TCGA-10-0925 TCGA-10-0926 
       20.68        44.52        57.76        17.98        54.31        25.91 
TCGA-10-0931 TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 TCGA-13-0714 TCGA-13-0720 
       32.88         6.71        36.92        19.99         6.21        44.55 
TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 TCGA-13-0751 TCGA-13-0755 TCGA-13-0761 
        2.73        31.20        15.19        55.17         2.50        38.01 
TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0797 TCGA-13-0803 TCGA-13-0804 
      111.78        45.67        40.24        69.73        43.86        35.28 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0887 TCGA-13-0889 TCGA-13-0899 
       13.61        68.94       107.18        66.67        95.15        66.15 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0912 TCGA-13-0913 TCGA-13-0921 TCGA-13-0923 
       50.37       123.16        37.64       109.32        48.76        83.74 

$subtype4
TCGA-04-1336 TCGA-04-1346 TCGA-04-1348 TCGA-04-1365 TCGA-04-1516 TCGA-04-1536 
       49.15        65.52        48.76        76.57        41.59        29.10 
TCGA-04-1654 TCGA-09-1662 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-2044 
       47.70        89.33        57.60        61.87        55.36         6.12 
TCGA-09-2051 TCGA-09-2056 TCGA-13-1410 TCGA-13-1484 TCGA-13-1488 TCGA-13-1496 
       63.09        12.46        81.01       124.44        70.82         4.24 
TCGA-13-1507 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-20-0987 TCGA-20-0991 
       65.52        77.88        76.90        65.52        23.05        26.20 
TCGA-23-1026 TCGA-23-1120 TCGA-23-1123 TCGA-23-2077 TCGA-23-2079 TCGA-23-2084 
       26.83         4.27        33.47       115.89        91.66        49.84 
TCGA-23-2649 TCGA-24-0980 TCGA-24-1104 TCGA-24-1417 TCGA-24-1428 TCGA-24-1435 
        3.81         7.66        63.55         7.82        17.39        43.53 
TCGA-24-1436 TCGA-24-1470 TCGA-24-1549 TCGA-24-1551 TCGA-24-1553 TCGA-24-1556 
        8.55         3.45        56.58        51.91        58.09        70.62 
TCGA-24-1842 TCGA-24-1843 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1924 
        8.32         3.48         3.81         4.37        11.28        30.21 
TCGA-24-1927 TCGA-24-1930 TCGA-24-2023 TCGA-24-2026 TCGA-24-2261 TCGA-24-2262 
       16.44        81.11        44.84        34.82         0.79         0.36 
TCGA-24-2267 TCGA-24-2281 TCGA-24-2288 TCGA-24-2290 TCGA-25-1313 TCGA-25-1322 
       47.54        44.61         0.82        36.23        26.96         2.99 
TCGA-25-1630 TCGA-25-1878 TCGA-25-2391 TCGA-25-2392 TCGA-25-2396 TCGA-25-2399 
       38.20        85.05        49.05         1.02         3.02        19.99 
TCGA-29-1688 TCGA-29-1699 TCGA-29-1701 TCGA-29-1707 TCGA-29-1711 TCGA-29-1761 
       78.90        36.36        16.93        41.98        34.62        17.36 
TCGA-29-1769 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1784 TCGA-29-1785 
       22.98        12.30        14.93         8.38         5.36        36.30 
TCGA-29-2427 TCGA-29-2428 TCGA-30-1718 TCGA-30-1856 TCGA-30-1860 TCGA-30-1887 
       62.47        45.11        51.91        15.68        44.91        24.26 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1953 TCGA-36-1574 TCGA-36-1578 
       45.57        30.18        18.77         6.71        22.55        27.85 
TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2542 
       24.69        35.05        33.01        29.49        29.82        21.60 
TCGA-36-2543 TCGA-36-2545 TCGA-36-2551 TCGA-42-2582 TCGA-42-2589 TCGA-42-2590 
        2.24        18.31        16.18        47.57        42.02        10.42 
TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2351 TCGA-61-1722 TCGA-61-1724 
       25.02       180.20        80.12       116.12         8.09        20.94 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1734 TCGA-61-1736 TCGA-61-1738 TCGA-61-1740 
       31.43        18.54        28.47        48.79        35.80         2.43 
TCGA-61-1895 TCGA-61-1899 TCGA-61-1903 TCGA-61-1906 TCGA-61-1907 TCGA-61-1911 
        1.45         8.42        13.02        34.13        31.30        42.51 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 TCGA-61-1995 TCGA-61-2000 
       48.92        56.61        67.76        15.75         2.01        14.50 
TCGA-61-2002 TCGA-61-2012 TCGA-61-2016 TCGA-61-2018 TCGA-61-2087 TCGA-61-2094 
       17.98        30.64         1.18        45.40         4.80        71.74 
TCGA-61-2104 TCGA-13-0723 TCGA-13-0725 TCGA-13-0758 TCGA-13-0760 TCGA-13-0764 
       76.87        39.58        12.39        11.38        11.54        61.84 
TCGA-13-0792 TCGA-13-0795 TCGA-13-0801 TCGA-13-0885 TCGA-13-0893 TCGA-13-0897 
      118.42        20.35        45.99       111.39        43.36        71.74 
TCGA-13-0903 TCGA-13-0924 
      127.79        85.94 

subtype1 subtype2 subtype3 subtype4 
    0.30     0.26     1.18     0.36 
subtype1 subtype2 subtype3 subtype4 
  152.02   153.37   123.16   180.20 
subtype1 subtype2 subtype3 subtype4 
  33.060   31.000   37.825   32.220 
[1] "0.3 - 152.0 (33.1)" "0.3 - 153.4 (31.0)" "1.2 - 123.2 (37.8)"
[4] "0.4 - 180.2 (32.2)"
D1V2, continuous
          vv
clus       OMENTUM OVARY PERITONEUM OVARY
  subtype1       0   181                0
  subtype2       1   111                1
  subtype3       0   120                0
  subtype4       1   147                1
D1V3, multiclass
                  clus
vv                 subtype1 subtype2 subtype3 subtype4
  OMENTUM                 0        1        0        1
  OVARY                 181      111      120      147
  PERITONEUM OVARY        0        1        0        1
[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"
D1V4, binary
          cls
clus         0   1
  subtype1 173   2
  subtype2 108   1
  subtype3 118   1
  subtype4 142   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  173    2
  subtype2  108    1
  subtype3  118    1
  subtype4  142    1
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       173      108      118      142
  YES        2        1        1        1
[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"
D1V5, continuous
          vv
clus       R0 R1 R2
  subtype1  7  7  0
  subtype2  1  8  1
  subtype3  1  3  0
  subtype4  5  9  0
D1V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0        7        1        1        5
  R1        7        8        3        9
  R2        0        1        0        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"
D1V7, binary
          cls
clus         0   1
  subtype1   5 109
  subtype2   0  69
  subtype3   2  73
  subtype4   4  79
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  109
  subtype2    0   69
  subtype3    2   73
  subtype4    4   79
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            5        0        2        4
  NOT HISPANIC OR LATINO      109       69       73       79
[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(2) Variable = MRNA_CHIERARCHICAL
D2V1, survival
          sevent
clus2        0   1
  subtype1 135 174
  subtype2  60 101
  subtype3  30  59
subtype1 subtype2 subtype3 
     309      161       89 
subtype1 subtype2 subtype3 
     174      101       59 
$subtype1
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 
       43.92         1.81        49.15         1.08        18.51        11.87 
TCGA-04-1346 TCGA-04-1348 TCGA-04-1349 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 
       65.52        48.76        21.57        49.28        32.52        44.32 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1369 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 
       76.57       103.40        21.11        41.59        19.99        38.37 
TCGA-04-1536 TCGA-04-1638 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 
       29.10        55.43        28.64        64.64        36.23        47.70 
TCGA-09-1659 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1670 
        9.99        89.33        74.93        41.62        57.60        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 
        5.85         3.02        97.55         6.18         6.12        35.15 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2055 TCGA-09-2056 TCGA-13-1403 TCGA-13-1410 
       63.09        39.75        26.93        12.46        77.10        81.01 
TCGA-13-1482 TCGA-13-1484 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 TCGA-13-1495 
       61.71       124.44        70.82        52.44       125.56        90.38 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1506 TCGA-13-1510 TCGA-13-1511 
        4.24       127.27        66.15        34.16        44.68        54.25 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-20-0987 TCGA-20-0991 
       78.48        77.88        76.90        65.52        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 
        2.76         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-24-0979 TCGA-24-0982 TCGA-24-1103 
        4.50         3.81         7.63        41.56        22.32        54.12 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1419 TCGA-24-1423 
       63.55        47.41         6.31         6.38         7.86         6.25 
TCGA-24-1426 TCGA-24-1428 TCGA-24-1431 TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 
        5.36        17.39        18.64         8.55        12.46        45.14 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1548 
      105.99         9.11         3.45         1.18        22.22        16.21 
TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 
       56.58        51.91        41.39        58.09        88.50        70.62 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1565 TCGA-24-1603 TCGA-24-1604 
       39.88        19.53        44.09        10.26        90.15        88.37 
TCGA-24-1614 TCGA-24-1616 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 
       48.33        38.24         3.48         3.72         3.81         4.37 
TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-2019 TCGA-24-2023 
       11.28         5.52         9.80        30.21         4.87        44.84 
TCGA-24-2026 TCGA-24-2030 TCGA-24-2036 TCGA-24-2038 TCGA-24-2260 TCGA-24-2261 
       34.82        55.92        64.01        44.52        36.16         0.79 
TCGA-24-2267 TCGA-24-2281 TCGA-24-2290 TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 
       47.54        44.61        36.23        33.11        55.86         1.02 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 TCGA-25-1322 
       26.96        33.01        34.98        65.00        33.96         2.99 
TCGA-25-1324 TCGA-25-1325 TCGA-25-1625 TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 
       34.03        32.09        27.62        12.95        38.20         0.30 
TCGA-25-1870 TCGA-25-1878 TCGA-25-2391 TCGA-25-2392 TCGA-25-2396 TCGA-25-2397 
       14.96        85.05        49.05         1.02         3.02        12.00 
TCGA-25-2399 TCGA-25-2400 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1696 
       19.99        42.02        78.90        47.61        48.33        33.93 
TCGA-29-1697 TCGA-29-1699 TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 TCGA-29-1761 
       31.20        36.36        23.93        59.67        41.98        17.36 
TCGA-29-1763 TCGA-29-1771 TCGA-29-1775 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 
       66.81        22.55        12.36        14.93         8.38         7.23 
TCGA-29-1784 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2434 TCGA-30-1856 
        5.36        62.47        45.11        13.84        11.47        15.68 
TCGA-30-1860 TCGA-30-1866 TCGA-31-1950 TCGA-31-1955 TCGA-36-1568 TCGA-36-1570 
       44.91        36.62        18.77        42.51        28.77        21.53 
TCGA-36-1571 TCGA-36-1578 TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       22.85        27.85        24.69        33.01        29.49        29.82 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 TCGA-36-2551 
       21.60         2.24        18.31        20.52         6.05        16.18 
TCGA-42-2582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 
       47.57        11.38        21.14        22.32        29.00        25.08 
TCGA-57-1994 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 
       25.02        80.12        22.32       116.12         9.40         2.14 
TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1734 TCGA-61-1736 
        8.09        31.43        18.54        27.88        28.47        48.79 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 
       35.80         2.43        33.67        43.69         1.45         8.42 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 
       11.41        13.02         9.07        34.13        31.30        37.05 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 
       42.51        48.92        67.76        43.43        15.75         2.01 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 
       30.64         1.18        45.96        45.40         4.80        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2104 TCGA-61-2109 
       71.74        61.64        58.39        60.62        76.87        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-09-0366 TCGA-09-0367 TCGA-10-0925 TCGA-10-0926 
       44.52       125.75        57.76        17.98        54.31        25.91 
TCGA-10-0931 TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 TCGA-13-0714 TCGA-13-0720 
       32.88         6.71        36.92        19.99         6.21        44.55 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0727 TCGA-13-0751 TCGA-13-0755 
       39.58         2.73        12.39        15.19        55.17         2.50 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0764 TCGA-13-0765 TCGA-13-0766 
       11.18        11.38        11.54        61.84        45.67        56.71 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 
       40.24       118.42        20.35        69.73        83.34        45.99 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0885 
       43.86        35.28        35.31        13.61        68.94       111.39 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0899 
      153.37        66.67        95.15       145.45       102.84        66.15 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0910 TCGA-13-0911 TCGA-13-0916 
      127.79        50.37       123.16       116.65        44.55        58.68 
TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       48.76        83.74        85.94 

$subtype2
TCGA-04-1332 TCGA-04-1337 TCGA-04-1338 TCGA-04-1353 TCGA-04-1530 TCGA-09-1667 
       41.00         2.01        46.62         0.53       119.08        61.87 
TCGA-09-1668 TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1411 TCGA-13-1412 
       55.36        81.17        28.54        55.23        17.46        32.35 
TCGA-13-1481 TCGA-13-1483 TCGA-13-1485 TCGA-13-1494 TCGA-13-1499 TCGA-13-1500 
       87.06        29.42        20.68        93.90       115.07        13.97 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1507 TCGA-13-1509 TCGA-13-1512 
       43.20        34.82        65.69        65.52        80.15        14.53 
TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1116 TCGA-23-1117 TCGA-23-2078 
       40.54        26.83        32.09        19.46        33.30        87.48 
TCGA-23-2081 TCGA-23-2647 TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-1417 
       77.00         4.44        11.64        21.80         7.66         7.82 
TCGA-24-1418 TCGA-24-1422 TCGA-24-1425 TCGA-24-1427 TCGA-24-1434 TCGA-24-1435 
        7.99         0.76         5.95         4.83        18.67        43.53 
TCGA-24-1463 TCGA-24-1545 TCGA-24-1546 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
       72.92        57.40        64.27        45.50        47.70        25.87 
TCGA-24-1842 TCGA-24-1849 TCGA-24-1923 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 
        8.32         5.79        22.68        16.44        11.05        81.11 
TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2254 TCGA-24-2262 TCGA-24-2271 
       14.43        18.48        28.18        57.07         0.36        31.63 
TCGA-24-2280 TCGA-24-2288 TCGA-24-2289 TCGA-24-2293 TCGA-24-2298 TCGA-25-1320 
       70.45         0.82        67.36        16.64        53.26        37.97 
TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1628 
       41.06        66.05        15.02        18.58        17.03        20.61 
TCGA-25-1633 TCGA-25-1635 TCGA-25-2042 TCGA-25-2398 TCGA-25-2401 TCGA-25-2404 
       62.17        52.04        13.02        45.01         2.96        29.03 
TCGA-25-2408 TCGA-25-2409 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1698 
       31.00        26.99       101.79        39.02        40.41        68.32 
TCGA-29-1701 TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 TCGA-29-1764 TCGA-29-1766 
       16.93        18.25        31.27        34.62        62.93        39.42 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1776 TCGA-29-1777 TCGA-29-1785 
       31.30        22.98        24.36        11.84        12.30        36.30 
TCGA-29-2432 TCGA-29-2436 TCGA-30-1718 TCGA-30-1855 TCGA-30-1857 TCGA-30-1861 
       21.47         9.76        51.91         2.47         0.26        34.78 
TCGA-30-1862 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 
        6.12         1.22        57.57        24.26        30.05        48.79 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 TCGA-31-1956 TCGA-31-1959 
       45.57        30.18        22.49         6.71        44.12         2.20 
TCGA-36-1569 TCGA-36-1574 TCGA-36-1576 TCGA-36-1580 TCGA-36-2529 TCGA-36-2538 
       29.10        22.55        30.08        24.23        35.05        25.08 
TCGA-36-2540 TCGA-36-2544 TCGA-36-2548 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 
       23.80        20.98        14.17        23.74        28.93        42.02 
TCGA-42-2590 TCGA-57-1582 TCGA-57-1585 TCGA-59-2348 TCGA-59-2354 TCGA-61-1721 
       10.42        24.03         1.74       180.20        34.39        11.11 
TCGA-61-1724 TCGA-61-1733 TCGA-61-1737 TCGA-61-1914 TCGA-61-1919 TCGA-61-1998 
       20.94        31.79        44.84        56.61        38.17         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2113 
       14.50        17.98         4.01        30.64        39.85        22.22 
TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-10-0930 TCGA-13-0726 TCGA-13-0761 
        6.35        31.07         8.61        34.19        31.20        38.01 
TCGA-13-0768 TCGA-13-0793 TCGA-13-0884 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 
       58.65       107.28       107.18        43.36        49.61        71.74 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0908 TCGA-13-0919 TCGA-13-2071 
      134.04        19.36        60.59        84.53        25.41 

$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-04-1519 TCGA-04-1542 TCGA-04-1644 TCGA-04-1646 TCGA-04-1652 TCGA-04-1655 
        0.79        84.20        48.89        27.88        31.86        45.37 
TCGA-09-1661 TCGA-09-1669 TCGA-09-1674 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 
       38.43        30.51         8.55         4.54       112.41        71.11 
TCGA-09-2054 TCGA-13-1407 TCGA-13-1409 TCGA-13-1477 TCGA-13-1487 TCGA-13-1489 
       20.94        83.31        57.27        54.64        22.39        83.93 
TCGA-13-2057 TCGA-13-2066 TCGA-20-0990 TCGA-23-1022 TCGA-23-1031 TCGA-23-1110 
       80.02        70.13        25.94        49.68        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        52.04        42.05 
TCGA-25-1317 TCGA-25-1323 TCGA-25-1632 TCGA-25-1634 TCGA-25-1871 TCGA-25-1877 
        2.01        12.99        59.15        35.87        24.99        24.00 
TCGA-25-2393 TCGA-29-1762 TCGA-29-1774 TCGA-29-2414 TCGA-29-2425 TCGA-29-2431 
       38.04        86.60        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 TCGA-09-0364 TCGA-09-0365 
        4.77        65.52        55.50         6.48        29.16         9.47 
TCGA-09-0369 TCGA-10-0927 TCGA-10-0928 TCGA-10-0933 TCGA-10-0935 TCGA-10-0938 
       35.57        81.86        18.51        14.66        35.44        20.91 
TCGA-13-0717 TCGA-13-0730 TCGA-13-0762 TCGA-13-0794 TCGA-13-0800 TCGA-13-0802 
       24.59        17.82       111.78        63.09        87.48        51.02 
TCGA-13-0888 TCGA-13-0906 TCGA-13-0912 TCGA-13-0913 TCGA-13-0920 
       92.42       118.98        37.64       109.32        48.79 

