[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/19775421/OV-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/OV-TP/20141012/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 
219 215 129 
  1   2   3 
219 215 129 
[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 
158 165 238 
  1   2   3 
158 165 238 
[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 
170 202 201 
  1   2   3 
170 202 201 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
175 180 220 
  1   2   3 
175 180 220 
[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 
 79 109 115 
  1   2   3 
 79 109 115 
[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 
124 185 144 
  1   2   3 
124 185 144 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
105  73 169 106 
  1   2   3   4 
105  73 169 106 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2 
12 10 
 1  2 
12 10 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
1 2 3 4 5 6 
6 2 2 6 4 2 
1 4 5 
6 6 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] "RACE"                                
[21] "ETHNICITY"                           

Input Data has 21 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=280,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=452,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'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:'RACE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'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 7 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"              "RACE"                       
[7] "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
RACE, nv=5, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
          sevent
clus2        0   1
  subtype1  92 126
  subtype2 117  95
  subtype3  50  79
subtype1 subtype2 subtype3 
     218      212      129 
subtype1 subtype2 subtype3 
     126       95       79 
$subtype1
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1341 TCGA-04-1342 TCGA-04-1347 
       43.92        41.00         1.81         1.08        18.51        63.09 
TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1364 TCGA-04-1367 TCGA-04-1369 
       63.98        65.46        49.28        33.67       103.40        21.11 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1542 
       82.39        56.55        19.99         0.79        38.37        84.20 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1652 TCGA-04-1655 
       55.43        48.89        27.88        28.64        31.86        45.37 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0369 TCGA-09-1661 TCGA-09-1664 TCGA-09-1669 
       29.16         9.47        35.57        38.43        74.93        30.51 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2048 TCGA-09-2049 
        5.85         3.02         8.55        97.55         4.54       112.41 
TCGA-09-2050 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-10-0925 TCGA-10-0926 
       71.11        39.75        20.94        26.93        54.31        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0938 
       81.86        18.51        14.66         6.71        35.44        20.91 
TCGA-13-0717 TCGA-13-0724 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 
       24.59         2.73        15.19        17.82        55.17        11.18 
TCGA-13-0762 TCGA-13-0766 TCGA-13-0794 TCGA-13-0799 TCGA-13-0800 TCGA-13-0802 
      111.78        56.71        30.35         7.79         8.12         8.19 
TCGA-13-0883 TCGA-13-0887 TCGA-13-0888 TCGA-13-0891 TCGA-13-0899 TCGA-13-0901 
       68.94        66.67        70.39        69.01        56.15        19.36 
TCGA-13-0906 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 
       44.94        37.08        34.06        29.98        21.17        13.81 
TCGA-13-0923 TCGA-13-1403 TCGA-13-1407 TCGA-13-1409 TCGA-13-1477 TCGA-13-1482 
        6.41        10.88         6.05         6.84        54.64        61.71 
TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1495 TCGA-13-1505 
       22.39        82.88        52.44        73.55        49.25         4.21 
TCGA-13-1506 TCGA-13-1510 TCGA-13-2057 TCGA-13-2066 TCGA-20-0990 TCGA-20-0996 
        4.41         2.56        80.02        70.13        25.94        72.20 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1686 TCGA-23-1021 TCGA-23-1022 TCGA-23-1024 
       25.38        19.10         2.93        47.54        49.68        15.39 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1107 TCGA-23-1109 
        8.81        29.13        18.90         2.76         0.30        51.35 
TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1119 TCGA-23-1121 
       54.51         3.22        31.20        68.68       129.96         6.38 
TCGA-23-1122 TCGA-23-1809 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 
       39.09         0.53         2.76         4.70         4.50         7.63 
TCGA-24-0979 TCGA-24-0982 TCGA-24-1103 TCGA-24-1413 TCGA-24-1419 TCGA-24-1423 
       41.56        22.32        54.12         6.31         7.86         6.25 
TCGA-24-1424 TCGA-24-1426 TCGA-24-1430 TCGA-24-1464 TCGA-24-1467 TCGA-24-1469 
        6.02         5.36        28.37        12.46       105.99         9.11 
TCGA-24-1544 TCGA-24-1548 TCGA-24-1552 TCGA-24-1555 TCGA-24-1557 TCGA-24-1558 
       26.96        16.21        41.39        88.50        39.88        19.53 
TCGA-24-1560 TCGA-24-1567 TCGA-24-1603 TCGA-24-1614 TCGA-24-1616 TCGA-24-1844 
       44.09        17.23        90.15        48.33        38.24         3.72 
TCGA-24-1923 TCGA-24-2019 TCGA-24-2020 TCGA-24-2024 TCGA-24-2027 TCGA-24-2030 
       22.68         4.87       152.02        58.16       109.71        55.92 
TCGA-24-2033 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2295 
       18.48        64.01        44.52        57.07        36.16        33.11 
TCGA-24-2297 TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
       55.86         1.02        33.01        52.04        42.05         2.01 
TCGA-25-1321 TCGA-25-1323 TCGA-25-1324 TCGA-25-1325 TCGA-25-1627 TCGA-25-1631 
       33.96        12.99        34.03        32.09        12.95         0.30 
TCGA-25-1632 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-2393 
       59.15        35.87        14.96        24.99        24.00        38.04 
TCGA-25-2400 TCGA-29-1691 TCGA-29-1697 TCGA-29-1702 TCGA-29-1703 TCGA-29-1762 
       42.02        48.33        31.20        23.93        59.67        86.60 
TCGA-29-1763 TCGA-29-1774 TCGA-29-1775 TCGA-29-2414 TCGA-29-2425 TCGA-29-2429 
       66.81        17.33        12.36        86.17        65.00        13.84 
TCGA-29-2431 TCGA-29-2434 TCGA-30-1714 TCGA-30-1853 TCGA-30-1859 TCGA-30-1866 
       42.25        11.47        38.07        36.26        48.10        36.62 
TCGA-31-1955 TCGA-36-1571 TCGA-36-1575 TCGA-36-1577 TCGA-36-2537 TCGA-36-2538 
       42.51        22.85         8.55        25.74        25.91        25.08 
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-59-2350 TCGA-59-2352 TCGA-59-2363 TCGA-59-2372 
       22.32        29.00        22.32         9.40         5.42        44.81 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1741 TCGA-61-1743 TCGA-61-1900 TCGA-61-1910 
       27.88         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-61-2101 
       43.43         4.77        51.72        58.39        65.52        55.50 
TCGA-61-2110 TCGA-61-2111 
       44.52       125.75 

$subtype2
TCGA-04-1336 TCGA-04-1346 TCGA-04-1348 TCGA-04-1349 TCGA-04-1353 TCGA-04-1361 
       49.15        65.52        48.76        21.57         0.53        32.52 
TCGA-04-1362 TCGA-04-1365 TCGA-04-1516 TCGA-04-1536 TCGA-04-1649 TCGA-04-1651 
       44.32        76.57        41.59        29.10        64.64        36.23 
TCGA-04-1654 TCGA-09-0366 TCGA-09-0367 TCGA-09-1659 TCGA-09-1662 TCGA-09-1665 
       47.70        57.76        17.98         9.99        89.33        41.62 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1670 TCGA-09-2043 TCGA-09-2044 
       57.60        61.87        55.36        17.98         6.18         6.12 
TCGA-09-2045 TCGA-09-2051 TCGA-09-2056 TCGA-10-0931 TCGA-10-0936 TCGA-10-0937 
       35.15        63.09        12.46        32.88        36.92        19.99 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0755 TCGA-13-0758 TCGA-13-0760 
       44.55        39.58        12.39         2.50        11.38        11.54 
TCGA-13-0761 TCGA-13-0764 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0795 
       38.01        61.84        28.57        40.24       118.42        19.59 
TCGA-13-0797 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0884 TCGA-13-0885 
        8.71         8.28        43.86        35.28       107.18        91.40 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0921 
       43.36        57.47        47.38        48.33        47.84         4.64 
TCGA-13-0924 TCGA-13-1410 TCGA-13-1484 TCGA-13-1488 TCGA-13-1496 TCGA-13-1497 
        6.08         4.70        98.04        70.82         4.24        54.31 
TCGA-13-1498 TCGA-13-1500 TCGA-13-1507 TCGA-13-1511 TCGA-13-2059 TCGA-13-2060 
       37.61        13.97         4.77         3.91        78.48        77.88 
TCGA-13-2061 TCGA-13-2065 TCGA-20-0987 TCGA-20-0991 TCGA-20-1685 TCGA-20-1687 
       76.90        65.52        23.05        26.20        16.70         2.66 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1118 TCGA-23-1120 TCGA-23-1123 
       26.83        32.09        49.41        86.01         4.27        33.47 
TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 
       58.13        24.95       115.89        91.66        77.00        49.84 
TCGA-23-2649 TCGA-24-0980 TCGA-24-1104 TCGA-24-1416 TCGA-24-1417 TCGA-24-1428 
        3.81         7.66        63.55         6.38         7.82        17.39 
TCGA-24-1431 TCGA-24-1436 TCGA-24-1466 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 
       18.64         8.55        45.14         3.45         1.18        22.22 
TCGA-24-1549 TCGA-24-1551 TCGA-24-1553 TCGA-24-1556 TCGA-24-1565 TCGA-24-1604 
       56.58        51.91        58.09        70.62        10.26        88.37 
TCGA-24-1842 TCGA-24-1843 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1920 
        8.32         3.48         3.81         4.37        11.28         9.80 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 TCGA-24-2023 TCGA-24-2026 TCGA-24-2261 
       30.21        16.44        81.11        44.84        34.82         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 TCGA-24-2290 TCGA-25-1313 
        0.36        47.54        31.63        44.61        36.23        26.96 
TCGA-25-1319 TCGA-25-1322 TCGA-25-1625 TCGA-25-1630 TCGA-25-1878 TCGA-25-2391 
       65.00         2.99        27.62        38.20        85.05        49.05 
TCGA-25-2392 TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 TCGA-25-2409 TCGA-29-1688 
        1.02         3.02        12.00        19.99        26.99        78.90 
TCGA-29-1694 TCGA-29-1696 TCGA-29-1699 TCGA-29-1707 TCGA-29-1711 TCGA-29-1761 
       39.02        33.93        36.36        41.98        34.62        17.36 
TCGA-29-1769 TCGA-29-1771 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 
       22.98        22.55        11.84        12.30        14.93         8.38 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2427 TCGA-29-2428 TCGA-30-1856 TCGA-30-1860 
        5.36        36.30        62.47        45.11        15.68        44.91 
TCGA-30-1880 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1953 TCGA-36-1568 
       57.57        45.57        30.18        18.77         6.71        28.77 
TCGA-36-1570 TCGA-36-1574 TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 
       21.53        22.55        27.85        24.69        35.05        33.01 
TCGA-36-2532 TCGA-36-2534 TCGA-36-2542 TCGA-36-2543 TCGA-36-2545 TCGA-36-2549 
       29.49        29.82        21.60         2.24        18.31         6.05 
TCGA-36-2551 TCGA-42-2582 TCGA-42-2589 TCGA-42-2590 TCGA-57-1584 TCGA-57-1993 
       16.18        47.57        42.02        10.42        21.14        25.08 
TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2351 TCGA-59-2355 TCGA-61-1722 
       25.02       180.20        80.12       116.12         2.14         8.09 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1734 TCGA-61-1736 TCGA-61-1738 
       20.94        31.43        18.54        28.47        48.79        35.80 
TCGA-61-1740 TCGA-61-1895 TCGA-61-1899 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 
        2.43         1.45         8.42        11.41        13.02         9.07 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 
       34.13        31.30        42.51        48.92        56.61        67.76 
TCGA-61-1918 TCGA-61-1995 TCGA-61-2000 TCGA-61-2002 TCGA-61-2008 TCGA-61-2012 
       15.75         2.01        14.50        17.98        30.64        30.64 
TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2094 TCGA-61-2097 
        1.18        45.96        45.40         4.80        71.74        60.62 
TCGA-61-2104 TCGA-61-2109 
       76.87        20.68 

$subtype3
TCGA-04-1337 TCGA-04-1338 TCGA-04-1343 TCGA-04-1530 TCGA-10-0930 TCGA-13-0714 
        2.01        46.62        11.87       119.08        34.19         6.21 
TCGA-13-0726 TCGA-13-0768 TCGA-13-0793 TCGA-13-0805 TCGA-13-0807 TCGA-13-0886 
       31.20        58.65       107.28        35.31        13.61        74.27 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0894 TCGA-13-0900 TCGA-13-0908 TCGA-13-0911 
       61.84        67.99        49.61        57.07        44.84        27.72 
TCGA-13-0919 TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1411 TCGA-13-1412 
       84.53         6.61         7.36         5.92         4.21         5.33 
TCGA-13-1481 TCGA-13-1483 TCGA-13-1485 TCGA-13-1494 TCGA-13-1499 TCGA-13-1501 
       87.06        29.42        20.68        38.20        38.40        32.84 
TCGA-13-1504 TCGA-13-1509 TCGA-13-1512 TCGA-13-2071 TCGA-20-1682 TCGA-23-1023 
       16.57         4.18         3.09        25.41        27.52        40.54 
TCGA-23-1116 TCGA-23-1117 TCGA-23-2078 TCGA-23-2647 TCGA-24-0970 TCGA-24-0975 
       19.46        33.30        87.48         4.44        11.64        21.80 
TCGA-24-1105 TCGA-24-1418 TCGA-24-1422 TCGA-24-1425 TCGA-24-1427 TCGA-24-1434 
       47.41         7.99         0.76         5.95         4.83        18.67 
TCGA-24-1435 TCGA-24-1463 TCGA-24-1545 TCGA-24-1546 TCGA-24-1550 TCGA-24-1562 
       43.53        72.92        57.40        64.27        41.06        45.50 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1849 TCGA-24-1850 TCGA-24-1928 TCGA-24-2029 
       47.70        25.87         5.79         5.52        11.05        14.43 
TCGA-24-2035 TCGA-24-2280 TCGA-24-2288 TCGA-24-2289 TCGA-24-2293 TCGA-24-2298 
       28.18        70.45         0.82        67.36        16.64        53.26 
TCGA-25-1318 TCGA-25-1320 TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 
       34.98        37.97        41.06        66.05        15.02        18.58 
TCGA-25-1626 TCGA-25-1628 TCGA-25-1633 TCGA-25-1635 TCGA-25-2042 TCGA-25-2398 
       17.03        20.61        62.17        52.04        13.02        45.01 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-29-1690 TCGA-29-1693 TCGA-29-1695 
        2.96        29.03        31.00        47.61       101.79        40.41 
TCGA-29-1698 TCGA-29-1701 TCGA-29-1705 TCGA-29-1710 TCGA-29-1764 TCGA-29-1766 
       68.32        16.93        18.25        31.27        62.93        39.42 
TCGA-29-1768 TCGA-29-1770 TCGA-29-1783 TCGA-29-2432 TCGA-29-2436 TCGA-30-1718 
       31.30        24.36         7.23        21.47         9.76        51.91 
TCGA-30-1855 TCGA-30-1857 TCGA-30-1861 TCGA-30-1862 TCGA-30-1867 TCGA-30-1887 
        2.47         0.26        34.78         6.12         1.22        24.26 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1951 TCGA-31-1956 TCGA-31-1959 TCGA-36-1569 
       30.05        48.79        22.49        44.12         2.20        29.10 
TCGA-36-1576 TCGA-36-1580 TCGA-36-2540 TCGA-36-2548 TCGA-42-2587 TCGA-42-2588 
       30.08        24.23        23.80        14.17        23.74        28.93 
TCGA-57-1585 TCGA-59-2354 TCGA-61-1721 TCGA-61-1733 TCGA-61-1737 TCGA-61-1919 
        1.74        34.39        11.11        31.79        44.84        38.17 
TCGA-61-1998 TCGA-61-2003 TCGA-61-2009 TCGA-61-2095 TCGA-61-2102 TCGA-61-2113 
        5.52         4.01        39.85        61.64         6.48        22.22 
TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
        6.35        31.07         8.61 

subtype1 subtype2 subtype3 
    0.30     0.36     0.26 
subtype1 subtype2 subtype3 
  152.02   180.20   119.08 
subtype1 subtype2 subtype3 
  30.855   30.195   28.930 
[1] "0.3 - 152.0 (30.9)" "0.4 - 180.2 (30.2)" "0.3 - 119.1 (28.9)"
D1V2, continuous
          vv
clus       OMENTUM OVARY PERITONEUM OVARY
  subtype1       0   219                0
  subtype2       1   213                1
  subtype3       1   127                1
D1V3, multiclass
                  clus
vv                 subtype1 subtype2 subtype3
  OMENTUM                 0        1        1
  OVARY                 219      213      127
  PERITONEUM OVARY        0        1        1
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V4, binary
          cls
clus         0   1
  subtype1 193   3
  subtype2 195   1
  subtype3 112   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  193    3
  subtype2  195    1
  subtype3  112    1
     clus
vv    subtype1 subtype2 subtype3
  NO       193      195      112
  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"
D1V5, continuous
          vv
clus       R0 R1 R2
  subtype1  6  9  0
  subtype2  7  9  0
  subtype3  1  9  1
D1V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0        6        7        1
  R1        9        9        9
  R2        0        0        1
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     7                        12
  subtype2                                0    12                         9
  subtype3                                2     1                         3
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0   187
  subtype2                                         1   181
  subtype3                                         0   118
D1V7, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 0        0        2
  ASIAN                                            7       12        1
  BLACK OR AFRICAN AMERICAN                       12        9        3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        1        0
  WHITE                                          187      181      118
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
          cls
clus         0   1
  subtype1   6 131
  subtype2   5 121
  subtype3   0  78
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  131
  subtype2    5  121
  subtype3    0   78
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            6        5        0
  NOT HISPANIC OR LATINO      131      121       78
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = MRNA_CHIERARCHICAL
D2V1, survival
          sevent
clus2        0   1
  subtype1 152 157
  subtype2  70  91
  subtype3  37  52
subtype1 subtype2 subtype3 
     309      161       89 
subtype1 subtype2 subtype3 
     157       91       52 
$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-09-0366 TCGA-09-0367 TCGA-09-1659 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       57.76        17.98         9.99        89.33        74.93        41.62 
TCGA-09-1666 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 
       57.60        17.98         5.85         3.02        97.55         6.18 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2051 TCGA-09-2053 TCGA-09-2055 TCGA-09-2056 
        6.12        35.15        63.09        39.75        26.93        12.46 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0931 TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 
       54.31        25.91        32.88         6.71        36.92        19.99 
TCGA-13-0714 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0727 
        6.21        44.55        39.58         2.73        12.39        15.19 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0764 
       55.17         2.50        11.18        11.38        11.54        61.84 
TCGA-13-0765 TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 TCGA-13-0795 TCGA-13-0797 
       28.57        56.71        40.24       118.42        19.59         8.71 
TCGA-13-0799 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
        7.79         8.28        43.86        35.28        35.31        13.61 
TCGA-13-0883 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 
       68.94        91.40        74.27        66.67        61.84        67.99 
TCGA-13-0891 TCGA-13-0899 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0910 
       69.01        56.15        47.38        48.33        47.84        37.08 
TCGA-13-0911 TCGA-13-0916 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 
       27.72        21.17         4.64         6.41         6.08        10.88 
TCGA-13-1410 TCGA-13-1482 TCGA-13-1484 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 
        4.70        61.71        98.04        70.82        52.44        73.55 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1506 TCGA-13-1510 
       49.25         4.24        54.31        37.61         4.41         2.56 
TCGA-13-1511 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-20-0987 
        3.91        78.48        77.88        76.90        65.52        23.05 
TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 
       26.20        72.20        27.52        25.38        19.10        16.70 
TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1024 TCGA-23-1028 TCGA-23-1029 
        2.93         2.66        47.54        15.39        49.41         8.81 
TCGA-23-1030 TCGA-23-1032 TCGA-23-1107 TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 
       29.13         2.76         0.30        51.35         3.22        31.20 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 
       86.01       129.96         4.27        39.09        33.47        58.13 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2079 TCGA-23-2084 TCGA-23-2641 
        0.53        24.95       115.89        91.66        49.84         2.76 
TCGA-23-2643 TCGA-23-2645 TCGA-23-2649 TCGA-24-0966 TCGA-24-0979 TCGA-24-0982 
        4.70         4.50         3.81         7.63        41.56        22.32 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1419 
       54.12        63.55        47.41         6.31         6.38         7.86 
TCGA-24-1423 TCGA-24-1426 TCGA-24-1428 TCGA-24-1431 TCGA-24-1436 TCGA-24-1464 
        6.25         5.36        17.39        18.64         8.55        12.46 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 
       45.14       105.99         9.11         3.45         1.18        22.22 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       16.21        56.58        51.91        41.39        58.09        88.50 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1565 TCGA-24-1603 
       70.62        39.88        19.53        44.09        10.26        90.15 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 
       88.37        48.33        38.24         3.48         3.72         3.81 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-2019 
        4.37        11.28         5.52         9.80        30.21         4.87 
TCGA-24-2023 TCGA-24-2026 TCGA-24-2030 TCGA-24-2036 TCGA-24-2038 TCGA-24-2260 
       44.84        34.82        55.92        64.01        44.52        36.16 
TCGA-24-2261 TCGA-24-2267 TCGA-24-2281 TCGA-24-2290 TCGA-24-2295 TCGA-24-2297 
        0.79        47.54        44.61        36.23        33.11        55.86 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 
        1.02        26.96        33.01        34.98        65.00        33.96 
TCGA-25-1322 TCGA-25-1324 TCGA-25-1325 TCGA-25-1625 TCGA-25-1627 TCGA-25-1630 
        2.99        34.03        32.09        27.62        12.95        38.20 
TCGA-25-1631 TCGA-25-1870 TCGA-25-1878 TCGA-25-2391 TCGA-25-2392 TCGA-25-2396 
        0.30        14.96        85.05        49.05         1.02         3.02 
TCGA-25-2397 TCGA-25-2399 TCGA-25-2400 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 
       12.00        19.99        42.02        78.90        47.61        48.33 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 
       33.93        31.20        36.36        23.93        59.67        41.98 
TCGA-29-1761 TCGA-29-1763 TCGA-29-1771 TCGA-29-1775 TCGA-29-1778 TCGA-29-1781 
       17.36        66.81        22.55        12.36        14.93         8.38 
TCGA-29-1783 TCGA-29-1784 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2434 
        7.23         5.36        62.47        45.11        13.84        11.47 
TCGA-30-1856 TCGA-30-1860 TCGA-30-1866 TCGA-31-1950 TCGA-31-1955 TCGA-36-1568 
       15.68        44.91        36.62        18.77        42.51        28.77 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1578 TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 
       21.53        22.85        27.85        24.69        33.01        29.49 
TCGA-36-2534 TCGA-36-2542 TCGA-36-2543 TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 
       29.82        21.60         2.24        18.31        20.52         6.05 
TCGA-36-2551 TCGA-42-2582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1992 
       16.18        47.57        11.38        21.14        22.32        29.00 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       25.08        25.02        80.12        22.32       116.12         9.40 
TCGA-59-2355 TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1734 
        2.14         8.09        31.43        18.54        27.88        28.47 
TCGA-61-1736 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 
       48.79        35.80         2.43        33.67        43.69         1.45 
TCGA-61-1899 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        8.42        11.41        13.02         9.07        34.13        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 
       37.05        42.51        48.92        67.76        43.43        15.75 
TCGA-61-1995 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
        2.01        30.64         1.18        45.96        45.40         4.80 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2104 
       51.72        71.74        61.64        58.39        60.62        76.87 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       20.68        44.52       125.75 

$subtype2
TCGA-04-1332 TCGA-04-1337 TCGA-04-1338 TCGA-04-1353 TCGA-04-1530 TCGA-09-1667 
       41.00         2.01        46.62         0.53       119.08        61.87 
TCGA-09-1668 TCGA-10-0930 TCGA-13-0726 TCGA-13-0761 TCGA-13-0768 TCGA-13-0793 
       55.36        34.19        31.20        38.01        58.65       107.28 
TCGA-13-0884 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 
      107.18        43.36        49.61        57.47        57.07        19.36 
TCGA-13-0908 TCGA-13-0919 TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1411 
       44.84        84.53         6.61         7.36         5.92         4.21 
TCGA-13-1412 TCGA-13-1481 TCGA-13-1483 TCGA-13-1485 TCGA-13-1494 TCGA-13-1499 
        5.33        87.06        29.42        20.68        38.20        38.40 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1507 TCGA-13-1509 
       13.97        32.84        16.57         4.21         4.77         4.18 
TCGA-13-1512 TCGA-13-2071 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1116 
        3.09        25.41        40.54        26.83        32.09        19.46 
TCGA-23-1117 TCGA-23-2078 TCGA-23-2081 TCGA-23-2647 TCGA-24-0970 TCGA-24-0975 
       33.30        87.48        77.00         4.44        11.64        21.80 
TCGA-24-0980 TCGA-24-1417 TCGA-24-1418 TCGA-24-1422 TCGA-24-1425 TCGA-24-1427 
        7.66         7.82         7.99         0.76         5.95         4.83 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1463 TCGA-24-1545 TCGA-24-1546 TCGA-24-1562 
       18.67        43.53        72.92        57.40        64.27        45.50 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1842 TCGA-24-1849 TCGA-24-1923 TCGA-24-1927 
       47.70        25.87         8.32         5.79        22.68        16.44 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2254 
       11.05        81.11        14.43        18.48        28.18        57.07 
TCGA-24-2262 TCGA-24-2271 TCGA-24-2280 TCGA-24-2288 TCGA-24-2289 TCGA-24-2293 
        0.36        31.63        70.45         0.82        67.36        16.64 
TCGA-24-2298 TCGA-25-1320 TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 
       53.26        37.97        41.06        66.05        15.02        18.58 
TCGA-25-1626 TCGA-25-1628 TCGA-25-1633 TCGA-25-1635 TCGA-25-2042 TCGA-25-2398 
       17.03        20.61        62.17        52.04        13.02        45.01 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1693 TCGA-29-1694 
        2.96        29.03        31.00        26.99       101.79        39.02 
TCGA-29-1695 TCGA-29-1698 TCGA-29-1701 TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 
       40.41        68.32        16.93        18.25        31.27        34.62 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1776 
       62.93        39.42        31.30        22.98        24.36        11.84 
TCGA-29-1777 TCGA-29-1785 TCGA-29-2432 TCGA-29-2436 TCGA-30-1718 TCGA-30-1855 
       12.30        36.30        21.47         9.76        51.91         2.47 
TCGA-30-1857 TCGA-30-1861 TCGA-30-1862 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 
        0.26        34.78         6.12         1.22        57.57        24.26 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 
       30.05        48.79        45.57        30.18        22.49         6.71 
TCGA-31-1956 TCGA-31-1959 TCGA-36-1569 TCGA-36-1574 TCGA-36-1576 TCGA-36-1580 
       44.12         2.20        29.10        22.55        30.08        24.23 
TCGA-36-2529 TCGA-36-2538 TCGA-36-2540 TCGA-36-2544 TCGA-36-2548 TCGA-42-2587 
       35.05        25.08        23.80        20.98        14.17        23.74 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-57-1582 TCGA-57-1585 TCGA-59-2348 
       28.93        42.02        10.42        24.03         1.74       180.20 
TCGA-59-2354 TCGA-61-1721 TCGA-61-1724 TCGA-61-1733 TCGA-61-1737 TCGA-61-1914 
       34.39        11.11        20.94        31.79        44.84        56.61 
TCGA-61-1919 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 
       38.17         5.52        14.50        17.98         4.01        30.64 
TCGA-61-2009 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       39.85        22.22         6.35        31.07         8.61 

$subtype3
TCGA-04-1347 TCGA-04-1350 TCGA-04-1351 TCGA-04-1364 TCGA-04-1371 TCGA-04-1514 
       63.09        63.98        65.46        33.67        82.39        56.55 
TCGA-04-1519 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-09-0364 TCGA-09-0365 TCGA-09-0369 TCGA-09-1661 TCGA-09-1669 TCGA-09-1674 
       29.16         9.47        35.57        38.43        30.51         8.55 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2054 TCGA-10-0927 TCGA-10-0928 
        4.54       112.41        71.11        20.94        81.86        18.51 
TCGA-10-0933 TCGA-10-0935 TCGA-10-0938 TCGA-13-0717 TCGA-13-0730 TCGA-13-0762 
       14.66        35.44        20.91        24.59        17.82       111.78 
TCGA-13-0794 TCGA-13-0800 TCGA-13-0802 TCGA-13-0888 TCGA-13-0906 TCGA-13-0912 
       30.35         8.12         8.19        70.39        44.94        34.06 
TCGA-13-0913 TCGA-13-0920 TCGA-13-1407 TCGA-13-1409 TCGA-13-1477 TCGA-13-1487 
       29.98        13.81         6.05         6.84        54.64        22.39 
TCGA-13-1489 TCGA-13-2057 TCGA-13-2066 TCGA-20-0990 TCGA-23-1022 TCGA-23-1031 
       82.88        80.02        70.13        25.94        49.68        18.90 
TCGA-23-1110 TCGA-23-1114 TCGA-23-1121 TCGA-24-1424 TCGA-24-1430 TCGA-24-1544 
       54.51        68.68         6.38         6.02        28.37        26.96 
TCGA-24-1550 TCGA-24-1567 TCGA-24-2020 TCGA-24-2024 TCGA-24-2027 TCGA-25-1315 
       41.06        17.23       152.02        58.16       109.71        52.04 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1323 TCGA-25-1632 TCGA-25-1634 TCGA-25-1871 
       42.05         2.01        12.99        59.15        35.87        24.99 
TCGA-25-1877 TCGA-25-2393 TCGA-29-1762 TCGA-29-1774 TCGA-29-2414 TCGA-29-2425 
       24.00        38.04        86.60        17.33        86.17        65.00 
TCGA-29-2431 TCGA-30-1714 TCGA-30-1853 TCGA-30-1859 TCGA-36-1575 TCGA-36-1577 
       42.25        38.07        36.26        48.10         8.55        25.74 
TCGA-36-2537 TCGA-36-2552 TCGA-42-2591 TCGA-59-2363 TCGA-59-2372 TCGA-61-1730 
       25.91        11.47        40.77         5.42        44.81         4.34 
TCGA-61-1900 TCGA-61-2088 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 
        5.79         4.77        65.52        55.50         6.48 

subtype1 subtype2 subtype3 
    0.30     0.26     0.79 
subtype1 subtype2 subtype3 
  129.96   180.20   152.02 
subtype1 subtype2 subtype3 
   30.21    26.99    34.06 
[1] "0.3 - 130.0 (30.2)" "0.3 - 180.2 (27.0)" "0.8 - 152.0 (34.1)"
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 279   3
  subtype2 143   1
  subtype3  78   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  279    3
  subtype2  143    1
  subtype3   78    1
     clus
vv    subtype1 subtype2 subtype3
  NO       279      143       78
  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"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    10                        14
  subtype2                                2     7                         6
  subtype3                                0     3                         4
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         1   274
  subtype2                                         0   136
  subtype3                                         0    76
D2V7, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 0        2        0
  ASIAN                                           10        7        3
  BLACK OR AFRICAN AMERICAN                       14        6        4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1        0        0
  WHITE                                          274      136       76
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
          cls
clus         0   1
  subtype1   8 179
  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  67  91
  subtype2  68  93
  subtype3 122 116
subtype1 subtype2 subtype3 
     158      161      238 
subtype1 subtype2 subtype3 
      91       93      116 
$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-04-1516 TCGA-04-1530 TCGA-04-1542 TCGA-04-1644 
        0.53        44.32        41.59       119.08        84.20        48.89 
TCGA-04-1649 TCGA-04-1651 TCGA-09-1664 TCGA-09-1665 TCGA-09-1670 TCGA-09-1672 
       64.64        36.23        74.93        41.62        17.98         5.85 
TCGA-09-1675 TCGA-09-2044 TCGA-09-2056 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 
       97.55         6.12        12.46        34.19        32.88        14.66 
TCGA-10-0936 TCGA-10-0938 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0758 
       36.92        20.91         2.73        12.39        31.20        11.38 
TCGA-13-0760 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0801 
       11.54        40.24       118.42       107.28        19.59         8.28 
TCGA-13-0803 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0893 TCGA-13-0903 
       43.86       107.18        91.40        74.27        43.36        47.38 
TCGA-13-0911 TCGA-13-0919 TCGA-13-0924 TCGA-13-1404 TCGA-13-1484 TCGA-13-1485 
       27.72        84.53         6.08         6.61        98.04        20.68 
TCGA-13-1488 TCGA-13-1494 TCGA-13-1500 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 
       70.82        38.20        13.97         4.18         3.91         3.09 
TCGA-13-2060 TCGA-13-2071 TCGA-20-0987 TCGA-20-1686 TCGA-23-1024 TCGA-23-1028 
       77.88        25.41        23.05         2.93        15.39        49.41 
TCGA-23-1032 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-2072 
        2.76        19.46        33.30        86.01       129.96        24.95 
TCGA-23-2643 TCGA-24-0966 TCGA-24-0970 TCGA-24-0979 TCGA-24-0980 TCGA-24-1413 
        4.70         7.63        11.64        41.56         7.66         6.31 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1434 TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 
        6.38         7.82        18.67         8.55        12.46        45.14 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1557 TCGA-24-1563 TCGA-24-1565 
       41.06        51.91        41.39        39.88        47.70        10.26 
TCGA-24-1842 TCGA-24-1844 TCGA-24-1846 TCGA-24-1850 TCGA-24-1924 TCGA-24-1927 
        8.32         3.72         4.37         5.52        30.21        16.44 
TCGA-24-1930 TCGA-24-2023 TCGA-24-2033 TCGA-24-2035 TCGA-24-2038 TCGA-24-2261 
       81.11        44.84        18.48        28.18        44.52         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2281 TCGA-24-2289 TCGA-24-2297 TCGA-24-2298 
        0.36        47.54        44.61        67.36        55.86        53.26 
TCGA-25-1313 TCGA-25-1315 TCGA-25-1320 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 
       26.96        52.04        37.97         2.99        15.02        18.58 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1633 TCGA-25-1634 TCGA-25-2391 TCGA-25-2400 
       12.95        20.61        62.17        35.87        49.05        42.02 
TCGA-25-2401 TCGA-25-2408 TCGA-29-1688 TCGA-29-1694 TCGA-29-1695 TCGA-29-1698 
        2.96        31.00        78.90        39.02        40.41        68.32 
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-36-2529 
       15.68         0.26        51.39        30.18         2.20        35.05 
TCGA-36-2534 TCGA-36-2537 TCGA-36-2540 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 
       29.82        25.91        23.80        20.52        14.17         6.05 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 TCGA-57-1584 
       47.57        23.74        10.42        40.77        24.03        21.14 
TCGA-57-1586 TCGA-57-1994 TCGA-59-2350 TCGA-59-2351 TCGA-59-2354 TCGA-61-1724 
       22.32        25.02        22.32       116.12        34.39        20.94 
TCGA-61-1895 TCGA-61-1903 TCGA-61-1907 TCGA-61-1914 TCGA-61-1919 TCGA-61-2009 
        1.45        13.02        31.30        56.61        38.17        39.85 
TCGA-61-2109 TCGA-61-2113 
       20.68        22.22 

$subtype2
TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1346 TCGA-04-1361 TCGA-04-1514 
       41.00         1.81         2.01        65.52        32.52        56.55 
TCGA-04-1525 TCGA-04-1648 TCGA-04-1655 TCGA-09-0364 TCGA-09-0369 TCGA-09-1661 
       38.37        28.64        45.37        29.16        35.57        38.43 
TCGA-09-1669 TCGA-09-2043 TCGA-09-2055 TCGA-10-0925 TCGA-10-0927 TCGA-10-0937 
       30.51         6.18        26.93        54.31        81.86        19.99 
TCGA-13-0714 TCGA-13-0727 TCGA-13-0755 TCGA-13-0757 TCGA-13-0766 TCGA-13-0768 
        6.21        15.19         2.50        11.18        56.71        58.65 
TCGA-13-0800 TCGA-13-0805 TCGA-13-0807 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 
        8.12        35.31        13.61        70.39        61.84        67.99 
TCGA-13-0894 TCGA-13-0897 TCGA-13-0900 TCGA-13-0906 TCGA-13-0913 TCGA-13-1405 
       49.61        57.47        57.07        44.94        29.98         7.36 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 TCGA-13-1483 TCGA-13-1487 TCGA-13-1495 
        4.21         5.33        87.06        29.42        22.39        49.25 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1510 TCGA-13-2057 TCGA-13-2059 
       32.84        16.57         4.21         2.56        80.02        78.48 
TCGA-20-1682 TCGA-20-1687 TCGA-23-1023 TCGA-23-1027 TCGA-23-1029 TCGA-23-1114 
       27.52         2.66        40.54        32.09         8.81        68.68 
TCGA-23-1120 TCGA-23-1809 TCGA-23-2077 TCGA-23-2647 TCGA-24-0975 TCGA-24-0982 
        4.27         0.53       115.89         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-24-1553 TCGA-24-1562 
      105.99        57.40        64.27        56.58        58.09        45.50 
TCGA-24-1567 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1847 TCGA-24-1849 
       17.23        88.37        48.33        38.24        11.28         5.79 
TCGA-24-1923 TCGA-24-2019 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2254 
       22.68         4.87        58.16       109.71        14.43        57.07 
TCGA-24-2271 TCGA-24-2293 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1321 
       31.63        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-25-1635 TCGA-25-2042 TCGA-25-2396 TCGA-25-2398 TCGA-25-2404 
        0.30        52.04        13.02         3.02        45.01        29.03 
TCGA-29-1691 TCGA-29-1693 TCGA-29-1696 TCGA-29-1705 TCGA-29-1710 TCGA-29-1763 
       48.33       101.79        33.93        18.25        31.27        66.81 
TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 TCGA-29-1778 TCGA-29-1783 
       24.36        22.55        17.33        11.84        14.93         7.23 
TCGA-29-2414 TCGA-29-2427 TCGA-29-2432 TCGA-29-2436 TCGA-30-1855 TCGA-30-1861 
       86.17        62.47        21.47         9.76         2.47        34.78 
TCGA-30-1862 TCGA-30-1867 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 
        6.12         1.22        24.26        30.05        48.79        45.57 
TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1574 TCGA-36-1580 
       42.51        44.12        28.77        29.10        22.55        24.23 
TCGA-36-2538 TCGA-36-2542 TCGA-42-2588 TCGA-57-1585 TCGA-57-1993 TCGA-59-2352 
       25.08        21.60        28.93         1.74        25.08         9.40 
TCGA-59-2355 TCGA-59-2363 TCGA-61-1721 TCGA-61-1722 TCGA-61-1730 TCGA-61-1736 
        2.14         5.42        11.11         8.09         4.34        48.79 
TCGA-61-1899 TCGA-61-1901 TCGA-61-1904 TCGA-61-1906 TCGA-61-1998 TCGA-61-2002 
        8.42        11.41         9.07        34.13         5.52        17.98 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2095 
        4.01        30.64         1.18        45.96        45.40        61.64 
TCGA-61-2097 TCGA-61-2101 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       60.62        55.50         6.35        31.07         8.61 

$subtype3
TCGA-04-1336 TCGA-04-1342 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 
       49.15        18.51        63.09        21.57        63.98        49.28 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1369 TCGA-04-1371 TCGA-04-1517 
       33.67        76.57       103.40        21.11        82.39        19.99 
TCGA-04-1519 TCGA-04-1638 TCGA-04-1646 TCGA-04-1652 TCGA-04-1654 TCGA-09-0365 
        0.79        55.43        27.88        31.86        47.70         9.47 
TCGA-09-0366 TCGA-09-0367 TCGA-09-1659 TCGA-09-1662 TCGA-09-1666 TCGA-09-1667 
       57.76        17.98         9.99        89.33        57.60        61.87 
TCGA-09-1668 TCGA-09-1673 TCGA-09-1674 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 
       55.36         3.02         8.55        35.15         4.54       112.41 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-10-0926 TCGA-10-0928 
       71.11        63.09        39.75        20.94        25.91        18.51 
TCGA-10-0934 TCGA-10-0935 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0730 
        6.71        35.44        24.59        44.55        39.58        17.82 
TCGA-13-0751 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0765 TCGA-13-0794 
       55.17        38.01       111.78        61.84        28.57        30.35 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0802 TCGA-13-0804 TCGA-13-0883 TCGA-13-0887 
        8.71         7.79         8.19        35.28        68.94        66.67 
TCGA-13-0891 TCGA-13-0899 TCGA-13-0901 TCGA-13-0904 TCGA-13-0905 TCGA-13-0908 
       69.01        56.15        19.36        48.33        47.84        44.84 
TCGA-13-0910 TCGA-13-0912 TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 
       37.08        34.06        21.17        13.81         4.64         6.41 
TCGA-13-1403 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1477 
       10.88         6.05         5.92         6.84         4.70        54.64 
TCGA-13-1482 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1496 TCGA-13-1497 
       61.71        82.88        52.44        73.55         4.24        54.31 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1506 TCGA-13-1507 TCGA-13-2061 TCGA-13-2065 
       37.61        38.40         4.41         4.77        76.90        65.52 
TCGA-13-2066 TCGA-20-0990 TCGA-20-0991 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 
       70.13        25.94        26.20        25.38        19.10        16.70 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1026 TCGA-23-1030 TCGA-23-1031 TCGA-23-1107 
       47.54        49.68        26.83        29.13        18.90         0.30 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1121 TCGA-23-1122 
       51.35        54.51         3.22        31.20         6.38        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 
       33.47        58.13        87.48        91.66        77.00        49.84 
TCGA-23-2641 TCGA-23-2645 TCGA-23-2649 TCGA-24-1103 TCGA-24-1418 TCGA-24-1419 
        2.76         4.50         3.81        54.12         7.99         7.86 
TCGA-24-1424 TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 
        6.02         5.36        17.39        28.37        18.64        43.53 
TCGA-24-1463 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
       72.92         9.11         3.45         1.18        22.22        26.96 
TCGA-24-1548 TCGA-24-1555 TCGA-24-1556 TCGA-24-1558 TCGA-24-1560 TCGA-24-1564 
       16.21        88.50        70.62        19.53        44.09        25.87 
TCGA-24-1603 TCGA-24-1843 TCGA-24-1845 TCGA-24-1920 TCGA-24-1928 TCGA-24-2020 
       90.15         3.48         3.81         9.80        11.05       152.02 
TCGA-24-2026 TCGA-24-2030 TCGA-24-2036 TCGA-24-2260 TCGA-24-2280 TCGA-24-2288 
       34.82        55.92        64.01        36.16        70.45         0.82 
TCGA-24-2290 TCGA-24-2295 TCGA-25-1312 TCGA-25-1314 TCGA-25-1319 TCGA-25-1324 
       36.23        33.11         1.02        33.01        65.00        34.03 
TCGA-25-1325 TCGA-25-1632 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 
       32.09        59.15        14.96        24.99        24.00        85.05 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2397 TCGA-25-2399 TCGA-25-2409 TCGA-29-1690 
        1.02        38.04        12.00        19.99        26.99        47.61 
TCGA-29-1697 TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 TCGA-29-1707 TCGA-29-1761 
       31.20        36.36        16.93        59.67        41.98        17.36 
TCGA-29-1762 TCGA-29-1764 TCGA-29-1769 TCGA-29-1775 TCGA-29-1777 TCGA-29-1781 
       86.60        62.93        22.98        12.36        12.30         8.38 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 TCGA-30-1714 
        5.36        36.30        13.84        42.25        11.47        38.07 
TCGA-30-1718 TCGA-30-1853 TCGA-30-1859 TCGA-30-1860 TCGA-30-1866 TCGA-30-1880 
       51.91        36.26        48.10        44.91        36.62        57.57 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-36-1570 TCGA-36-1571 TCGA-36-1575 
       18.77        22.49         6.71        21.53        22.85         8.55 
TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 
       30.08        25.74        27.85        24.69        33.01        29.49 
TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2551 TCGA-36-2552 TCGA-42-2589 
        2.24        20.98        18.31        16.18        11.47        42.02 
TCGA-57-1583 TCGA-57-1992 TCGA-59-2348 TCGA-59-2349 TCGA-59-2372 TCGA-61-1725 
       11.38        29.00       180.20        80.12        44.81        31.43 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 TCGA-61-1734 TCGA-61-1737 TCGA-61-1738 
       18.54        27.88        31.79        28.47        44.84        35.80 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1900 TCGA-61-1910 TCGA-61-1913 
        2.43        33.67        43.69         5.79        37.05        48.92 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 TCGA-61-2000 TCGA-61-2012 
       67.76        43.43        15.75         2.01        14.50        30.64 
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-61-2110 TCGA-61-2111 
        6.48        76.87        44.52       125.75 