subtype1 subtype2 subtype3 
    0.30     0.26     0.79 
subtype1 subtype2 subtype3 
  153.37   180.20   152.02 
subtype1 subtype2 subtype3 
   33.93    30.08    38.43 
[1] "0.3 - 153.4 (33.9)" "0.3 - 180.2 (30.1)" "0.8 - 152.0 (38.4)"
D2V2, continuous
          vv
clus       OMENTUM OVARY PERITONEUM OVARY
  subtype1       1   312                0
  subtype2       1   158                2
  subtype3       0    89                0
D2V3, multiclass
                  clus
vv                 subtype1 subtype2 subtype3
  OMENTUM                 1        1        0
  OVARY                 312      158       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, binary
          cls
clus         0   1
  subtype1 301   3
  subtype2 154   1
  subtype3  86   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  301    3
  subtype2  154    1
  subtype3   86    1
     clus
vv    subtype1 subtype2 subtype3
  NO       301      154       86
  YES        3        1        1
[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"
D2V5, continuous
          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"
D2V7, binary
          cls
clus         0   1
  subtype1   8 179
  subtype2   0  94
  subtype3   3  57
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8  179
  subtype2    0   94
  subtype3    3   57
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            8        0        3
  NOT HISPANIC OR LATINO      179       94       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  70 111
  subtype2  44  85
  subtype3 109 138
subtype1 subtype2 subtype3 
     181      129      247 
subtype1 subtype2 subtype3 
     111       85      138 
$subtype1
TCGA-04-1331 TCGA-04-1338 TCGA-04-1341 TCGA-04-1343 TCGA-04-1348 TCGA-04-1351 
       43.92        46.62         1.08        11.87        48.76        65.46 
TCGA-04-1353 TCGA-04-1362 TCGA-04-1365 TCGA-04-1516 TCGA-04-1530 TCGA-04-1542 
        0.53        44.32        76.57        41.59       119.08        84.20 
TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-09-1664 TCGA-09-1665 
       48.89        28.64        64.64        36.23        74.93        41.62 
TCGA-09-1670 TCGA-09-1675 TCGA-09-2044 TCGA-09-2056 TCGA-13-1404 TCGA-13-1484 
       17.98        97.55         6.12        12.46        81.17       124.44 
TCGA-13-1485 TCGA-13-1488 TCGA-13-1494 TCGA-13-1496 TCGA-13-1500 TCGA-13-1509 
       20.68        70.82        93.90         4.24        13.97        80.15 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2060 TCGA-20-0987 TCGA-20-1683 TCGA-20-1684 
       54.25        14.53        77.88        23.05        25.38        19.10 
TCGA-20-1686 TCGA-23-1024 TCGA-23-1028 TCGA-23-1032 TCGA-23-1116 TCGA-23-1117 
        2.93        15.39        49.41         2.76        19.46        33.30 
TCGA-23-1118 TCGA-23-1119 TCGA-23-2072 TCGA-23-2643 TCGA-24-0966 TCGA-24-0970 
       86.01       129.96        24.95         4.70         7.63        11.64 
TCGA-24-0979 TCGA-24-0980 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1428 
       41.56         7.66         6.31         6.38         7.82        17.39 
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-24-1843 
       41.39        39.88        47.70        10.26         8.32         3.48 
TCGA-24-1844 TCGA-24-1846 TCGA-24-1850 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 
        3.72         4.37         5.52        30.21        16.44        11.05 
TCGA-24-1930 TCGA-24-2023 TCGA-24-2033 TCGA-24-2038 TCGA-24-2260 TCGA-24-2261 
       81.11        44.84        18.48        44.52        36.16         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 
        0.36        47.54        44.61         0.82        67.36        36.23 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1320 TCGA-25-1322 
       55.86        53.26        26.96        52.04        37.97         2.99 
TCGA-25-1325 TCGA-25-1329 TCGA-25-1623 TCGA-25-1627 TCGA-25-1628 TCGA-25-1633 
       32.09        15.02        18.58        12.95        20.61        62.17 
TCGA-25-1634 TCGA-25-1635 TCGA-25-2391 TCGA-25-2392 TCGA-25-2400 TCGA-25-2401 
       35.87        52.04        49.05         1.02        42.02         2.96 
TCGA-25-2408 TCGA-29-1688 TCGA-29-1694 TCGA-29-1695 TCGA-29-1698 TCGA-29-1699 
       31.00        78.90        39.02        40.41        68.32        36.36 
TCGA-29-1702 TCGA-29-1711 TCGA-29-1766 TCGA-29-1768 TCGA-29-2425 TCGA-29-2428 
       23.93        34.62        39.42        31.30        65.00        45.11 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1869 TCGA-31-1946 TCGA-31-1959 TCGA-36-1571 
       15.68         0.26        51.39        30.18         2.20        22.85 
TCGA-36-2529 TCGA-36-2534 TCGA-36-2537 TCGA-36-2540 TCGA-36-2547 TCGA-36-2548 
       35.05        29.82        25.91        23.80        20.52        14.17 
TCGA-36-2549 TCGA-42-2582 TCGA-42-2587 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
        6.05        47.57        23.74        42.02        10.42        40.77 
TCGA-57-1582 TCGA-57-1584 TCGA-57-1586 TCGA-57-1994 TCGA-59-2350 TCGA-59-2351 
       24.03        21.14        22.32        25.02        22.32       116.12 
TCGA-59-2354 TCGA-61-1724 TCGA-61-1736 TCGA-61-1738 TCGA-61-1895 TCGA-61-1903 
       34.39        20.94        48.79        35.80         1.45        13.02 
TCGA-61-1907 TCGA-61-1913 TCGA-61-1914 TCGA-61-1919 TCGA-61-1995 TCGA-61-2009 
       31.30        48.92        56.61        38.17         2.01        39.85 
TCGA-61-2087 TCGA-61-2094 TCGA-61-2109 TCGA-61-2113 TCGA-10-0928 TCGA-10-0930 
        4.80        71.74        20.68        22.22        18.51        34.19 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0936 TCGA-10-0938 TCGA-13-0724 TCGA-13-0725 
       32.88        14.66        36.92        20.91         2.73        12.39 
TCGA-13-0726 TCGA-13-0758 TCGA-13-0760 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       31.20        11.38        11.54        40.24       118.42       107.28 
TCGA-13-0795 TCGA-13-0801 TCGA-13-0803 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 
       20.35        45.99        43.86       107.18       111.39       153.37 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0903 TCGA-13-0911 TCGA-13-0919 TCGA-13-0924 
      102.84        43.36       127.79        44.55        84.53        85.94 
TCGA-13-2071 
       25.41 

$subtype2
TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1346 TCGA-04-1361 TCGA-04-1525 
       41.00         1.81         2.01        65.52        32.52        38.37 
TCGA-09-1661 TCGA-09-1672 TCGA-09-2043 TCGA-09-2055 TCGA-13-1405 TCGA-13-1411 
       38.43         5.85         6.18        26.93        28.54        17.46 
TCGA-13-1412 TCGA-13-1483 TCGA-13-1487 TCGA-13-1495 TCGA-13-1501 TCGA-13-1504 
       32.35        29.42        22.39        90.38        43.20        34.82 
TCGA-13-1505 TCGA-13-1510 TCGA-13-2057 TCGA-20-1682 TCGA-20-1687 TCGA-23-1027 
       65.69        44.68        80.02        27.52         2.66        32.09 
TCGA-23-1029 TCGA-23-1120 TCGA-23-1809 TCGA-23-2647 TCGA-24-0975 TCGA-24-0982 
        8.81         4.27         0.53         4.44        21.80        22.32 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1427 
       63.55        47.41         0.76         6.25         5.95         4.83 
TCGA-24-1467 TCGA-24-1545 TCGA-24-1546 TCGA-24-1549 TCGA-24-1562 TCGA-24-1616 
      105.99        57.40        64.27        56.58        45.50        38.24 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1923 TCGA-24-2024 TCGA-24-2029 TCGA-24-2035 
       11.28         5.79        22.68        58.16        14.43        28.18 
TCGA-24-2254 TCGA-24-2293 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1321 
       57.07        16.64        42.05         2.01        34.98        33.96 
TCGA-25-1323 TCGA-25-1326 TCGA-25-1328 TCGA-25-1625 TCGA-25-1626 TCGA-25-1630 
       12.99        41.06        66.05        27.62        17.03        38.20 
TCGA-25-1631 TCGA-25-2042 TCGA-25-2398 TCGA-25-2404 TCGA-29-1691 TCGA-29-1693 
        0.30        13.02        45.01        29.03        48.33       101.79 
TCGA-29-1696 TCGA-29-1705 TCGA-29-1710 TCGA-29-1770 TCGA-29-1771 TCGA-29-1776 
       33.93        18.25        31.27        24.36        22.55        11.84 
TCGA-29-1783 TCGA-29-2414 TCGA-29-2427 TCGA-29-2436 TCGA-30-1861 TCGA-30-1862 
        7.23        86.17        62.47         9.76        34.78         6.12 
TCGA-30-1867 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1955 
        1.22        24.26        30.05        48.79        45.57        42.51 
TCGA-31-1956 TCGA-36-1569 TCGA-36-1574 TCGA-36-1580 TCGA-36-2538 TCGA-42-2588 
       44.12        29.10        22.55        24.23        25.08        28.93 
TCGA-57-1585 TCGA-57-1993 TCGA-59-2352 TCGA-59-2355 TCGA-61-1721 TCGA-61-1722 
        1.74        25.08         9.40         2.14        11.11         8.09 
TCGA-61-1901 TCGA-61-1904 TCGA-61-1906 TCGA-61-1998 TCGA-61-2002 TCGA-61-2008 
       11.41         9.07        34.13         5.52        17.98        30.64 
TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2095 TCGA-61-2097 TCGA-61-2101 
        1.18        45.96        45.40        61.64        60.62        55.50 
TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-09-0364 TCGA-09-0369 TCGA-10-0925 
        6.35        31.07         8.61        29.16        35.57        54.31 
TCGA-10-0927 TCGA-10-0937 TCGA-13-0714 TCGA-13-0727 TCGA-13-0755 TCGA-13-0766 
       81.86        19.99         6.21        15.19         2.50        56.71 
TCGA-13-0768 TCGA-13-0800 TCGA-13-0805 TCGA-13-0807 TCGA-13-0888 TCGA-13-0890 
       58.65        87.48        35.31        13.61        92.42       145.45 
TCGA-13-0894 TCGA-13-0897 TCGA-13-0900 
       49.61        71.74       134.04 

$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-04-1367 TCGA-04-1369 TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 
       33.67       103.40        21.11        82.39        56.55        19.99 
TCGA-04-1519 TCGA-04-1638 TCGA-04-1646 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 
        0.79        55.43        27.88        31.86        47.70        45.37 
TCGA-09-1659 TCGA-09-1662 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 
        9.99        89.33        57.60        61.87        55.36        30.51 
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-13-1403 TCGA-13-1407 TCGA-13-1408 
       63.09        39.75        20.94        77.10        83.31        55.23 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1489 
       57.27        81.01        54.64        87.06        61.71        83.93 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1506 
       52.44       125.56       127.27        66.15       115.07        34.16 
TCGA-13-1507 TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 TCGA-13-2066 TCGA-20-0990 
       65.52        78.48        76.90        65.52        70.13        25.94 
TCGA-20-0991 TCGA-20-1685 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 
       26.20        16.70        47.54        49.68        40.54        26.83 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1107 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
       29.13        18.90         0.30        51.35        54.51         3.22 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 
       31.20        68.68         6.38        39.09        33.47        58.13 
TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
      115.89        87.48        91.66        77.00        49.84         2.76 
TCGA-23-2645 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-24-1430 TCGA-24-1431 TCGA-24-1435 TCGA-24-1463 TCGA-24-1469 
        5.36        28.37        18.64        43.53        72.92         9.11 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1548 TCGA-24-1553 
        3.45         1.18        22.22        26.96        16.21        58.09 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1558 TCGA-24-1560 TCGA-24-1564 TCGA-24-1567 
       88.50        70.62        19.53        44.09        25.87        17.23 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1845 TCGA-24-1920 TCGA-24-2019 
       90.15        88.37        48.33         3.81         9.80         4.87 
TCGA-24-2020 TCGA-24-2026 TCGA-24-2027 TCGA-24-2030 TCGA-24-2036 TCGA-24-2271 
      152.02        34.82       109.71        55.92        64.01        31.63 
TCGA-24-2280 TCGA-24-2295 TCGA-25-1312 TCGA-25-1314 TCGA-25-1319 TCGA-25-1324 
       70.45        33.11         1.02        33.01        65.00        34.03 
TCGA-25-1632 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2393 
       59.15        14.96        24.99        24.00        85.05        38.04 
TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 TCGA-25-2409 TCGA-29-1690 TCGA-29-1697 
        3.02        12.00        19.99        26.99        47.61        31.20 
TCGA-29-1701 TCGA-29-1703 TCGA-29-1707 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
       16.93        59.67        41.98        17.36        86.60        66.81 
TCGA-29-1764 TCGA-29-1769 TCGA-29-1774 TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 
       62.93        22.98        17.33        12.36        12.30        14.93 
TCGA-29-1781 TCGA-29-1784 TCGA-29-1785 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 
        8.38         5.36        36.30        13.84        42.25        21.47 
TCGA-29-2434 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1859 
       11.47        38.07        51.91        36.26         2.47        48.10 
TCGA-30-1860 TCGA-30-1866 TCGA-30-1880 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 
       44.91        36.62        57.57        18.77        22.49         6.71 
TCGA-36-1568 TCGA-36-1570 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 
       28.77        21.53         8.55        30.08        25.74        27.85 
TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 
       24.69        33.01        29.49        21.60         2.24        20.98 
TCGA-36-2545 TCGA-36-2551 TCGA-36-2552 TCGA-57-1583 TCGA-57-1992 TCGA-59-2348 
       18.31        16.18        11.47        11.38        29.00       180.20 
TCGA-59-2349 TCGA-59-2363 TCGA-59-2372 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 
       80.12         5.42        44.81        31.43        18.54        27.88 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1737 TCGA-61-1740 TCGA-61-1741 
        4.34        31.79        28.47        44.84         2.43        33.67 
TCGA-61-1743 TCGA-61-1899 TCGA-61-1900 TCGA-61-1910 TCGA-61-1915 TCGA-61-1917 
       43.69         8.42         5.79        37.05        67.76        43.43 
TCGA-61-1918 TCGA-61-2000 TCGA-61-2003 TCGA-61-2012 TCGA-61-2088 TCGA-61-2092 
       15.75        14.50         4.01        30.64         4.77        51.72 
TCGA-61-2096 TCGA-61-2098 TCGA-61-2102 TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 
       58.39        65.52         6.48        76.87        44.52       125.75 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-10-0926 TCGA-10-0934 TCGA-10-0935 
        9.47        57.76        17.98        25.91         6.71        35.44 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 
       24.59        44.55        39.58        17.82        55.17        11.18 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0765 TCGA-13-0794 TCGA-13-0797 
       38.01       111.78        61.84        45.67        63.09        69.73 
TCGA-13-0799 TCGA-13-0802 TCGA-13-0804 TCGA-13-0883 TCGA-13-0887 TCGA-13-0889 
       83.34        51.02        35.28        68.94        66.67        95.15 
TCGA-13-0899 TCGA-13-0901 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 
       66.15        19.36        50.37       123.16       118.98        60.59 
TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 
      116.65        37.64       109.32        58.68        48.79        48.76 
TCGA-13-0923 
       83.74 

subtype1 subtype2 subtype3 
    0.26     0.30     0.30 
subtype1 subtype2 subtype3 
  153.37   145.45   180.20 
subtype1 subtype2 subtype3 
   32.09    29.10    36.30 
[1] "0.3 - 153.4 (32.1)" "0.3 - 145.4 (29.1)" "0.3 - 180.2 (36.3)"
D3V2, continuous
          vv
clus       OMENTUM OVARY PERITONEUM OVARY
  subtype1       1   178                2
  subtype2       1   132                0
  subtype3       0   247                0
D3V3, multiclass
                  clus
vv                 subtype1 subtype2 subtype3
  OMENTUM                 1        1        0
  OVARY                 178      132      247
  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, binary
          cls
clus         0   1
  subtype1 173   1
  subtype2 127   1
  subtype3 239   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  173    1
  subtype2  127    1
  subtype3  239    3
     clus
vv    subtype1 subtype2 subtype3
  NO       173      127      239
  YES        1        1        3
[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"
D3V5, continuous
          vv
clus       R0 R1 R2
  subtype1  5 12  0
  subtype2  2  7  1
  subtype3  7  8  0
D3V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0        5        2        7
  R1       12        7        8
  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"
D3V7, binary
          cls
clus         0   1
  subtype1   5 101
  subtype2   1  79
  subtype3   5 149
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  101
  subtype2    1   79
  subtype3    5  149
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            5        1        5
  NOT HISPANIC OR LATINO      101       79      149
[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  31 52
  subtype10 26 30
  subtype2  21 37
  subtype3  38 48
  subtype4   8 26
  subtype5  31 43
  subtype6  11 25
  subtype7  20 16
  subtype8  22 28
  subtype9  15 29
 subtype1 subtype10  subtype2  subtype3  subtype4  subtype5  subtype6  subtype7 
       83        56        58        86        34        74        36        36 
 subtype8  subtype9 
       50        44 
 subtype1 subtype10  subtype2  subtype3  subtype4  subtype5  subtype6  subtype7 
       52        30        37        48        26        43        25        16 
 subtype8  subtype9 
       28        29 
$subtype1
TCGA-04-1331 TCGA-04-1353 TCGA-04-1362 TCGA-04-1516 TCGA-04-1530 TCGA-04-1644 
       43.92         0.53        44.32        41.59       119.08        48.89 
TCGA-04-1651 TCGA-09-1672 TCGA-09-2056 TCGA-13-1404 TCGA-13-1485 TCGA-13-1494 
       36.23         5.85        12.46        81.17        20.68        93.90 
TCGA-13-1500 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-20-0987 TCGA-20-1686 
       13.97        80.15        54.25        14.53        23.05         2.93 
TCGA-23-1024 TCGA-23-1028 TCGA-23-1116 TCGA-23-1117 TCGA-23-1119 TCGA-23-1120 
       15.39        49.41        19.46        33.30       129.96         4.27 
TCGA-23-2072 TCGA-23-2643 TCGA-24-0970 TCGA-24-0980 TCGA-24-1416 TCGA-24-1464 
       24.95         4.70        11.64         7.66         6.38        12.46 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1557 TCGA-24-1563 TCGA-24-1565 TCGA-24-1846 
       41.06        51.91        39.88        47.70        10.26         4.37 
TCGA-24-1850 TCGA-24-1930 TCGA-24-2023 TCGA-24-2038 TCGA-24-2254 TCGA-24-2261 
        5.52        81.11        44.84        44.52        57.07         0.79 
TCGA-24-2262 TCGA-24-2281 TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1320 
        0.36        44.61        55.86        53.26        26.96        37.97 
TCGA-25-1322 TCGA-25-1329 TCGA-25-1627 TCGA-25-1628 TCGA-25-1633 TCGA-25-2391 
        2.99        15.02        12.95        20.61        62.17        49.05 
TCGA-25-2408 TCGA-29-1694 TCGA-29-1711 TCGA-29-1768 TCGA-29-2428 TCGA-30-1857 
       31.00        39.02        34.62        31.30        45.11         0.26 
TCGA-31-1946 TCGA-31-1959 TCGA-36-1580 TCGA-36-2529 TCGA-36-2537 TCGA-36-2540 
       30.18         2.20        24.23        35.05        25.91        23.80 
TCGA-36-2547 TCGA-42-2587 TCGA-42-2590 TCGA-57-1582 TCGA-59-2351 TCGA-59-2354 
       20.52        23.74        10.42        24.03       116.12        34.39 
TCGA-61-1914 TCGA-61-2009 TCGA-10-0931 TCGA-13-0724 TCGA-13-0726 TCGA-13-0760 
       56.61        39.85        32.88         2.73        31.20        11.54 
TCGA-13-0791 TCGA-13-0801 TCGA-13-0886 TCGA-13-0919 TCGA-13-2071 
       40.24        45.99       153.37        84.53        25.41 

$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-13-1477 TCGA-13-1489 TCGA-13-2059 TCGA-20-1685 TCGA-23-2077 TCGA-24-0966 
       54.64        83.93        78.48        16.70       115.89         7.63 
TCGA-24-0979 TCGA-24-1103 TCGA-24-1413 TCGA-24-1426 TCGA-24-1844 TCGA-24-1923 
       41.56        54.12         6.31         5.36         3.72        22.68 
TCGA-24-2019 TCGA-24-2036 TCGA-25-1317 TCGA-25-1321 TCGA-25-1625 TCGA-25-1870 
        4.87        64.01         2.01        33.96        27.62        14.96 
TCGA-25-2404 TCGA-29-1695 TCGA-29-1703 TCGA-29-1771 TCGA-29-1783 TCGA-36-1570 
       29.03        40.41        59.67        22.55         7.23        21.53 
TCGA-36-1571 TCGA-36-2538 TCGA-42-2582 TCGA-42-2591 TCGA-57-1993 TCGA-59-2352 
       22.85        25.08        47.57        40.77        25.08         9.40 
TCGA-61-1721 TCGA-61-1728 TCGA-61-1734 TCGA-61-1736 TCGA-61-1899 TCGA-61-1901 
       11.11        27.88        28.47        48.79         8.42        11.41 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1918 TCGA-61-2008 TCGA-61-2018 TCGA-61-2096 
        9.07        34.13        15.75        30.64        45.40        58.39 
TCGA-61-2102 TCGA-10-0925 TCGA-10-0936 TCGA-10-0938 TCGA-13-0751 TCGA-13-0755 
        6.48        54.31        36.92        20.91        55.17         2.50 
TCGA-13-0912 TCGA-13-0913 
       37.64       109.32 

$subtype2
TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 
       41.00         1.81         2.01         1.08        18.51        11.87 
TCGA-04-1517 TCGA-04-1519 TCGA-04-1542 TCGA-04-1638 TCGA-04-1646 TCGA-04-1648 
       19.99         0.79        84.20        55.43        27.88        28.64 
TCGA-04-1649 TCGA-04-1652 TCGA-09-1661 TCGA-09-1670 TCGA-13-1482 TCGA-13-1487 
       64.64        31.86        38.43        17.98        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        34.16        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 
       52.04        65.00        38.20         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 TCGA-10-0928 TCGA-13-0921 
       61.64        60.62        18.51        48.76 

$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       103.40 
TCGA-04-1369 TCGA-04-1371 TCGA-04-1654 TCGA-09-1659 TCGA-09-1666 TCGA-09-2051 
       21.11        82.39        47.70         9.99        57.60        63.09 
TCGA-13-1403 TCGA-13-1408 TCGA-13-1410 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
       77.10        55.23        81.01         4.24       127.27        66.15 
TCGA-13-2061 TCGA-23-1021 TCGA-23-1026 TCGA-23-1032 TCGA-23-1107 TCGA-23-1118 
       76.90        47.54        26.83         2.76         0.30        86.01 
TCGA-23-1123 TCGA-23-1124 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2649 
       33.47        58.13        91.66        77.00        49.84         3.81 
TCGA-24-1422 TCGA-24-1430 TCGA-24-1436 TCGA-24-1466 TCGA-24-1469 TCGA-24-1471 
        0.76        28.37         8.55        45.14         9.11         1.18 
TCGA-24-1474 TCGA-24-1548 TCGA-24-1555 TCGA-24-1560 TCGA-24-1843 TCGA-24-2030 
       22.22        16.21        88.50        44.09         3.48        55.92 
TCGA-24-2288 TCGA-24-2290 TCGA-25-1314 TCGA-25-1632 TCGA-25-1878 TCGA-25-2397 
        0.82        36.23        33.01        59.15        85.05        12.00 
TCGA-25-2409 TCGA-29-1781 TCGA-29-1784 TCGA-29-2434 TCGA-30-1860 TCGA-30-1866 
       26.99         8.38         5.36        11.47        44.91        36.62 
TCGA-31-1950 TCGA-31-1953 TCGA-36-1576 TCGA-36-1578 TCGA-36-2530 TCGA-36-2532 
       18.77         6.71        30.08        27.85        33.01        29.49 
TCGA-36-2543 TCGA-36-2551 TCGA-59-2349 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 
        2.24        16.18        80.12        44.84        35.80         2.43 
TCGA-61-1910 TCGA-61-2000 TCGA-61-2087 TCGA-61-2092 TCGA-61-2111 TCGA-09-0367 
       37.05        14.50         4.80        51.72       125.75        17.98 
TCGA-10-0930 TCGA-10-0934 TCGA-13-0720 TCGA-13-0723 TCGA-13-0764 TCGA-13-0765 
       34.19         6.71        44.55        39.58        61.84        45.67 
TCGA-13-0797 TCGA-13-0804 TCGA-13-0887 TCGA-13-0901 TCGA-13-0905 TCGA-13-0908 
       69.73        35.28        66.67        19.36       123.16        60.59 
TCGA-13-0916 TCGA-13-0923 
       58.68        83.74 