subtype1 subtype2 subtype3 
    0.26     0.30     0.30 
subtype1 subtype2 subtype3 
  129.96   115.89   180.20 
subtype1 subtype2 subtype3 
  30.000   28.930   31.315 
[1] "0.3 - 130.0 (30.0)" "0.3 - 115.9 (28.9)" "0.3 - 180.2 (31.3)"
D3V2, continuous
          vv
clus       OMENTUM OVARY PERITONEUM OVARY
  subtype1       0   156                2
  subtype2       1   164                0
  subtype3       1   237                0
D3V3, multiclass
                  clus
vv                 subtype1 subtype2 subtype3
  OMENTUM                 0        1        1
  OVARY                 156      164      237
  PERITONEUM OVARY        2        0        0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V4, binary
          cls
clus         0   1
  subtype1 142   1
  subtype2 146   1
  subtype3 210   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  142    1
  subtype2  146    1
  subtype3  210    3
     clus
vv    subtype1 subtype2 subtype3
  NO       142      146      210
  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  4 12  0
  subtype2  3  9  1
  subtype3  7  6  0
D3V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0        4        3        7
  R1       12        9        6
  R2        0        1        0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     3                         8
  subtype2                                2     6                         5
  subtype3                                0    11                        10
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0   137
  subtype2                                         0   143
  subtype3                                         1   205
D3V7, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 0        2        0
  ASIAN                                            3        6       11
  BLACK OR AFRICAN AMERICAN                        8        5       10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        1
  WHITE                                          137      143      205
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
          cls
clus         0   1
  subtype1   5  88
  subtype2   1  97
  subtype3   5 144
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   88
  subtype2    1   97
  subtype3    5  144
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            5        1        5
  NOT HISPANIC OR LATINO       88       97      144
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = MIR_CHIERARCHICAL
D4V1, survival
           sevent
clus2        0  1
  subtype1  34 49
  subtype10 28 28
  subtype2  23 35
  subtype3  43 43
  subtype4   9 25
  subtype5  36 38
  subtype6  16 20
  subtype7  23 13
  subtype8  25 25
  subtype9  20 24
 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 
       49        28        35        43        25        38        20        13 
 subtype8  subtype9 
       25        24 
$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-10-0931 TCGA-13-0724 TCGA-13-0726 
       36.23         5.85        12.46        32.88         2.73        31.20 
TCGA-13-0760 TCGA-13-0791 TCGA-13-0801 TCGA-13-0886 TCGA-13-0919 TCGA-13-1404 
       11.54        40.24         8.28        74.27        84.53         6.61 
TCGA-13-1485 TCGA-13-1494 TCGA-13-1500 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 
       20.68        38.20        13.97         4.18         3.91         3.09 
TCGA-13-2071 TCGA-20-0987 TCGA-20-1686 TCGA-23-1024 TCGA-23-1028 TCGA-23-1116 
       25.41        23.05         2.93        15.39        49.41        19.46 
TCGA-23-1117 TCGA-23-1119 TCGA-23-1120 TCGA-23-2072 TCGA-23-2643 TCGA-24-0970 
       33.30       129.96         4.27        24.95         4.70        11.64 
TCGA-24-0980 TCGA-24-1416 TCGA-24-1464 TCGA-24-1550 TCGA-24-1551 TCGA-24-1557 
        7.66         6.38        12.46        41.06        51.91        39.88 
TCGA-24-1563 TCGA-24-1565 TCGA-24-1846 TCGA-24-1850 TCGA-24-1930 TCGA-24-2023 
       47.70        10.26         4.37         5.52        81.11        44.84 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2261 TCGA-24-2262 TCGA-24-2281 TCGA-24-2297 
       44.52        57.07         0.79         0.36        44.61        55.86 
TCGA-24-2298 TCGA-25-1313 TCGA-25-1320 TCGA-25-1322 TCGA-25-1329 TCGA-25-1627 
       53.26        26.96        37.97         2.99        15.02        12.95 
TCGA-25-1628 TCGA-25-1633 TCGA-25-2391 TCGA-25-2408 TCGA-29-1694 TCGA-29-1711 
       20.61        62.17        49.05        31.00        39.02        34.62 
TCGA-29-1768 TCGA-29-2428 TCGA-30-1857 TCGA-31-1946 TCGA-31-1959 TCGA-36-1580 
       31.30        45.11         0.26        30.18         2.20        24.23 
TCGA-36-2529 TCGA-36-2537 TCGA-36-2540 TCGA-36-2547 TCGA-42-2587 TCGA-42-2590 
       35.05        25.91        23.80        20.52        23.74        10.42 
TCGA-57-1582 TCGA-59-2351 TCGA-59-2354 TCGA-61-1914 TCGA-61-2009 
       24.03       116.12        34.39        56.61        39.85 

$subtype10
TCGA-04-1525 TCGA-09-1664 TCGA-09-1675 TCGA-09-2043 TCGA-09-2045 TCGA-09-2055 
       38.37        74.93        97.55         6.18        35.15        26.93 
TCGA-10-0925 TCGA-10-0936 TCGA-10-0938 TCGA-13-0751 TCGA-13-0755 TCGA-13-0912 
       54.31        36.92        20.91        55.17         2.50        34.06 
TCGA-13-0913 TCGA-13-1477 TCGA-13-1489 TCGA-13-2059 TCGA-20-1685 TCGA-23-2077 
       29.98        54.64        82.88        78.48        16.70       115.89 
TCGA-24-0966 TCGA-24-0979 TCGA-24-1103 TCGA-24-1413 TCGA-24-1426 TCGA-24-1844 
        7.63        41.56        54.12         6.31         5.36         3.72 
TCGA-24-1923 TCGA-24-2019 TCGA-24-2036 TCGA-25-1317 TCGA-25-1321 TCGA-25-1625 
       22.68         4.87        64.01         2.01        33.96        27.62 
TCGA-25-1870 TCGA-25-2404 TCGA-29-1695 TCGA-29-1703 TCGA-29-1771 TCGA-29-1783 
       14.96        29.03        40.41        59.67        22.55         7.23 
TCGA-36-1570 TCGA-36-1571 TCGA-36-2538 TCGA-42-2582 TCGA-42-2591 TCGA-57-1993 
       21.53        22.85        25.08        47.57        40.77        25.08 
TCGA-59-2352 TCGA-61-1721 TCGA-61-1728 TCGA-61-1734 TCGA-61-1736 TCGA-61-1899 
        9.40        11.11        27.88        28.47        48.79         8.42 
TCGA-61-1901 TCGA-61-1904 TCGA-61-1906 TCGA-61-1918 TCGA-61-2008 TCGA-61-2018 
       11.41         9.07        34.13        15.75        30.64        45.40 
TCGA-61-2096 TCGA-61-2102 
       58.39         6.48 

$subtype2
TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1341 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-10-0928 TCGA-13-0921 
       64.64        31.86        38.43        17.98        18.51         4.64 
TCGA-13-1482 TCGA-13-1487 TCGA-13-1488 TCGA-13-1491 TCGA-13-1506 TCGA-20-1684 
       61.71        22.39        70.82        52.44         4.41        19.10 
TCGA-23-1031 TCGA-23-1111 TCGA-23-2641 TCGA-24-0982 TCGA-24-1435 TCGA-24-1467 
       18.90         3.22         2.76        22.32        43.53       105.99 
TCGA-24-1544 TCGA-24-1552 TCGA-24-1556 TCGA-24-1603 TCGA-24-1616 TCGA-24-1842 
       26.96        41.39        70.62        90.15        38.24         8.32 
TCGA-24-1845 TCGA-24-2024 TCGA-25-1315 TCGA-25-1319 TCGA-25-1630 TCGA-25-1631 
        3.81        58.16        52.04        65.00        38.20         0.30 
TCGA-25-2400 TCGA-29-1707 TCGA-29-1778 TCGA-29-2425 TCGA-31-1955 TCGA-36-1574 
       42.02        41.98        14.93        65.00        42.51        22.55 
TCGA-36-2548 TCGA-36-2549 TCGA-57-1583 TCGA-57-1584 TCGA-57-1994 TCGA-61-1724 
       14.17         6.05        11.38        21.14        25.02        20.94 
TCGA-61-1915 TCGA-61-1995 TCGA-61-2095 TCGA-61-2097 
       67.76         2.01        61.64        60.62 

$subtype3
TCGA-04-1336 TCGA-04-1349 TCGA-04-1351 TCGA-04-1356 TCGA-04-1365 TCGA-04-1367 
       49.15        21.57        65.46        49.28        76.57       103.40 
TCGA-04-1369 TCGA-04-1371 TCGA-04-1654 TCGA-09-0367 TCGA-09-1659 TCGA-09-1666 
       21.11        82.39        47.70        17.98         9.99        57.60 
TCGA-09-2051 TCGA-10-0930 TCGA-10-0934 TCGA-13-0720 TCGA-13-0723 TCGA-13-0764 
       63.09        34.19         6.71        44.55        39.58        61.84 
TCGA-13-0765 TCGA-13-0797 TCGA-13-0804 TCGA-13-0887 TCGA-13-0901 TCGA-13-0905 
       28.57         8.71        35.28        66.67        19.36        47.84 
TCGA-13-0908 TCGA-13-0916 TCGA-13-0923 TCGA-13-1403 TCGA-13-1408 TCGA-13-1410 
       44.84        21.17         6.41        10.88         5.92         4.70 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-2061 TCGA-23-1021 TCGA-23-1026 
        4.24        54.31        37.61        76.90        47.54        26.83 
TCGA-23-1032 TCGA-23-1107 TCGA-23-1118 TCGA-23-1123 TCGA-23-1124 TCGA-23-2079 
        2.76         0.30        86.01        33.47        58.13        91.66 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2649 TCGA-24-1422 TCGA-24-1430 TCGA-24-1436 
       77.00        49.84         3.81         0.76        28.37         8.55 
TCGA-24-1466 TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 TCGA-24-1548 TCGA-24-1555 
       45.14         9.11         1.18        22.22        16.21        88.50 
TCGA-24-1560 TCGA-24-1843 TCGA-24-2030 TCGA-24-2288 TCGA-24-2290 TCGA-25-1314 
       44.09         3.48        55.92         0.82        36.23        33.01 
TCGA-25-1632 TCGA-25-1878 TCGA-25-2397 TCGA-25-2409 TCGA-29-1781 TCGA-29-1784 
       59.15        85.05        12.00        26.99         8.38         5.36 
TCGA-29-2434 TCGA-30-1860 TCGA-30-1866 TCGA-31-1950 TCGA-31-1953 TCGA-36-1576 
       11.47        44.91        36.62        18.77         6.71        30.08 
TCGA-36-1578 TCGA-36-2530 TCGA-36-2532 TCGA-36-2543 TCGA-36-2551 TCGA-59-2349 
       27.85        33.01        29.49         2.24        16.18        80.12 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1910 TCGA-61-2000 TCGA-61-2087 
       44.84        35.80         2.43        37.05        14.50         4.80 
TCGA-61-2092 TCGA-61-2111 
       51.72       125.75 

$subtype4
TCGA-04-1338 TCGA-09-1665 TCGA-13-0725 TCGA-13-0766 TCGA-13-0793 TCGA-13-0807 
       46.62        41.62        12.39        56.71       107.28        13.61 
TCGA-13-0900 TCGA-13-0911 TCGA-13-0924 TCGA-24-1434 TCGA-24-1545 TCGA-24-1546 
       57.07        27.72         6.08        18.67        57.40        64.27 
TCGA-24-1928 TCGA-24-2033 TCGA-24-2035 TCGA-24-2260 TCGA-24-2289 TCGA-25-1326 
       11.05        18.48        28.18        36.16        67.36        41.06 
TCGA-25-1623 TCGA-25-1626 TCGA-25-2401 TCGA-29-1693 TCGA-29-1698 TCGA-29-1701 
       18.58        17.03         2.96       101.79        68.32        16.93 
TCGA-29-1766 TCGA-30-1856 TCGA-30-1867 TCGA-30-1869 TCGA-61-1895 TCGA-61-1919 
       39.42        15.68         1.22        51.39         1.45        38.17 
TCGA-61-1998 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 
        5.52        22.22         6.35        31.07 

$subtype5
TCGA-04-1346 TCGA-09-1662 TCGA-09-1673 TCGA-09-2053 TCGA-09-2054 TCGA-10-0927 
       65.52        89.33         3.02        39.75        20.94        81.86 
TCGA-13-0727 TCGA-13-0757 TCGA-13-0761 TCGA-13-0768 TCGA-13-0799 TCGA-13-0805 
       15.19        11.18        38.01        58.65         7.79        35.31 
TCGA-13-0883 TCGA-13-0889 TCGA-13-0890 TCGA-13-0910 TCGA-13-1405 TCGA-13-1411 
       68.94        61.84        67.99        37.08         7.36         4.21 
TCGA-13-1481 TCGA-13-1495 TCGA-13-1499 TCGA-13-1505 TCGA-13-1507 TCGA-20-1683 
       87.06        49.25        38.40         4.21         4.77        25.38 
TCGA-23-1023 TCGA-23-1109 TCGA-23-1122 TCGA-24-0975 TCGA-24-1423 TCGA-24-1425 
       40.54        51.35        39.09        21.80         6.25         5.95 
TCGA-24-1428 TCGA-24-1463 TCGA-24-1470 TCGA-24-1553 TCGA-24-1564 TCGA-24-1604 
       17.39        72.92         3.45        58.09        25.87        88.37 
TCGA-24-1614 TCGA-24-1849 TCGA-24-2026 TCGA-24-2271 TCGA-24-2280 TCGA-24-2293 
       48.33         5.79        34.82        31.63        70.45        16.64 
TCGA-25-1328 TCGA-25-2042 TCGA-25-2396 TCGA-25-2398 TCGA-29-1710 TCGA-29-1763 
       66.05        13.02         3.02        45.01        31.27        66.81 
TCGA-29-1764 TCGA-29-1769 TCGA-29-1770 TCGA-29-1777 TCGA-29-1785 TCGA-29-2414 
       62.93        22.98        24.36        12.30        36.30        86.17 
TCGA-29-2427 TCGA-29-2431 TCGA-29-2432 TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 
       62.47        42.25        21.47        38.07        51.91         2.47 
TCGA-30-1862 TCGA-30-1892 TCGA-31-1951 TCGA-31-1956 TCGA-36-2542 TCGA-36-2544 
        6.12        48.79        22.49        44.12        21.60        20.98 
TCGA-57-1585 TCGA-57-1586 TCGA-59-2348 TCGA-61-2003 TCGA-61-2101 TCGA-61-2104 
        1.74        22.32       180.20         4.01        55.50        76.87 
TCGA-61-2110 TCGA-61-2614 
       44.52         8.61 

$subtype6
TCGA-04-1347 TCGA-04-1350 TCGA-09-0365 TCGA-09-2050 TCGA-10-0935 TCGA-13-0762 
       63.09        63.98         9.47        71.11        35.44       111.78 
TCGA-13-0794 TCGA-13-0899 TCGA-13-0904 TCGA-13-1407 TCGA-13-1409 TCGA-13-1492 
       30.35        56.15        48.33         6.05         6.84        73.55 
TCGA-13-2066 TCGA-20-0990 TCGA-23-1030 TCGA-23-1110 TCGA-23-1113 TCGA-24-1424 
       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 

$subtype7
TCGA-04-1348 TCGA-09-1667 TCGA-09-1668 TCGA-09-2044 TCGA-13-0758 TCGA-13-0795 
       48.76        61.87        55.36         6.12        11.38        19.59 
TCGA-13-0885 TCGA-13-0891 TCGA-13-1484 TCGA-13-2060 TCGA-13-2065 TCGA-20-0991 
       91.40        69.01        98.04        77.88        65.52        26.20 
TCGA-23-2078 TCGA-24-1417 TCGA-24-1924 TCGA-24-1927 TCGA-24-2029 TCGA-24-2267 
       87.48         7.82        30.21        16.44        14.43        47.54 
TCGA-25-1325 TCGA-25-1635 TCGA-29-1688 TCGA-29-1690 TCGA-29-1699 TCGA-36-1581 
       32.09        52.04        78.90        47.61        36.36        24.69 
TCGA-36-2534 TCGA-36-2545 TCGA-42-2589 TCGA-59-2350 TCGA-61-1722 TCGA-61-1727 
       29.82        18.31        42.02        22.32         8.09        18.54 
TCGA-61-1903 TCGA-61-1907 TCGA-61-1913 TCGA-61-2012 TCGA-61-2094 TCGA-61-2109 
       13.02        31.30        48.92        30.64        71.74        20.68 

$subtype8
TCGA-04-1364 TCGA-04-1514 TCGA-04-1655 TCGA-09-0364 TCGA-09-0369 TCGA-09-1669 
       33.67        56.55        45.37        29.16        35.57        30.51 
TCGA-09-1674 TCGA-09-2048 TCGA-09-2049 TCGA-10-0926 TCGA-10-0933 TCGA-13-0717 
        8.55         4.54       112.41        25.91        14.66        24.59 
TCGA-13-0730 TCGA-13-0800 TCGA-13-0802 TCGA-13-0888 TCGA-13-0906 TCGA-13-0920 
       17.82         8.12         8.19        70.39        44.94        13.81 
TCGA-13-2057 TCGA-20-1682 TCGA-23-1022 TCGA-23-1029 TCGA-23-1114 TCGA-23-1121 
       80.02        27.52        49.68         8.81        68.68         6.38 
TCGA-23-1809 TCGA-23-2645 TCGA-24-1418 TCGA-24-1419 TCGA-24-1567 TCGA-24-1920 
        0.53         4.50         7.99         7.86        17.23         9.80 
TCGA-24-2020 TCGA-24-2027 TCGA-25-1316 TCGA-25-1323 TCGA-25-1634 TCGA-25-1871 
      152.02       109.71        42.05        12.99        35.87        24.99 
TCGA-25-1877 TCGA-25-2393 TCGA-29-1702 TCGA-29-1762 TCGA-29-1774 TCGA-29-1775 
       24.00        38.04        23.93        86.60        17.33        12.36 
TCGA-36-1577 TCGA-36-2552 TCGA-57-1992 TCGA-59-2363 TCGA-61-1730 TCGA-61-1741 
       25.74        11.47        29.00         5.42         4.34        33.67 
TCGA-61-1900 TCGA-61-2098 
        5.79        65.52 