$subtype4
TCGA-04-1338 TCGA-09-1665 TCGA-24-1434 TCGA-24-1545 TCGA-24-1546 TCGA-24-1928 
       46.62        41.62        18.67        57.40        64.27        11.05 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2260 TCGA-24-2289 TCGA-25-1326 TCGA-25-1623 
       18.48        28.18        36.16        67.36        41.06        18.58 
TCGA-25-1626 TCGA-25-2401 TCGA-29-1693 TCGA-29-1698 TCGA-29-1701 TCGA-29-1766 
       17.03         2.96       101.79        68.32        16.93        39.42 
TCGA-30-1856 TCGA-30-1867 TCGA-30-1869 TCGA-61-1895 TCGA-61-1919 TCGA-61-1998 
       15.68         1.22        51.39         1.45        38.17         5.52 
TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-13-0725 TCGA-13-0766 TCGA-13-0793 
       22.22         6.35        31.07        12.39        56.71       107.28 
TCGA-13-0807 TCGA-13-0900 TCGA-13-0911 TCGA-13-0924 
       13.61       134.04        44.55        85.94 

$subtype5
TCGA-04-1346 TCGA-09-1662 TCGA-09-1673 TCGA-09-2053 TCGA-09-2054 TCGA-13-1405 
       65.52        89.33         3.02        39.75        20.94        28.54 
TCGA-13-1411 TCGA-13-1481 TCGA-13-1495 TCGA-13-1499 TCGA-13-1505 TCGA-13-1507 
       17.46        87.06        90.38       115.07        65.69        65.52 
TCGA-20-1683 TCGA-23-1023 TCGA-23-1109 TCGA-23-1122 TCGA-24-0975 TCGA-24-1423 
       25.38        40.54        51.35        39.09        21.80         6.25 
TCGA-24-1425 TCGA-24-1428 TCGA-24-1463 TCGA-24-1470 TCGA-24-1553 TCGA-24-1564 
        5.95        17.39        72.92         3.45        58.09        25.87 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1849 TCGA-24-2026 TCGA-24-2271 TCGA-24-2280 
       88.37        48.33         5.79        34.82        31.63        70.45 
TCGA-24-2293 TCGA-25-1328 TCGA-25-2042 TCGA-25-2396 TCGA-25-2398 TCGA-29-1710 
       16.64        66.05        13.02         3.02        45.01        31.27 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1769 TCGA-29-1770 TCGA-29-1777 TCGA-29-1785 
       66.81        62.93        22.98        24.36        12.30        36.30 
TCGA-29-2414 TCGA-29-2427 TCGA-29-2431 TCGA-29-2432 TCGA-30-1714 TCGA-30-1718 
       86.17        62.47        42.25        21.47        38.07        51.91 
TCGA-30-1855 TCGA-30-1862 TCGA-30-1892 TCGA-31-1951 TCGA-31-1956 TCGA-36-2542 
        2.47         6.12        48.79        22.49        44.12        21.60 
TCGA-36-2544 TCGA-57-1585 TCGA-57-1586 TCGA-59-2348 TCGA-61-2003 TCGA-61-2101 
       20.98         1.74        22.32       180.20         4.01        55.50 
TCGA-61-2104 TCGA-61-2110 TCGA-61-2614 TCGA-10-0927 TCGA-13-0727 TCGA-13-0757 
       76.87        44.52         8.61        81.86        15.19        11.18 
TCGA-13-0761 TCGA-13-0768 TCGA-13-0799 TCGA-13-0805 TCGA-13-0883 TCGA-13-0889 
       38.01        58.65        83.34        35.31        68.94        95.15 
TCGA-13-0890 TCGA-13-0910 
      145.45       116.65 

$subtype6
TCGA-04-1347 TCGA-04-1350 TCGA-09-2050 TCGA-13-1407 TCGA-13-1409 TCGA-13-1492 
       63.09        63.98        71.11        83.31        57.27       125.56 
TCGA-13-2066 TCGA-20-0990 TCGA-23-1030 TCGA-23-1110 TCGA-23-1113 TCGA-24-1424 
       70.13        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 
       18.64        19.53        33.11         1.02        34.03        33.93 
TCGA-29-1697 TCGA-29-1761 TCGA-29-2429 TCGA-30-1853 TCGA-30-1859 TCGA-30-1880 
       31.20        17.36        13.84        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 
TCGA-09-0365 TCGA-10-0935 TCGA-13-0762 TCGA-13-0794 TCGA-13-0899 TCGA-13-0904 
        9.47        35.44       111.78        63.09        66.15        50.37 

$subtype7
TCGA-04-1348 TCGA-09-1667 TCGA-09-1668 TCGA-09-2044 TCGA-13-1484 TCGA-13-2060 
       48.76        61.87        55.36         6.12       124.44        77.88 
TCGA-13-2065 TCGA-20-0991 TCGA-23-2078 TCGA-24-1417 TCGA-24-1924 TCGA-24-1927 
       65.52        26.20        87.48         7.82        30.21        16.44 
TCGA-24-2029 TCGA-24-2267 TCGA-25-1325 TCGA-25-1635 TCGA-29-1688 TCGA-29-1690 
       14.43        47.54        32.09        52.04        78.90        47.61 
TCGA-29-1699 TCGA-36-1581 TCGA-36-2534 TCGA-36-2545 TCGA-42-2589 TCGA-59-2350 
       36.36        24.69        29.82        18.31        42.02        22.32 
TCGA-61-1722 TCGA-61-1727 TCGA-61-1903 TCGA-61-1907 TCGA-61-1913 TCGA-61-2012 
        8.09        18.54        13.02        31.30        48.92        30.64 
TCGA-61-2094 TCGA-61-2109 TCGA-13-0758 TCGA-13-0795 TCGA-13-0885 TCGA-13-0891 
       71.74        20.68        11.38        20.35       111.39       102.84 

$subtype8
TCGA-04-1364 TCGA-04-1514 TCGA-04-1655 TCGA-09-1669 TCGA-09-1674 TCGA-09-2048 
       33.67        56.55        45.37        30.51         8.55         4.54 
TCGA-09-2049 TCGA-13-2057 TCGA-20-1682 TCGA-23-1022 TCGA-23-1029 TCGA-23-1114 
      112.41        80.02        27.52        49.68         8.81        68.68 
TCGA-23-1121 TCGA-23-1809 TCGA-23-2645 TCGA-24-1418 TCGA-24-1419 TCGA-24-1567 
        6.38         0.53         4.50         7.99         7.86        17.23 
TCGA-24-1920 TCGA-24-2020 TCGA-24-2027 TCGA-25-1316 TCGA-25-1323 TCGA-25-1634 
        9.80       152.02       109.71        42.05        12.99        35.87 
TCGA-25-1871 TCGA-25-1877 TCGA-25-2393 TCGA-29-1702 TCGA-29-1762 TCGA-29-1774 
       24.99        24.00        38.04        23.93        86.60        17.33 
TCGA-29-1775 TCGA-36-1577 TCGA-36-2552 TCGA-57-1992 TCGA-59-2363 TCGA-61-1730 
       12.36        25.74        11.47        29.00         5.42         4.34 
TCGA-61-1741 TCGA-61-1900 TCGA-61-2098 TCGA-09-0364 TCGA-09-0369 TCGA-10-0926 
       33.67         5.79        65.52        29.16        35.57        25.91 
TCGA-10-0933 TCGA-13-0717 TCGA-13-0730 TCGA-13-0800 TCGA-13-0802 TCGA-13-0888 
       14.66        24.59        17.82        87.48        51.02        92.42 
TCGA-13-0906 TCGA-13-0920 
      118.98        48.79 

$subtype9
TCGA-04-1361 TCGA-13-1412 TCGA-13-1483 TCGA-13-1501 TCGA-13-1504 TCGA-13-1510 
       32.52        32.35        29.42        43.20        34.82        44.68 
TCGA-20-1687 TCGA-23-1027 TCGA-23-2647 TCGA-24-1104 TCGA-24-1105 TCGA-24-1427 
        2.66        32.09         4.44        63.55        47.41         4.83 
TCGA-24-1549 TCGA-24-1562 TCGA-24-1847 TCGA-25-1318 TCGA-25-2392 TCGA-25-2399 
       56.58        45.50        11.28        34.98         1.02        19.99 
TCGA-29-1691 TCGA-29-1705 TCGA-29-1776 TCGA-29-2436 TCGA-30-1861 TCGA-30-1887 
       48.33        18.25        11.84         9.76        34.78        24.26 
TCGA-30-1891 TCGA-31-1944 TCGA-36-1568 TCGA-36-1569 TCGA-42-2588 TCGA-59-2355 
       30.05        45.57        28.77        29.10        28.93         2.14 
TCGA-61-1725 TCGA-61-2002 TCGA-61-2016 TCGA-61-2017 TCGA-09-0366 TCGA-10-0937 
       31.43        17.98         1.18        45.96        57.76        19.99 
TCGA-13-0714 TCGA-13-0792 TCGA-13-0803 TCGA-13-0884 TCGA-13-0893 TCGA-13-0894 
        6.21       118.42        43.86       107.18        43.36        49.61 
TCGA-13-0897 TCGA-13-0903 
       71.74       127.79 

 subtype1 subtype10  subtype2  subtype3  subtype4  subtype5  subtype6  subtype7 
     0.26      2.01      0.30      0.30      1.22      1.74      1.02      6.12 
 subtype8  subtype9 
     0.53      1.02 
 subtype1 subtype10  subtype2  subtype3  subtype4  subtype5  subtype6  subtype7 
   153.37    115.89    105.99    127.27    134.04    180.20    125.56    124.44 
 subtype8  subtype9 
   152.02    127.79 
 subtype1 subtype10  subtype2  subtype3  subtype4  subtype5  subtype6  subtype7 
   31.200    28.175    28.260    36.835    33.615    38.580    35.850    31.695 
 subtype8  subtype9 
   26.715    32.220 
 [1] "0.3 - 153.4 (31.2)" "2.0 - 115.9 (28.2)" "0.3 - 106.0 (28.3)"
 [4] "0.3 - 127.3 (36.8)" "1.2 - 134.0 (33.6)" "1.7 - 180.2 (38.6)"
 [7] "1.0 - 125.6 (35.8)" "6.1 - 124.4 (31.7)" "0.5 - 152.0 (26.7)"
[10] "1.0 - 127.8 (32.2)"
D4V2, continuous
           vv
clus        OMENTUM OVARY PERITONEUM OVARY
  subtype1        0    82                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                  82        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, binary
           cls
clus         0  1
  subtype1  77  1
  subtype10 55  0
  subtype2  56  1
  subtype3  85  0
  subtype4  34  0
  subtype5  74  0
  subtype6  35  0
  subtype7  33  1
  subtype8  48  2
  subtype9  42  0
[1] "tbl2"
           cls
clus        [,1] [,2]
  subtype1    77    1
  subtype10   55    0
  subtype2    56    1
  subtype3    85    0
  subtype4    34    0
  subtype5    74    0
  subtype6    35    0
  subtype7    33    1
  subtype8    48    2
  subtype9    42    0
     clus
vv    subtype1 subtype10 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        77        55       56       85       34       74       35       33
  YES        1         0        1        0        0        0        0        1
     clus
vv    subtype8 subtype9
  NO        48       42
  YES        2        0
[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"
D4V5, continuous
           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"  "subtype5"  "subtype2" 
 [7] "subtype5"  "subtype1"  "subtype5"  "subtype5"  "subtype3"  "subtype1" 
[13] "subtype3"  "subtype3"  "subtype7"  "subtype1"  "subtype10" "subtype1" 
[19] "subtype5"  "subtype3"  "subtype5"  "subtype7"  "subtype1"  "subtype2" 
[25] "subtype2"  "subtype3"  "subtype10" "subtype1"  "subtype7"  "subtype1" 
[31] "subtype10" "subtype4"  "subtype4"  "subtype5"  "subtype4"  "subtype4" 
    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"
D4V7, binary
           cls
clus         0  1
  subtype1   3 46
  subtype10  0 36
  subtype2   0 25
  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   46
  subtype10    0   36
  subtype2     0   25
  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       46        36       25       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  97 138
  subtype2  46  80
  subtype3  85 113
subtype1 subtype2 subtype3 
     235      126      198 
subtype1 subtype2 subtype3 
     138       80      113 
$subtype1
TCGA-3P-A9WA TCGA-5X-AA5U TCGA-04-1331 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 
       13.81        11.87        43.92         1.08        18.51        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1364 TCGA-04-1371 TCGA-04-1516 
       65.52        63.09        48.76        33.67        82.39        41.59 
TCGA-04-1517 TCGA-04-1525 TCGA-04-1536 TCGA-04-1542 TCGA-04-1649 TCGA-04-1652 
       19.99        38.37        29.10        84.20        64.64        31.86 
TCGA-04-1655 TCGA-09-1659 TCGA-09-1661 TCGA-09-1667 TCGA-09-1670 TCGA-09-1673 
       45.37         9.99        38.43        61.87        17.98         3.02 
TCGA-09-1674 TCGA-09-2043 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
        8.55         6.18         4.54       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2054 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
       39.75        20.94        83.31        55.23        57.27        81.01 
TCGA-13-1484 TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1495 
      124.44        22.39        83.93        52.44       125.56        90.38 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 
        4.24       127.27        66.15        34.82        34.16        65.52 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
       80.15        44.68        54.25        80.02        78.48        77.88 
TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 
       76.90        65.52         8.42        25.94        26.20        27.52 
TCGA-20-1683 TCGA-20-1684 TCGA-23-1022 TCGA-23-1024 TCGA-23-1030 TCGA-23-1031 
       25.38        19.10        49.68        15.39        29.13        18.90 
TCGA-23-1032 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 TCGA-23-1121 TCGA-23-1123 
        2.76        54.51         3.22        68.68         6.38        33.47 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2084 TCGA-23-2643 TCGA-24-0982 
        0.53        24.95       115.89        49.84         4.70        22.32 
TCGA-24-1413 TCGA-24-1418 TCGA-24-1422 TCGA-24-1424 TCGA-24-1426 TCGA-24-1430 
        6.31         7.99         0.76         6.02         5.36        28.37 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1469 TCGA-24-1544 TCGA-24-1548 
       18.64        18.67         8.55         9.11        26.96        16.21 
TCGA-24-1552 TCGA-24-1614 TCGA-24-1616 TCGA-24-1843 TCGA-24-1845 TCGA-24-1850 
       41.39        48.33        38.24         3.48         3.81         5.52 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2026 
       11.05        81.11         4.87       152.02        44.84        34.82 
TCGA-24-2027 TCGA-24-2033 TCGA-24-2260 TCGA-24-2261 TCGA-24-2280 TCGA-24-2288 
      109.71        18.48        36.16         0.79        70.45         0.82 
TCGA-24-2290 TCGA-24-2295 TCGA-24-2298 TCGA-25-1312 TCGA-25-1315 TCGA-25-1317 
       36.23        33.11        53.26         1.02        52.04         2.01 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1323 TCGA-25-1329 TCGA-25-1627 TCGA-25-1628 
       37.97        33.96        12.99        15.02        12.95        20.61 
TCGA-25-1631 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
        0.30        35.87        52.04        14.96        24.99        24.00 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 TCGA-29-1691 TCGA-29-1695 TCGA-29-1697 
       38.04         3.02        45.01        48.33        40.41        31.20 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1703 TCGA-29-1710 TCGA-29-1761 TCGA-29-1762 
       68.32        36.36        59.67        31.27        17.36        86.60 
TCGA-29-1763 TCGA-29-1766 TCGA-29-1769 TCGA-29-1774 TCGA-29-1778 TCGA-29-1783 
       66.81        39.42        22.98        17.33        14.93         7.23 
TCGA-29-2414 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 TCGA-29-A5NZ 
       86.17        45.11        13.84        42.25        11.47        35.77 
TCGA-30-1714 TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 TCGA-30-1862 TCGA-30-1866 
       38.07         2.47        15.68        48.10         6.12        36.62 
TCGA-30-1867 TCGA-30-1887 TCGA-31-1951 TCGA-31-1953 TCGA-31-1959 TCGA-36-1571 
        1.22        24.26        22.49         6.71         2.20        22.85 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1581 TCGA-36-2529 TCGA-36-2543 TCGA-36-2547 
        8.55        30.08        24.69        35.05         2.24        20.52 
TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2589 TCGA-42-2593 TCGA-57-1586 
       14.17        16.18        11.47        42.02         1.48        22.32 
TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2351 TCGA-59-2352 
       29.00        25.08        25.02       180.20       116.12         9.40 
TCGA-59-2363 TCGA-59-2372 TCGA-61-1722 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 
        5.42        44.81         8.09        27.88         4.34        31.79 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1899 TCGA-61-1904 TCGA-61-1906 TCGA-61-1911 
       33.67        43.69         8.42         9.07        34.13        42.51 
TCGA-61-1917 TCGA-61-2000 TCGA-61-2003 TCGA-61-2012 TCGA-61-2087 TCGA-61-2088 
       43.43        14.50         4.01        30.64         4.80         4.77 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2111 TCGA-61-2113 
       60.62        65.52        55.50         6.48       125.75        22.22 
TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-09-0365 TCGA-09-0366 
        6.35         8.61        39.68        18.94         9.47        57.76 
TCGA-09-0369 TCGA-10-0927 TCGA-10-0933 TCGA-10-0935 TCGA-10-0938 TCGA-13-0717 
       35.57        81.86        14.66        35.44        20.91        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-13-0791 TCGA-13-0794 TCGA-13-0795 TCGA-13-0800 TCGA-13-0807 
       11.54        40.24        63.09        20.35        87.48        13.61 
TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0891 TCGA-13-0910 TCGA-13-0911 
      111.39        66.67        92.42       102.84       116.65        44.55 
TCGA-13-0923 
       83.74 

$subtype2
TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1350 TCGA-04-1351 TCGA-04-1367 
       41.00         1.81         2.01        63.98        65.46       103.40 
TCGA-04-1514 TCGA-04-1519 TCGA-04-1530 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 
       56.55         0.79       119.08        55.43        48.89        28.64 
TCGA-09-1664 TCGA-09-1672 TCGA-09-2055 TCGA-09-2056 TCGA-13-1405 TCGA-13-1411 
       74.93         5.85        26.93        12.46        28.54        17.46 
TCGA-13-1477 TCGA-13-1485 TCGA-13-1494 TCGA-13-1499 TCGA-13-1500 TCGA-20-0987 
       54.64        20.68        93.90       115.07        13.97        23.05 
TCGA-20-0996 TCGA-23-1113 TCGA-23-1116 TCGA-23-1118 TCGA-23-2078 TCGA-24-0966 
       72.20        31.20        19.46        86.01        87.48         7.63 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-1105 TCGA-24-1416 TCGA-24-1463 
       11.64        21.80         7.66        47.41         6.38        72.92 
TCGA-24-1464 TCGA-24-1467 TCGA-24-1471 TCGA-24-1545 TCGA-24-1546 TCGA-24-1549 
       12.46       105.99         1.18        57.40        64.27        56.58 
TCGA-24-1551 TCGA-24-1555 TCGA-24-1560 TCGA-24-1562 TCGA-24-1564 TCGA-24-1565 
       51.91        88.50        44.09        45.50        25.87        10.26 
TCGA-24-1603 TCGA-24-1849 TCGA-24-1923 TCGA-24-2024 TCGA-24-2029 TCGA-24-2035 
       90.15         5.79        22.68        58.16        14.43        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2271 TCGA-24-2281 TCGA-24-2293 TCGA-25-1316 
       64.01        44.52        31.63        44.61        16.64        42.05 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1630 TCGA-25-1633 TCGA-25-2042 
       18.58        27.62        17.03        38.20        62.17        13.02 
TCGA-25-2399 TCGA-25-2408 TCGA-29-1690 TCGA-29-1771 TCGA-29-1785 TCGA-29-2427 
       19.99        31.00        47.61        22.55        36.30        62.47 
TCGA-29-2436 TCGA-30-1853 TCGA-30-1880 TCGA-30-1892 TCGA-31-1950 TCGA-31-1955 
        9.76        36.26        57.57        48.79        18.77        42.51 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1577 TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 
       28.77        29.10        25.74        24.23        33.01        29.49 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-42-2587 TCGA-42-2590 TCGA-59-2349 
       25.91        25.08        23.80        23.74        10.42        80.12 
TCGA-59-2350 TCGA-59-2354 TCGA-59-2355 TCGA-61-1721 TCGA-61-1727 TCGA-61-1734 
       22.32        34.39         2.14        11.11        18.54        28.47 
TCGA-61-1736 TCGA-61-1995 TCGA-61-1998 TCGA-61-2002 TCGA-61-2009 TCGA-61-2016 
       48.79         2.01         5.52        17.98        39.85         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 
       45.96        45.40        51.72        71.74        61.64        58.39 
TCGA-61-2110 TCGA-61-2613 TCGA-09-0364 TCGA-10-0926 TCGA-10-0930 TCGA-10-0934 
       44.52        31.07        29.16        25.91        34.19         6.71 
TCGA-13-0714 TCGA-13-0762 TCGA-13-0768 TCGA-13-0799 TCGA-13-0804 TCGA-13-0886 
        6.21       111.78        58.65        83.34        35.28       153.37 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0899 TCGA-13-0912 TCGA-13-0919 TCGA-13-0921 
       95.15       145.45        66.15        37.64        84.53        48.76 

$subtype3
TCGA-59-A5PD TCGA-04-1336 TCGA-04-1338 TCGA-04-1349 TCGA-04-1353 TCGA-04-1356 
       20.52        49.15        46.62        21.57         0.53        49.28 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 TCGA-04-1646 TCGA-04-1651 TCGA-04-1654 
       32.52        44.32        76.57        27.88        36.23        47.70 
TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 TCGA-09-1675 
       89.33        41.62        57.60        55.36        30.51        97.55 
TCGA-09-2044 TCGA-09-2045 TCGA-13-1403 TCGA-13-1404 TCGA-13-1412 TCGA-13-1481 
        6.12        35.15        77.10        81.17        32.35        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1488 TCGA-13-1501 TCGA-13-1505 TCGA-13-1512 
       61.71        29.42        70.82        43.20        65.69        14.53 
TCGA-13-A5FT TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1023 
       70.45        16.70         2.93         2.66        47.54        40.54 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1109 TCGA-23-1117 
       26.83        32.09        49.41         8.81        51.35        33.30 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 TCGA-23-1124 TCGA-23-2079 TCGA-23-2081 
      129.96         4.27        39.09        58.13        91.66        77.00 
TCGA-23-2641 TCGA-23-2645 TCGA-24-0979 TCGA-24-1103 TCGA-24-1104 TCGA-24-1417 
        2.76         4.50        41.56        54.12        63.55         7.82 
TCGA-24-1419 TCGA-24-1423 TCGA-24-1425 TCGA-24-1427 TCGA-24-1428 TCGA-24-1435 
        7.86         6.25         5.95         4.83        17.39        43.53 
TCGA-24-1466 TCGA-24-1470 TCGA-24-1474 TCGA-24-1550 TCGA-24-1553 TCGA-24-1556 
       45.14         3.45        22.22        41.06        58.09        70.62 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1563 TCGA-24-1567 TCGA-24-1604 TCGA-24-1842 
       39.88        19.53        47.70        17.23        88.37         8.32 
TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 TCGA-24-1920 TCGA-24-1924 TCGA-24-1927 
        3.72         4.37        11.28         9.80        30.21        16.44 
TCGA-24-2030 TCGA-24-2254 TCGA-24-2262 TCGA-24-2267 TCGA-24-2289 TCGA-24-2297 
       55.92        57.07         0.36        47.54        67.36        55.86 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1318 TCGA-25-1319 TCGA-25-1322 TCGA-25-1632 
       26.96        33.01        34.98        65.00         2.99        59.15 
TCGA-25-1878 TCGA-25-2391 TCGA-25-2392 TCGA-25-2397 TCGA-25-2400 TCGA-25-2401 
       85.05        49.05         1.02        12.00        42.02         2.96 
TCGA-25-2404 TCGA-25-2409 TCGA-29-1688 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 
       29.03        26.99        78.90       101.79        39.02        33.93 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 TCGA-29-1764 
       16.93        23.93        18.25        41.98        34.62        62.93 
TCGA-29-1768 TCGA-29-1770 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 
       31.30        24.36        12.36        11.84        12.30         8.38 
TCGA-29-1784 TCGA-29-2425 TCGA-29-2432 TCGA-30-1718 TCGA-30-1857 TCGA-30-1860 
        5.36        65.00        21.47        51.91         0.26        44.91 
TCGA-30-1861 TCGA-30-1891 TCGA-31-1944 TCGA-31-1946 TCGA-31-1956 TCGA-36-1570 
       34.78        30.05        45.57        30.18        44.12        21.53 
TCGA-36-1574 TCGA-36-1578 TCGA-36-2534 TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 
       22.55        27.85        29.82        21.60        20.98        18.31 
TCGA-36-2549 TCGA-42-2582 TCGA-42-2588 TCGA-42-2591 TCGA-57-1582 TCGA-57-1583 
        6.05        47.57        28.93        40.77        24.03        11.38 
TCGA-57-1584 TCGA-57-1585 TCGA-61-1724 TCGA-61-1725 TCGA-61-1737 TCGA-61-1738 
       21.14         1.74        20.94        31.43        44.84        35.80 
TCGA-61-1740 TCGA-61-1895 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1907 
        2.43         1.45         5.79        11.41        13.02        31.30 
TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 TCGA-61-1919 
       37.05        48.92        56.61        67.76        15.75        38.17 
TCGA-61-2008 TCGA-61-2104 TCGA-61-2109 TCGA-VG-A8LO TCGA-WR-A838 TCGA-09-0367 
       30.64        76.87        20.68         0.79         9.99        17.98 
TCGA-10-0925 TCGA-10-0928 TCGA-10-0931 TCGA-10-0936 TCGA-10-0937 TCGA-13-0720 
       54.31        18.51        32.88        36.92        19.99        44.55 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0755 TCGA-13-0758 TCGA-13-0761 TCGA-13-0764 
       12.39        31.20         2.50        11.38        38.01        61.84 
TCGA-13-0766 TCGA-13-0792 TCGA-13-0793 TCGA-13-0797 TCGA-13-0801 TCGA-13-0802 
       56.71       118.42       107.28        69.73        45.99        51.02 
TCGA-13-0803 TCGA-13-0805 TCGA-13-0883 TCGA-13-0884 TCGA-13-0893 TCGA-13-0897 
       43.86        35.31        68.94       107.18        43.36        71.74 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
      134.04        19.36       127.79        50.37       123.16       118.98 
TCGA-13-0908 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0924 TCGA-13-2071 
       60.59       109.32        58.68        48.79        85.94        25.41 

subtype1 subtype2 subtype3 
    0.30     0.79     0.26 
subtype1 subtype2 subtype3 
  180.20   153.37   134.04 
subtype1 subtype2 subtype3 
   29.13    33.60    34.88 
[1] "0.3 - 180.2 (29.1)" "0.8 - 153.4 (33.6)" "0.3 - 134.0 (34.9)"
D5V2, continuous
          vv
clus       OMENTUM OVARY PERITONEUM OVARY
  subtype1       2   233                2
  subtype2       1   126                0
  subtype3       0   199                0
D5V3, multiclass
                  clus
vv                 subtype1 subtype2 subtype3
  OMENTUM                 2        1        0
  OVARY                 233      126      199
  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"
D5V4, binary
          cls
clus         0   1
  subtype1 229   1
  subtype2 118   3
  subtype3 194   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  229    1
  subtype2  118    3
  subtype3  194    1
     clus
vv    subtype1 subtype2 subtype3
  NO       229      118      194
  YES        1        3        1
[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"
D5V5, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 10 12  3  2
  subtype2  2  9  0  0
  subtype3  3  5  2  1
D5V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       10        2        3
  R1       12        9        5
  R2        3        0        2
  RX        2        0        1
[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"
D5V7, binary
          cls
clus         0   1
  subtype1   5 139
  subtype2   1  74
  subtype3   4 114
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  139
  subtype2    1   74
  subtype3    4  114
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            5        1        4
  NOT HISPANIC OR LATINO      139       74      114
[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 = METHLYATION_CNMF
D6V1, survival
          sevent
clus2        0   1
  subtype1  45  71
  subtype2  34  61
  subtype3  77 107
  subtype4  68  97
subtype1 subtype2 subtype3 subtype4 
     116       95      184      165 
subtype1 subtype2 subtype3 subtype4 
      71       61      107       97 
$subtype1
TCGA-04-1331 TCGA-04-1337 TCGA-04-1338 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 
       43.92         2.01        46.62         1.08        18.51        11.87 
TCGA-04-1353 TCGA-04-1365 TCGA-04-1516 TCGA-09-1665 TCGA-09-2044 TCGA-09-2055 
        0.53        76.57        41.59        41.62         6.12        26.93 
TCGA-13-1408 TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 TCGA-13-1483 TCGA-13-1484 
       55.23        17.46        32.35        87.06        29.42       124.44 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1494 TCGA-13-1497 TCGA-13-1499 TCGA-13-1500 
       22.39        70.82        93.90       127.27       115.07        13.97 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1506 TCGA-13-1509 TCGA-13-1512 TCGA-13-2066 
       43.20        34.82        34.16        80.15        14.53        70.13 
TCGA-20-0987 TCGA-20-0991 TCGA-20-1682 TCGA-20-1685 TCGA-23-1023 TCGA-23-1032 
       23.05        26.20        27.52        16.70        40.54         2.76 
TCGA-23-1107 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1809 
        0.30        19.46        33.30        86.01       129.96         0.53 
TCGA-23-2078 TCGA-23-2081 TCGA-23-2645 TCGA-23-2647 TCGA-24-0970 TCGA-24-0975 
       87.48        77.00         4.50         4.44        11.64        21.80 
TCGA-24-1434 TCGA-24-1545 TCGA-24-1550 TCGA-24-1553 TCGA-24-1564 TCGA-24-1850 
       18.67        57.40        41.06        58.09        25.87         5.52 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2030 TCGA-24-2288 TCGA-24-2289 
       11.05        81.11         4.87        55.92         0.82        67.36 
TCGA-24-2293 TCGA-25-1321 TCGA-25-1325 TCGA-25-1326 TCGA-25-1329 TCGA-25-1623 
       16.64        33.96        32.09        41.06        15.02        18.58 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1635 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 
       17.03        12.95        52.04        24.00        85.05        13.02 
TCGA-29-1698 TCGA-29-1710 TCGA-29-1761 TCGA-29-1763 TCGA-29-2429 TCGA-30-1860 
       68.32        31.27        17.36        66.81        13.84        44.91 
TCGA-30-1861 TCGA-30-1867 TCGA-30-1887 TCGA-31-1959 TCGA-36-1576 TCGA-36-1577 
       34.78         1.22        24.26         2.20        30.08        25.74 
TCGA-36-2543 TCGA-36-2548 TCGA-42-2589 TCGA-57-1582 TCGA-57-1585 TCGA-57-1992 
        2.24        14.17        42.02        24.03         1.74        29.00 
TCGA-57-1993 TCGA-61-1722 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1911 
       25.08         8.09        44.84        35.80         2.43        42.51 
TCGA-61-2000 TCGA-61-2003 TCGA-61-2012 TCGA-61-2111 TCGA-61-2612 TCGA-09-0366 
       14.50         4.01        30.64       125.75         6.35        57.76 
TCGA-10-0930 TCGA-13-0768 TCGA-13-0795 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
       34.19        58.65        20.35        35.28        35.31        13.61 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0889 TCGA-13-0890 TCGA-13-0900 TCGA-13-0903 
      111.39       153.37        95.15       145.45       134.04       127.79 
TCGA-13-0919 TCGA-13-0920 
       84.53        48.79 

$subtype2
TCGA-04-1332 TCGA-04-1346 TCGA-04-1351 TCGA-04-1356 TCGA-04-1362 TCGA-04-1514 
       41.00        65.52        65.46        49.28        44.32        56.55 
TCGA-04-1519 TCGA-04-1644 TCGA-04-1655 TCGA-09-2048 TCGA-09-2053 TCGA-13-1409 
        0.79        48.89        45.37         4.54        39.75        57.27 
TCGA-13-1477 TCGA-13-1489 TCGA-13-1498 TCGA-13-2057 TCGA-23-1031 TCGA-23-1122 
       54.64        83.93        66.15        80.02        18.90        39.09 
TCGA-23-2077 TCGA-23-2641 TCGA-23-2643 TCGA-24-0979 TCGA-24-0982 TCGA-24-1105 
      115.89         2.76         4.70        41.56        22.32        47.41 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1426 TCGA-24-1427 TCGA-24-1474 TCGA-24-1557 
        0.76         6.25         5.36         4.83        22.22        39.88 
TCGA-24-1560 TCGA-24-1567 TCGA-24-1923 TCGA-24-2280 TCGA-25-1313 TCGA-25-1316 
       44.09        17.23        22.68        70.45        26.96        42.05 
TCGA-25-1317 TCGA-25-1323 TCGA-25-1628 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
        2.01        12.99        20.61        59.15        62.17        35.87 
TCGA-25-1871 TCGA-25-2392 TCGA-25-2393 TCGA-25-2398 TCGA-29-1769 TCGA-29-1774 
       24.99         1.02        38.04        45.01        22.98        17.33 
TCGA-29-2414 TCGA-29-2431 TCGA-29-2432 TCGA-30-1853 TCGA-30-1855 TCGA-30-1866 
       86.17        42.25        21.47        36.26         2.47        36.62 
TCGA-31-1944 TCGA-31-1955 TCGA-36-1569 TCGA-36-1580 TCGA-36-2537 TCGA-36-2544 
       45.57        42.51        29.10        24.23        25.91        20.98 
TCGA-42-2590 TCGA-42-2591 TCGA-57-1586 TCGA-57-1994 TCGA-59-2350 TCGA-59-2363 
       10.42        40.77        22.32        25.02        22.32         5.42 
TCGA-61-1721 TCGA-61-1730 TCGA-61-1733 TCGA-61-1900 TCGA-61-2008 TCGA-61-2009 
       11.11         4.34        31.79         5.79        30.64        39.85 
TCGA-61-2096 TCGA-61-2098 TCGA-61-2102 TCGA-61-2109 TCGA-61-2613 TCGA-61-2614 
       58.39        65.52         6.48        20.68        31.07         8.61 
TCGA-09-0364 TCGA-09-0365 TCGA-10-0926 TCGA-10-0928 TCGA-10-0933 TCGA-10-0934 
       29.16         9.47        25.91        18.51        14.66         6.71 
TCGA-10-0935 TCGA-13-0727 TCGA-13-0730 TCGA-13-0757 TCGA-13-0758 TCGA-13-0800 
       35.44        15.19        17.82        11.18        11.38        87.48 
TCGA-13-0802 TCGA-13-0894 TCGA-13-0901 TCGA-13-0910 TCGA-13-0912 
       51.02        49.61        19.36       116.65        37.64 

$subtype3
TCGA-04-1335 TCGA-04-1336 TCGA-04-1349 TCGA-04-1361 TCGA-04-1367 TCGA-04-1536 
        1.81        49.15        21.57        32.52       103.40        29.10 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-09-1662 TCGA-09-1664 
       28.64        64.64        36.23        47.70        89.33        74.93 
TCGA-09-1666 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 TCGA-09-1675 TCGA-09-2043 
       57.60        55.36        17.98         5.85        97.55         6.18 
TCGA-09-2045 TCGA-09-2051 TCGA-09-2056 TCGA-13-1404 TCGA-13-1405 TCGA-13-1482 
       35.15        63.09        12.46        81.17        28.54        61.71 
TCGA-13-1485 TCGA-13-1511 TCGA-13-2059 TCGA-13-2065 TCGA-20-0996 TCGA-20-1687 
       20.68        54.25        78.48        65.52        72.20         2.66 
TCGA-23-1021 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1113 TCGA-23-2072 
       47.54        26.83        32.09        49.41        31.20        24.95 
TCGA-23-2079 TCGA-23-2084 TCGA-23-2649 TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 
       91.66        49.84         3.81         7.66        54.12        63.55 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1425 TCGA-24-1430 TCGA-24-1435 TCGA-24-1463 
        6.38         7.82         5.95        28.37        43.53        72.92 
TCGA-24-1464 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1546 TCGA-24-1551 
       12.46       105.99         3.45         1.18        64.27        51.91 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1562 TCGA-24-1563 TCGA-24-1565 TCGA-24-1603 
       88.50        70.62        45.50        47.70        10.26        90.15 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1846 TCGA-24-1847 
       88.37        48.33        38.24         8.32         4.37        11.28 
TCGA-24-1849 TCGA-24-1927 TCGA-24-2023 TCGA-24-2024 TCGA-24-2029 TCGA-24-2035 
        5.79        16.44        44.84        58.16        14.43        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 
       64.01        44.52        57.07         0.36        47.54        31.63 
TCGA-24-2290 TCGA-24-2298 TCGA-25-1314 TCGA-25-1318 TCGA-25-1322 TCGA-25-1328 
       36.23        53.26        33.01        34.98         2.99        66.05 
TCGA-25-1625 TCGA-25-1630 TCGA-25-1631 TCGA-25-2391 TCGA-25-2397 TCGA-25-2401 
       27.62        38.20         0.30        49.05        12.00         2.96 
TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1694 
       29.03        31.00        26.99        78.90        47.61        39.02 
TCGA-29-1696 TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 TCGA-29-1764 TCGA-29-1768 
       33.93        18.25        41.98        34.62        62.93        31.30 
TCGA-29-1770 TCGA-29-1771 TCGA-29-1776 TCGA-29-1781 TCGA-29-2427 TCGA-29-2436 
       24.36        22.55        11.84         8.38        62.47         9.76 
TCGA-30-1718 TCGA-30-1857 TCGA-30-1869 TCGA-30-1880 TCGA-30-1891 TCGA-30-1892 
       51.91         0.26        51.39        57.57        30.05        48.79 
TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 TCGA-31-1956 TCGA-36-1568 TCGA-36-1570 
       30.18        22.49         6.71        44.12        28.77        21.53 
TCGA-36-1574 TCGA-36-1578 TCGA-36-2532 TCGA-36-2534 TCGA-36-2538 TCGA-36-2540 
       22.55        27.85        29.49        29.82        25.08        23.80 
TCGA-36-2542 TCGA-36-2545 TCGA-36-2549 TCGA-42-2582 TCGA-42-2588 TCGA-57-1584 
       21.60        18.31         6.05        47.57        28.93        21.14 
TCGA-59-2348 TCGA-59-2354 TCGA-59-2355 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
      180.20        34.39         2.14        20.94        31.43        18.54 
TCGA-61-1734 TCGA-61-1736 TCGA-61-1895 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 
       28.47        48.79         1.45        11.41        13.02         9.07 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1913 TCGA-61-1995 TCGA-61-2002 TCGA-61-2016 
       34.13        31.30        48.92         2.01        17.98         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 
       45.96        45.40         4.80        71.74        61.64        60.62 
TCGA-61-2110 TCGA-09-0367 TCGA-10-0925 TCGA-10-0931 TCGA-10-0937 TCGA-13-0714 
       44.52        17.98        54.31        32.88        19.99         6.21 
TCGA-13-0720 TCGA-13-0725 TCGA-13-0726 TCGA-13-0765 TCGA-13-0766 TCGA-13-0791 
       44.55        12.39        31.20        45.67        56.71        40.24 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0799 TCGA-13-0801 TCGA-13-0883 TCGA-13-0884 
      118.42       107.28        83.34        45.99        68.94       107.18 
TCGA-13-0887 TCGA-13-0893 TCGA-13-0897 TCGA-13-0905 TCGA-13-0908 TCGA-13-0911 
       66.67        43.36        71.74       123.16        60.59        44.55 
TCGA-13-0916 TCGA-13-0921 TCGA-13-0924 TCGA-13-2071 
       58.68        48.76        85.94        25.41 