$subtype9
TCGA-04-1361 TCGA-09-0366 TCGA-10-0937 TCGA-13-0714 TCGA-13-0792 TCGA-13-0803 
       32.52        57.76        19.99         6.21       118.42        43.86 
TCGA-13-0884 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0903 TCGA-13-1412 
      107.18        43.36        49.61        57.47        47.38         5.33 
TCGA-13-1483 TCGA-13-1501 TCGA-13-1504 TCGA-13-1510 TCGA-20-1687 TCGA-23-1027 
       29.42        32.84        16.57         2.56         2.66        32.09 
TCGA-23-2647 TCGA-24-1104 TCGA-24-1105 TCGA-24-1427 TCGA-24-1549 TCGA-24-1562 
        4.44        63.55        47.41         4.83        56.58        45.50 
TCGA-24-1847 TCGA-25-1318 TCGA-25-2392 TCGA-25-2399 TCGA-29-1691 TCGA-29-1705 
       11.28        34.98         1.02        19.99        48.33        18.25 
TCGA-29-1776 TCGA-29-2436 TCGA-30-1861 TCGA-30-1887 TCGA-30-1891 TCGA-31-1944 
       11.84         9.76        34.78        24.26        30.05        45.57 
TCGA-36-1568 TCGA-36-1569 TCGA-42-2588 TCGA-59-2355 TCGA-61-1725 TCGA-61-2002 
       28.77        29.10        28.93         2.14        31.43        17.98 
TCGA-61-2016 TCGA-61-2017 
        1.18        45.96 

 subtype1 subtype10  subtype2  subtype3  subtype4  subtype5  subtype6  subtype7 
     0.26      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 
   129.96    115.89    105.99    125.75    107.28    180.20    111.78     98.04 
 subtype8  subtype9 
   152.02    118.42 
 subtype1 subtype10  subtype2  subtype3  subtype4  subtype5  subtype6  subtype7 
   25.910    28.175    25.990    33.010    27.950    35.805    33.520    31.695 
 subtype8  subtype9 
   24.790    29.735 
 [1] "0.3 - 130.0 (25.9)" "2.0 - 115.9 (28.2)" "0.3 - 106.0 (26.0)"
 [4] "0.3 - 125.8 (33.0)" "1.2 - 107.3 (27.9)" "1.7 - 180.2 (35.8)"
 [7] "1.0 - 111.8 (33.5)" "6.1 - 98.0 (31.7)"  "0.5 - 152.0 (24.8)"
[10] "1.0 - 118.4 (29.7)"
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  71  1
  subtype10 55  0
  subtype2  53  1
  subtype3  77  0
  subtype4  32  0
  subtype5  66  0
  subtype6  31  0
  subtype7  32  1
  subtype8  43  2
  subtype9  38  0
[1] "tbl2"
           cls
clus        [,1] [,2]
  subtype1    71    1
  subtype10   55    0
  subtype2    53    1
  subtype3    77    0
  subtype4    32    0
  subtype5    66    0
  subtype6    31    0
  subtype7    32    1
  subtype8    43    2
  subtype9    38    0
     clus
vv    subtype1 subtype10 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        71        55       53       77       32       66       31       32
  YES        1         0        1        0        0        0        0        1
     clus
vv    subtype8 subtype9
  NO        43       38
  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"  "subtype4"  "subtype4" 
 [7] "subtype5"  "subtype2"  "subtype5"  "subtype1"  "subtype5"  "subtype5" 
[13] "subtype3"  "subtype1"  "subtype3"  "subtype3"  "subtype7"  "subtype1" 
[19] "subtype10" "subtype1"  "subtype5"  "subtype3"  "subtype5"  "subtype7" 
[25] "subtype1"  "subtype2"  "subtype2"  "subtype3"  "subtype10" "subtype1" 
[31] "subtype7"  "subtype1"  "subtype10" "subtype4"  "subtype4"  "subtype5" 
    clus
vv   subtype1 subtype10 subtype2 subtype3 subtype4 subtype5 subtype7
  R0        2         2        1        2        0        1        2
  R1        7         1        2        4        5        6        1
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
           vv
clus        AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                 0     2                         3
  subtype10                                1     2                         4
  subtype2                                 0     2                         5
  subtype3                                 0     4                         4
  subtype4                                 0     0                         1
  subtype5                                 1     3                         2
  subtype6                                 0     1                         0
  subtype7                                 0     1                         1
  subtype8                                 0     4                         1
  subtype9                                 0     1                         2
           vv
clus        NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                          0    71
  subtype10                                         0    47
  subtype2                                          0    48
  subtype3                                          1    73
  subtype4                                          0    33
  subtype5                                          0    66
  subtype6                                          0    34
  subtype7                                          0    32
  subtype8                                          0    42
  subtype9                                          0    39
D4V7, multiclass
                                           clus
vv                                          subtype1 subtype10 subtype2
  AMERICAN INDIAN OR ALASKA NATIVE                 0         1        0
  ASIAN                                            2         2        2
  BLACK OR AFRICAN AMERICAN                        3         4        5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0         0        0
  WHITE                                           71        47       48
                                           clus
vv                                          subtype3 subtype4 subtype5 subtype6
  AMERICAN INDIAN OR ALASKA NATIVE                 0        0        1        0
  ASIAN                                            4        0        3        1
  BLACK OR AFRICAN AMERICAN                        4        1        2        0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1        0        0        0
  WHITE                                           73       33       66       34
                                           clus
vv                                          subtype7 subtype8 subtype9
  AMERICAN INDIAN OR ALASKA NATIVE                 0        0        0
  ASIAN                                            1        4        1
  BLACK OR AFRICAN AMERICAN                        1        1        2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        0
  WHITE                                           32       42       39
[1]  5 10
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
           cls
clus         0  1
  subtype1   3 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  70  96
  subtype2  98  99
  subtype3  93 103
subtype1 subtype2 subtype3 
     166      197      196 
subtype1 subtype2 subtype3 
      96       99      103 
$subtype1
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1350 TCGA-04-1351 
       43.92        41.00         1.81         2.01        63.98        65.46 
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-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0369 TCGA-09-1659 TCGA-09-1664 
       29.16         9.47        57.76        35.57         9.99        74.93 
TCGA-09-1666 TCGA-09-1672 TCGA-09-2048 TCGA-09-2055 TCGA-09-2056 TCGA-10-0926 
       57.60         5.85         4.54        26.93        12.46        25.91 
TCGA-10-0930 TCGA-10-0934 TCGA-10-0935 TCGA-10-0938 TCGA-13-0720 TCGA-13-0762 
       34.19         6.71        35.44        20.91        44.55       111.78 
TCGA-13-0768 TCGA-13-0793 TCGA-13-0799 TCGA-13-0800 TCGA-13-0803 TCGA-13-0804 
       58.65       107.28         7.79         8.12        43.86        35.28 
TCGA-13-0805 TCGA-13-0886 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0899 
       35.31        74.27        61.84        67.99        69.01        56.15 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0919 TCGA-13-0921 TCGA-13-1405 
       37.08        27.72        34.06        84.53         4.64         7.36 
TCGA-13-1411 TCGA-13-1477 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 
        4.21        54.64        29.42        98.04        20.68        22.39 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1499 TCGA-13-1500 TCGA-13-1507 TCGA-13-1510 
       73.55        38.20        38.40        13.97         4.77         2.56 
TCGA-20-0987 TCGA-20-0991 TCGA-20-0996 TCGA-23-1023 TCGA-23-1030 TCGA-23-1031 
       23.05        26.20        72.20        40.54        29.13        18.90 
TCGA-23-1032 TCGA-23-1113 TCGA-23-1116 TCGA-23-1118 TCGA-23-2072 TCGA-23-2078 
        2.76        31.20        19.46        86.01        24.95        87.48 
TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-1105 TCGA-24-1416 
        7.63        11.64        21.80         7.66        47.41         6.38 
TCGA-24-1422 TCGA-24-1430 TCGA-24-1463 TCGA-24-1467 TCGA-24-1471 TCGA-24-1545 
        0.76        28.37        72.92       105.99         1.18        57.40 
TCGA-24-1546 TCGA-24-1550 TCGA-24-1551 TCGA-24-1555 TCGA-24-1560 TCGA-24-1562 
       64.27        41.06        51.91        88.50        44.09        45.50 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1603 TCGA-24-1844 TCGA-24-1849 TCGA-24-1923 
       25.87        10.26        90.15         3.72         5.79        22.68 
TCGA-24-2024 TCGA-24-2029 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2271 
       58.16        14.43        28.18        64.01        44.52        31.63 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2293 TCGA-24-2298 TCGA-25-1316 TCGA-25-1623 
       70.45        44.61        16.64        53.26        42.05        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1628 TCGA-25-1633 TCGA-25-2042 TCGA-25-2399 
       27.62        17.03        20.61        62.17        13.02        19.99 
TCGA-25-2408 TCGA-29-1690 TCGA-29-1707 TCGA-29-1762 TCGA-29-1771 TCGA-29-1785 
       31.00        47.61        41.98        86.60        22.55        36.30 
TCGA-29-2427 TCGA-29-2436 TCGA-30-1853 TCGA-30-1880 TCGA-30-1892 TCGA-31-1950 
       62.47         9.76        36.26        57.57        48.79        18.77 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1576 TCGA-36-1577 TCGA-36-1580 TCGA-36-2532 
       28.77        29.10        30.08        25.74        24.23        29.49 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2543 TCGA-3P-A9WA TCGA-42-2587 
       25.91        25.08        23.80         2.24        13.81        23.74 
TCGA-42-2590 TCGA-59-2349 TCGA-59-2350 TCGA-59-2354 TCGA-59-2355 TCGA-61-1721 
       10.42        80.12        22.32        34.39         2.14        11.11 
TCGA-61-1727 TCGA-61-1730 TCGA-61-1734 TCGA-61-1736 TCGA-61-1743 TCGA-61-1901 
       18.54         4.34        28.47        48.79        43.69        11.41 
TCGA-61-1911 TCGA-61-1995 TCGA-61-1998 TCGA-61-2002 TCGA-61-2009 TCGA-61-2016 
       42.51         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-61-2097 TCGA-61-2110 TCGA-61-2612 TCGA-61-2613 
       60.62        44.52         6.35        31.07 

$subtype2
TCGA-04-1336 TCGA-04-1338 TCGA-04-1349 TCGA-04-1353 TCGA-04-1356 TCGA-04-1361 
       49.15        46.62        21.57         0.53        49.28        32.52 
TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 TCGA-04-1536 TCGA-04-1651 TCGA-04-1654 
       44.32        76.57       103.40        29.10        36.23        47.70 
TCGA-09-0367 TCGA-09-1662 TCGA-09-1665 TCGA-09-1668 TCGA-09-1669 TCGA-09-1675 
       17.98        89.33        41.62        55.36        30.51        97.55 
TCGA-09-2045 TCGA-10-0925 TCGA-10-0928 TCGA-10-0931 TCGA-10-0937 TCGA-13-0714 
       35.15        54.31        18.51        32.88        19.99         6.21 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0755 TCGA-13-0758 TCGA-13-0761 TCGA-13-0766 
       12.39        31.20         2.50        11.38        38.01        56.71 
TCGA-13-0792 TCGA-13-0797 TCGA-13-0801 TCGA-13-0802 TCGA-13-0883 TCGA-13-0884 
      118.42         8.71         8.28         8.19        68.94       107.18 
TCGA-13-0887 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       66.67        43.36        57.47        57.07        19.36        47.38 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0913 TCGA-13-0916 
       48.33        47.84        44.94        44.84        29.98        21.17 
TCGA-13-0920 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1412 TCGA-13-1481 
       13.81         6.08        10.88         6.61         5.33        87.06 
TCGA-13-1482 TCGA-13-1488 TCGA-13-1497 TCGA-13-1501 TCGA-13-1505 TCGA-13-1512 
       61.71        70.82        54.31        32.84         4.21         3.09 
TCGA-13-2059 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-20-1682 TCGA-20-1685 
       78.48        65.52        25.41        70.45        27.52        16.70 
TCGA-20-1686 TCGA-20-1687 TCGA-23-1022 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
        2.93         2.66        49.68        26.83        32.09        49.41 
TCGA-23-1029 TCGA-23-1109 TCGA-23-1117 TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 
        8.81        51.35        33.30       129.96         4.27        39.09 
TCGA-23-1124 TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
       58.13       115.89        91.66        77.00        49.84         2.76 
TCGA-23-2645 TCGA-24-0979 TCGA-24-1103 TCGA-24-1104 TCGA-24-1417 TCGA-24-1419 
        4.50        41.56        54.12        63.55         7.82         7.86 
TCGA-24-1423 TCGA-24-1425 TCGA-24-1427 TCGA-24-1428 TCGA-24-1435 TCGA-24-1436 
        6.25         5.95         4.83        17.39        43.53         8.55 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1470 TCGA-24-1474 TCGA-24-1553 TCGA-24-1556 
       12.46        45.14         3.45        22.22        58.09        70.62 
TCGA-24-1557 TCGA-24-1563 TCGA-24-1567 TCGA-24-1604 TCGA-24-1842 TCGA-24-1846 
       39.88        47.70        17.23        88.37         8.32         4.37 
TCGA-24-1847 TCGA-24-1920 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-2030 
       11.28         9.80        30.21        16.44        11.05        55.92 
TCGA-24-2254 TCGA-24-2262 TCGA-24-2267 TCGA-24-2289 TCGA-24-2297 TCGA-25-1313 
       57.07         0.36        47.54        67.36        55.86        26.96 
TCGA-25-1314 TCGA-25-1318 TCGA-25-1322 TCGA-25-1630 TCGA-25-1632 TCGA-25-1878 
       33.01        34.98         2.99        38.20        59.15        85.05 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2397 TCGA-25-2401 TCGA-25-2409 TCGA-29-1688 
       49.05         1.02        12.00         2.96        26.99        78.90 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1701 TCGA-29-1702 TCGA-29-1705 
      101.79        39.02        33.93        16.93        23.93        18.25 
TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1775 TCGA-29-1776 
       62.93        31.30        22.98        24.36        12.36        11.84 
TCGA-29-1777 TCGA-29-1781 TCGA-29-1784 TCGA-29-2425 TCGA-29-2432 TCGA-30-1718 
       12.30         8.38         5.36        65.00        21.47        51.91 
TCGA-30-1857 TCGA-30-1860 TCGA-30-1861 TCGA-30-1891 TCGA-31-1944 TCGA-31-1946 
        0.26        44.91        34.78        30.05        45.57        30.18 
TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1570 TCGA-36-1574 TCGA-36-1578 
       42.51        44.12         2.20        21.53        22.55        27.85 
TCGA-36-2530 TCGA-36-2534 TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 TCGA-36-2549 
       33.01        29.82        21.60        20.98        18.31         6.05 
TCGA-42-2582 TCGA-42-2588 TCGA-42-2591 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 
       47.57        28.93        40.77        24.03        11.38        21.14 
TCGA-57-1585 TCGA-59-A5PD TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1737 
        1.74        20.52         8.09        20.94        31.43        44.84 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1895 TCGA-61-1900 TCGA-61-1903 TCGA-61-1907 
       35.80         2.43         1.45         5.79        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 
       30.64        76.87        20.68         0.79         9.99 

$subtype3
TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 
        1.08        18.51        11.87        65.52        63.09        48.76 
TCGA-04-1364 TCGA-04-1371 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1542 
       33.67        82.39        41.59        19.99        38.37        84.20 
TCGA-04-1646 TCGA-04-1649 TCGA-04-1652 TCGA-04-1655 TCGA-09-1661 TCGA-09-1667 
       27.88        64.64        31.86        45.37        38.43        61.87 
TCGA-09-1670 TCGA-09-1673 TCGA-09-1674 TCGA-09-2043 TCGA-09-2044 TCGA-09-2049 
       17.98         3.02         8.55         6.18         6.12       112.41 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-10-0927 TCGA-10-0933 
       71.11        63.09        39.75        20.94        81.86        14.66 
TCGA-10-0936 TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 TCGA-13-0727 TCGA-13-0730 
       36.92        24.59        39.58         2.73        15.19        17.82 
TCGA-13-0751 TCGA-13-0757 TCGA-13-0760 TCGA-13-0764 TCGA-13-0791 TCGA-13-0794 
       55.17        11.18        11.54        61.84        40.24        30.35 
TCGA-13-0795 TCGA-13-0807 TCGA-13-0885 TCGA-13-0888 TCGA-13-0923 TCGA-13-1407 
       19.59        13.61        91.40        70.39         6.41         6.05 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1489 TCGA-13-1491 TCGA-13-1495 
        5.92         6.84         4.70        82.88        52.44        49.25 
TCGA-13-1496 TCGA-13-1498 TCGA-13-1504 TCGA-13-1506 TCGA-13-1509 TCGA-13-1511 
        4.24        37.61        16.57         4.41         4.18         3.91 
TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-A5FU TCGA-20-0990 TCGA-20-1683 
       80.02        77.88        76.90         8.42        25.94        25.38 
TCGA-20-1684 TCGA-23-1021 TCGA-23-1024 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 
       19.10        47.54        15.39        54.51         3.22        68.68 
TCGA-23-1121 TCGA-23-1123 TCGA-23-1809 TCGA-23-2643 TCGA-24-0982 TCGA-24-1413 
        6.38        33.47         0.53         4.70        22.32         6.31 
TCGA-24-1418 TCGA-24-1424 TCGA-24-1426 TCGA-24-1431 TCGA-24-1434 TCGA-24-1469 
        7.99         6.02         5.36        18.64        18.67         9.11 
TCGA-24-1544 TCGA-24-1548 TCGA-24-1549 TCGA-24-1552 TCGA-24-1558 TCGA-24-1614 
       26.96        16.21        56.58        41.39        19.53        48.33 
TCGA-24-1616 TCGA-24-1843 TCGA-24-1845 TCGA-24-1850 TCGA-24-1930 TCGA-24-2019 
       38.24         3.48         3.81         5.52        81.11         4.87 
TCGA-24-2020 TCGA-24-2023 TCGA-24-2026 TCGA-24-2027 TCGA-24-2033 TCGA-24-2260 
      152.02        44.84        34.82       109.71        18.48        36.16 
TCGA-24-2261 TCGA-24-2288 TCGA-24-2290 TCGA-24-2295 TCGA-25-1312 TCGA-25-1315 
        0.79         0.82        36.23        33.11         1.02        52.04 
TCGA-25-1317 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1323 TCGA-25-1329 
        2.01        65.00        37.97        33.96        12.99        15.02 
TCGA-25-1627 TCGA-25-1631 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 
       12.95         0.30        35.87        52.04        14.96        24.99 
TCGA-25-1877 TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 TCGA-25-2400 TCGA-25-2404 
       24.00        38.04         3.02        45.01        42.02        29.03 
TCGA-29-1691 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1703 
       48.33        40.41        31.20        68.32        36.36        59.67 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1763 TCGA-29-1766 TCGA-29-1774 
       31.27        34.62        17.36        66.81        39.42        17.33 
TCGA-29-1778 TCGA-29-1783 TCGA-29-2414 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 
       14.93         7.23        86.17        45.11        13.84        42.25 
TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 
       11.47        35.77        38.07         2.47        15.68        48.10 
TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1887 TCGA-31-1951 TCGA-31-1953 
        6.12        36.62         1.22        24.26        22.49         6.71 
TCGA-36-1571 TCGA-36-1575 TCGA-36-1581 TCGA-36-2529 TCGA-36-2547 TCGA-36-2548 
       22.85         8.55        24.69        35.05        20.52        14.17 
TCGA-36-2551 TCGA-36-2552 TCGA-42-2589 TCGA-42-2593 TCGA-57-1586 TCGA-57-1992 
       16.18        11.47        42.02         1.48        22.32        29.00 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2351 TCGA-59-2352 TCGA-59-2363 
       25.08        25.02       180.20       116.12         9.40         5.42 
TCGA-59-2372 TCGA-5X-AA5U TCGA-61-1728 TCGA-61-1733 TCGA-61-1741 TCGA-61-1899 
       44.81        11.87        27.88        31.79        33.67         8.42 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1917 TCGA-61-2000 TCGA-61-2003 TCGA-61-2012 
        9.07        34.13        43.43        14.50         4.01        30.64 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2111 
        4.80         4.77        65.52        55.50         6.48       125.75 
TCGA-61-2113 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
       22.22         8.61        39.68        18.94 

subtype1 subtype2 subtype3 
    0.76     0.26     0.30 
subtype1 subtype2 subtype3 
  119.08   129.96   180.20 
subtype1 subtype2 subtype3 
  30.540   30.640   25.005 
[1] "0.8 - 119.1 (30.5)" "0.3 - 130.0 (30.6)" "0.3 - 180.2 (25.0)"
D5V2, continuous
          vv
clus       OMENTUM OVARY PERITONEUM OVARY
  subtype1       1   166                0
  subtype2       0   199                0
  subtype3       2   193                2
D5V3, multiclass
                  clus
vv                 subtype1 subtype2 subtype3
  OMENTUM                 1        0        2
  OVARY                 166      199      193
  PERITONEUM OVARY        0        0        2
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V4, binary
          cls
clus         0   1
  subtype1 145   2
  subtype2 179   2
  subtype3 176   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  145    2
  subtype2  179    2
  subtype3  176    1
     clus
vv    subtype1 subtype2 subtype3
  NO       145      179      176
  YES        2        2        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  2 11  0  1
  subtype2  3  6  2  1
  subtype3 10  9  3  1
D5V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0        2        3       10
  R1       11        6        9
  R2        0        2        3
  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"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     3                         7
  subtype2                                0    10                        15
  subtype3                                2     6                        12
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0   145
  subtype2                                         1   163
  subtype3                                         0   168
D5V7, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 1        0        2
  ASIAN                                            3       10        6
  BLACK OR AFRICAN AMERICAN                        7       15       12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        1        0
  WHITE                                          145      163      168
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
          cls
clus         0   1
  subtype1   1 101
  subtype2   4 112
  subtype3   5 114
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  101
  subtype2    4  112
  subtype3    5  114
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        4        5
  NOT HISPANIC OR LATINO      101      112      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  68 103
  subtype2  85  88
  subtype3 105 111
subtype1 subtype2 subtype3 
     171      173      216 
subtype1 subtype2 subtype3 
     103       88      111 
$subtype1
TCGA-04-1331 TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1347 TCGA-04-1350 
       43.92         1.08        18.51        11.87        63.09        63.98 
TCGA-04-1364 TCGA-04-1369 TCGA-04-1371 TCGA-04-1514 TCGA-04-1530 TCGA-04-1542 
       33.67        21.11        82.39        56.55       119.08        84.20 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1652 TCGA-09-0364 TCGA-09-0365 
       55.43        48.89        27.88        31.86        29.16         9.47 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1665 TCGA-09-1669 TCGA-09-1673 
       35.57         9.99        38.43        41.62        30.51         3.02 
TCGA-09-1674 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2054 TCGA-09-2055 
        8.55         4.54       112.41        71.11        20.94        26.93 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 
       25.91        81.86        14.66         6.71        35.44        36.92 
TCGA-10-0938 TCGA-13-0717 TCGA-13-0724 TCGA-13-0730 TCGA-13-0757 TCGA-13-0762 
       20.91        24.59         2.73        17.82        11.18       111.78 
TCGA-13-0764 TCGA-13-0794 TCGA-13-0800 TCGA-13-0802 TCGA-13-0888 TCGA-13-0891 
       61.84        30.35         8.12         8.19        70.39        69.01 
TCGA-13-0899 TCGA-13-0904 TCGA-13-0906 TCGA-13-0913 TCGA-13-0920 TCGA-13-0921 
       56.15        48.33        44.94        29.98        13.81         4.64 
TCGA-13-0923 TCGA-13-1407 TCGA-13-1410 TCGA-13-1481 TCGA-13-1487 TCGA-13-1491 
        6.41         6.05         4.70        87.06        22.39        52.44 
TCGA-13-1492 TCGA-13-1496 TCGA-13-1505 TCGA-13-1507 TCGA-13-2057 TCGA-13-2060 
       73.55         4.24         4.21         4.77        80.02        77.88 
TCGA-13-2061 TCGA-13-2066 TCGA-20-0990 TCGA-20-1684 TCGA-20-1686 TCGA-23-1022 
       76.90        70.13        25.94        19.10         2.93        49.68 
TCGA-23-1024 TCGA-23-1030 TCGA-23-1032 TCGA-23-1107 TCGA-23-1109 TCGA-23-1110 
       15.39        29.13         2.76         0.30        51.35        54.51 
TCGA-23-1111 TCGA-23-1114 TCGA-23-1120 TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 
        3.22        68.68         4.27         6.38        33.47        58.13 
TCGA-23-1809 TCGA-24-1418 TCGA-24-1419 TCGA-24-1424 TCGA-24-1431 TCGA-24-1434 
        0.53         7.99         7.86         6.02        18.64        18.67 
TCGA-24-1469 TCGA-24-1544 TCGA-24-1552 TCGA-24-1558 TCGA-24-1567 TCGA-24-1843 
        9.11        26.96        41.39        19.53        17.23         3.48 
TCGA-24-1844 TCGA-24-1850 TCGA-24-1920 TCGA-24-2020 TCGA-24-2026 TCGA-24-2027 
        3.72         5.52         9.80       152.02        34.82       109.71 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2260 TCGA-24-2280 TCGA-24-2295 TCGA-24-2297 
       55.92        18.48        36.16        70.45        33.11        55.86 
TCGA-25-1312 TCGA-25-1315 TCGA-25-1316 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 
        1.02        52.04        42.05        65.00        37.97        33.96 
TCGA-25-1323 TCGA-25-1324 TCGA-25-1627 TCGA-25-1634 TCGA-25-1870 TCGA-25-1877 
       12.99        34.03        12.95        35.87        14.96        24.00 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2399 TCGA-25-2400 TCGA-29-1691 TCGA-29-1695 
       38.04         3.02        19.99        42.02        48.33        40.41 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 
       31.20        68.32        36.36        16.93        23.93        59.67 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1766 TCGA-29-1774 TCGA-29-1775 
       17.36        86.60        66.81        39.42        17.33        12.36 
TCGA-29-1778 TCGA-29-1783 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 
       14.93         7.23        86.17        65.00        45.11        13.84 
TCGA-29-2434 TCGA-30-1714 TCGA-30-1853 TCGA-30-1859 TCGA-30-1867 TCGA-36-1571 
       11.47        38.07        36.26        48.10         1.22        22.85 
TCGA-36-1575 TCGA-36-2551 TCGA-36-2552 TCGA-42-2593 TCGA-57-1992 TCGA-57-1993 
        8.55        16.18        11.47         1.48        29.00        25.08 
TCGA-59-2352 TCGA-59-2372 TCGA-61-1728 TCGA-61-1730 TCGA-61-1738 TCGA-61-1741 
        9.40        44.81        27.88         4.34        35.80        33.67 
TCGA-61-1743 TCGA-61-1910 TCGA-61-1917 TCGA-61-1919 TCGA-61-2088 TCGA-61-2092 
       43.69        37.05        43.43        38.17         4.77        51.72 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2111 
       55.50         6.48       125.75 

$subtype2
TCGA-04-1332 TCGA-04-1337 TCGA-04-1338 TCGA-04-1346 TCGA-04-1351 TCGA-04-1356 
       41.00         2.01        46.62        65.52        65.46        49.28 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 TCGA-04-1519 TCGA-04-1655 TCGA-09-1662 
       32.52        44.32        76.57         0.79        45.37        89.33 
TCGA-09-1666 TCGA-09-2045 TCGA-09-2053 TCGA-10-0928 TCGA-13-0725 TCGA-13-0727 
       57.60        35.15        39.75        18.51        12.39        15.19 
TCGA-13-0758 TCGA-13-0765 TCGA-13-0766 TCGA-13-0792 TCGA-13-0799 TCGA-13-0883 
       11.38        28.57        56.71       118.42         7.79        68.94 
TCGA-13-0884 TCGA-13-0890 TCGA-13-0893 TCGA-13-0894 TCGA-13-0901 TCGA-13-0908 
      107.18        67.99        43.36        49.61        19.36        44.84 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-1409 TCGA-13-1411 TCGA-13-1477 
       37.08        27.72        34.06         6.84         4.21        54.64 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1489 TCGA-13-1494 TCGA-13-1498 TCGA-13-1499 
       98.04        20.68        82.88        38.20        37.61        38.40 
TCGA-13-1501 TCGA-13-1509 TCGA-13-1512 TCGA-13-2071 TCGA-20-0991 TCGA-20-0996 
       32.84         4.18         3.09        25.41        26.20        72.20 
TCGA-23-1023 TCGA-23-1031 TCGA-23-1113 TCGA-23-1117 TCGA-23-1118 TCGA-23-1122 
       40.54        18.90        31.20        33.30        86.01        39.09 
TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 
      115.89        87.48        91.66         2.76         4.70         4.50 
TCGA-23-2647 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0982 TCGA-24-1104 
        4.44        11.64        21.80        41.56        22.32        63.55 
TCGA-24-1105 TCGA-24-1416 TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 
       47.41         6.38         0.76         6.25         5.95         5.36 
TCGA-24-1427 TCGA-24-1430 TCGA-24-1463 TCGA-24-1471 TCGA-24-1474 TCGA-24-1545 
        4.83        28.37        72.92         1.18        22.22        57.40 
TCGA-24-1546 TCGA-24-1550 TCGA-24-1551 TCGA-24-1553 TCGA-24-1557 TCGA-24-1560 
       64.27        41.06        51.91        58.09        39.88        44.09 
TCGA-24-1562 TCGA-24-1564 TCGA-24-1603 TCGA-24-1847 TCGA-24-1849 TCGA-24-1923 
       45.50        25.87        90.15        11.28         5.79        22.68 
TCGA-24-1927 TCGA-24-2029 TCGA-24-2036 TCGA-24-2038 TCGA-24-2298 TCGA-25-1313 
       16.44        14.43        64.01        44.52        53.26        26.96 
TCGA-25-1314 TCGA-25-1317 TCGA-25-1328 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 
       33.01         2.01        66.05        18.58        27.62        17.03 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1632 TCGA-25-1633 TCGA-25-1871 TCGA-25-2042 
       20.61        38.20        59.15        62.17        24.99        13.02 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2398 TCGA-25-2408 TCGA-25-2409 TCGA-29-1694 
       49.05         1.02        45.01        31.00        26.99        39.02 
TCGA-29-1705 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1781 TCGA-29-2427 
       18.25        31.30        22.98        24.36         8.38        62.47 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2436 TCGA-30-1855 TCGA-30-1861 TCGA-30-1866 
       42.25        21.47         9.76         2.47        34.78        36.62 
TCGA-30-1880 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1951 TCGA-31-1955 
       57.57        30.05        48.79        45.57        22.49        42.51 
TCGA-31-1956 TCGA-31-1959 TCGA-36-1569 TCGA-36-1576 TCGA-36-1577 TCGA-36-1580 
       44.12         2.20        29.10        30.08        25.74        24.23 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2544 TCGA-36-2548 TCGA-42-2589 
       25.91        25.08        23.80        20.98        14.17        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-57-1586 TCGA-57-1994 TCGA-59-2348 TCGA-59-2350 
       10.42        40.77        22.32        25.02       180.20        22.32 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-61-1721 TCGA-61-1722 TCGA-61-1725 
       34.39         2.14         5.42        11.11         8.09        31.43 
TCGA-61-1733 TCGA-61-1734 TCGA-61-1895 TCGA-61-1900 TCGA-61-1995 TCGA-61-1998 
       31.79        28.47         1.45         5.79         2.01         5.52 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 
        4.01        30.64        39.85        61.64        58.39        65.52 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       20.68        44.52         6.35        31.07         8.61 

$subtype3
TCGA-04-1335 TCGA-04-1336 TCGA-04-1348 TCGA-04-1349 TCGA-04-1353 TCGA-04-1367 
        1.81        49.15        48.76        21.57         0.53       103.40 
TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1536 TCGA-04-1648 TCGA-04-1649 
       41.59        19.99        38.37        29.10        28.64        64.64 
TCGA-04-1651 TCGA-04-1654 TCGA-09-0366 TCGA-09-0367 TCGA-09-1664 TCGA-09-1667 
       36.23        47.70        57.76        17.98        74.93        61.87 
TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 
       55.36        17.98         5.85        97.55         6.18         6.12 
TCGA-09-2051 TCGA-09-2056 TCGA-10-0925 TCGA-10-0930 TCGA-10-0931 TCGA-10-0937 
       63.09        12.46        54.31        34.19        32.88        19.99 
TCGA-13-0714 TCGA-13-0720 TCGA-13-0723 TCGA-13-0726 TCGA-13-0751 TCGA-13-0755 
        6.21        44.55        39.58        31.20        55.17         2.50 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0768 TCGA-13-0791 TCGA-13-0793 TCGA-13-0795 
       11.54        38.01        58.65        40.24       107.28        19.59 
TCGA-13-0797 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
        8.71         8.28        43.86        35.28        35.31        13.61 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0897 TCGA-13-0900 
       91.40        74.27        66.67        61.84        57.47        57.07 
TCGA-13-0903 TCGA-13-0905 TCGA-13-0916 TCGA-13-0919 TCGA-13-0924 TCGA-13-1403 
       47.38        47.84        21.17        84.53         6.08        10.88 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1412 TCGA-13-1482 TCGA-13-1483 
        6.61         7.36         5.92         5.33        61.71        29.42 
TCGA-13-1488 TCGA-13-1495 TCGA-13-1497 TCGA-13-1500 TCGA-13-1504 TCGA-13-1506 
       70.82        49.25        54.31        13.97        16.57         4.41 
TCGA-13-1510 TCGA-13-1511 TCGA-13-2059 TCGA-13-2065 TCGA-20-0987 TCGA-20-1682 
        2.56         3.91        78.48        65.52        23.05        27.52 
TCGA-20-1683 TCGA-20-1685 TCGA-20-1687 TCGA-23-1021 TCGA-23-1026 TCGA-23-1027 
       25.38        16.70         2.66        47.54        26.83        32.09 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1116 TCGA-23-1119 TCGA-23-2072 TCGA-23-2081 
       49.41         8.81        19.46       129.96        24.95        77.00 
TCGA-23-2084 TCGA-23-2649 TCGA-24-0966 TCGA-24-0980 TCGA-24-1103 TCGA-24-1413 
       49.84         3.81         7.63         7.66        54.12         6.31 
TCGA-24-1417 TCGA-24-1428 TCGA-24-1435 TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 
        7.82        17.39        43.53         8.55        12.46        45.14 
TCGA-24-1467 TCGA-24-1470 TCGA-24-1548 TCGA-24-1549 TCGA-24-1555 TCGA-24-1556 
      105.99         3.45        16.21        56.58        88.50        70.62 
TCGA-24-1563 TCGA-24-1565 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 
       47.70        10.26        88.37        48.33        38.24         8.32 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1924 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 
        3.81         4.37        30.21        11.05        81.11         4.87 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2035 TCGA-24-2254 TCGA-24-2261 TCGA-24-2262 
       44.84        58.16        28.18        57.07         0.79         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 
       47.54        31.63        44.61         0.82        67.36        36.23 
TCGA-24-2293 TCGA-25-1318 TCGA-25-1322 TCGA-25-1325 TCGA-25-1326 TCGA-25-1329 
       16.64        34.98         2.99        32.09        41.06        15.02 
TCGA-25-1631 TCGA-25-1635 TCGA-25-1878 TCGA-25-2397 TCGA-25-2401 TCGA-25-2404 
        0.30        52.04        85.05        12.00         2.96        29.03 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1696 TCGA-29-1707 TCGA-29-1710 
       78.90        47.61       101.79        33.93        41.98        31.27 
TCGA-29-1711 TCGA-29-1764 TCGA-29-1771 TCGA-29-1776 TCGA-29-1777 TCGA-29-1784 
       34.62        62.93        22.55        11.84        12.30         5.36 
TCGA-29-1785 TCGA-30-1718 TCGA-30-1856 TCGA-30-1857 TCGA-30-1860 TCGA-30-1862 
       36.30        51.91        15.68         0.26        44.91         6.12 
TCGA-30-1869 TCGA-30-1887 TCGA-31-1946 TCGA-31-1950 TCGA-31-1953 TCGA-36-1568 
       51.39        24.26        30.18        18.77         6.71        28.77 
TCGA-36-1570 TCGA-36-1574 TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 TCGA-36-2532 
       21.53        22.55        27.85        24.69        35.05        29.49 
TCGA-36-2534 TCGA-36-2542 TCGA-36-2543 TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 
       29.82        21.60         2.24        18.31        20.52         6.05 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 
       47.57        23.74        28.93        24.03        11.38        21.14 
TCGA-57-1585 TCGA-59-2349 TCGA-59-2351 TCGA-61-1724 TCGA-61-1727 TCGA-61-1736 
        1.74        80.12       116.12        20.94        18.54        48.79 
TCGA-61-1737 TCGA-61-1740 TCGA-61-1899 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 
       44.84         2.43         8.42        11.41        13.02         9.07 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 
       34.13        31.30        42.51        48.92        56.61        67.76 
TCGA-61-1918 TCGA-61-2000 TCGA-61-2002 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 
       15.75        14.50        17.98        30.64         1.18        45.96 
TCGA-61-2018 TCGA-61-2087 TCGA-61-2094 TCGA-61-2097 TCGA-61-2104 TCGA-61-2113 
       45.40         4.80        71.74        60.62        76.87        22.22 

subtype1 subtype2 subtype3 
    0.30     0.76     0.26 
subtype1 subtype2 subtype3 
  152.02   180.20   129.96 
subtype1 subtype2 subtype3 
  29.160   30.640   29.455 
[1] "0.3 - 152.0 (29.2)" "0.8 - 180.2 (30.6)" "0.3 - 130.0 (29.5)"
D6V2, continuous
          vv
clus       OMENTUM OVARY PERITONEUM OVARY
  subtype1       0   170                1
  subtype2       0   175                0
  subtype3       2   216                1
D6V3, multiclass
                  clus
vv                 subtype1 subtype2 subtype3
  OMENTUM                 0        0        2
  OVARY                 170      175      216
  PERITONEUM OVARY        1        0        1
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V4, binary
          cls
clus         0   1
  subtype1 153   1
  subtype2 155   3
  subtype3 193   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  153    1
  subtype2  155    3
  subtype3  193    1
     clus
vv    subtype1 subtype2 subtype3
  NO       153      155      193
  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"
D6V5, continuous
          vv
clus       R0 R1 R2
  subtype1  4  8  1
  subtype2  4 12  0
  subtype3  6  6  1
D6V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0        4        4        6
  R1        8       12        6
  R2        1        0        1
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     3                         9
  subtype2                                1     8                         4
  subtype3                                1     8                        11
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0   152
  subtype2                                         0   151
  subtype3                                         1   184
D6V7, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 1        1        1
  ASIAN                                            3        8        8
  BLACK OR AFRICAN AMERICAN                        9        4       11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        1
  WHITE                                          152      151      184
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
          cls
clus         0   1
  subtype1   5 103
  subtype2   2 104
  subtype3   4 124
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  103
  subtype2    2  104
  subtype3    4  124
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            5        2        4
  NOT HISPANIC OR LATINO      103      104      124
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = RPPA_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1  61  86
  subtype2 103  88
  subtype3  31  47
subtype1 subtype2 subtype3 
     147      191       78 
subtype1 subtype2 subtype3 
      86       88       47 
$subtype1
TCGA-04-1335 TCGA-04-1338 TCGA-04-1342 TCGA-04-1349 TCGA-04-1519 TCGA-04-1525 
        1.81        46.62        18.51        21.57         0.79        38.37 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-09-1664 TCGA-09-1665 
       84.20        55.43        48.89        28.64        74.93        41.62 
TCGA-09-2049 TCGA-09-2056 TCGA-10-0925 TCGA-10-0933 TCGA-13-0725 TCGA-13-0793 
      112.41        12.46        54.31        14.66        12.39       107.28 
TCGA-13-0886 TCGA-13-0894 TCGA-13-0901 TCGA-13-0903 TCGA-13-0906 TCGA-13-0910 
       74.27        49.61        19.36        47.38        44.94        37.08 
TCGA-13-0913 TCGA-13-1408 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
       29.98         5.92         4.21         5.33        54.64        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1488 TCGA-13-1491 TCGA-13-1494 
       61.71        29.42        98.04        70.82        52.44        38.20 
TCGA-13-1495 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-2059 
       49.25        37.61        38.40        13.97        32.84        78.48 
TCGA-13-2065 TCGA-13-A5FT TCGA-20-1686 TCGA-20-1687 TCGA-23-1122 TCGA-23-2078 
       65.52        70.45         2.93         2.66        39.09        87.48 
TCGA-24-0970 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1104 TCGA-24-1422 
       11.64        41.56         7.66        22.32        63.55         0.76 
TCGA-24-1423 TCGA-24-1427 TCGA-24-1466 TCGA-24-1545 TCGA-24-1546 TCGA-24-1550 
        6.25         4.83        45.14        57.40        64.27        41.06 
TCGA-24-1553 TCGA-24-1563 TCGA-24-1614 TCGA-24-1849 TCGA-24-1850 TCGA-24-1923 
       58.09        47.70        48.33         5.79         5.52        22.68 
TCGA-24-1924 TCGA-24-2029 TCGA-24-2033 TCGA-24-2038 TCGA-24-2260 TCGA-24-2262 
       30.21        14.43        18.48        44.52        36.16         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2293 
       47.54        31.63        44.61         0.82        67.36        16.64 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1319 TCGA-25-1320 TCGA-25-1323 
       55.86        53.26        26.96        65.00        37.97        12.99 
TCGA-25-1326 TCGA-25-1328 TCGA-25-1623 TCGA-25-1626 TCGA-25-1630 TCGA-25-2042 
       41.06        66.05        18.58        17.03        38.20        13.02 
TCGA-25-2398 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-29-1690 TCGA-29-1699 
       45.01         2.96        29.03        31.00        47.61        36.36 
TCGA-29-1701 TCGA-29-1710 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 
       16.93        31.27        39.42        31.30        22.98        22.55 
TCGA-29-1776 TCGA-29-2425 TCGA-29-2427 TCGA-29-2429 TCGA-29-2432 TCGA-30-1856 
       11.84        65.00        62.47        13.84        21.47        15.68 
TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 TCGA-31-1950 TCGA-36-1568 TCGA-36-1569 
       24.26        48.79        45.57        18.77        28.77        29.10 
TCGA-36-1576 TCGA-36-1577 TCGA-36-1580 TCGA-36-1581 TCGA-36-2537 TCGA-36-2540 
       30.08        25.74        24.23        24.69        25.91        23.80 
TCGA-36-2543 TCGA-36-2549 TCGA-42-2587 TCGA-42-2591 TCGA-59-2351 TCGA-59-2363 
        2.24         6.05        23.74        40.77       116.12         5.42 
TCGA-59-A5PD TCGA-61-1722 TCGA-61-1724 TCGA-61-1895 TCGA-61-1900 TCGA-61-1903 
       20.52         8.09        20.94         1.45         5.79        13.02 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1919 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 
       34.13        31.30        38.17         4.01        30.64        39.85 
TCGA-61-2012 TCGA-61-2094 TCGA-61-2095 TCGA-61-2101 TCGA-61-2111 TCGA-61-2113 
       30.64        71.74        61.64        55.50       125.75        22.22 
TCGA-61-2610 TCGA-61-2613 TCGA-VG-A8LO 
       51.91        31.07         0.79 

$subtype2
TCGA-04-1336 TCGA-04-1348 TCGA-04-1356 TCGA-04-1361 TCGA-04-1369 TCGA-04-1514 
       49.15        48.76        49.28        32.52        21.11        56.55 
TCGA-04-1516 TCGA-04-1517 TCGA-04-1649 TCGA-04-1651 TCGA-09-1666 TCGA-09-1670 
       41.59        19.99        64.64        36.23        57.60        17.98 
TCGA-09-1673 TCGA-09-2043 TCGA-09-2044 TCGA-09-2051 TCGA-09-2054 TCGA-10-0931 
        3.02         6.18         6.12        63.09        20.94        32.88 
TCGA-10-0936 TCGA-13-0720 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 
       36.92        44.55        30.35         8.71         7.79         8.12 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0884 TCGA-13-0887 TCGA-13-0888 
        8.28         8.19        35.28       107.18        66.67        70.39 
TCGA-13-0891 TCGA-13-0897 TCGA-13-0899 TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 
       69.01        57.47        56.15        21.17        13.81         4.64 
TCGA-13-1404 TCGA-13-1409 TCGA-13-1410 TCGA-13-1487 TCGA-13-1489 TCGA-13-1492 
        6.61         6.84         4.70        22.39        82.88        73.55 
TCGA-13-1496 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 TCGA-13-1511 
        4.24        16.57         4.21         4.41         4.18         3.91 
TCGA-13-1512 TCGA-13-2060 TCGA-13-2061 TCGA-13-2066 TCGA-13-A5FU TCGA-20-1683 
        3.09        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-5X-AA5U 
        1.48        22.32       180.20         9.40        44.81        11.87 
TCGA-61-1730 TCGA-61-1734 TCGA-61-1736 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 
        4.34        28.47        48.79         2.43        33.67        43.69 
TCGA-61-1899 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1915 TCGA-61-1995 
        8.42        37.05        42.51        48.92        67.76         2.01 
TCGA-61-2000 TCGA-61-2018 TCGA-61-2088 TCGA-61-2092 TCGA-61-2096 TCGA-61-2098 
       14.50        45.40         4.77        51.72        58.39        65.52 
TCGA-61-2104 TCGA-61-2109 TCGA-OY-A56P TCGA-OY-A56Q TCGA-WR-A838 
       76.87        20.68        39.68        18.94         9.99 