$subtype4
TCGA-04-1347 TCGA-04-1348 TCGA-04-1350 TCGA-04-1364 TCGA-04-1369 TCGA-04-1371 
       63.09        48.76        63.98        33.67        21.11        82.39 
TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1646 
       19.99        38.37       119.08        84.20        55.43        27.88 
TCGA-04-1652 TCGA-09-1659 TCGA-09-1661 TCGA-09-1667 TCGA-09-1669 TCGA-09-1673 
       31.86         9.99        38.43        61.87        30.51         3.02 
TCGA-09-1674 TCGA-09-2049 TCGA-09-2050 TCGA-09-2054 TCGA-13-1403 TCGA-13-1407 
        8.55       112.41        71.11        20.94        77.10        83.31 
TCGA-13-1410 TCGA-13-1491 TCGA-13-1492 TCGA-13-1495 TCGA-13-1496 TCGA-13-1505 
       81.01        52.44       125.56        90.38         4.24        65.69 
TCGA-13-1507 TCGA-13-1510 TCGA-13-2060 TCGA-13-2061 TCGA-20-0990 TCGA-20-1683 
       65.52        44.68        77.88        76.90        25.94        25.38 
TCGA-20-1684 TCGA-20-1686 TCGA-23-1022 TCGA-23-1024 TCGA-23-1029 TCGA-23-1030 
       19.10         2.93        49.68        15.39         8.81        29.13 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 TCGA-23-1120 TCGA-23-1121 
       51.35        54.51         3.22        68.68         4.27         6.38 
TCGA-23-1123 TCGA-23-1124 TCGA-24-0966 TCGA-24-1413 TCGA-24-1418 TCGA-24-1419 
       33.47        58.13         7.63         6.31         7.99         7.86 
TCGA-24-1424 TCGA-24-1428 TCGA-24-1431 TCGA-24-1436 TCGA-24-1466 TCGA-24-1469 
        6.02        17.39        18.64         8.55        45.14         9.11 
TCGA-24-1544 TCGA-24-1548 TCGA-24-1549 TCGA-24-1552 TCGA-24-1558 TCGA-24-1843 
       26.96        16.21        56.58        41.39        19.53         3.48 
TCGA-24-1844 TCGA-24-1845 TCGA-24-1920 TCGA-24-1924 TCGA-24-2020 TCGA-24-2026 
        3.72         3.81         9.80        30.21       152.02        34.82 
TCGA-24-2027 TCGA-24-2033 TCGA-24-2260 TCGA-24-2261 TCGA-24-2281 TCGA-24-2295 
      109.71        18.48        36.16         0.79        44.61        33.11 
TCGA-24-2297 TCGA-25-1312 TCGA-25-1315 TCGA-25-1319 TCGA-25-1320 TCGA-25-1324 
       55.86         1.02        52.04        65.00        37.97        34.03 
TCGA-25-1870 TCGA-25-2396 TCGA-25-2399 TCGA-25-2400 TCGA-29-1691 TCGA-29-1693 
       14.96         3.02        19.99        42.02        48.33       101.79 
TCGA-29-1695 TCGA-29-1697 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 
       40.41        31.20        36.36        16.93        23.93        59.67 
TCGA-29-1762 TCGA-29-1766 TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 TCGA-29-1783 
       86.60        39.42        12.36        12.30        14.93         7.23 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2425 TCGA-29-2428 TCGA-29-2434 TCGA-30-1714 
        5.36        36.30        65.00        45.11        11.47        38.07 
TCGA-30-1856 TCGA-30-1859 TCGA-30-1862 TCGA-31-1950 TCGA-36-1571 TCGA-36-1575 
       15.68        48.10         6.12        18.77        22.85         8.55 
TCGA-36-1581 TCGA-36-2529 TCGA-36-2547 TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 
       24.69        35.05        20.52        16.18        11.47        23.74 
TCGA-42-2593 TCGA-57-1583 TCGA-59-2349 TCGA-59-2351 TCGA-59-2352 TCGA-59-2372 
        1.48        11.38        80.12       116.12         9.40        44.81 
TCGA-61-1728 TCGA-61-1741 TCGA-61-1743 TCGA-61-1899 TCGA-61-1910 TCGA-61-1914 
       27.88        33.67        43.69         8.42        37.05        56.61 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1998 TCGA-61-2088 
       67.76        43.43        15.75        38.17         5.52         4.77 
TCGA-61-2092 TCGA-61-2101 TCGA-61-2104 TCGA-61-2113 TCGA-09-0369 TCGA-10-0927 
       51.72        55.50        76.87        22.22        35.57        81.86 
TCGA-10-0936 TCGA-10-0938 TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 TCGA-13-0751 
       36.92        20.91        24.59        39.58         2.73        55.17 
TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0794 
        2.50        11.54        38.01       111.78        61.84        63.09 
TCGA-13-0797 TCGA-13-0803 TCGA-13-0888 TCGA-13-0891 TCGA-13-0899 TCGA-13-0904 
       69.73        43.86        92.42       102.84        66.15        50.37 
TCGA-13-0906 TCGA-13-0913 TCGA-13-0923 
      118.98       109.32        83.74 

subtype1 subtype2 subtype3 subtype4 
    0.30     0.76     0.26     0.79 
subtype1 subtype2 subtype3 subtype4 
  153.37   116.65   180.20   152.02 
subtype1 subtype2 subtype3 subtype4 
  30.955   29.100   34.260   35.050 
[1] "0.3 - 153.4 (31.0)" "0.8 - 116.7 (29.1)" "0.3 - 180.2 (34.3)"
[4] "0.8 - 152.0 (35.0)"
D6V2, continuous
          vv
clus       OMENTUM OVARY PERITONEUM OVARY
  subtype1       1   117                0
  subtype2       0    97                0
  subtype3       1   184                0
  subtype4       0   163                2
D6V3, multiclass
                  clus
vv                 subtype1 subtype2 subtype3 subtype4
  OMENTUM                 1        0        1        0
  OVARY                 117       97      184      163
  PERITONEUM OVARY        0        0        0        2
[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"
D6V4, binary
          cls
clus         0   1
  subtype1 111   3
  subtype2  90   2
  subtype3 180   0
  subtype4 161   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  111    3
  subtype2   90    2
  subtype3  180    0
  subtype4  161    0
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       111       90      180      161
  YES        3        2        0        0
[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"
D6V5, continuous
          vv
clus       R0 R1 R2
  subtype1  3  5  0
  subtype2  2  8  0
  subtype3  5  6  1
  subtype4  4  7  1
D6V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0        3        2        5        4
  R1        5        8        6        7
  R2        0        0        1        1
[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"
D6V7, binary
          cls
clus         0   1
  subtype1   2  80
  subtype2   1  57
  subtype3   3 104
  subtype4   5  90
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   80
  subtype2    1   57
  subtype3    3  104
  subtype4    5   90
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        1        3        5
  NOT HISPANIC OR LATINO       80       57      104       90
[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(7) Variable = RPPA_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1  53  94
  subtype2  88 103
  subtype3  28  50
subtype1 subtype2 subtype3 
     147      191       78 
subtype1 subtype2 subtype3 
      94      103       50 
$subtype1
TCGA-59-A5PD TCGA-04-1335 TCGA-04-1338 TCGA-04-1342 TCGA-04-1349 TCGA-04-1519 
       20.52         1.81        46.62        18.51        21.57         0.79 
TCGA-04-1525 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-09-1664 
       38.37        84.20        55.43        48.89        28.64        74.93 
TCGA-09-1665 TCGA-09-2049 TCGA-09-2056 TCGA-13-1408 TCGA-13-1411 TCGA-13-1412 
       41.62       112.41        12.46        55.23        17.46        32.35 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1488 
       54.64        87.06        61.71        29.42       124.44        70.82 
TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 
       52.44        93.90        90.38        66.15       115.07        13.97 
TCGA-13-1501 TCGA-13-2059 TCGA-13-2065 TCGA-13-A5FT TCGA-20-1686 TCGA-20-1687 
       43.20        78.48        65.52        70.45         2.93         2.66 
TCGA-23-1122 TCGA-23-2078 TCGA-24-0970 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
       39.09        87.48        11.64        41.56         7.66        22.32 
TCGA-24-1104 TCGA-24-1422 TCGA-24-1423 TCGA-24-1427 TCGA-24-1466 TCGA-24-1545 
       63.55         0.76         6.25         4.83        45.14        57.40 
TCGA-24-1546 TCGA-24-1550 TCGA-24-1553 TCGA-24-1563 TCGA-24-1614 TCGA-24-1849 
       64.27        41.06        58.09        47.70        48.33         5.79 
TCGA-24-1850 TCGA-24-1923 TCGA-24-1924 TCGA-24-2029 TCGA-24-2033 TCGA-24-2038 
        5.52        22.68        30.21        14.43        18.48        44.52 
TCGA-24-2260 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 
       36.16         0.36        47.54        31.63        44.61         0.82 
TCGA-24-2289 TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1319 
       67.36        16.64        55.86        53.26        26.96        65.00 
TCGA-25-1320 TCGA-25-1323 TCGA-25-1326 TCGA-25-1328 TCGA-25-1623 TCGA-25-1626 
       37.97        12.99        41.06        66.05        18.58        17.03 
TCGA-25-1630 TCGA-25-2042 TCGA-25-2398 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 
       38.20        13.02        45.01         2.96        29.03        31.00 
TCGA-29-1690 TCGA-29-1699 TCGA-29-1701 TCGA-29-1710 TCGA-29-1766 TCGA-29-1768 
       47.61        36.36        16.93        31.27        39.42        31.30 
TCGA-29-1769 TCGA-29-1771 TCGA-29-1776 TCGA-29-2425 TCGA-29-2427 TCGA-29-2429 
       22.98        22.55        11.84        65.00        62.47        13.84 
TCGA-29-2432 TCGA-30-1856 TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 TCGA-31-1950 
       21.47        15.68        24.26        48.79        45.57        18.77 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1576 TCGA-36-1577 TCGA-36-1580 TCGA-36-1581 
       28.77        29.10        30.08        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-61-1724 TCGA-61-1895 TCGA-61-1900 
      116.12         5.42         8.09        20.94         1.45         5.79 
TCGA-61-1903 TCGA-61-1906 TCGA-61-1907 TCGA-61-1919 TCGA-61-2003 TCGA-61-2008 
       13.02        34.13        31.30        38.17         4.01        30.64 
TCGA-61-2009 TCGA-61-2012 TCGA-61-2094 TCGA-61-2095 TCGA-61-2101 TCGA-61-2111 
       39.85        30.64        71.74        61.64        55.50       125.75 
TCGA-61-2113 TCGA-61-2610 TCGA-61-2613 TCGA-VG-A8LO TCGA-10-0925 TCGA-10-0933 
       22.22        51.91        31.07         0.79        54.31        14.66 
TCGA-13-0725 TCGA-13-0793 TCGA-13-0886 TCGA-13-0894 TCGA-13-0901 TCGA-13-0903 
       12.39       107.28       153.37        49.61        19.36       127.79 
TCGA-13-0906 TCGA-13-0910 TCGA-13-0913 
      118.98       116.65       109.32 

$subtype2
TCGA-5X-AA5U TCGA-04-1336 TCGA-04-1348 TCGA-04-1356 TCGA-04-1361 TCGA-04-1369 
       11.87        49.15        48.76        49.28        32.52        21.11 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1649 TCGA-04-1651 TCGA-09-1666 
       56.55        41.59        19.99        64.64        36.23        57.60 
TCGA-09-1670 TCGA-09-1673 TCGA-09-2043 TCGA-09-2044 TCGA-09-2051 TCGA-09-2054 
       17.98         3.02         6.18         6.12        63.09        20.94 
TCGA-13-1404 TCGA-13-1409 TCGA-13-1410 TCGA-13-1487 TCGA-13-1489 TCGA-13-1492 
       81.17        57.27        81.01        22.39        83.93       125.56 
TCGA-13-1496 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 TCGA-13-1511 
        4.24        34.82        65.69        34.16        80.15        54.25 
TCGA-13-1512 TCGA-13-2060 TCGA-13-2061 TCGA-13-2066 TCGA-13-A5FU TCGA-20-1683 
       14.53        77.88        76.90        70.13         8.42        25.38 
TCGA-20-1684 TCGA-20-1685 TCGA-23-1109 TCGA-23-1110 TCGA-23-1121 TCGA-23-1123 
       19.10        16.70        51.35        54.51         6.38        33.47 
TCGA-23-1809 TCGA-23-2077 TCGA-23-2643 TCGA-23-2645 TCGA-23-2649 TCGA-24-0966 
        0.53       115.89         4.70         4.50         3.81         7.63 
TCGA-24-1103 TCGA-24-1105 TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 TCGA-24-1424 
       54.12        47.41         6.38         7.82         7.86         6.02 
TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 TCGA-24-1436 TCGA-24-1464 
       17.39        28.37        18.64        43.53         8.55        12.46 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1548 
      105.99         9.11         1.18        22.22        26.96        16.21 
TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       56.58        51.91        41.39        88.50        70.62        39.88 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       19.53        44.09        45.50        10.26        17.23        90.15 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1930 
       38.24         8.32         3.72         3.81         4.37        81.11 
TCGA-24-2020 TCGA-24-2023 TCGA-24-2027 TCGA-24-2030 TCGA-24-2036 TCGA-24-2261 
      152.02        44.84       109.71        55.92        64.01         0.79 
TCGA-24-2290 TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 TCGA-25-1318 TCGA-25-1321 
       36.23         1.02        33.01        52.04        34.98        33.96 
TCGA-25-1329 TCGA-25-1627 TCGA-25-1631 TCGA-25-1635 TCGA-25-1878 TCGA-25-2393 
       15.02        12.95         0.30        52.04        85.05        38.04 
TCGA-25-2396 TCGA-25-2397 TCGA-25-2400 TCGA-25-2409 TCGA-29-1688 TCGA-29-1691 
        3.02        12.00        42.02        26.99        78.90        48.33 
TCGA-29-1693 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1703 TCGA-29-1705 
      101.79        40.41        31.20        68.32        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        17.36        86.60        62.93        17.33 
TCGA-29-1778 TCGA-29-1781 TCGA-29-2428 TCGA-29-2431 TCGA-29-2434 TCGA-29-2435 
       14.93         8.38        45.11        42.25        11.47         1.12 
TCGA-29-A5NZ TCGA-30-1859 TCGA-30-1869 TCGA-31-1951 TCGA-31-1955 TCGA-36-1570 
       35.77        48.10        51.39        22.49        42.51        21.53 
TCGA-36-1571 TCGA-36-1575 TCGA-36-1578 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 
       22.85         8.55        27.85        35.05        33.01        29.49 
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-61-1730 
        1.48        22.32       180.20         9.40        44.81         4.34 
TCGA-61-1734 TCGA-61-1736 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1899 
       28.47        48.79         2.43        33.67        43.69         8.42 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1915 TCGA-61-1995 TCGA-61-2000 
       37.05        42.51        48.92        67.76         2.01        14.50 
TCGA-61-2018 TCGA-61-2088 TCGA-61-2092 TCGA-61-2096 TCGA-61-2098 TCGA-61-2104 
       45.40         4.77        51.72        58.39        65.52        76.87 
TCGA-61-2109 TCGA-OY-A56P TCGA-OY-A56Q TCGA-WR-A838 TCGA-10-0931 TCGA-10-0936 
       20.68        39.68        18.94         9.99        32.88        36.92 
TCGA-13-0720 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
       44.55        63.09        69.73        83.34        87.48        45.99 
TCGA-13-0802 TCGA-13-0804 TCGA-13-0884 TCGA-13-0887 TCGA-13-0888 TCGA-13-0891 
       51.02        35.28       107.18        66.67        92.42       102.84 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 
       71.74        66.15        58.68        48.79        48.76 

$subtype3
TCGA-3P-A9WA TCGA-04-1341 TCGA-04-1343 TCGA-04-1362 TCGA-04-1370 TCGA-04-1646 
       13.81         1.08        11.87        44.32        59.97        27.88 
TCGA-04-1654 TCGA-09-1662 TCGA-09-1674 TCGA-09-2045 TCGA-09-2055 TCGA-13-1405 
       47.70        89.33         8.55        35.15        26.93        28.54 
TCGA-13-1507 TCGA-20-1682 TCGA-23-1111 TCGA-23-1124 TCGA-23-2079 TCGA-23-2081 
       65.52        27.52         3.22        58.13        91.66        77.00 
TCGA-23-2641 TCGA-23-2647 TCGA-24-1434 TCGA-24-1463 TCGA-24-1470 TCGA-24-1564 
        2.76         4.44        18.67        72.92         3.45        25.87 
TCGA-24-1604 TCGA-24-1920 TCGA-24-1927 TCGA-24-2024 TCGA-24-2026 TCGA-24-2254 
       88.37         9.80        16.44        58.16        34.82        57.07 
TCGA-24-2295 TCGA-25-1316 TCGA-25-1322 TCGA-25-1325 TCGA-25-1625 TCGA-25-1628 
       33.11        42.05         2.99        32.09        27.62        20.61 
TCGA-25-1632 TCGA-25-1633 TCGA-25-2391 TCGA-25-2399 TCGA-29-1694 TCGA-29-1696 
       59.15        62.17        49.05        19.99        39.02        33.93 
TCGA-29-1702 TCGA-29-1770 TCGA-29-1775 TCGA-29-1777 TCGA-29-1783 TCGA-29-1785 
       23.93        24.36        12.36        12.30         7.23        36.30 
TCGA-29-2414 TCGA-29-2436 TCGA-30-1718 TCGA-30-1855 TCGA-30-1860 TCGA-30-1861 
       86.17         9.76        51.91         2.47        44.91        34.78 
TCGA-30-1891 TCGA-31-1946 TCGA-36-2534 TCGA-36-2544 TCGA-36-2545 TCGA-36-2551 
       30.05        30.18        29.82        20.98        18.31        16.18 
TCGA-42-2582 TCGA-42-2588 TCGA-42-2590 TCGA-59-2349 TCGA-59-2354 TCGA-61-1721 
       47.57        28.93        10.42        80.12        34.39        11.11 
TCGA-61-1727 TCGA-61-1733 TCGA-61-1738 TCGA-61-1914 TCGA-61-1918 TCGA-61-2017 
       18.54        31.79        35.80        56.61        15.75        45.96 
TCGA-61-2087 TCGA-61-2102 TCGA-61-2612 TCGA-61-2614 TCGA-10-0926 TCGA-13-0911 
        4.80         6.48         6.35         8.61        25.91        44.55 

subtype1 subtype2 subtype3 
    0.36     0.30     1.08 
subtype1 subtype2 subtype3 
  153.37   180.20    91.66 
subtype1 subtype2 subtype3 
  31.630   35.770   28.735 
[1] "0.4 - 153.4 (31.6)" "0.3 - 180.2 (35.8)" "1.1 - 91.7 (28.7)" 
D7V2, continuous
          vv
clus       OMENTUM OVARY PERITONEUM OVARY
  subtype1       1   148                1
  subtype2       2   189                1
  subtype3       0    78                0
D7V3, multiclass
                  clus
vv                 subtype1 subtype2 subtype3
  OMENTUM                 1        2        0
  OVARY                 148      189       78
  PERITONEUM OVARY        1        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"
D7V4, binary
          cls
clus         0   1
  subtype1 141   2
  subtype2 186   1
  subtype3  74   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  141    2
  subtype2  186    1
  subtype3   74    1
     clus
vv    subtype1 subtype2 subtype3
  NO       141      186       74
  YES        2        1        1
[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"
D7V5, continuous
          vv
clus       R0 R1 R2 RX
  subtype1  2 12  1  1
  subtype2  9  8  3  1
  subtype3  3  9  1  1
D7V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0        2        9        3
  R1       12        8        9
  R2        1        3        1
  RX        1        1        1
[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"
D7V7, binary
          cls
clus        0  1
  subtype1  2 79
  subtype2  5 98
  subtype3  1 38
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   79
  subtype2    5   98
  subtype3    1   38
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        5        1
  NOT HISPANIC OR LATINO       79       98       38
[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(8) Variable = RPPA_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 56 89
  subtype2 15 42
  subtype3 30 31
  subtype4 68 85
subtype1 subtype2 subtype3 subtype4 
     145       57       61      153 
subtype1 subtype2 subtype3 subtype4 
      89       42       31       85 
$subtype1
TCGA-59-A5PD TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1342 TCGA-04-1349 
       20.52         1.81        49.15        46.62        18.51        21.57 
TCGA-04-1361 TCGA-04-1638 TCGA-04-1649 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       32.52        55.43        64.64        89.33        74.93        41.62 
TCGA-09-2056 TCGA-13-1405 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
       12.46        28.54        55.23        57.27        81.01        17.46 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1488 TCGA-13-1494 TCGA-13-1501 
       32.35        54.64        87.06        70.82        93.90        43.20 
TCGA-13-1505 TCGA-13-1507 TCGA-13-2065 TCGA-13-A5FU TCGA-20-1682 TCGA-20-1686 
       65.69        65.52        65.52         8.42        27.52         2.93 
TCGA-23-1122 TCGA-23-2078 TCGA-24-0980 TCGA-24-0982 TCGA-24-1423 TCGA-24-1427 
       39.09        87.48         7.66        22.32         6.25         4.83 
TCGA-24-1434 TCGA-24-1466 TCGA-24-1545 TCGA-24-1546 TCGA-24-1553 TCGA-24-1563 
       18.67        45.14        57.40        64.27        58.09        47.70 
TCGA-24-1565 TCGA-24-1614 TCGA-24-1844 TCGA-24-1849 TCGA-24-1850 TCGA-24-1923 
       10.26        48.33         3.72         5.79         5.52        22.68 
TCGA-24-1924 TCGA-24-2027 TCGA-24-2029 TCGA-24-2038 TCGA-24-2262 TCGA-24-2271 
       30.21       109.71        14.43        44.52         0.36        31.63 
TCGA-24-2288 TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1319 
        0.82        16.64        55.86        53.26        26.96        65.00 
TCGA-25-1322 TCGA-25-1323 TCGA-25-1325 TCGA-25-1328 TCGA-25-1623 TCGA-25-1625 
        2.99        12.99        32.09        66.05        18.58        27.62 
TCGA-25-1626 TCGA-25-1628 TCGA-25-1630 TCGA-25-1633 TCGA-25-2042 TCGA-25-2398 
       17.03        20.61        38.20        62.17        13.02        45.01 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 TCGA-29-1694 
        2.96        29.03        31.00        78.90        47.61        39.02 
TCGA-29-1695 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1710 TCGA-29-1768 
       40.41        68.32        36.36        16.93        31.27        31.30 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1776 TCGA-29-1783 TCGA-29-2414 
       22.98        24.36        22.55        11.84         7.23        86.17 
TCGA-29-2425 TCGA-29-2428 TCGA-29-2431 TCGA-29-2432 TCGA-29-2436 TCGA-30-1856 
       65.00        45.11        42.25        21.47         9.76        15.68 
TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 
       24.26        30.05        48.79        45.57        30.18        18.77 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1576 TCGA-36-1580 TCGA-36-1581 TCGA-36-2534 
       28.77        29.10        30.08        24.23        24.69        29.82 
TCGA-36-2538 TCGA-36-2540 TCGA-36-2543 TCGA-36-2547 TCGA-36-2549 TCGA-36-2551 
       25.08        23.80         2.24        20.52         6.05        16.18 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 TCGA-59-2348 TCGA-59-2354 TCGA-61-1721 
       23.74        28.93        10.42       180.20        34.39        11.11 
TCGA-61-1724 TCGA-61-1740 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1906 
       20.94         2.43         1.45         8.42         5.79        34.13 
TCGA-61-1914 TCGA-61-1918 TCGA-61-1919 TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 
       56.61        15.75        38.17        14.50         4.01        30.64 
TCGA-61-2012 TCGA-61-2017 TCGA-61-2095 TCGA-61-2101 TCGA-61-2111 TCGA-61-2113 
       30.64        45.96        61.64        55.50       125.75        22.22 
TCGA-61-2610 TCGA-61-2613 TCGA-OY-A56P TCGA-13-0886 TCGA-13-0894 TCGA-13-0906 
       51.91        31.07        39.68       153.37        49.61       118.98 
TCGA-13-0913 
      109.32 

$subtype2
TCGA-3P-A9WA TCGA-04-1341 TCGA-04-1343 TCGA-04-1356 TCGA-04-1369 TCGA-04-1370 
       13.81         1.08        11.87        49.28        21.11        59.97 
TCGA-04-1654 TCGA-09-2055 TCGA-13-1483 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 
       47.70        26.93        29.42        90.38         4.24        66.15 
TCGA-13-1500 TCGA-13-1509 TCGA-23-1111 TCGA-23-1124 TCGA-23-2647 TCGA-24-1422 
       13.97        80.15         3.22        58.13         4.44         0.76 
TCGA-24-1435 TCGA-24-1463 TCGA-24-1469 TCGA-24-1470 TCGA-24-1562 TCGA-24-1564 
       43.53        72.92         9.11         3.45        45.50        25.87 
TCGA-24-1920 TCGA-24-1927 TCGA-24-2024 TCGA-24-2026 TCGA-24-2030 TCGA-24-2261 
        9.80        16.44        58.16        34.82        55.92         0.79 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2295 TCGA-25-1320 TCGA-25-2399 TCGA-25-2409 
       67.36        36.23        33.11        37.97        19.99        26.99 
TCGA-29-1705 TCGA-29-1711 TCGA-29-1766 TCGA-29-1777 TCGA-29-1785 TCGA-29-A5NZ 
       18.25        34.62        39.42        12.30        36.30        35.77 
TCGA-30-1718 TCGA-30-1855 TCGA-30-1860 TCGA-30-1861 TCGA-36-2544 TCGA-36-2545 
       51.91         2.47        44.91        34.78        20.98        18.31 
TCGA-42-2582 TCGA-42-2589 TCGA-61-1738 TCGA-61-1743 TCGA-61-2612 TCGA-61-2614 
       47.57        42.02        35.80        43.69         6.35         8.61 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0911 
       71.74        66.15        44.55 

$subtype3
TCGA-04-1348 TCGA-04-1516 TCGA-04-1519 TCGA-04-1525 TCGA-04-1651 TCGA-09-2044 
       48.76        41.59         0.79        38.37        36.23         6.12 
TCGA-13-1404 TCGA-13-1482 TCGA-13-1487 TCGA-13-1489 TCGA-13-1492 TCGA-13-1499 
       81.17        61.71        22.39        83.93       125.56       115.07 
TCGA-13-1504 TCGA-13-1506 TCGA-13-1512 TCGA-13-2060 TCGA-13-2061 TCGA-13-2066 
       34.82        34.16        14.53        77.88        76.90        70.13 
TCGA-20-1684 TCGA-20-1685 TCGA-23-1121 TCGA-23-2643 TCGA-24-0970 TCGA-24-1105 
       19.10        16.70         6.38         4.70        11.64        47.41 
TCGA-24-1417 TCGA-24-1436 TCGA-24-1467 TCGA-24-1474 TCGA-24-1552 TCGA-24-1556 
        7.82         8.55       105.99        22.22        41.39        70.62 
TCGA-24-1558 TCGA-24-1842 TCGA-24-1845 TCGA-24-1846 TCGA-24-1930 TCGA-24-2260 
       19.53         8.32         3.81         4.37        81.11        36.16 
TCGA-25-1635 TCGA-25-1878 TCGA-25-2393 TCGA-29-1693 TCGA-29-1703 TCGA-29-1764 
       52.04        85.05        38.04       101.79        59.67        62.93 
TCGA-29-2427 TCGA-36-1575 TCGA-36-1577 TCGA-36-2530 TCGA-36-2537 TCGA-36-2542 
       62.47         8.55        25.74        33.01        25.91        21.60 
TCGA-36-2548 TCGA-36-2552 TCGA-57-1586 TCGA-10-0933 TCGA-10-0936 TCGA-13-0725 
       14.17        11.47        22.32        14.66        36.92        12.39 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0802 TCGA-13-0884 TCGA-13-0903 TCGA-13-0910 
      107.28        63.09        51.02       107.18       127.79       116.65 
TCGA-13-0920 
       48.79 

$subtype4
TCGA-5X-AA5U TCGA-04-1362 TCGA-04-1514 TCGA-04-1517 TCGA-04-1542 TCGA-04-1644 
       11.87        44.32        56.55        19.99        84.20        48.89 
TCGA-04-1646 TCGA-04-1648 TCGA-09-1666 TCGA-09-1670 TCGA-09-1673 TCGA-09-1674 
       27.88        28.64        57.60        17.98         3.02         8.55 
TCGA-09-2043 TCGA-09-2045 TCGA-09-2049 TCGA-09-2051 TCGA-09-2054 TCGA-13-1484 
        6.18        35.15       112.41        63.09        20.94       124.44 
TCGA-13-1491 TCGA-13-1511 TCGA-13-2059 TCGA-13-A5FT TCGA-20-1683 TCGA-20-1687 
       52.44        54.25        78.48        70.45        25.38         2.66 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1123 TCGA-23-1809 TCGA-23-2077 TCGA-23-2079 
       51.35        54.51        33.47         0.53       115.89        91.66 
TCGA-23-2081 TCGA-23-2641 TCGA-23-2645 TCGA-23-2649 TCGA-24-0966 TCGA-24-0979 
       77.00         2.76         4.50         3.81         7.63        41.56 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1416 TCGA-24-1419 TCGA-24-1424 TCGA-24-1428 
       54.12        63.55         6.38         7.86         6.02        17.39 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1464 TCGA-24-1471 TCGA-24-1544 TCGA-24-1548 
       28.37        18.64        12.46         1.18        26.96        16.21 
TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1555 TCGA-24-1557 TCGA-24-1560 
       56.58        41.06        51.91        88.50        39.88        44.09 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-2020 TCGA-24-2023 
       17.23        90.15        88.37        38.24       152.02        44.84 
TCGA-24-2033 TCGA-24-2036 TCGA-24-2254 TCGA-24-2267 TCGA-24-2281 TCGA-25-1312 
       18.48        64.01        57.07        47.54        44.61         1.02 
TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1318 TCGA-25-1321 TCGA-25-1326 
       33.01        52.04        42.05        34.98        33.96        41.06 
TCGA-25-1329 TCGA-25-1627 TCGA-25-1631 TCGA-25-1632 TCGA-25-2391 TCGA-25-2396 
       15.02        12.95         0.30        59.15        49.05         3.02 
TCGA-25-2397 TCGA-25-2400 TCGA-29-1691 TCGA-29-1696 TCGA-29-1697 TCGA-29-1702 
       12.00        42.02        48.33        33.93        31.20        23.93 
TCGA-29-1707 TCGA-29-1761 TCGA-29-1762 TCGA-29-1774 TCGA-29-1775 TCGA-29-1778 
       41.98        17.36        86.60        17.33        12.36        14.93 
TCGA-29-1781 TCGA-29-2429 TCGA-29-2434 TCGA-29-2435 TCGA-30-1859 TCGA-30-1869 
        8.38        13.84        11.47         1.12        48.10        51.39 
TCGA-31-1951 TCGA-31-1955 TCGA-36-1570 TCGA-36-1571 TCGA-36-1578 TCGA-36-2529 
       22.49        42.51        21.53        22.85        27.85        35.05 
TCGA-36-2532 TCGA-42-2591 TCGA-42-2593 TCGA-59-2349 TCGA-59-2351 TCGA-59-2352 
       29.49        40.77         1.48        80.12       116.12         9.40 
TCGA-59-2363 TCGA-59-2372 TCGA-61-1722 TCGA-61-1727 TCGA-61-1730 TCGA-61-1733 
        5.42        44.81         8.09        18.54         4.34        31.79 
TCGA-61-1734 TCGA-61-1736 TCGA-61-1741 TCGA-61-1903 TCGA-61-1907 TCGA-61-1910 
       28.47        48.79        33.67        13.02        31.30        37.05 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1915 TCGA-61-1995 TCGA-61-2009 TCGA-61-2018 
       42.51        48.92        67.76         2.01        39.85        45.40 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2096 TCGA-61-2098 
        4.80         4.77        51.72        71.74        58.39        65.52 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
        6.48        76.87        20.68        18.94         0.79         9.99 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0931 TCGA-13-0720 TCGA-13-0797 TCGA-13-0799 
       54.31        25.91        32.88        44.55        69.73        83.34 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0804 TCGA-13-0887 TCGA-13-0888 TCGA-13-0891 
       87.48        45.99        35.28        66.67        92.42       102.84 
TCGA-13-0901 TCGA-13-0916 TCGA-13-0921 
       19.36        58.68        48.76 

subtype1 subtype2 subtype3 subtype4 
    0.36     0.76     0.79     0.30 
subtype1 subtype2 subtype3 subtype4 
  180.20    90.38   127.79   152.02 
subtype1 subtype2 subtype3 subtype4 
   30.21    34.78    36.92    35.05 
[1] "0.4 - 180.2 (30.2)" "0.8 - 90.4 (34.8)"  "0.8 - 127.8 (36.9)"
[4] "0.3 - 152.0 (35.0)"
D8V2, continuous
          vv
clus       OMENTUM OVARY PERITONEUM OVARY
  subtype1       1   145                0
  subtype2       2    54                1
  subtype3       0    61                0
  subtype4       0   155                1
D8V3, multiclass
                  clus
vv                 subtype1 subtype2 subtype3 subtype4
  OMENTUM                 1        2        0        0
  OVARY                 145       54       61      155
  PERITONEUM OVARY        0        1        0        1
[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"
D8V4, binary
          cls
clus         0   1
  subtype1 140   1
  subtype2  56   0
  subtype3  59   1
  subtype4 146   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  140    1
  subtype2   56    0
  subtype3   59    1
  subtype4  146    2
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       140       56       59      146
  YES        1        0        1        2
[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"
D8V5, continuous
          vv
clus       R0 R1 R2 RX
  subtype1  4 13  3  0
  subtype2  3  6  0  1
  subtype3  2  5  0  0
  subtype4  5  5  2  2
D8V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0        4        3        2        5
  R1       13        6        5        5
  R2        3        0        0        2
  RX        0        1        0        2
[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"
D8V7, binary
          cls
clus        0  1
  subtype1  1 75
  subtype2  2 25
  subtype3  3 32
  subtype4  2 83
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   75
  subtype2    2   25
  subtype3    3   32
  subtype4    2   83
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        2        3        2
  NOT HISPANIC OR LATINO       75       25       32       83
[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(9) Variable = MRNASEQ_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 34 44
  subtype2 41 69
  subtype3 44 70
subtype1 subtype2 subtype3 
      78      110      114 
subtype1 subtype2 subtype3 
      44       69       70 
$subtype1
TCGA-3P-A9WA TCGA-04-1348 TCGA-04-1362 TCGA-04-1365 TCGA-09-1666 TCGA-09-1670 
       13.81        48.76        44.32        76.57        57.60        17.98 
TCGA-09-2045 TCGA-09-2051 TCGA-09-2056 TCGA-13-1498 TCGA-20-1685 TCGA-23-1026 
       35.15        63.09        12.46        66.15        16.70        26.83 
TCGA-23-2081 TCGA-23-2084 TCGA-24-1103 TCGA-24-1413 TCGA-24-1416 TCGA-24-1423 
       77.00        49.84        54.12         6.31         6.38         6.25 
TCGA-24-1428 TCGA-24-1467 TCGA-24-1551 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       17.39       105.99        51.91        88.50        70.62        39.88 
TCGA-24-1847 TCGA-24-1924 TCGA-24-2019 TCGA-24-2023 TCGA-24-2026 TCGA-24-2267 
       11.28        30.21         4.87        44.84        34.82        47.54 
TCGA-24-2281 TCGA-25-1313 TCGA-25-1322 TCGA-25-1625 TCGA-25-1630 TCGA-25-2391 
       44.61        26.96         2.99        27.62        38.20        49.05 
TCGA-25-2392 TCGA-25-2396 TCGA-25-2397 TCGA-25-2404 TCGA-25-2409 TCGA-29-1688 
        1.02         3.02        12.00        29.03        26.99        78.90 
TCGA-29-1690 TCGA-29-1694 TCGA-29-1696 TCGA-29-1776 TCGA-29-1778 TCGA-29-1784 
       47.61        39.02        33.93        11.84        14.93         5.36 
TCGA-30-1860 TCGA-31-1944 TCGA-36-1570 TCGA-36-1574 TCGA-36-1581 TCGA-57-1584 
       44.91        45.57        21.53        22.55        24.69        21.14 
TCGA-57-1993 TCGA-59-2351 TCGA-59-2354 TCGA-59-2355 TCGA-61-1724 TCGA-61-1725 
       25.08       116.12        34.39         2.14        20.94        31.43 
TCGA-61-1736 TCGA-61-1907 TCGA-61-1910 TCGA-61-1914 TCGA-61-1918 TCGA-61-2016 
       48.79        31.30        37.05        56.61        15.75         1.18 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2097 TCGA-61-2104 TCGA-61-2109 TCGA-VG-A8LO 
       51.72        71.74        60.62        76.87        20.68         0.79 
TCGA-09-0366 TCGA-09-0367 TCGA-10-0936 TCGA-13-0801 TCGA-13-0893 TCGA-13-0924 
       57.76        17.98        36.92        45.99        43.36        85.94 

$subtype2
TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1364 TCGA-04-1514 TCGA-04-1519 TCGA-09-1669 
       20.52        11.87        33.67        56.55         0.79        30.51 
TCGA-09-1673 TCGA-09-1674 TCGA-09-2044 TCGA-09-2048 TCGA-09-2054 TCGA-13-1506 
        3.02         8.55         6.12         4.54        20.94        34.16 
TCGA-13-A5FT TCGA-20-1683 TCGA-20-1684 TCGA-23-1029 TCGA-23-1111 TCGA-23-1114 
       70.45        25.38        19.10         8.81         3.22        68.68 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1809 TCGA-23-2077 TCGA-24-1419 TCGA-24-1424 
       39.09        33.47         0.53       115.89         7.86         6.02 
TCGA-24-1430 TCGA-24-1469 TCGA-24-1474 TCGA-24-1544 TCGA-24-1548 TCGA-24-1549 
       28.37         9.11        22.22        26.96        16.21        56.58 
TCGA-24-1553 TCGA-24-1558 TCGA-24-1560 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 
       58.09        19.53        44.09        17.23        90.15        88.37 
TCGA-24-1616 TCGA-24-1843 TCGA-24-1844 TCGA-24-2020 TCGA-24-2027 TCGA-24-2036 
       38.24         3.48         3.72       152.02       109.71        64.01 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2297 TCGA-25-1312 TCGA-25-1315 TCGA-25-1316 
       44.52        57.07        55.86         1.02        52.04        42.05 
TCGA-25-1317 TCGA-25-1319 TCGA-25-1321 TCGA-25-1323 TCGA-25-1324 TCGA-25-1627 
        2.01        65.00        33.96        12.99        34.03        12.95 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-2393 
        0.30        59.15        35.87        14.96        24.99        38.04 
TCGA-25-2400 TCGA-29-1691 TCGA-29-1697 TCGA-29-1702 TCGA-29-1703 TCGA-29-1761 
       42.02        48.33        31.20        23.93        59.67        17.36 
TCGA-29-1762 TCGA-29-1763 TCGA-29-1783 TCGA-29-2414 TCGA-29-2425 TCGA-29-A5NZ 
       86.60        66.81         7.23        86.17        65.00        35.77 
TCGA-36-1571 TCGA-36-1575 TCGA-36-1577 TCGA-57-1583 TCGA-57-1994 TCGA-59-2350 
       22.85         8.55        25.74        11.38        25.02        22.32 
TCGA-59-2352 TCGA-59-2363 TCGA-61-1728 TCGA-61-1733 TCGA-61-1738 TCGA-61-1741 
        9.40         5.42        27.88        31.79        35.80        33.67 
TCGA-61-1743 TCGA-61-1900 TCGA-61-1917 TCGA-61-1995 TCGA-61-1998 TCGA-61-2008 
       43.69         5.79        43.43         2.01         5.52        30.64 
TCGA-61-2012 TCGA-61-2088 TCGA-61-2095 TCGA-61-2098 TCGA-61-2102 TCGA-61-2110 
       30.64         4.77        61.64        65.52         6.48        44.52 
TCGA-61-2111 TCGA-OY-A56P TCGA-OY-A56Q TCGA-WR-A838 TCGA-09-0364 TCGA-09-0369 
      125.75        39.68        18.94         9.99        29.16        35.57 
TCGA-10-0928 TCGA-13-0730 TCGA-13-0799 TCGA-13-0800 TCGA-13-0899 TCGA-13-0913 
       18.51        17.82        83.34        87.48        66.15       109.32 
TCGA-13-0916 TCGA-13-0920 
       58.68        48.79 

$subtype3
TCGA-09-1659 TCGA-09-1662 TCGA-09-1667 TCGA-09-1668 TCGA-13-1403 TCGA-13-1405 
        9.99        89.33        61.87        55.36        77.10        28.54 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 TCGA-13-1497 TCGA-13-1505 TCGA-13-1507 
       81.01        17.46        87.06       127.27        65.69        65.52 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2060 TCGA-20-1682 TCGA-20-1687 TCGA-23-1023 
       54.25        14.53        77.88        27.52         2.66        40.54 
TCGA-23-1027 TCGA-23-1109 TCGA-23-1120 TCGA-23-2078 TCGA-24-0975 TCGA-24-1417 
       32.09        51.35         4.27        87.48        21.80         7.82 
TCGA-24-1418 TCGA-24-1425 TCGA-24-1427 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
        7.99         5.95         4.83        18.67        43.53         8.55 
TCGA-24-1463 TCGA-24-1545 TCGA-24-1546 TCGA-24-1550 TCGA-24-1552 TCGA-24-1562 
       72.92        57.40        64.27        41.06        41.39        45.50 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1842 TCGA-24-1846 TCGA-24-1849 TCGA-24-1850 
       47.70        25.87         8.32         4.37         5.79         5.52 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2024 TCGA-24-2033 TCGA-24-2035 TCGA-24-2261 
       11.05        81.11        58.16        18.48        28.18         0.79 
TCGA-24-2262 TCGA-24-2271 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 
        0.36        31.63         0.82        67.36        36.23        16.64 
TCGA-24-2298 TCGA-25-1314 TCGA-25-1318 TCGA-25-1320 TCGA-25-1326 TCGA-25-1328 
       53.26        33.01        34.98        37.97        41.06        66.05 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1628 TCGA-25-1633 TCGA-25-1635 
       15.02        18.58        17.03        20.61        62.17        52.04 
TCGA-25-2042 TCGA-25-2398 TCGA-25-2399 TCGA-25-2401 TCGA-29-1693 TCGA-29-1695 
       13.02        45.01        19.99         2.96       101.79        40.41 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 
       68.32        36.36        16.93        18.25        31.27        34.62 
TCGA-29-1770 TCGA-29-1781 TCGA-29-1785 TCGA-29-2427 TCGA-29-2428 TCGA-30-1718 
       24.36         8.38        36.30        62.47        45.11        51.91 
TCGA-30-1855 TCGA-30-1857 TCGA-30-1861 TCGA-30-1862 TCGA-30-1891 TCGA-31-1946 
        2.47         0.26        34.78         6.12        30.05        30.18 
TCGA-31-1951 TCGA-31-1953 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 
       22.49         6.71        44.12         2.20        28.77        29.10 
TCGA-36-1576 TCGA-36-1578 TCGA-36-1580 TCGA-57-1582 TCGA-57-1585 TCGA-59-2348 
       30.08        27.85        24.23        24.03         1.74       180.20 
TCGA-61-1721 TCGA-61-1737 TCGA-61-1740 TCGA-61-1919 TCGA-61-2000 TCGA-61-2002 
       11.11        44.84         2.43        38.17        14.50        17.98 
TCGA-61-2003 TCGA-61-2009 TCGA-61-2101 TCGA-61-2113 TCGA-13-0890 TCGA-13-0897 
        4.01        39.85        55.50        22.22       145.45        71.74 

subtype1 subtype2 subtype3 
    0.79     0.30     0.26 
subtype1 subtype2 subtype3 
  116.12   152.02   180.20 
subtype1 subtype2 subtype3 
  34.605   30.640   30.130 
[1] "0.8 - 116.1 (34.6)" "0.3 - 152.0 (30.6)" "0.3 - 180.2 (30.1)"
D9V2, continuous
          vv
clus       OMENTUM OVARY
  subtype1       0    79
  subtype2       1   109
  subtype3       2   112
D9V3, multiclass
         clus
vv        subtype1 subtype2 subtype3
  OMENTUM        0        1        2
  OVARY         79      109      112
[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, binary
          cls
clus         0   1
  subtype1  75   0
  subtype2 104   2
  subtype3 109   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   75    0
  subtype2  104    2
  subtype3  109    0
     clus
vv    subtype1 subtype2 subtype3
  NO        75      104      109
  YES        0        2        0
[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"
D9V5, continuous
          vv
clus       R0 R1 R2 RX
  subtype1  1  0  1  1
  subtype2  2  2  1  2
  subtype3  0  3  0  0
D9V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0        1        2        0
  R1        0        2        3
  R2        1        1        0
  RX        1        2        0
[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"
D9V7, binary
          cls
clus        0  1
  subtype1  3 41
  subtype2  0 60
  subtype3  0 62
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   41
  subtype2    0   60
  subtype3    0   62
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        0        0
  NOT HISPANIC OR LATINO       41       60       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"