$subtype3
TCGA-04-1341 TCGA-04-1343 TCGA-04-1362 TCGA-04-1370 TCGA-04-1646 TCGA-04-1654 
        1.08        11.87        44.32        59.97        27.88        47.70 
TCGA-09-1662 TCGA-09-1674 TCGA-09-2045 TCGA-09-2055 TCGA-10-0926 TCGA-13-0911 
       89.33         8.55        35.15        26.93        25.91        27.72 
TCGA-13-1405 TCGA-13-1507 TCGA-20-1682 TCGA-23-1111 TCGA-23-1124 TCGA-23-2079 
        7.36         4.77        27.52         3.22        58.13        91.66 
TCGA-23-2081 TCGA-23-2641 TCGA-23-2647 TCGA-24-1434 TCGA-24-1463 TCGA-24-1470 
       77.00         2.76         4.44        18.67        72.92         3.45 
TCGA-24-1564 TCGA-24-1604 TCGA-24-1920 TCGA-24-1927 TCGA-24-2024 TCGA-24-2026 
       25.87        88.37         9.80        16.44        58.16        34.82 
TCGA-24-2254 TCGA-24-2295 TCGA-25-1316 TCGA-25-1322 TCGA-25-1325 TCGA-25-1625 
       57.07        33.11        42.05         2.99        32.09        27.62 
TCGA-25-1628 TCGA-25-1632 TCGA-25-1633 TCGA-25-2391 TCGA-25-2399 TCGA-29-1694 
       20.61        59.15        62.17        49.05        19.99        39.02 
TCGA-29-1696 TCGA-29-1702 TCGA-29-1770 TCGA-29-1775 TCGA-29-1777 TCGA-29-1783 
       33.93        23.93        24.36        12.36        12.30         7.23 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2436 TCGA-30-1718 TCGA-30-1855 TCGA-30-1860 
       36.30        86.17         9.76        51.91         2.47        44.91 
TCGA-30-1861 TCGA-30-1891 TCGA-31-1946 TCGA-36-2534 TCGA-36-2544 TCGA-36-2545 
       34.78        30.05        30.18        29.82        20.98        18.31 
TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2588 TCGA-42-2590 TCGA-59-2349 
       16.18        13.81        47.57        28.93        10.42        80.12 
TCGA-59-2354 TCGA-61-1721 TCGA-61-1727 TCGA-61-1733 TCGA-61-1738 TCGA-61-1914 
       34.39        11.11        18.54        31.79        35.80        56.61 
TCGA-61-1918 TCGA-61-2017 TCGA-61-2087 TCGA-61-2102 TCGA-61-2612 TCGA-61-2614 
       15.75        45.96         4.80         6.48         6.35         8.61 

subtype1 subtype2 subtype3 
    0.36     0.30     1.08 
subtype1 subtype2 subtype3 
  125.75   180.20    91.66 
subtype1 subtype2 subtype3 
   31.27    28.47    27.67 
[1] "0.4 - 125.8 (31.3)" "0.3 - 180.2 (28.5)" "1.1 - 91.7 (27.7)" 
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 134   2
  subtype2 165   1
  subtype3  72   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  134    2
  subtype2  165    1
  subtype3   72    1
     clus
vv    subtype1 subtype2 subtype3
  NO       134      165       72
  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"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                2     6                        10
  subtype2                                1     9                        16
  subtype3                                0     2                         3
          vv
clus       WHITE
  subtype1   121
  subtype2   156
  subtype3    68
D7V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        2        1        0
  ASIAN                                   6        9        2
  BLACK OR AFRICAN AMERICAN              10       16        3
  WHITE                                 121      156       68
[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"
D7V8, 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 64 81
  subtype2 20 37
  subtype3 37 24
  subtype4 74 79
subtype1 subtype2 subtype3 subtype4 
     145       57       61      153 
subtype1 subtype2 subtype3 subtype4 
      81       37       24       79 
$subtype1
TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1342 TCGA-04-1349 TCGA-04-1361 
        1.81        49.15        46.62        18.51        21.57        32.52 
TCGA-04-1638 TCGA-04-1649 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-2056 
       55.43        64.64        89.33        74.93        41.62        12.46 
TCGA-13-0886 TCGA-13-0894 TCGA-13-0906 TCGA-13-0913 TCGA-13-1405 TCGA-13-1408 
       74.27        49.61        44.94        29.98         7.36         5.92 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
        6.84         4.70         4.21         5.33        54.64        87.06 
TCGA-13-1488 TCGA-13-1494 TCGA-13-1501 TCGA-13-1505 TCGA-13-1507 TCGA-13-2065 
       70.82        38.20        32.84         4.21         4.77        65.52 
TCGA-13-A5FU TCGA-20-1682 TCGA-20-1686 TCGA-23-1122 TCGA-23-2078 TCGA-24-0980 
        8.42        27.52         2.93        39.09        87.48         7.66 
TCGA-24-0982 TCGA-24-1423 TCGA-24-1427 TCGA-24-1434 TCGA-24-1466 TCGA-24-1545 
       22.32         6.25         4.83        18.67        45.14        57.40 
TCGA-24-1546 TCGA-24-1553 TCGA-24-1563 TCGA-24-1565 TCGA-24-1614 TCGA-24-1844 
       64.27        58.09        47.70        10.26        48.33         3.72 
TCGA-24-1849 TCGA-24-1850 TCGA-24-1923 TCGA-24-1924 TCGA-24-2027 TCGA-24-2029 
        5.79         5.52        22.68        30.21       109.71        14.43 
TCGA-24-2038 TCGA-24-2262 TCGA-24-2271 TCGA-24-2288 TCGA-24-2293 TCGA-24-2297 
       44.52         0.36        31.63         0.82        16.64        55.86 
TCGA-24-2298 TCGA-25-1313 TCGA-25-1319 TCGA-25-1322 TCGA-25-1323 TCGA-25-1325 
       53.26        26.96        65.00         2.99        12.99        32.09 
TCGA-25-1328 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1628 TCGA-25-1630 
       66.05        18.58        27.62        17.03        20.61        38.20 
TCGA-25-1633 TCGA-25-2042 TCGA-25-2398 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 
       62.17        13.02        45.01         2.96        29.03        31.00 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1694 TCGA-29-1695 TCGA-29-1698 TCGA-29-1699 
       78.90        47.61        39.02        40.41        68.32        36.36 
TCGA-29-1701 TCGA-29-1710 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 
       16.93        31.27        31.30        22.98        24.36        22.55 
TCGA-29-1776 TCGA-29-1783 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2431 
       11.84         7.23        86.17        65.00        45.11        42.25 
TCGA-29-2432 TCGA-29-2436 TCGA-30-1856 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 
       21.47         9.76        15.68        24.26        30.05        48.79 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-36-1568 TCGA-36-1569 TCGA-36-1576 
       45.57        30.18        18.77        28.77        29.10        30.08 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2534 TCGA-36-2538 TCGA-36-2540 TCGA-36-2543 
       24.23        24.69        29.82        25.08        23.80         2.24 
TCGA-36-2547 TCGA-36-2549 TCGA-36-2551 TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 
       20.52         6.05        16.18        23.74        28.93        10.42 
TCGA-59-2348 TCGA-59-2354 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1724 TCGA-61-1740 
      180.20        34.39        20.52        11.11        20.94         2.43 
TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1906 TCGA-61-1914 TCGA-61-1918 
        1.45         8.42         5.79        34.13        56.61        15.75 
TCGA-61-1919 TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 TCGA-61-2017 
       38.17        14.50         4.01        30.64        30.64        45.96 
TCGA-61-2095 TCGA-61-2101 TCGA-61-2111 TCGA-61-2113 TCGA-61-2610 TCGA-61-2613 
       61.64        55.50       125.75        22.22        51.91        31.07 
TCGA-OY-A56P 
       39.68 

$subtype2
TCGA-04-1341 TCGA-04-1343 TCGA-04-1356 TCGA-04-1369 TCGA-04-1370 TCGA-04-1654 
        1.08        11.87        49.28        21.11        59.97        47.70 
TCGA-09-2055 TCGA-13-0897 TCGA-13-0899 TCGA-13-0911 TCGA-13-1483 TCGA-13-1495 
       26.93        57.47        56.15        27.72        29.42        49.25 
TCGA-13-1496 TCGA-13-1498 TCGA-13-1500 TCGA-13-1509 TCGA-23-1111 TCGA-23-1124 
        4.24        37.61        13.97         4.18         3.22        58.13 
TCGA-23-2647 TCGA-24-1422 TCGA-24-1435 TCGA-24-1463 TCGA-24-1469 TCGA-24-1470 
        4.44         0.76        43.53        72.92         9.11         3.45 
TCGA-24-1562 TCGA-24-1564 TCGA-24-1920 TCGA-24-1927 TCGA-24-2024 TCGA-24-2026 
       45.50        25.87         9.80        16.44        58.16        34.82 
TCGA-24-2030 TCGA-24-2261 TCGA-24-2289 TCGA-24-2290 TCGA-24-2295 TCGA-25-1320 
       55.92         0.79        67.36        36.23        33.11        37.97 
TCGA-25-2399 TCGA-25-2409 TCGA-29-1705 TCGA-29-1711 TCGA-29-1766 TCGA-29-1777 
       19.99        26.99        18.25        34.62        39.42        12.30 
TCGA-29-1785 TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1855 TCGA-30-1860 TCGA-30-1861 
       36.30        35.77        51.91         2.47        44.91        34.78 
TCGA-36-2544 TCGA-36-2545 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2589 TCGA-61-1738 
       20.98        18.31        13.81        47.57        42.02        35.80 
TCGA-61-1743 TCGA-61-2612 TCGA-61-2614 
       43.69         6.35         8.61 

$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-10-0933 TCGA-10-0936 TCGA-13-0725 TCGA-13-0793 TCGA-13-0794 TCGA-13-0802 
       14.66        36.92        12.39       107.28        30.35         8.19 
TCGA-13-0884 TCGA-13-0903 TCGA-13-0910 TCGA-13-0920 TCGA-13-1404 TCGA-13-1482 
      107.18        47.38        37.08        13.81         6.61        61.71 
TCGA-13-1487 TCGA-13-1489 TCGA-13-1492 TCGA-13-1499 TCGA-13-1504 TCGA-13-1506 
       22.39        82.88        73.55        38.40        16.57         4.41 
TCGA-13-1512 TCGA-13-2060 TCGA-13-2061 TCGA-13-2066 TCGA-20-1684 TCGA-20-1685 
        3.09        77.88        76.90        70.13        19.10        16.70 
TCGA-23-1121 TCGA-23-2643 TCGA-24-0970 TCGA-24-1105 TCGA-24-1417 TCGA-24-1436 
        6.38         4.70        11.64        47.41         7.82         8.55 
TCGA-24-1467 TCGA-24-1474 TCGA-24-1552 TCGA-24-1556 TCGA-24-1558 TCGA-24-1842 
      105.99        22.22        41.39        70.62        19.53         8.32 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1930 TCGA-24-2260 TCGA-25-1635 TCGA-25-1878 
        3.81         4.37        81.11        36.16        52.04        85.05 
TCGA-25-2393 TCGA-29-1693 TCGA-29-1703 TCGA-29-1764 TCGA-29-2427 TCGA-36-1575 
       38.04       101.79        59.67        62.93        62.47         8.55 
TCGA-36-1577 TCGA-36-2530 TCGA-36-2537 TCGA-36-2542 TCGA-36-2548 TCGA-36-2552 
       25.74        33.01        25.91        21.60        14.17        11.47 
TCGA-57-1586 
       22.32 

$subtype4
TCGA-04-1362 TCGA-04-1514 TCGA-04-1517 TCGA-04-1542 TCGA-04-1644 TCGA-04-1646 
       44.32        56.55        19.99        84.20        48.89        27.88 
TCGA-04-1648 TCGA-09-1666 TCGA-09-1670 TCGA-09-1673 TCGA-09-1674 TCGA-09-2043 
       28.64        57.60        17.98         3.02         8.55         6.18 
TCGA-09-2045 TCGA-09-2049 TCGA-09-2051 TCGA-09-2054 TCGA-10-0925 TCGA-10-0926 
       35.15       112.41        63.09        20.94        54.31        25.91 
TCGA-10-0931 TCGA-13-0720 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
       32.88        44.55         8.71         7.79         8.12         8.28 
TCGA-13-0804 TCGA-13-0887 TCGA-13-0888 TCGA-13-0891 TCGA-13-0901 TCGA-13-0916 
       35.28        66.67        70.39        69.01        19.36        21.17 
TCGA-13-0921 TCGA-13-1484 TCGA-13-1491 TCGA-13-1511 TCGA-13-2059 TCGA-13-A5FT 
        4.64        98.04        52.44         3.91        78.48        70.45 
TCGA-20-1683 TCGA-20-1687 TCGA-23-1109 TCGA-23-1110 TCGA-23-1123 TCGA-23-1809 
       25.38         2.66        51.35        54.51        33.47         0.53 
TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-23-2641 TCGA-23-2645 TCGA-23-2649 
      115.89        91.66        77.00         2.76         4.50         3.81 
TCGA-24-0966 TCGA-24-0979 TCGA-24-1103 TCGA-24-1104 TCGA-24-1416 TCGA-24-1419 
        7.63        41.56        54.12        63.55         6.38         7.86 
TCGA-24-1424 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1464 TCGA-24-1471 
        6.02        17.39        28.37        18.64        12.46         1.18 
TCGA-24-1544 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1555 
       26.96        16.21        56.58        41.06        51.91        88.50 
TCGA-24-1557 TCGA-24-1560 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 
       39.88        44.09        17.23        90.15        88.37        38.24 
TCGA-24-2020 TCGA-24-2023 TCGA-24-2033 TCGA-24-2036 TCGA-24-2254 TCGA-24-2267 
      152.02        44.84        18.48        64.01        57.07        47.54 
TCGA-24-2281 TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1318 
       44.61         1.02        33.01        52.04        42.05        34.98 
TCGA-25-1321 TCGA-25-1326 TCGA-25-1329 TCGA-25-1627 TCGA-25-1631 TCGA-25-1632 
       33.96        41.06        15.02        12.95         0.30        59.15 
TCGA-25-2391 TCGA-25-2396 TCGA-25-2397 TCGA-25-2400 TCGA-29-1691 TCGA-29-1696 
       49.05         3.02        12.00        42.02        48.33        33.93 
TCGA-29-1697 TCGA-29-1702 TCGA-29-1707 TCGA-29-1761 TCGA-29-1762 TCGA-29-1774 
       31.20        23.93        41.98        17.36        86.60        17.33 
TCGA-29-1775 TCGA-29-1778 TCGA-29-1781 TCGA-29-2429 TCGA-29-2434 TCGA-29-2435 
       12.36        14.93         8.38        13.84        11.47         1.12 
TCGA-30-1859 TCGA-30-1869 TCGA-31-1951 TCGA-31-1955 TCGA-36-1570 TCGA-36-1571 
       48.10        51.39        22.49        42.51        21.53        22.85 
TCGA-36-1578 TCGA-36-2529 TCGA-36-2532 TCGA-42-2591 TCGA-42-2593 TCGA-59-2349 
       27.85        35.05        29.49        40.77         1.48        80.12 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2363 TCGA-59-2372 TCGA-5X-AA5U TCGA-61-1722 
      116.12         9.40         5.42        44.81        11.87         8.09 
TCGA-61-1727 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1741 
       18.54         4.34        31.79        28.47        48.79        33.67 
TCGA-61-1903 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1915 
       13.02        31.30        37.05        42.51        48.92        67.76 
TCGA-61-1995 TCGA-61-2009 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 
        2.01        39.85        45.40         4.80         4.77        51.72 
TCGA-61-2094 TCGA-61-2096 TCGA-61-2098 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       71.74        58.39        65.52         6.48        76.87        20.68 
TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       18.94         0.79         9.99 

subtype1 subtype2 subtype3 subtype4 
    0.36     0.76     0.79     0.30 
subtype1 subtype2 subtype3 subtype4 
  180.20    72.92   107.28   152.02 
subtype1 subtype2 subtype3 subtype4 
   29.03    33.11    30.35    32.88 
[1] "0.4 - 180.2 (29.0)" "0.8 - 72.9 (33.1)"  "0.8 - 107.3 (30.4)"
[4] "0.3 - 152.0 (32.9)"
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 130   1
  subtype2  55   0
  subtype3  51   1
  subtype4 135   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  130    1
  subtype2   55    0
  subtype3   51    1
  subtype4  135    2
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       130       55       51      135
  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"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                2     2                        10
  subtype2                                0     1                         6
  subtype3                                0     5                         3
  subtype4                                1     9                        10
          vv
clus       WHITE
  subtype1   121
  subtype2    48
  subtype3    46
  subtype4   130
D8V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        2        0        0        1
  ASIAN                                   2        1        5        9
  BLACK OR AFRICAN AMERICAN              10        6        3       10
  WHITE                                 121       48       46      130
[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"
D8V8, 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 35 43
  subtype2 44 65
  subtype3 51 64
subtype1 subtype2 subtype3 
      78      109      115 
subtype1 subtype2 subtype3 
      43       65       64 
$subtype1
TCGA-04-1348 TCGA-04-1362 TCGA-04-1365 TCGA-09-0366 TCGA-09-0367 TCGA-09-1666 
       48.76        44.32        76.57        57.76        17.98        57.60 
TCGA-09-1670 TCGA-09-2045 TCGA-09-2051 TCGA-09-2056 TCGA-10-0936 TCGA-13-0801 
       17.98        35.15        63.09        12.46        36.92         8.28 
TCGA-13-0893 TCGA-13-0924 TCGA-13-1498 TCGA-20-1685 TCGA-23-1026 TCGA-23-2081 
       43.36         6.08        37.61        16.70        26.83        77.00 
TCGA-23-2084 TCGA-24-1103 TCGA-24-1413 TCGA-24-1416 TCGA-24-1423 TCGA-24-1428 
       49.84        54.12         6.31         6.38         6.25        17.39 
TCGA-24-1467 TCGA-24-1551 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1847 
      105.99        51.91        88.50        70.62        39.88        11.28 
TCGA-24-1924 TCGA-24-2019 TCGA-24-2023 TCGA-24-2026 TCGA-24-2038 TCGA-24-2267 
       30.21         4.87        44.84        34.82        44.52        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-3P-A9WA 
       44.91        45.57        21.53        22.55        24.69        13.81 
TCGA-57-1584 TCGA-57-1993 TCGA-59-2351 TCGA-59-2354 TCGA-59-2355 TCGA-61-1724 
       21.14        25.08       116.12        34.39         2.14        20.94 
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 

$subtype2
TCGA-04-1364 TCGA-04-1514 TCGA-04-1519 TCGA-09-0364 TCGA-09-0369 TCGA-09-1669 
       33.67        56.55         0.79        29.16        35.57        30.51 
TCGA-09-1673 TCGA-09-1674 TCGA-09-2044 TCGA-09-2048 TCGA-09-2054 TCGA-10-0928 
        3.02         8.55         6.12         4.54        20.94        18.51 
TCGA-13-0730 TCGA-13-0799 TCGA-13-0800 TCGA-13-0899 TCGA-13-0913 TCGA-13-0916 
       17.82         7.79         8.12        56.15        29.98        21.17 
TCGA-13-0920 TCGA-13-1506 TCGA-13-A5FT TCGA-20-1683 TCGA-20-1684 TCGA-23-1029 
       13.81         4.41        70.45        25.38        19.10         8.81 
TCGA-23-1111 TCGA-23-1114 TCGA-23-1122 TCGA-23-1123 TCGA-23-1809 TCGA-23-2077 
        3.22        68.68        39.09        33.47         0.53       115.89 
TCGA-24-1419 TCGA-24-1424 TCGA-24-1430 TCGA-24-1469 TCGA-24-1474 TCGA-24-1544 
        7.86         6.02        28.37         9.11        22.22        26.96 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1553 TCGA-24-1558 TCGA-24-1560 TCGA-24-1567 
       16.21        56.58        58.09        19.53        44.09        17.23 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-1843 TCGA-24-1844 TCGA-24-2020 
       90.15        88.37        38.24         3.48         3.72       152.02 
TCGA-24-2027 TCGA-24-2036 TCGA-24-2254 TCGA-24-2297 TCGA-25-1312 TCGA-25-1315 
      109.71        64.01        57.07        55.86         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-25-1627 TCGA-25-1631 TCGA-25-1632 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 
       12.95         0.30        59.15        35.87        14.96        24.99 
TCGA-25-2393 TCGA-25-2400 TCGA-29-1691 TCGA-29-1697 TCGA-29-1702 TCGA-29-1703 
       38.04        42.02        48.33        31.20        23.93        59.67 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1783 TCGA-29-2414 TCGA-29-2425 
       17.36        86.60        66.81         7.23        86.17        65.00 
TCGA-29-A5NZ TCGA-36-1571 TCGA-36-1575 TCGA-36-1577 TCGA-57-1583 TCGA-57-1994 
       35.77        22.85         8.55        25.74        11.38        25.02 
TCGA-59-2350 TCGA-59-2352 TCGA-59-2363 TCGA-59-A5PD TCGA-5X-AA5U TCGA-61-1728 
       22.32         9.40         5.42        20.52        11.87        27.88 
TCGA-61-1733 TCGA-61-1738 TCGA-61-1741 TCGA-61-1743 TCGA-61-1900 TCGA-61-1917 
       31.79        35.80        33.67        43.69         5.79        43.43 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2008 TCGA-61-2012 TCGA-61-2088 TCGA-61-2095 
        2.01         5.52        30.64        30.64         4.77        61.64 
TCGA-61-2098 TCGA-61-2102 TCGA-61-2110 TCGA-61-2111 TCGA-OY-A56P TCGA-OY-A56Q 
       65.52         6.48        44.52       125.75        39.68        18.94 
TCGA-WR-A838 
        9.99 