Clustering(10) Variable = MRNASEQ_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 63 83
  subtype2 20 40
  subtype3 36 60
subtype1 subtype2 subtype3 
     146       60       96 
subtype1 subtype2 subtype3 
      83       40       60 
$subtype1
TCGA-3P-A9WA TCGA-04-1348 TCGA-04-1362 TCGA-04-1365 TCGA-04-1519 TCGA-09-1659 
       13.81        48.76        44.32        76.57         0.79         9.99 
TCGA-09-1662 TCGA-09-1666 TCGA-09-1670 TCGA-09-2044 TCGA-09-2045 TCGA-09-2051 
       89.33        57.60        17.98         6.12        35.15        63.09 
TCGA-09-2056 TCGA-13-1403 TCGA-13-1497 TCGA-13-1498 TCGA-13-1506 TCGA-13-2060 
       12.46        77.10       127.27        66.15        34.16        77.88 
TCGA-13-A5FT TCGA-20-1682 TCGA-20-1683 TCGA-20-1685 TCGA-23-1026 TCGA-23-1029 
       70.45        27.52        25.38        16.70        26.83         8.81 
TCGA-23-1111 TCGA-23-1120 TCGA-23-1122 TCGA-23-1809 TCGA-23-2077 TCGA-23-2084 
        3.22         4.27        39.09         0.53       115.89        49.84 
TCGA-24-1103 TCGA-24-1413 TCGA-24-1416 TCGA-24-1419 TCGA-24-1423 TCGA-24-1428 
       54.12         6.31         6.38         7.86         6.25        17.39 
TCGA-24-1430 TCGA-24-1467 TCGA-24-1474 TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 
       28.37       105.99        22.22        56.58        51.91        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1603 TCGA-24-1604 
       58.09        88.50        70.62        39.88        90.15        88.37 
TCGA-24-1616 TCGA-24-1843 TCGA-24-1844 TCGA-24-1847 TCGA-24-1850 TCGA-24-1924 
       38.24         3.48         3.72        11.28         5.52        30.21 
TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2036 TCGA-24-2038 
        4.87        44.84        58.16        34.82        64.01        44.52 
TCGA-24-2254 TCGA-24-2262 TCGA-24-2267 TCGA-24-2281 TCGA-24-2290 TCGA-24-2297 
       57.07         0.36        47.54        44.61        36.23        55.86 
TCGA-25-1313 TCGA-25-1318 TCGA-25-1322 TCGA-25-1328 TCGA-25-1625 TCGA-25-1627 
       26.96        34.98         2.99        66.05        27.62        12.95 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1635 TCGA-25-2391 TCGA-25-2392 TCGA-25-2396 
       38.20         0.30        52.04        49.05         1.02         3.02 
TCGA-25-2397 TCGA-25-2399 TCGA-25-2400 TCGA-25-2404 TCGA-29-1690 TCGA-29-1691 
       12.00        19.99        42.02        29.03        47.61        48.33 
TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 TCGA-29-1703 TCGA-29-1761 
       39.02        33.93        31.20        36.36        59.67        17.36 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 
       14.93         8.38         7.23         5.36        36.30        86.17 
TCGA-29-2425 TCGA-29-2428 TCGA-30-1860 TCGA-31-1944 TCGA-36-1568 TCGA-36-1570 
       65.00        45.11        44.91        45.57        28.77        21.53 
TCGA-36-1578 TCGA-36-1581 TCGA-57-1583 TCGA-57-1584 TCGA-57-1993 TCGA-59-2348 
       27.85        24.69        11.38        21.14        25.08       180.20 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-61-1721 TCGA-61-1724 
       22.32       116.12         9.40         2.14        11.11        20.94 
TCGA-61-1736 TCGA-61-1738 TCGA-61-1740 TCGA-61-1907 TCGA-61-1910 TCGA-61-1914 
       48.79        35.80         2.43        31.30        37.05        56.61 
TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 TCGA-61-2003 TCGA-61-2008 
       43.43        15.75         2.01         5.52         4.01        30.64 
TCGA-61-2012 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-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-VG-A8LO TCGA-09-0366 
       76.87        20.68        44.52       125.75         0.79        57.76 
TCGA-09-0367 TCGA-10-0936 TCGA-13-0799 TCGA-13-0801 TCGA-13-0893 TCGA-13-0899 
       17.98        36.92        83.34        45.99        43.36        66.15 
TCGA-13-0916 TCGA-13-0924 
       58.68        85.94 

$subtype2
TCGA-59-A5PD TCGA-5X-AA5U TCGA-04-1364 TCGA-04-1514 TCGA-09-1669 TCGA-09-1673 
       20.52        11.87        33.67        56.55        30.51         3.02 
TCGA-09-1674 TCGA-09-2048 TCGA-09-2054 TCGA-20-1684 TCGA-23-1114 TCGA-23-1123 
        8.55         4.54        20.94        19.10        68.68        33.47 
TCGA-24-1424 TCGA-24-1469 TCGA-24-1544 TCGA-24-1548 TCGA-24-1550 TCGA-24-1558 
        6.02         9.11        26.96        16.21        41.06        19.53 
TCGA-24-1560 TCGA-24-1567 TCGA-24-2020 TCGA-24-2027 TCGA-25-1312 TCGA-25-1315 
       44.09        17.23       152.02       109.71         1.02        52.04 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1319 TCGA-25-1321 TCGA-25-1323 TCGA-25-1324 
       42.05         2.01        65.00        33.96        12.99        34.03 
TCGA-25-1632 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-2393 TCGA-29-1702 
       59.15        35.87        14.96        24.99        38.04        23.93 
TCGA-29-1762 TCGA-29-1763 TCGA-36-1571 TCGA-36-1575 TCGA-36-1577 TCGA-57-1994 
       86.60        66.81        22.85         8.55        25.74        25.02 
TCGA-59-2363 TCGA-61-1728 TCGA-61-1741 TCGA-61-1743 TCGA-61-1900 TCGA-61-2088 
        5.42        27.88        33.67        43.69         5.79         4.77 
TCGA-61-2098 TCGA-61-2102 TCGA-OY-A56P TCGA-OY-A56Q TCGA-WR-A838 TCGA-09-0364 
       65.52         6.48        39.68        18.94         9.99        29.16 
TCGA-09-0369 TCGA-10-0928 TCGA-13-0730 TCGA-13-0800 TCGA-13-0913 TCGA-13-0920 
       35.57        18.51        17.82        87.48       109.32        48.79 

$subtype3
TCGA-09-1667 TCGA-09-1668 TCGA-13-1405 TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 
       61.87        55.36        28.54        81.01        17.46        87.06 
TCGA-13-1505 TCGA-13-1507 TCGA-13-1511 TCGA-13-1512 TCGA-20-1687 TCGA-23-1023 
       65.69        65.52        54.25        14.53         2.66        40.54 
TCGA-23-1027 TCGA-23-1109 TCGA-23-2078 TCGA-23-2081 TCGA-24-0975 TCGA-24-1417 
       32.09        51.35        87.48        77.00        21.80         7.82 
TCGA-24-1418 TCGA-24-1425 TCGA-24-1427 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
        7.99         5.95         4.83        18.67        43.53         8.55 
TCGA-24-1463 TCGA-24-1545 TCGA-24-1546 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
       72.92        57.40        64.27        45.50        47.70        25.87 
TCGA-24-1842 TCGA-24-1846 TCGA-24-1849 TCGA-24-1928 TCGA-24-1930 TCGA-24-2033 
        8.32         4.37         5.79        11.05        81.11        18.48 
TCGA-24-2035 TCGA-24-2261 TCGA-24-2271 TCGA-24-2288 TCGA-24-2289 TCGA-24-2293 
       28.18         0.79        31.63         0.82        67.36        16.64 
TCGA-24-2298 TCGA-25-1314 TCGA-25-1320 TCGA-25-1326 TCGA-25-1329 TCGA-25-1623 
       53.26        33.01        37.97        41.06        15.02        18.58 
TCGA-25-1626 TCGA-25-1628 TCGA-25-1633 TCGA-25-2042 TCGA-25-2398 TCGA-25-2401 
       17.03        20.61        62.17        13.02        45.01         2.96 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1693 TCGA-29-1695 TCGA-29-1698 TCGA-29-1701 
       26.99        78.90       101.79        40.41        68.32        16.93 
TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 TCGA-29-1770 TCGA-29-1776 TCGA-29-2427 
       18.25        31.27        34.62        24.36        11.84        62.47 
TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1855 TCGA-30-1857 TCGA-30-1861 TCGA-30-1862 
       35.77        51.91         2.47         0.26        34.78         6.12 
TCGA-30-1891 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 TCGA-31-1956 TCGA-31-1959 
       30.05        30.18        22.49         6.71        44.12         2.20 
TCGA-36-1569 TCGA-36-1574 TCGA-36-1576 TCGA-36-1580 TCGA-57-1582 TCGA-57-1585 
       29.10        22.55        30.08        24.23        24.03         1.74 
TCGA-59-2354 TCGA-61-1725 TCGA-61-1733 TCGA-61-1737 TCGA-61-1919 TCGA-61-2000 
       34.39        31.43        31.79        44.84        38.17        14.50 
TCGA-61-2002 TCGA-61-2009 TCGA-61-2101 TCGA-61-2113 TCGA-13-0890 TCGA-13-0897 
       17.98        39.85        55.50        22.22       145.45        71.74 

subtype1 subtype2 subtype3 
    0.30     1.02     0.26 
subtype1 subtype2 subtype3 
  180.20   152.02   145.45 
subtype1 subtype2 subtype3 
  35.475   26.350   30.130 
[1] "0.3 - 180.2 (35.5)" "1.0 - 152.0 (26.4)" "0.3 - 145.4 (30.1)"
D10V2, continuous
          vv
clus       OMENTUM OVARY
  subtype1       1   146
  subtype2       0    60
  subtype3       2    94
D10V3, multiclass
         clus
vv        subtype1 subtype2 subtype3
  OMENTUM        1        0        2
  OVARY        146       60       94
[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"
D10V4, binary
          cls
clus         0   1
  subtype1 138   1
  subtype2  58   1
  subtype3  92   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  138    1
  subtype2   58    1
  subtype3   92    0
     clus
vv    subtype1 subtype2 subtype3
  NO       138       58       92
  YES        1        1        0
[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"
D10V5, continuous
          vv
clus       R0 R1 R2 RX
  subtype1  1  3  1  2
  subtype2  2  0  1  1
  subtype3  0  2  0  0
D10V6, multiclass
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 
       7        4        2 
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [7] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1"
    clus
vv   subtype1 subtype2
  R0        1        2
  R1        3        0
  R2        1        1
  RX        2        1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
          cls
clus        0  1
  subtype1  3 73
  subtype2  0 39
  subtype3  0 51
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   73
  subtype2    0   39
  subtype3    0   51
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        0        0
  NOT HISPANIC OR LATINO       73       39       51
[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_CNMF
D11V1, survival
          sevent
clus2       0  1
  subtype1 23 51
  subtype2 40 94
  subtype3 58 82
  subtype4 47 56
subtype1 subtype2 subtype3 subtype4 
      74      134      140      103 
subtype1 subtype2 subtype3 subtype4 
      51       94       82       56 
$subtype1
TCGA-04-1331 TCGA-04-1332 TCGA-04-1349 TCGA-09-1662 TCGA-09-2054 TCGA-13-1408 
       43.92        41.00        21.57        89.33        20.94        55.23 
TCGA-13-1411 TCGA-13-1477 TCGA-13-1481 TCGA-13-1485 TCGA-13-1499 TCGA-23-1026 
       17.46        54.64        87.06        20.68       115.07        26.83 
TCGA-23-1121 TCGA-24-0970 TCGA-24-1418 TCGA-24-1422 TCGA-24-1427 TCGA-24-1434 
        6.38        11.64         7.99         0.76         4.83        18.67 
TCGA-24-1550 TCGA-24-1563 TCGA-24-1842 TCGA-24-1843 TCGA-24-1849 TCGA-24-1928 
       41.06        47.70         8.32         3.48         5.79        11.05 
TCGA-24-2020 TCGA-24-2033 TCGA-24-2035 TCGA-24-2261 TCGA-24-2271 TCGA-24-2281 
      152.02        18.48        28.18         0.79        31.63        44.61 
TCGA-24-2293 TCGA-24-2298 TCGA-25-1316 TCGA-25-1326 TCGA-25-1328 TCGA-25-1626 
       16.64        53.26        42.05        41.06        66.05        17.03 
TCGA-25-1628 TCGA-25-1633 TCGA-25-1877 TCGA-25-2042 TCGA-25-2398 TCGA-25-2401 
       20.61        62.17        24.00        13.02        45.01         2.96 
TCGA-25-2408 TCGA-29-1698 TCGA-29-1702 TCGA-29-1705 TCGA-29-1710 TCGA-29-1766 
       31.00        68.32        23.93        18.25        31.27        39.42 
TCGA-29-1768 TCGA-29-2427 TCGA-30-1857 TCGA-30-1861 TCGA-30-1862 TCGA-30-1867 
       31.30        62.47         0.26        34.78         6.12         1.22 
TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1953 
       24.26        30.05        48.79        45.57        30.18         6.71 
TCGA-31-1956 TCGA-31-1959 TCGA-36-1574 TCGA-36-1576 TCGA-57-1585 TCGA-59-2354 
       44.12         2.20        22.55        30.08         1.74        34.39 
TCGA-61-1721 TCGA-61-2002 TCGA-61-2009 TCGA-61-2101 TCGA-13-0768 TCGA-13-0890 
       11.11        17.98        39.85        55.50        58.65       145.45 
TCGA-13-0894 TCGA-13-0900 
       49.61       134.04 

$subtype2
TCGA-04-1336 TCGA-04-1337 TCGA-04-1341 TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 
       49.15         2.01         1.08        18.51        65.52        63.09 
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       103.40       119.08 
TCGA-04-1536 TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 TCGA-09-1674 TCGA-13-1403 
       29.10        41.62        61.87        55.36         8.55        77.10 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1412 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 
       81.17        28.54        32.35        29.42       124.44        22.39 
TCGA-13-1488 TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1500 
       70.82        52.44        93.90        90.38         4.24        13.97 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 
       43.20        34.82        34.16        65.52        80.15        44.68 
TCGA-13-1512 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1683 TCGA-20-1684 
       14.53        23.05        25.94        26.20        25.38        19.10 
TCGA-20-1687 TCGA-23-1023 TCGA-23-1027 TCGA-23-1032 TCGA-23-1109 TCGA-23-1113 
        2.66        40.54        32.09         2.76        51.35        31.20 
TCGA-23-1114 TCGA-23-1118 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 
       68.68        86.01         4.27        39.09        33.47        58.13 
TCGA-24-0975 TCGA-24-1104 TCGA-24-1105 TCGA-24-1417 TCGA-24-1423 TCGA-24-1425 
       21.80        63.55        47.41         7.82         6.25         5.95 
TCGA-24-1428 TCGA-24-1431 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 
       17.39        18.64        43.53         8.55        72.92        45.14 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1549 
        9.11         3.45        26.96        57.40        64.27        56.58 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1558 TCGA-24-1564 
       51.91        41.39        58.09        88.50        19.53        25.87 
TCGA-24-1614 TCGA-25-1312 TCGA-25-1314 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 
       48.33         1.02        33.01        34.98        65.00        37.97 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1635 TCGA-25-2397 TCGA-29-1688 TCGA-29-1690 
       15.02        18.58        52.04        12.00        78.90        47.61 
TCGA-29-1701 TCGA-29-1770 TCGA-29-1776 TCGA-29-1777 TCGA-30-1718 TCGA-30-1855 
       16.93        24.36        11.84        12.30        51.91         2.47 
TCGA-30-1856 TCGA-30-1880 TCGA-36-1581 TCGA-57-1582 TCGA-57-1583 TCGA-61-1740 
       15.68        57.57        24.69        24.03        11.38         2.43 
TCGA-09-0366 TCGA-10-0926 TCGA-10-0927 TCGA-13-0714 TCGA-13-0724 TCGA-13-0751 
       57.76        25.91        81.86         6.21         2.73        55.17 
TCGA-13-0757 TCGA-13-0760 TCGA-13-0766 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 
       11.18        11.54        56.71        69.73        83.34        45.99 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0805 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 
       51.02        43.86        35.31        68.94       107.18       111.39 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0903 
      153.37        66.67        95.15       102.84        43.36       127.79 
TCGA-13-0904 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0916 TCGA-13-0919 
       50.37        60.59       116.65        44.55        58.68        84.53 
TCGA-13-0923 TCGA-13-0924 
       83.74        85.94 

$subtype3
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1514 TCGA-04-1517 TCGA-04-1519 
       32.52        44.32        33.67        56.55        19.99         0.79 
TCGA-04-1525 TCGA-04-1542 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 
       38.37        84.20        28.64        64.64        36.23        31.86 
TCGA-04-1655 TCGA-09-1661 TCGA-09-1669 TCGA-09-2045 TCGA-09-2048 TCGA-09-2053 
       45.37        38.43        30.51        35.15         4.54        39.75 
TCGA-09-2056 TCGA-13-1489 TCGA-20-1685 TCGA-20-1686 TCGA-23-1022 TCGA-23-1029 
       12.46        83.93        16.70         2.93        49.68         8.81 
TCGA-23-1110 TCGA-23-1111 TCGA-23-1119 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 
       54.51         3.22       129.96         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-24-1557 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-24-2297 TCGA-25-1313 TCGA-25-1315 
       64.01        44.52        57.07        55.86        26.96        52.04 
TCGA-25-1317 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1625 TCGA-25-1627 
        2.01        33.96         2.99        12.99        27.62        12.95 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 
       38.20         0.30        59.15        35.87        14.96        24.99 
TCGA-25-1878 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2400 TCGA-25-2404 
       85.05        49.05         1.02        38.04        42.02        29.03 
TCGA-29-1694 TCGA-29-1696 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1771 
       39.02        33.93        17.36        86.60        66.81        22.55 
TCGA-29-1774 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-30-1714 TCGA-36-1568 
       17.33        14.93         8.38         7.23        38.07        28.77 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1575 TCGA-36-1577 TCGA-36-1580 TCGA-57-1584 
       21.53        22.85         8.55        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-61-1899 
        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-61-1915 TCGA-61-1918 
        5.79        11.41        34.13        56.61        67.76        15.75 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2003 TCGA-61-2008 TCGA-61-2016 TCGA-61-2092 
        2.01         5.52         4.01        30.64         1.18        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 TCGA-61-2098 TCGA-61-2109 TCGA-61-2110 
       71.74        61.64        60.62        65.52        20.68        44.52 
TCGA-09-0364 TCGA-10-0928 TCGA-10-0933 TCGA-10-0934 TCGA-13-0755 TCGA-13-0791 
       29.16        18.51        14.66         6.71         2.50        40.24 
TCGA-13-0792 TCGA-13-0800 TCGA-13-0888 TCGA-13-0906 TCGA-13-0912 TCGA-13-0913 
      118.42        87.48        92.42       118.98        37.64       109.32 
TCGA-13-0920 TCGA-13-0921 
       48.79        48.76 