$subtype3
TCGA-09-1659 TCGA-09-1662 TCGA-09-1667 TCGA-09-1668 TCGA-13-0890 TCGA-13-0897 
        9.99        89.33        61.87        55.36        67.99        57.47 
TCGA-13-1403 TCGA-13-1405 TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 TCGA-13-1497 
       10.88         7.36         4.70         4.21        87.06        54.31 
TCGA-13-1505 TCGA-13-1507 TCGA-13-1511 TCGA-13-1512 TCGA-13-2060 TCGA-20-1682 
        4.21         4.77         3.91         3.09        77.88        27.52 
TCGA-20-1687 TCGA-23-1023 TCGA-23-1027 TCGA-23-1109 TCGA-23-1120 TCGA-23-2078 
        2.66        40.54        32.09        51.35         4.27        87.48 
TCGA-24-0975 TCGA-24-1417 TCGA-24-1418 TCGA-24-1425 TCGA-24-1427 TCGA-24-1434 
       21.80         7.82         7.99         5.95         4.83        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1545 TCGA-24-1546 TCGA-24-1550 
       43.53         8.55        72.92        57.40        64.27        41.06 
TCGA-24-1552 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1842 TCGA-24-1846 
       41.39        45.50        47.70        25.87         8.32         4.37 
TCGA-24-1849 TCGA-24-1850 TCGA-24-1928 TCGA-24-1930 TCGA-24-2024 TCGA-24-2033 
        5.79         5.52        11.05        81.11        58.16        18.48 
TCGA-24-2035 TCGA-24-2261 TCGA-24-2262 TCGA-24-2271 TCGA-24-2288 TCGA-24-2289 
       28.18         0.79         0.36        31.63         0.82        67.36 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2298 TCGA-25-1314 TCGA-25-1318 TCGA-25-1320 
       36.23        16.64        53.26        33.01        34.98        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-25-2399 TCGA-25-2401 
       62.17        52.04        13.02        45.01        19.99         2.96 
TCGA-29-1693 TCGA-29-1695 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1705 
      101.79        40.41        68.32        36.36        16.93        18.25 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1770 TCGA-29-1781 TCGA-29-1785 TCGA-29-2427 
       31.27        34.62        24.36         8.38        36.30        62.47 
TCGA-29-2428 TCGA-30-1718 TCGA-30-1855 TCGA-30-1857 TCGA-30-1861 TCGA-30-1862 
       45.11        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-36-1568 TCGA-36-1569 TCGA-36-1576 TCGA-36-1578 TCGA-36-1580 TCGA-57-1582 
       28.77        29.10        30.08        27.85        24.23        24.03 
TCGA-57-1585 TCGA-59-2348 TCGA-61-1721 TCGA-61-1725 TCGA-61-1737 TCGA-61-1740 
        1.74       180.20        11.11        31.43        44.84         2.43 
TCGA-61-1919 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2009 TCGA-61-2101 
       38.17        14.50        17.98         4.01        39.85        55.50 
TCGA-61-2113 
       22.22 

subtype1 subtype2 subtype3 
    0.79     0.30     0.26 
subtype1 subtype2 subtype3 
  116.12   152.02   180.20 
subtype1 subtype2 subtype3 
   34.16    26.96    28.18 
[1] "0.8 - 116.1 (34.2)" "0.3 - 152.0 (27.0)" "0.3 - 180.2 (28.2)"
D9V2, continuous
          vv
clus       OMENTUM OVARY
  subtype1       0    79
  subtype2       1   108
  subtype3       2   113
D9V3, multiclass
         clus
vv        subtype1 subtype2 subtype3
  OMENTUM        0        1        2
  OVARY         79      108      113
[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  71   0
  subtype2  97   2
  subtype3 101   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   71    0
  subtype2   97    2
  subtype3  101    0
     clus
vv    subtype1 subtype2 subtype3
  NO        71       97      101
  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"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     2                         7
  subtype2                                0     6                        15
  subtype3                                1     4                         4
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         1    66
  subtype2                                         0    85
  subtype3                                         0   100
D9V7, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 1        0        1
  ASIAN                                            2        6        4
  BLACK OR AFRICAN AMERICAN                        7       15        4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1        0        0
  WHITE                                           66       85      100
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
          cls
clus        0  1
  subtype1  3 40
  subtype2  0 60
  subtype3  0 63
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   40
  subtype2    0   60
  subtype3    0   63
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        0        0
  NOT HISPANIC OR LATINO       40       60       63
[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 68 78
  subtype2 21 39
  subtype3 41 55
subtype1 subtype2 subtype3 
     146       60       96 
subtype1 subtype2 subtype3 
      78       39       55 
$subtype1
TCGA-04-1348 TCGA-04-1362 TCGA-04-1365 TCGA-04-1519 TCGA-09-0366 TCGA-09-0367 
       48.76        44.32        76.57         0.79        57.76        17.98 
TCGA-09-1659 TCGA-09-1662 TCGA-09-1666 TCGA-09-1670 TCGA-09-2044 TCGA-09-2045 
        9.99        89.33        57.60        17.98         6.12        35.15 
TCGA-09-2051 TCGA-09-2056 TCGA-10-0936 TCGA-13-0799 TCGA-13-0801 TCGA-13-0893 
       63.09        12.46        36.92         7.79         8.28        43.36 
TCGA-13-0899 TCGA-13-0916 TCGA-13-0924 TCGA-13-1403 TCGA-13-1497 TCGA-13-1498 
       56.15        21.17         6.08        10.88        54.31        37.61 
TCGA-13-1506 TCGA-13-2060 TCGA-13-A5FT TCGA-20-1682 TCGA-20-1683 TCGA-20-1685 
        4.41        77.88        70.45        27.52        25.38        16.70 
TCGA-23-1026 TCGA-23-1029 TCGA-23-1111 TCGA-23-1120 TCGA-23-1122 TCGA-23-1809 
       26.83         8.81         3.22         4.27        39.09         0.53 
TCGA-23-2077 TCGA-23-2084 TCGA-24-1103 TCGA-24-1413 TCGA-24-1416 TCGA-24-1419 
      115.89        49.84        54.12         6.31         6.38         7.86 
TCGA-24-1423 TCGA-24-1428 TCGA-24-1430 TCGA-24-1467 TCGA-24-1474 TCGA-24-1549 
        6.25        17.39        28.37       105.99        22.22        56.58 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       51.91        41.39        58.09        88.50        70.62        39.88 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-1843 TCGA-24-1844 TCGA-24-1847 
       90.15        88.37        38.24         3.48         3.72        11.28 
TCGA-24-1850 TCGA-24-1924 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 
        5.52        30.21         4.87        44.84        58.16        34.82 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2262 TCGA-24-2267 TCGA-24-2281 
       64.01        44.52        57.07         0.36        47.54        44.61 
TCGA-24-2290 TCGA-24-2297 TCGA-25-1313 TCGA-25-1318 TCGA-25-1322 TCGA-25-1328 
       36.23        55.86        26.96        34.98         2.99        66.05 
TCGA-25-1625 TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 TCGA-25-1635 TCGA-25-2391 
       27.62        12.95        38.20         0.30        52.04        49.05 
TCGA-25-2392 TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 TCGA-25-2400 TCGA-25-2404 
        1.02         3.02        12.00        19.99        42.02        29.03 
TCGA-29-1690 TCGA-29-1691 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 
       47.61        48.33        39.02        33.93        31.20        36.36 
TCGA-29-1703 TCGA-29-1761 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
       59.67        17.36        14.93         8.38         7.23         5.36 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-30-1860 TCGA-31-1944 
       36.30        86.17        65.00        45.11        44.91        45.57 
TCGA-36-1568 TCGA-36-1570 TCGA-36-1578 TCGA-36-1581 TCGA-3P-A9WA TCGA-57-1583 
       28.77        21.53        27.85        24.69        13.81        11.38 
TCGA-57-1584 TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       21.14        25.08       180.20        22.32       116.12         9.40 
TCGA-59-2355 TCGA-61-1721 TCGA-61-1724 TCGA-61-1736 TCGA-61-1738 TCGA-61-1740 
        2.14        11.11        20.94        48.79        35.80         2.43 
TCGA-61-1907 TCGA-61-1910 TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 
       31.30        37.05        56.61        43.43        15.75         2.01 
TCGA-61-1998 TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 TCGA-61-2016 TCGA-61-2092 
        5.52         4.01        30.64        30.64         1.18        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       71.74        61.64        60.62        76.87        20.68        44.52 
TCGA-61-2111 TCGA-VG-A8LO 
      125.75         0.79 

$subtype2
TCGA-04-1364 TCGA-04-1514 TCGA-09-0364 TCGA-09-0369 TCGA-09-1669 TCGA-09-1673 
       33.67        56.55        29.16        35.57        30.51         3.02 
TCGA-09-1674 TCGA-09-2048 TCGA-09-2054 TCGA-10-0928 TCGA-13-0730 TCGA-13-0800 
        8.55         4.54        20.94        18.51        17.82         8.12 
TCGA-13-0913 TCGA-13-0920 TCGA-20-1684 TCGA-23-1114 TCGA-23-1123 TCGA-24-1424 
       29.98        13.81        19.10        68.68        33.47         6.02 
TCGA-24-1469 TCGA-24-1544 TCGA-24-1548 TCGA-24-1550 TCGA-24-1558 TCGA-24-1560 
        9.11        26.96        16.21        41.06        19.53        44.09 
TCGA-24-1567 TCGA-24-2020 TCGA-24-2027 TCGA-25-1312 TCGA-25-1315 TCGA-25-1316 
       17.23       152.02       109.71         1.02        52.04        42.05 
TCGA-25-1317 TCGA-25-1319 TCGA-25-1321 TCGA-25-1323 TCGA-25-1324 TCGA-25-1632 
        2.01        65.00        33.96        12.99        34.03        59.15 
TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-2393 TCGA-29-1702 TCGA-29-1762 
       35.87        14.96        24.99        38.04        23.93        86.60 
TCGA-29-1763 TCGA-36-1571 TCGA-36-1575 TCGA-36-1577 TCGA-57-1994 TCGA-59-2363 
       66.81        22.85         8.55        25.74        25.02         5.42 
TCGA-59-A5PD TCGA-5X-AA5U TCGA-61-1728 TCGA-61-1741 TCGA-61-1743 TCGA-61-1900 
       20.52        11.87        27.88        33.67        43.69         5.79 
TCGA-61-2088 TCGA-61-2098 TCGA-61-2102 TCGA-OY-A56P TCGA-OY-A56Q TCGA-WR-A838 
        4.77        65.52         6.48        39.68        18.94         9.99 

$subtype3
TCGA-09-1667 TCGA-09-1668 TCGA-13-0890 TCGA-13-0897 TCGA-13-1405 TCGA-13-1410 
       61.87        55.36        67.99        57.47         7.36         4.70 
TCGA-13-1411 TCGA-13-1481 TCGA-13-1505 TCGA-13-1507 TCGA-13-1511 TCGA-13-1512 
        4.21        87.06         4.21         4.77         3.91         3.09 
TCGA-20-1687 TCGA-23-1023 TCGA-23-1027 TCGA-23-1109 TCGA-23-2078 TCGA-23-2081 
        2.66        40.54        32.09        51.35        87.48        77.00 
TCGA-24-0975 TCGA-24-1417 TCGA-24-1418 TCGA-24-1425 TCGA-24-1427 TCGA-24-1434 
       21.80         7.82         7.99         5.95         4.83        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1545 TCGA-24-1546 TCGA-24-1562 
       43.53         8.55        72.92        57.40        64.27        45.50 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1842 TCGA-24-1846 TCGA-24-1849 TCGA-24-1928 
       47.70        25.87         8.32         4.37         5.79        11.05 
TCGA-24-1930 TCGA-24-2033 TCGA-24-2035 TCGA-24-2261 TCGA-24-2271 TCGA-24-2288 
       81.11        18.48        28.18         0.79        31.63         0.82 
TCGA-24-2289 TCGA-24-2293 TCGA-24-2298 TCGA-25-1314 TCGA-25-1320 TCGA-25-1326 
       67.36        16.64        53.26        33.01        37.97        41.06 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1628 TCGA-25-1633 TCGA-25-2042 
       15.02        18.58        17.03        20.61        62.17        13.02 
TCGA-25-2398 TCGA-25-2401 TCGA-25-2409 TCGA-29-1688 TCGA-29-1693 TCGA-29-1695 
       45.01         2.96        26.99        78.90       101.79        40.41 
TCGA-29-1698 TCGA-29-1701 TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 TCGA-29-1770 
       68.32        16.93        18.25        31.27        34.62        24.36 
TCGA-29-1776 TCGA-29-2427 TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1855 TCGA-30-1857 
       11.84        62.47        35.77        51.91         2.47         0.26 
TCGA-30-1861 TCGA-30-1862 TCGA-30-1891 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 
       34.78         6.12        30.05        30.18        22.49         6.71 
TCGA-31-1956 TCGA-31-1959 TCGA-36-1569 TCGA-36-1574 TCGA-36-1576 TCGA-36-1580 
       44.12         2.20        29.10        22.55        30.08        24.23 
TCGA-57-1582 TCGA-57-1585 TCGA-59-2354 TCGA-61-1725 TCGA-61-1733 TCGA-61-1737 
       24.03         1.74        34.39        31.43        31.79        44.84 
TCGA-61-1919 TCGA-61-2000 TCGA-61-2002 TCGA-61-2009 TCGA-61-2101 TCGA-61-2113 
       38.17        14.50        17.98        39.85        55.50        22.22 

subtype1 subtype2 subtype3 
    0.30     1.02     0.26 
subtype1 subtype2 subtype3 
  180.20   152.02   101.79 
subtype1 subtype2 subtype3 
  31.250   25.005   27.585 
[1] "0.3 - 180.2 (31.2)" "1.0 - 152.0 (25.0)" "0.3 - 101.8 (27.6)"
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 130   1
  subtype2  55   1
  subtype3  84   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  130    1
  subtype2   55    1
  subtype3   84    0
     clus
vv    subtype1 subtype2 subtype3
  NO       130       55       84
  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" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [7] "subtype2" "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"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     6                        12
  subtype2                                0     2                         9
  subtype3                                1     4                         5
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         1   122
  subtype2                                         0    48
  subtype3                                         0    81
D10V7, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE                 1        0        1
  ASIAN                                            6        2        4
  BLACK OR AFRICAN AMERICAN                       12        9        5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1        0        0
  WHITE                                          122       48       81
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, 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 45 78
  subtype2 86 99
  subtype3 66 77
subtype1 subtype2 subtype3 
     123      185      143 
subtype1 subtype2 subtype3 
      78       99       77 
$subtype1
TCGA-04-1331 TCGA-04-1332 TCGA-04-1346 TCGA-04-1349 TCGA-04-1530 TCGA-09-1662 
       43.92        41.00        65.52        21.57       119.08        89.33 
TCGA-09-2054 TCGA-13-0768 TCGA-13-0890 TCGA-13-0894 TCGA-13-0900 TCGA-13-0908 
       20.94        58.65        67.99        49.61        57.07        44.84 
TCGA-13-1405 TCGA-13-1408 TCGA-13-1411 TCGA-13-1477 TCGA-13-1481 TCGA-13-1485 
        7.36         5.92         4.21        54.64        87.06        20.68 
TCGA-13-1487 TCGA-13-1499 TCGA-13-1501 TCGA-13-1505 TCGA-13-2060 TCGA-23-1026 
       22.39        38.40        32.84         4.21        77.88        26.83 
TCGA-23-1121 TCGA-23-2078 TCGA-23-2081 TCGA-24-0970 TCGA-24-1418 TCGA-24-1422 
        6.38        87.48        77.00        11.64         7.99         0.76 
TCGA-24-1425 TCGA-24-1427 TCGA-24-1434 TCGA-24-1546 TCGA-24-1550 TCGA-24-1556 
        5.95         4.83        18.67        64.27        41.06        70.62 
TCGA-24-1563 TCGA-24-1842 TCGA-24-1843 TCGA-24-1846 TCGA-24-1849 TCGA-24-1850 
       47.70         8.32         3.48         4.37         5.79         5.52 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1928 TCGA-24-1930 TCGA-24-2020 TCGA-24-2024 
        9.80        22.68        11.05        81.11       152.02        58.16 
TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 
       14.43        18.48        28.18        36.16         0.79         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 
       47.54        31.63        70.45        44.61         0.82        67.36 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2298 TCGA-25-1316 TCGA-25-1320 TCGA-25-1326 
       36.23        16.64        53.26        42.05        37.97        41.06 
TCGA-25-1328 TCGA-25-1626 TCGA-25-1628 TCGA-25-1633 TCGA-25-1635 TCGA-25-1877 
       66.05        17.03        20.61        62.17        52.04        24.00 
TCGA-25-2042 TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 
       13.02         3.02        45.01        19.99         2.96        29.03 
TCGA-25-2408 TCGA-25-2409 TCGA-29-1695 TCGA-29-1698 TCGA-29-1702 TCGA-29-1703 
       31.00        26.99        40.41        68.32        23.93        59.67 
TCGA-29-1705 TCGA-29-1710 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1770 
       18.25        31.27        62.93        39.42        31.30        24.36 
TCGA-29-2414 TCGA-29-2427 TCGA-30-1857 TCGA-30-1861 TCGA-30-1862 TCGA-30-1867 
       86.17        62.47         0.26        34.78         6.12         1.22 
TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 
       57.57        24.26        30.05        48.79        45.57        30.18 
TCGA-31-1951 TCGA-31-1953 TCGA-31-1956 TCGA-31-1959 TCGA-36-1574 TCGA-36-1575 
       22.49         6.71        44.12         2.20        22.55         8.55 
TCGA-36-1576 TCGA-57-1585 TCGA-59-2354 TCGA-61-1721 TCGA-61-1724 TCGA-61-1733 
       30.08         1.74        34.39        11.11        20.94        31.79 
TCGA-61-1919 TCGA-61-2002 TCGA-61-2003 TCGA-61-2009 TCGA-61-2101 TCGA-61-2102 
       38.17        17.98         4.01        39.85        55.50         6.48 
TCGA-61-2104 TCGA-61-2111 TCGA-61-2113 
       76.87       125.75        22.22 

$subtype2
TCGA-04-1336 TCGA-04-1337 TCGA-04-1341 TCGA-04-1342 TCGA-04-1347 TCGA-04-1348 
       49.15         2.01         1.08        18.51        63.09        48.76 
TCGA-04-1350 TCGA-04-1356 TCGA-04-1365 TCGA-04-1367 TCGA-04-1536 TCGA-04-1646 
       63.98        49.28        76.57       103.40        29.10        27.88 
TCGA-04-1654 TCGA-09-0366 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 
       47.70        57.76        41.62        57.60        61.87        55.36 
TCGA-09-1673 TCGA-09-1674 TCGA-10-0926 TCGA-10-0927 TCGA-13-0714 TCGA-13-0720 
        3.02         8.55        25.91        81.86         6.21        44.55 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0751 TCGA-13-0757 TCGA-13-0760 TCGA-13-0766 
       39.58         2.73        55.17        11.18        11.54        56.71 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0805 
        8.71         7.79         8.28         8.19        43.86        35.31 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 
       68.94       107.18        91.40        74.27        66.67        61.84 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       69.01        43.36        19.36        47.38        48.33        47.84 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0916 TCGA-13-0919 TCGA-13-0923 TCGA-13-0924 
       37.08        27.72        21.17        84.53         6.41         6.08 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 TCGA-13-1412 
       10.88         6.61         6.05         6.84         4.70         5.33 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 
       61.71        29.42        98.04        70.82        52.44        73.55 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 
       38.20        49.25         4.24        54.31        37.61        13.97 
TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
       16.57         4.41         4.77         4.18         2.56         3.91 
TCGA-13-1512 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 
        3.09        23.05        25.94        26.20        27.52        25.38 
TCGA-20-1684 TCGA-20-1687 TCGA-23-1021 TCGA-23-1023 TCGA-23-1027 TCGA-23-1028 
       19.10         2.66        47.54        40.54        32.09        49.41 
TCGA-23-1030 TCGA-23-1032 TCGA-23-1107 TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 
       29.13         2.76         0.30        51.35        54.51        31.20 
TCGA-23-1114 TCGA-23-1118 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2079 
       68.68        86.01        39.09        33.47        58.13        91.66 
TCGA-24-0975 TCGA-24-1104 TCGA-24-1105 TCGA-24-1417 TCGA-24-1423 TCGA-24-1428 
       21.80        63.55        47.41         7.82         6.25        17.39 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 
       28.37        18.64        43.53         8.55        72.92        45.14 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 
        9.11         3.45         1.18        22.22        26.96        57.40 
TCGA-24-1548 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1558 
       16.21        51.91        41.39        58.09        88.50        19.53 
TCGA-24-1562 TCGA-24-1564 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1845 
       45.50        25.87        90.15        88.37        48.33         3.81 
TCGA-24-1924 TCGA-24-2026 TCGA-24-2030 TCGA-25-1312 TCGA-25-1314 TCGA-25-1318 
       30.21        34.82        55.92         1.02        33.01        34.98 
TCGA-25-1319 TCGA-25-1324 TCGA-25-1325 TCGA-25-1329 TCGA-25-1623 TCGA-25-1632 
       65.00        34.03        32.09        15.02        18.58        59.15 
TCGA-25-2397 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1697 
       12.00        78.90        47.61        48.33       101.79        31.20 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1707 TCGA-29-1711 TCGA-29-1769 TCGA-29-1776 
       36.36        16.93        41.98        34.62        22.98        11.84 
TCGA-29-1777 TCGA-29-1784 TCGA-29-1785 TCGA-29-2425 TCGA-29-2428 TCGA-30-1718 
       12.30         5.36        36.30        65.00        45.11        51.91 
TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 TCGA-30-1860 TCGA-30-1866 
       36.26         2.47        15.68        48.10        44.91        36.62 
TCGA-36-1569 TCGA-36-1578 TCGA-36-1581 TCGA-57-1582 TCGA-57-1583 TCGA-59-2348 
       29.10        27.85        24.69        24.03        11.38       180.20 
TCGA-59-2350 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 TCGA-61-1907 
       22.32        35.80         2.43        33.67         1.45        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-2000 TCGA-61-2012 
       37.05        42.51        48.92        14.50        30.64 

$subtype3
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1514 TCGA-04-1517 TCGA-04-1519 
       32.52        44.32        33.67        56.55        19.99         0.79 
TCGA-04-1525 TCGA-04-1542 TCGA-04-1638 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 
       38.37        84.20        55.43        28.64        64.64        36.23 
TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 TCGA-09-1661 TCGA-09-1669 TCGA-09-1670 
       31.86        45.37        29.16        38.43        30.51        17.98 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 
        6.12        35.15         4.54        71.11        63.09        39.75 
TCGA-09-2056 TCGA-10-0928 TCGA-10-0933 TCGA-10-0934 TCGA-13-0755 TCGA-13-0791 
       12.46        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         8.12        70.39        44.94        34.06        29.98 
TCGA-13-0920 TCGA-13-0921 TCGA-13-1489 TCGA-20-1685 TCGA-20-1686 TCGA-23-1022 
       13.81         4.64        82.88        16.70         2.93        49.68 
TCGA-23-1029 TCGA-23-1111 TCGA-23-1119 TCGA-23-1120 TCGA-23-1809 TCGA-23-2072 
        8.81         3.22       129.96         4.27         0.53        24.95 
TCGA-23-2077 TCGA-23-2084 TCGA-24-0966 TCGA-24-0979 TCGA-24-0982 TCGA-24-1103 
      115.89        49.84         7.63        41.56        22.32        54.12 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1419 TCGA-24-1424 TCGA-24-1426 TCGA-24-1464 
        6.31         6.38         7.86         6.02         5.36        12.46 
TCGA-24-1467 TCGA-24-1549 TCGA-24-1557 TCGA-24-1560 TCGA-24-1565 TCGA-24-1567 
      105.99        56.58        39.88        44.09        10.26        17.23 
TCGA-24-1616 TCGA-24-1844 TCGA-24-1847 TCGA-24-2019 TCGA-24-2023 TCGA-24-2027 
       38.24         3.72        11.28         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-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 
       38.20         0.30        35.87        14.96        24.99        85.05 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2400 TCGA-29-1694 TCGA-29-1696 
       49.05         1.02        38.04        42.02        39.02        33.93 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1771 TCGA-29-1774 TCGA-29-1778 
       17.36        86.60        66.81        22.55        17.33        14.93 
TCGA-29-1781 TCGA-29-1783 TCGA-30-1714 TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 
        8.38         7.23        38.07        28.77        21.53        22.85 
TCGA-36-1577 TCGA-36-1580 TCGA-57-1584 TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 
       25.74        24.23        21.14        22.32        25.08        25.02 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 TCGA-61-1725 TCGA-61-1728 
      116.12         9.40         2.14         5.42        31.43        27.88 
TCGA-61-1736 TCGA-61-1737 TCGA-61-1743 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 
       48.79        44.84        43.69         8.42         5.79        11.41 
TCGA-61-1906 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 
       34.13        56.61        67.76        43.43        15.75         2.01 
TCGA-61-1998 TCGA-61-2008 TCGA-61-2016 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 
        5.52        30.64         1.18         4.77        51.72        71.74 
TCGA-61-2095 TCGA-61-2097 TCGA-61-2098 TCGA-61-2109 TCGA-61-2110 
       61.64        60.62        65.52        20.68        44.52 

subtype1 subtype2 subtype3 
    0.26     0.30     0.30 
subtype1 subtype2 subtype3 
  152.02   180.20   129.96 
subtype1 subtype2 subtype3 
   30.18    33.67    28.77 
[1] "0.3 - 152.0 (30.2)" "0.3 - 180.2 (33.7)" "0.3 - 130.0 (28.8)"
D11V2, continuous
          vv
clus       OMENTUM OVARY PERITONEUM OVARY
  subtype1       2   121                1
  subtype2       0   185                0
  subtype3       0   144                0
D11V3, multiclass
                  clus
vv                 subtype1 subtype2 subtype3
  OMENTUM                 2        0        0
  OVARY                 121      185      144
  PERITONEUM OVARY        1        0        0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V4, binary
          cls
clus         0   1
  subtype1 115   0
  subtype2 152   2
  subtype3 130   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  115    0
  subtype2  152    2
  subtype3  130    1
     clus
vv    subtype1 subtype2 subtype3
  NO       115      152      130
  YES        0        2        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"
D11V5, continuous
          vv
clus       R0 R1
  subtype1  0  3
  subtype2  0  3
  subtype3  2  0
D11V6, multiclass
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 
       3        3        2 
[1] "subtype2" "subtype1" "subtype1" "subtype2" "subtype1" "subtype2"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                2     3                         6
  subtype2                                0     6                        10
  subtype3                                0     6                         5
          vv
clus       WHITE
  subtype1   106
  subtype2   167
  subtype3   128
D11V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        2        0        0
  ASIAN                                   3        6        6
  BLACK OR AFRICAN AMERICAN               6       10        5
  WHITE                                 106      167      128
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
          cls
clus         0   1
  subtype1   0  66
  subtype2   7 114
  subtype3   1  83
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   66
  subtype2    7  114
  subtype3    1   83
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        7        1
  NOT HISPANIC OR LATINO       66      114       83
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = MIRSEQ_CHIERARCHICAL
D12V1, survival
          sevent
clus2       0  1
  subtype1 51 54
  subtype2 27 46
  subtype3 69 99
  subtype4 50 55
subtype1 subtype2 subtype3 subtype4 
     105       73      168      105 
subtype1 subtype2 subtype3 subtype4 
      54       46       99       55 
$subtype1
TCGA-04-1331 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 TCGA-04-1347 TCGA-09-0366 
       43.92        49.15         2.01        18.51        63.09        57.76 
TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 TCGA-13-0714 TCGA-13-0720 TCGA-13-0724 
       41.62        61.87        55.36         6.21        44.55         2.73 
TCGA-13-0751 TCGA-13-0760 TCGA-13-0766 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 
       55.17        11.54        56.71         8.71         7.79         8.28 
TCGA-13-0803 TCGA-13-0805 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
       43.86        35.31       107.18        91.40        74.27        66.67 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0900 TCGA-13-0903 
       61.84        67.99        69.01        43.36        57.07        47.38 
TCGA-13-0905 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0916 TCGA-13-0919 
       47.84        44.84        37.08        27.72        21.17        84.53 
TCGA-13-0924 TCGA-13-1404 TCGA-13-1411 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
        6.08         6.61         4.21        61.71        29.42        98.04 
TCGA-13-1485 TCGA-13-1500 TCGA-13-1501 TCGA-13-1511 TCGA-13-1512 TCGA-20-0990 
       20.68        13.97        32.84         3.91         3.09        25.94 
TCGA-20-0991 TCGA-20-1687 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       26.20         2.66        40.54        26.83        32.09        49.41 
TCGA-23-1109 TCGA-23-1113 TCGA-23-1118 TCGA-23-2079 TCGA-23-2081 TCGA-24-0970 
       51.35        31.20        86.01        91.66        77.00        11.64 
TCGA-24-0975 TCGA-24-1105 TCGA-24-1417 TCGA-24-1425 TCGA-24-1428 TCGA-24-1435 
       21.80        47.41         7.82         5.95        17.39        43.53 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 TCGA-24-1470 TCGA-24-1545 TCGA-24-1546 
        8.55        72.92        45.14         3.45        57.40        64.27 
TCGA-24-1551 TCGA-24-1555 TCGA-24-1563 TCGA-24-1614 TCGA-24-1845 TCGA-24-1846 
       51.91        88.50        47.70        48.33         3.81         4.37 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2271 TCGA-24-2298 TCGA-25-1314 TCGA-25-1623 
       36.16         0.79        31.63        53.26        33.01        18.58 
TCGA-25-1626 TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1711 
       17.03         2.96        31.00        26.99        78.90        34.62 
TCGA-29-1764 TCGA-29-1768 TCGA-29-1770 TCGA-29-2427 TCGA-30-1856 TCGA-30-1857 
       62.93        31.30        24.36        62.47        15.68         0.26 
TCGA-30-1860 TCGA-31-1953 TCGA-31-1956 TCGA-36-1574 TCGA-36-1578 TCGA-59-2354 
       44.91         6.71        44.12        22.55        27.85        34.39 
TCGA-61-1740 TCGA-61-1907 TCGA-61-1913 
        2.43        31.30        48.92 

$subtype2
TCGA-04-1332 TCGA-04-1346 TCGA-04-1349 TCGA-04-1364 TCGA-04-1514 TCGA-04-1517 
       41.00        65.52        21.57        33.67        56.55        19.99 
TCGA-04-1519 TCGA-04-1536 TCGA-04-1655 TCGA-09-0364 TCGA-09-1662 TCGA-09-2044 
        0.79        29.10        45.37        29.16        89.33         6.12 
TCGA-09-2048 TCGA-09-2050 TCGA-10-0927 TCGA-13-0755 TCGA-13-0791 TCGA-13-0800 
        4.54        71.11        81.86         2.50        40.24         8.12 
TCGA-13-0883 TCGA-13-0888 TCGA-13-0906 TCGA-13-1409 TCGA-13-1477 TCGA-20-1686 
       68.94        70.39        44.94         6.84        54.64         2.93 
TCGA-23-1022 TCGA-23-1032 TCGA-23-1110 TCGA-23-1114 TCGA-23-1120 TCGA-23-1121 
       49.68         2.76        54.51        68.68         4.27         6.38 
TCGA-23-1123 TCGA-23-2084 TCGA-24-0982 TCGA-24-1104 TCGA-24-1423 TCGA-24-1424 
       33.47        49.84        22.32        63.55         6.25         6.02 
TCGA-24-1544 TCGA-24-1549 TCGA-24-1558 TCGA-24-1567 TCGA-24-1604 TCGA-24-1923 
       26.96        56.58        19.53        17.23        88.37        22.68 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1315 TCGA-25-1322 TCGA-25-1324 TCGA-25-1328 
        1.02        26.96        52.04         2.99        34.03        66.05 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-2392 TCGA-25-2393 
       62.17        35.87        14.96        24.99         1.02        38.04 
TCGA-29-1690 TCGA-29-1761 TCGA-29-1762 TCGA-29-1774 TCGA-29-1776 TCGA-29-1778 
       47.61        17.36        86.60        17.33        11.84        14.93 
TCGA-29-1781 TCGA-29-1784 TCGA-31-1944 TCGA-36-1575 TCGA-36-1577 TCGA-36-1580 
        8.38         5.36        45.57         8.55        25.74        24.23 
TCGA-61-1721 TCGA-61-1743 TCGA-61-1915 TCGA-61-1917 TCGA-61-1998 TCGA-61-2003 
       11.11        43.69        67.76        43.43         5.52         4.01 
TCGA-61-2104 
       76.87 

$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-10-0926 TCGA-13-0723 TCGA-13-0757 TCGA-13-0768 TCGA-13-0802 
       20.94        25.91        39.58        11.18        58.65         8.19 
TCGA-13-0894 TCGA-13-0901 TCGA-13-0904 TCGA-13-0923 TCGA-13-1403 TCGA-13-1405 
       49.61        19.36        48.33         6.41        10.88         7.36 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1412 TCGA-13-1481 TCGA-13-1487 
        6.05         5.92         4.70         5.33        87.06        22.39 
TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
       70.82        52.44        73.55        38.20        49.25         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       54.31        37.61        38.40        16.57         4.21         4.41 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-2060 TCGA-20-1682 TCGA-20-1683 
        4.77         4.18         2.56        77.88        27.52        25.38 
TCGA-20-1684 TCGA-23-1021 TCGA-23-1030 TCGA-23-1107 TCGA-23-1122 TCGA-23-1124 
       19.10        47.54        29.13         0.30        39.09        58.13 
TCGA-23-2078 TCGA-24-1418 TCGA-24-1422 TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 
       87.48         7.99         0.76         4.83        28.37        18.64 
TCGA-24-1434 TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 TCGA-24-1548 TCGA-24-1550 
       18.67         9.11         1.18        22.22        16.21        41.06 
TCGA-24-1552 TCGA-24-1556 TCGA-24-1562 TCGA-24-1564 TCGA-24-1603 TCGA-24-1842 
       41.39        70.62        45.50        25.87        90.15         8.32 
TCGA-24-1843 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-1928 
        3.48         5.79         5.52         9.80        30.21        11.05 
TCGA-24-1930 TCGA-24-2020 TCGA-24-2024 TCGA-24-2026 TCGA-24-2029 TCGA-24-2030 
       81.11       152.02        58.16        34.82        14.43        55.92 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2262 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
       18.48        28.18         0.36        70.45        44.61         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-25-1316 TCGA-25-1318 TCGA-25-1319 
       67.36        36.23        16.64        42.05        34.98        65.00 
TCGA-25-1320 TCGA-25-1325 TCGA-25-1326 TCGA-25-1329 TCGA-25-1628 TCGA-25-1632 
       37.97        32.09        41.06        15.02        20.61        59.15 
TCGA-25-1635 TCGA-25-1877 TCGA-25-2042 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 
       52.04        24.00        13.02         3.02        12.00        45.01 
TCGA-25-2399 TCGA-29-1691 TCGA-29-1693 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 
       19.99        48.33       101.79        40.41        31.20        68.32 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
       36.36        16.93        23.93        59.67        18.25        41.98 
TCGA-29-1710 TCGA-29-1766 TCGA-29-1769 TCGA-29-1777 TCGA-29-1785 TCGA-29-2414 
       31.27        39.42        22.98        12.30        36.30        86.17 
TCGA-29-2425 TCGA-29-2428 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1859 
       65.00        45.11        51.91        36.26         2.47        48.10 
TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 
       34.78         6.12        36.62         1.22        57.57        24.26 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1946 TCGA-31-1951 TCGA-31-1959 TCGA-36-1569 
       30.05        48.79        30.18        22.49         2.20        29.10 
TCGA-36-1576 TCGA-36-1581 TCGA-57-1582 TCGA-57-1583 TCGA-57-1585 TCGA-59-2348 
       30.08        24.69        24.03        11.38         1.74       180.20 
TCGA-59-2350 TCGA-61-1724 TCGA-61-1733 TCGA-61-1738 TCGA-61-1741 TCGA-61-1895 
       22.32        20.94        31.79        35.80        33.67         1.45 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1919 TCGA-61-2000 TCGA-61-2002 TCGA-61-2009 
       37.05        42.51        38.17        14.50        17.98        39.85 
TCGA-61-2012 TCGA-61-2088 TCGA-61-2101 TCGA-61-2102 TCGA-61-2111 TCGA-61-2113 
       30.64         4.77        55.50         6.48       125.75        22.22 

$subtype4
TCGA-04-1361 TCGA-04-1362 TCGA-04-1525 TCGA-04-1542 TCGA-04-1638 TCGA-04-1648 
       32.52        44.32        38.37        84.20        55.43        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-09-1661 TCGA-09-1669 TCGA-09-1670 
       64.64        36.23        31.86        38.43        30.51        17.98 
TCGA-09-2045 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-10-0928 TCGA-10-0933 
       35.15        63.09        39.75        12.46        18.51        14.66 
TCGA-10-0934 TCGA-13-0792 TCGA-13-0912 TCGA-13-0913 TCGA-13-0920 TCGA-13-0921 
        6.71       118.42        34.06        29.98        13.81         4.64 
TCGA-13-1489 TCGA-20-0987 TCGA-20-1685 TCGA-23-1029 TCGA-23-1111 TCGA-23-1119 
       82.88        23.05        16.70         8.81         3.22       129.96 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-24-0966 TCGA-24-0979 TCGA-24-1103 
        0.53        24.95       115.89         7.63        41.56        54.12 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1419 TCGA-24-1426 TCGA-24-1464 TCGA-24-1467 
        6.31         6.38         7.86         5.36        12.46       105.99 
TCGA-24-1553 TCGA-24-1557 TCGA-24-1560 TCGA-24-1565 TCGA-24-1616 TCGA-24-1844 
       58.09        39.88        44.09        10.26        38.24         3.72 
TCGA-24-1847 TCGA-24-2019 TCGA-24-2023 TCGA-24-2027 TCGA-24-2036 TCGA-24-2038 
       11.28         4.87        44.84       109.71        64.01        44.52 
TCGA-24-2254 TCGA-24-2267 TCGA-24-2297 TCGA-25-1317 TCGA-25-1321 TCGA-25-1323 
       57.07        47.54        55.86         2.01        33.96        12.99 
TCGA-25-1625 TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 TCGA-25-1878 TCGA-25-2391 
       27.62        12.95        38.20         0.30        85.05        49.05 
TCGA-25-2400 TCGA-25-2404 TCGA-29-1694 TCGA-29-1696 TCGA-29-1763 TCGA-29-1771 
       42.02        29.03        39.02        33.93        66.81        22.55 
TCGA-29-1783 TCGA-30-1714 TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 TCGA-57-1584 
        7.23        38.07        28.77        21.53        22.85        21.14 
TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 
       22.32        25.08        25.02       116.12         9.40         2.14 
TCGA-59-2363 TCGA-61-1725 TCGA-61-1728 TCGA-61-1736 TCGA-61-1737 TCGA-61-1899 
        5.42        31.43        27.88        48.79        44.84         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1906 TCGA-61-1914 TCGA-61-1918 TCGA-61-1995 
        5.79        11.41        34.13        56.61        15.75         2.01 
TCGA-61-2008 TCGA-61-2016 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 
       30.64         1.18        51.72        71.74        61.64        60.62 
TCGA-61-2098 TCGA-61-2109 TCGA-61-2110 
       65.52        20.68        44.52 

subtype1 subtype2 subtype3 subtype4 
    0.26     0.79     0.30     0.30 
subtype1 subtype2 subtype3 subtype4 
  107.18    89.33   180.20   129.96 
subtype1 subtype2 subtype3 subtype4 
  34.620   26.960   30.065   30.640 
[1] "0.3 - 107.2 (34.6)" "0.8 - 89.3 (27.0)"  "0.3 - 180.2 (30.1)"
[4] "0.3 - 130.0 (30.6)"
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  86   0
  subtype2  66   1
  subtype3 146   2
  subtype4  99   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   86    0
  subtype2   66    1
  subtype3  146    2
  subtype4   99    0
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        86       66      146       99
  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"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     6                         4
  subtype2                                0     3                         4
  subtype3                                1     3                         8
  subtype4                                1     3                         5
          vv
clus       WHITE
  subtype1    94
  subtype2    61
  subtype3   152
  subtype4    94
D12V7, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1        1
  ASIAN                                   6        3        3        3
  BLACK OR AFRICAN AMERICAN               4        4        8        5
  WHITE                                  94       61      152       94
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, 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 4 8
  subtype2 4 6
subtype1 subtype2 
      12       10 
subtype1 subtype2 
       8        6 
$subtype1
TCGA-04-1652 TCGA-13-0908 TCGA-24-2288 TCGA-24-2290 TCGA-25-2392 TCGA-25-2399 
       31.86        44.84         0.82        36.23         1.02        19.99 
TCGA-25-2400 TCGA-57-1994 TCGA-61-1918 TCGA-61-2088 TCGA-61-2109 TCGA-61-2111 
       42.02        25.02        15.75         4.77        20.68       125.75 

$subtype2
TCGA-09-2050 TCGA-09-2054 TCGA-23-2077 TCGA-24-1928 TCGA-24-2036 TCGA-24-2289 
       71.11        20.94       115.89        11.05        64.01        67.36 
TCGA-24-2297 TCGA-25-2404 TCGA-59-2363 TCGA-61-2098 
       55.86        29.03         5.42        65.52 

subtype1 subtype2 
    0.82     5.42 
subtype1 subtype2 
  125.75   115.89 
subtype1 subtype2 
  22.850   59.935 
[1] "0.8 - 125.8 (22.9)" "5.4 - 115.9 (59.9)"
[1] "hr=" "2.1"
D13V2, continuous
          vv
clus       OMENTUM OVARY
  subtype1       1    11
  subtype2       0    10
D13V3, multiclass
         clus
vv        subtype1 subtype2
  OMENTUM        1        0
  OVARY         11       10
[1] 2 2
[1] FALSE
D13V4, binary
          cls
clus        0
  subtype1 11
  subtype2  9
[1] "NOT AVAILABLE: table only has an event [0]"
D13V5, continuous
          vv
clus       R0
  subtype1  0
  subtype2  1
[1] "NOT AVAILABLE: table dimension [2x1]"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         0
  subtype2                                1     1                         1
          vv
clus       WHITE
  subtype1    12
  subtype2     7
D13V7, multiclass
                                  clus
vv                                 subtype1 subtype2
  AMERICAN INDIAN OR ALASKA NATIVE        0        1
  ASIAN                                   0        1
  BLACK OR AFRICAN AMERICAN               0        1
  WHITE                                  12        7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V8, binary
          cls
clus       0
  subtype1 8
  subtype2 5
[1] "NOT AVAILABLE: table only has an event [0]"

Clustering(14) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D14V1, survival
          sevent
clus2      0 1
  subtype1 1 5
  subtype4 4 2
  subtype5 1 3
subtype1 subtype4 subtype5 
       6        6        4 
subtype1 subtype4 subtype5 
       5        2        3 
$subtype1
TCGA-04-1652 TCGA-25-2400 TCGA-25-2404 TCGA-61-1918 TCGA-61-2088 TCGA-61-2109 
       31.86        42.02        29.03        15.75         4.77        20.68 

$subtype4
TCGA-23-2077 TCGA-24-2036 TCGA-24-2297 TCGA-57-1994 TCGA-59-2363 TCGA-61-2098 
      115.89        64.01        55.86        25.02         5.42        65.52 

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

subtype1 subtype4 subtype5 
    4.77     5.42    11.05 
subtype1 subtype4 subtype5 
   42.02   115.89   125.75 
subtype1 subtype4 subtype5 
  24.855   59.935   51.795 
[1] "4.8 - 42.0 (24.9)"   "5.4 - 115.9 (59.9)"  "11.1 - 125.8 (51.8)"
D14V2, continuous
          vv
clus       OMENTUM OVARY
  subtype1       0     6
  subtype4       0     6
  subtype5       1     3
D14V3, multiclass
         clus
vv        subtype1 subtype4 subtype5
  OMENTUM        0        0        1
  OVARY          6        6        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"
D14V4, binary
          cls
clus       0
  subtype1 5
  subtype4 5
  subtype5 4
[1] "NOT AVAILABLE: table only has an event [0]"
D14V5, continuous
          vv
clus       R0
  subtype1  0
  subtype4  1
  subtype5  0
[1] "NOT AVAILABLE: table dimension [3x1]"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN WHITE
  subtype1                                1     0     5
  subtype4                                0     1     5
  subtype5                                0     0     4
D14V7, multiclass
                                  clus
vv                                 subtype1 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   0        1        0
  WHITE                                   5        5        4
[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"
D14V8, binary
          cls
clus       0
  subtype1 5
  subtype4 2
  subtype5 1
[1] "NOT AVAILABLE: table only has an event [0]"