$subtype4
TCGA-04-1638 TCGA-04-1646 TCGA-04-1654 TCGA-09-1666 TCGA-09-1670 TCGA-09-1673 
       55.43        27.88        47.70        57.60        17.98         3.02 
TCGA-09-2044 TCGA-09-2050 TCGA-09-2051 TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 
        6.12        71.11        63.09        83.31        57.27        81.01 
TCGA-13-1482 TCGA-13-1492 TCGA-13-1497 TCGA-13-1498 TCGA-13-1505 TCGA-13-1511 
       61.71       125.56       127.27        66.15        65.69        54.25 
TCGA-13-2060 TCGA-20-1682 TCGA-23-1021 TCGA-23-1028 TCGA-23-1030 TCGA-23-1107 
       77.88        27.52        47.54        49.41        29.13         0.30 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-24-1430 TCGA-24-1471 TCGA-24-1474 
       87.48        91.66        77.00        28.37         1.18        22.22 
TCGA-24-1548 TCGA-24-1556 TCGA-24-1562 TCGA-24-1603 TCGA-24-1845 TCGA-24-1846 
       16.21        70.62        45.50        90.15         3.81         4.37 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-1930 TCGA-24-2024 TCGA-24-2026 
        5.52         9.80        30.21        81.11        58.16        34.82 
TCGA-24-2029 TCGA-24-2030 TCGA-24-2260 TCGA-24-2262 TCGA-24-2267 TCGA-24-2280 
       14.43        55.92        36.16         0.36        47.54        70.45 
TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-25-1324 TCGA-25-1325 TCGA-25-2396 
        0.82        67.36        36.23        34.03        32.09         3.02 
TCGA-25-2399 TCGA-25-2409 TCGA-29-1691 TCGA-29-1693 TCGA-29-1695 TCGA-29-1697 
       19.99        26.99        48.33       101.79        40.41        31.20 
TCGA-29-1699 TCGA-29-1703 TCGA-29-1707 TCGA-29-1711 TCGA-29-1764 TCGA-29-1769 
       36.36        59.67        41.98        34.62        62.93        22.98 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-30-1853 
        5.36        36.30        86.17        65.00        45.11        36.26 
TCGA-30-1859 TCGA-30-1860 TCGA-30-1866 TCGA-31-1951 TCGA-36-1569 TCGA-36-1578 
       48.10        44.91        36.62        22.49        29.10        27.85 
TCGA-59-2348 TCGA-59-2350 TCGA-61-1724 TCGA-61-1733 TCGA-61-1738 TCGA-61-1741 
      180.20        22.32        20.94        31.79        35.80        33.67 
TCGA-61-1743 TCGA-61-1895 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 
       43.69         1.45        31.30        37.05        42.51        48.92 
TCGA-61-1917 TCGA-61-1919 TCGA-61-2000 TCGA-61-2012 TCGA-61-2088 TCGA-61-2102 
       43.43        38.17        14.50        30.64         4.77         6.48 
TCGA-61-2104 TCGA-61-2111 TCGA-61-2113 TCGA-13-0720 TCGA-13-0723 TCGA-13-0901 
       76.87       125.75        22.22        44.55        39.58        19.36 
TCGA-13-0905 
      123.16 

subtype1 subtype2 subtype3 subtype4 
    0.26     1.02     0.30     0.30 
subtype1 subtype2 subtype3 subtype4 
  152.02   153.37   129.96   180.20 
subtype1 subtype2 subtype3 subtype4 
  30.065   43.695   29.835   37.050 
[1] "0.3 - 152.0 (30.1)" "1.0 - 153.4 (43.7)" "0.3 - 130.0 (29.8)"
[4] "0.3 - 180.2 (37.0)"
D11V2, continuous
          vv
clus       OMENTUM OVARY PERITONEUM OVARY
  subtype1       1    72                1
  subtype2       0   135                0
  subtype3       0   141                0
  subtype4       1   102                0
D11V3, multiclass
                  clus
vv                 subtype1 subtype2 subtype3 subtype4
  OMENTUM                 1        0        0        1
  OVARY                  72      135      141      102
  PERITONEUM OVARY        1        0        0        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, binary
          cls
clus         0   1
  subtype1  72   0
  subtype2 132   1
  subtype3 135   1
  subtype4  99   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   72    0
  subtype2  132    1
  subtype3  135    1
  subtype4   99    1
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        72      132      135       99
  YES        0        1        1        1
[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"
D11V5, continuous
          vv
clus       R0 R1
  subtype1  0  2
  subtype2  0  1
  subtype3  2  0
  subtype4  0  3
D11V6, multiclass
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 
       2        1        2        3 
[1] "subtype4" "subtype4" "subtype4"
D11V7, binary
          cls
clus        0  1
  subtype1  0 44
  subtype2  4 89
  subtype3  2 79
  subtype4  2 51
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   44
  subtype2    4   89
  subtype3    2   79
  subtype4    2   51
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            0        4        2        2
  NOT HISPANIC OR LATINO       44       89       79       51
[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_CHIERARCHICAL
D12V1, survival
          sevent
clus2        0   1
  subtype1  42  63
  subtype2  25  48
  subtype3  55 113
  subtype4  46  59
subtype1 subtype2 subtype3 subtype4 
     105       73      168      105 
subtype1 subtype2 subtype3 subtype4 
      63       48      113       59 
$subtype1
TCGA-04-1331 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 TCGA-04-1347 TCGA-09-1665 
       43.92        49.15         2.01        18.51        63.09        41.62 
TCGA-09-1667 TCGA-09-1668 TCGA-13-1404 TCGA-13-1411 TCGA-13-1482 TCGA-13-1483 
       61.87        55.36        81.17        17.46        61.71        29.42 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1500 TCGA-13-1501 TCGA-13-1511 TCGA-13-1512 
      124.44        20.68        13.97        43.20        54.25        14.53 
TCGA-20-0990 TCGA-20-0991 TCGA-20-1687 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 
       25.94        26.20         2.66        40.54        26.83        32.09 
TCGA-23-1028 TCGA-23-1109 TCGA-23-1113 TCGA-23-1118 TCGA-23-2079 TCGA-23-2081 
       49.41        51.35        31.20        86.01        91.66        77.00 
TCGA-24-0970 TCGA-24-0975 TCGA-24-1105 TCGA-24-1417 TCGA-24-1425 TCGA-24-1428 
       11.64        21.80        47.41         7.82         5.95        17.39 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 TCGA-24-1470 TCGA-24-1545 
       43.53         8.55        72.92        45.14         3.45        57.40 
TCGA-24-1546 TCGA-24-1551 TCGA-24-1555 TCGA-24-1563 TCGA-24-1614 TCGA-24-1845 
       64.27        51.91        88.50        47.70        48.33         3.81 
TCGA-24-1846 TCGA-24-2260 TCGA-24-2261 TCGA-24-2271 TCGA-24-2298 TCGA-25-1314 
        4.37        36.16         0.79        31.63        53.26        33.01 
TCGA-25-1623 TCGA-25-1626 TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 
       18.58        17.03         2.96        31.00        26.99        78.90 
TCGA-29-1711 TCGA-29-1764 TCGA-29-1768 TCGA-29-1770 TCGA-29-2427 TCGA-30-1856 
       34.62        62.93        31.30        24.36        62.47        15.68 
TCGA-30-1857 TCGA-30-1860 TCGA-31-1953 TCGA-31-1956 TCGA-36-1574 TCGA-36-1578 
        0.26        44.91         6.71        44.12        22.55        27.85 
TCGA-59-2354 TCGA-61-1740 TCGA-61-1907 TCGA-61-1913 TCGA-09-0366 TCGA-13-0714 
       34.39         2.43        31.30        48.92        57.76         6.21 
TCGA-13-0720 TCGA-13-0724 TCGA-13-0751 TCGA-13-0760 TCGA-13-0766 TCGA-13-0797 
       44.55         2.73        55.17        11.54        56.71        69.73 
TCGA-13-0799 TCGA-13-0801 TCGA-13-0803 TCGA-13-0805 TCGA-13-0884 TCGA-13-0885 
       83.34        45.99        43.86        35.31       107.18       111.39 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
      153.37        66.67        95.15       145.45       102.84        43.36 
TCGA-13-0900 TCGA-13-0903 TCGA-13-0905 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
      134.04       127.79       123.16        60.59       116.65        44.55 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0924 
       58.68        84.53        85.94 

$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-04-1519 TCGA-04-1536 TCGA-04-1655 TCGA-09-1662 TCGA-09-2044 TCGA-09-2048 
        0.79        29.10        45.37        89.33         6.12         4.54 
TCGA-09-2050 TCGA-13-1409 TCGA-13-1477 TCGA-20-1686 TCGA-23-1022 TCGA-23-1032 
       71.11        57.27        54.64         2.93        49.68         2.76 
TCGA-23-1110 TCGA-23-1114 TCGA-23-1120 TCGA-23-1121 TCGA-23-1123 TCGA-23-2084 
       54.51        68.68         4.27         6.38        33.47        49.84 
TCGA-24-0982 TCGA-24-1104 TCGA-24-1423 TCGA-24-1424 TCGA-24-1544 TCGA-24-1549 
       22.32        63.55         6.25         6.02        26.96        56.58 
TCGA-24-1558 TCGA-24-1567 TCGA-24-1604 TCGA-24-1923 TCGA-25-1312 TCGA-25-1313 
       19.53        17.23        88.37        22.68         1.02        26.96 
TCGA-25-1315 TCGA-25-1322 TCGA-25-1324 TCGA-25-1328 TCGA-25-1633 TCGA-25-1634 
       52.04         2.99        34.03        66.05        62.17        35.87 
TCGA-25-1870 TCGA-25-1871 TCGA-25-2392 TCGA-25-2393 TCGA-29-1690 TCGA-29-1761 
       14.96        24.99         1.02        38.04        47.61        17.36 
TCGA-29-1762 TCGA-29-1774 TCGA-29-1776 TCGA-29-1778 TCGA-29-1781 TCGA-29-1784 
       86.60        17.33        11.84        14.93         8.38         5.36 
TCGA-31-1944 TCGA-36-1575 TCGA-36-1577 TCGA-36-1580 TCGA-61-1721 TCGA-61-1743 
       45.57         8.55        25.74        24.23        11.11        43.69 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1998 TCGA-61-2003 TCGA-61-2104 TCGA-09-0364 
       67.76        43.43         5.52         4.01        76.87        29.16 
TCGA-10-0927 TCGA-13-0755 TCGA-13-0791 TCGA-13-0800 TCGA-13-0883 TCGA-13-0888 
       81.86         2.50        40.24        87.48        68.94        92.42 
TCGA-13-0906 
      118.98 

$subtype3
TCGA-04-1341 TCGA-04-1348 TCGA-04-1350 TCGA-04-1356 TCGA-04-1365 TCGA-04-1367 
        1.08        48.76        63.98        49.28        76.57       103.40 
TCGA-04-1530 TCGA-04-1646 TCGA-04-1654 TCGA-09-1666 TCGA-09-1673 TCGA-09-1674 
      119.08        27.88        47.70        57.60         3.02         8.55 
TCGA-09-2054 TCGA-13-1403 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 
       20.94        77.10        28.54        83.31        55.23        81.01 
TCGA-13-1412 TCGA-13-1481 TCGA-13-1487 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 
       32.35        87.06        22.39        70.82        52.44       125.56 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 
       93.90        90.38         4.24       127.27        66.15       115.07 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 
       34.82        65.69        34.16        65.52        80.15        44.68 
TCGA-13-2060 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-23-1021 TCGA-23-1030 
       77.88        27.52        25.38        19.10        47.54        29.13 
TCGA-23-1107 TCGA-23-1122 TCGA-23-1124 TCGA-23-2078 TCGA-24-1418 TCGA-24-1422 
        0.30        39.09        58.13        87.48         7.99         0.76 
TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1469 TCGA-24-1471 
        4.83        28.37        18.64        18.67         9.11         1.18 
TCGA-24-1474 TCGA-24-1548 TCGA-24-1550 TCGA-24-1552 TCGA-24-1556 TCGA-24-1562 
       22.22        16.21        41.06        41.39        70.62        45.50 
TCGA-24-1564 TCGA-24-1603 TCGA-24-1842 TCGA-24-1843 TCGA-24-1849 TCGA-24-1850 
       25.87        90.15         8.32         3.48         5.79         5.52 
TCGA-24-1920 TCGA-24-1924 TCGA-24-1928 TCGA-24-1930 TCGA-24-2020 TCGA-24-2024 
        9.80        30.21        11.05        81.11       152.02        58.16 
TCGA-24-2026 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2262 
       34.82        14.43        55.92        18.48        28.18         0.36 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 
       70.45        44.61         0.82        67.36        36.23        16.64 
TCGA-25-1316 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1325 TCGA-25-1326 
       42.05        34.98        65.00        37.97        32.09        41.06 
TCGA-25-1329 TCGA-25-1628 TCGA-25-1632 TCGA-25-1635 TCGA-25-1877 TCGA-25-2042 
       15.02        20.61        59.15        52.04        24.00        13.02 
TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-29-1691 TCGA-29-1693 
        3.02        12.00        45.01        19.99        48.33       101.79 
TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 
       40.41        31.20        68.32        36.36        16.93        23.93 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1766 TCGA-29-1769 
       59.67        18.25        41.98        31.27        39.42        22.98 
TCGA-29-1777 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-30-1718 
       12.30        36.30        86.17        65.00        45.11        51.91 
TCGA-30-1853 TCGA-30-1855 TCGA-30-1859 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 
       36.26         2.47        48.10        34.78         6.12        36.62 
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-31-1959 TCGA-36-1569 TCGA-36-1576 TCGA-36-1581 TCGA-57-1582 
       22.49         2.20        29.10        30.08        24.69        24.03 
TCGA-57-1583 TCGA-57-1585 TCGA-59-2348 TCGA-59-2350 TCGA-61-1724 TCGA-61-1733 
       11.38         1.74       180.20        22.32        20.94        31.79 
TCGA-61-1738 TCGA-61-1741 TCGA-61-1895 TCGA-61-1910 TCGA-61-1911 TCGA-61-1919 
       35.80        33.67         1.45        37.05        42.51        38.17 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2009 TCGA-61-2012 TCGA-61-2088 TCGA-61-2101 
       14.50        17.98        39.85        30.64         4.77        55.50 
TCGA-61-2102 TCGA-61-2111 TCGA-61-2113 TCGA-10-0926 TCGA-13-0723 TCGA-13-0757 
        6.48       125.75        22.22        25.91        39.58        11.18 
TCGA-13-0768 TCGA-13-0802 TCGA-13-0894 TCGA-13-0901 TCGA-13-0904 TCGA-13-0923 
       58.65        51.02        49.61        19.36        50.37        83.74 

$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-13-1489 TCGA-20-0987 
       35.15        63.09        39.75        12.46        83.93        23.05 
TCGA-20-1685 TCGA-23-1029 TCGA-23-1111 TCGA-23-1119 TCGA-23-1809 TCGA-23-2072 
       16.70         8.81         3.22       129.96         0.53        24.95 
TCGA-23-2077 TCGA-24-0966 TCGA-24-0979 TCGA-24-1103 TCGA-24-1413 TCGA-24-1416 
      115.89         7.63        41.56        54.12         6.31         6.38 
TCGA-24-1419 TCGA-24-1426 TCGA-24-1464 TCGA-24-1467 TCGA-24-1553 TCGA-24-1557 
        7.86         5.36        12.46       105.99        58.09        39.88 
TCGA-24-1560 TCGA-24-1565 TCGA-24-1616 TCGA-24-1844 TCGA-24-1847 TCGA-24-2019 
       44.09        10.26        38.24         3.72        11.28         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-25-1317 TCGA-25-1321 TCGA-25-1323 TCGA-25-1625 TCGA-25-1627 
       55.86         2.01        33.96        12.99        27.62        12.95 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1878 TCGA-25-2391 TCGA-25-2400 TCGA-25-2404 
       38.20         0.30        85.05        49.05        42.02        29.03 
TCGA-29-1694 TCGA-29-1696 TCGA-29-1763 TCGA-29-1771 TCGA-29-1783 TCGA-30-1714 
       39.02        33.93        66.81        22.55         7.23        38.07 
TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 TCGA-57-1584 TCGA-57-1586 TCGA-57-1993 
       28.77        21.53        22.85        21.14        22.32        25.08 
TCGA-57-1994 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 TCGA-61-1725 
       25.02       116.12         9.40         2.14         5.42        31.43 
TCGA-61-1728 TCGA-61-1736 TCGA-61-1737 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 
       27.88        48.79        44.84         8.42         5.79        11.41 
TCGA-61-1906 TCGA-61-1914 TCGA-61-1918 TCGA-61-1995 TCGA-61-2008 TCGA-61-2016 
       34.13        56.61        15.75         2.01        30.64         1.18 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 TCGA-61-2098 TCGA-61-2109 
       51.72        71.74        61.64        60.62        65.52        20.68 
TCGA-61-2110 TCGA-10-0928 TCGA-10-0933 TCGA-10-0934 TCGA-13-0792 TCGA-13-0912 
       44.52        18.51        14.66         6.71       118.42        37.64 
TCGA-13-0913 TCGA-13-0920 TCGA-13-0921 
      109.32        48.79        48.76 

subtype1 subtype2 subtype3 subtype4 
    0.26     0.79     0.30     0.30 
subtype1 subtype2 subtype3 subtype4 
  153.37   118.98   180.20   129.96 
subtype1 subtype2 subtype3 subtype4 
   43.92    29.16    34.82    32.52 
[1] "0.3 - 153.4 (43.9)" "0.8 - 119.0 (29.2)" "0.3 - 180.2 (34.8)"
[4] "0.3 - 130.0 (32.5)"
D12V2, continuous
          vv
clus       OMENTUM OVARY PERITONEUM OVARY
  subtype1       0   105                0
  subtype2       0    73                0
  subtype3       2   166                1
  subtype4       0   106                0
D12V3, 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"
D12V4, binary
          cls
clus         0   1
  subtype1 103   0
  subtype2  70   1
  subtype3 162   2
  subtype4 103   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  103    0
  subtype2   70    1
  subtype3  162    2
  subtype4  103    0
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       103       70      162      103
  YES        0        1        2        0
[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"
D12V5, continuous
          vv
clus       R0 R1
  subtype1  0  2
  subtype2  0  0
  subtype3  0  4
  subtype4  2  0
D12V6, multiclass
[1] "Remove cluster labels:" "subtype1"               "subtype4"              
clus
subtype1 subtype3 subtype4 
       2        4        2 
[1] "subtype3" "subtype3" "subtype3" "subtype3"
D12V7, binary
          cls
clus        0  1
  subtype1  3 70
  subtype2  2 45
  subtype3  2 91
  subtype4  1 57
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   70
  subtype2    2   45
  subtype3    2   91
  subtype4    1   57
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        2        2        1
  NOT HISPANIC OR LATINO       70       45       91       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(13) Variable = MIRSEQ_MATURE_CNMF
D13V1, survival
          sevent
clus2      0 1
  subtype1 1 5
  subtype2 4 2
  subtype3 0 5
  subtype4 2 3
subtype1 subtype2 subtype3 subtype4 
       6        6        5        5 
subtype1 subtype2 subtype3 subtype4 
       5        2        5        3 
$subtype1
TCGA-04-1652 TCGA-24-2290 TCGA-24-2297 TCGA-57-1994 TCGA-61-1918 TCGA-61-2109 
       31.86        36.23        55.86        25.02        15.75        20.68 

$subtype2
TCGA-09-2050 TCGA-09-2054 TCGA-23-2077 TCGA-24-2036 TCGA-59-2363 TCGA-61-2098 
       71.11        20.94       115.89        64.01         5.42        65.52 

$subtype3
TCGA-24-1928 TCGA-24-2289 TCGA-25-2399 TCGA-25-2404 TCGA-13-0908 
       11.05        67.36        19.99        29.03        60.59 

$subtype4
TCGA-24-2288 TCGA-25-2392 TCGA-25-2400 TCGA-61-2088 TCGA-61-2111 
        0.82         1.02        42.02         4.77       125.75 

subtype1 subtype2 subtype3 subtype4 
   15.75     5.42    11.05     0.82 
subtype1 subtype2 subtype3 subtype4 
   55.86   115.89    67.36   125.75 
subtype1 subtype2 subtype3 subtype4 
  28.440   64.765   29.030    4.770 
[1] "15.8 - 55.9 (28.4)" "5.4 - 115.9 (64.8)" "11.1 - 67.4 (29.0)"
[4] "0.8 - 125.8 (4.8)" 
D13V2, continuous
          vv
clus       OMENTUM OVARY
  subtype1       1     5
  subtype2       0     6
  subtype3       0     5
  subtype4       0     5
D13V3, multiclass
         clus
vv        subtype1 subtype2 subtype3 subtype4
  OMENTUM        1        0        0        0
  OVARY          5        6        5        5
[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"
D13V4, binary
          cls
clus       0
  subtype1 6
  subtype2 6
  subtype3 5
  subtype4 5
[1] "NOT AVAILABLE: table only has an event [0]"
D13V5, continuous
          vv
clus       R0
  subtype1  0
  subtype2  1
  subtype3  0
  subtype4  0
[1] "NOT AVAILABLE: table dimension [4x1]"
D13V7, binary
          cls
clus       0
  subtype1 2
  subtype2 4
  subtype3 3
  subtype4 4
[1] "NOT AVAILABLE: table only has an event [0]"

Clustering(14) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D14V1, survival
          sevent
clus2      0 1
  subtype1 1 4
  subtype4 3 1
  subtype5 1 4
  subtype6 1 3
subtype1 subtype4 subtype5 subtype6 
       5        4        5        4 
subtype1 subtype4 subtype5 subtype6 
       4        1        4        3 
$subtype1
TCGA-04-1652 TCGA-24-2297 TCGA-25-2404 TCGA-57-1994 TCGA-61-1918 
       31.86        55.86        29.03        25.02        15.75 

$subtype4
TCGA-23-2077 TCGA-24-2036 TCGA-59-2363 TCGA-61-2098 
      115.89        64.01         5.42        65.52 

$subtype5
TCGA-24-1928 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-61-2111 
       11.05         0.82        67.36        36.23       125.75 

$subtype6
TCGA-25-2392 TCGA-25-2400 TCGA-61-2088 TCGA-61-2109 
        1.02        42.02         4.77        20.68 

subtype1 subtype4 subtype5 subtype6 
   15.75     5.42     0.82     1.02 
subtype1 subtype4 subtype5 subtype6 
   55.86   115.89   125.75    42.02 
subtype1 subtype4 subtype5 subtype6 
  29.030   64.765   36.230   12.725 
[1] "15.8 - 55.9 (29.0)" "5.4 - 115.9 (64.8)" "0.8 - 125.8 (36.2)"
[4] "1.0 - 42.0 (12.7)" 
D14V2, continuous
          vv
clus       OMENTUM OVARY
  subtype1       0     5
  subtype4       0     4
  subtype5       1     4
  subtype6       0     4
D14V3, multiclass
         clus
vv        subtype1 subtype4 subtype5 subtype6
  OMENTUM        0        0        1        0
  OVARY          5        4        4        4
[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"
D14V4, binary
          cls
clus       0
  subtype1 5
  subtype4 4
  subtype5 5
  subtype6 4
[1] "NOT AVAILABLE: table only has an event [0]"
D14V5, continuous
          vv
clus       R0
  subtype1  0
  subtype4  1
  subtype5  0
  subtype6  0
[1] "NOT AVAILABLE: table dimension [4x1]"
D14V7, binary
          cls
clus       0
  subtype1 2
  subtype4 2
  subtype5 1
  subtype6 4
[1] "NOT AVAILABLE: table only has an event [0]"
