[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"      "-oTOV-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/OV-TP/10006099/OV-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/OV-TP/10686040/transformed.cor.cli.txt"

nPatients in clinical file=586, in cluster file=316, common to both=316
[1]  19 316
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           273             43 
  TP53 MUTATED TP53 WILD-TYPE 
           273             43 
[1] "BRCA1 MUTATION ANALYSIS"
[1] 3
  BRCA1 MUTATED BRCA1 WILD-TYPE 
             12             304 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
             12             304 
[1] "FAM86B2 MUTATION ANALYSIS"
[1] 3
  FAM86B2 MUTATED FAM86B2 WILD-TYPE 
                6               310 
  FAM86B2 MUTATED FAM86B2 WILD-TYPE 
                6               310 
[1] "TBP MUTATION ANALYSIS"
[1] 3
  TBP MUTATED TBP WILD-TYPE 
            4           312 
  TBP MUTATED TBP WILD-TYPE 
            4           312 
[1] "NBPF10 MUTATION ANALYSIS"
[1] 3
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               4              312 
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               4              312 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           14           302 
  NF1 MUTATED NF1 WILD-TYPE 
           14           302 
[1] "C10ORF140 MUTATION ANALYSIS"
[1] 3
  C10ORF140 MUTATED C10ORF140 WILD-TYPE 
                  5                 311 
  C10ORF140 MUTATED C10ORF140 WILD-TYPE 
                  5                 311 
[1] "BRCA2 MUTATION ANALYSIS"
[1] 3
  BRCA2 MUTATED BRCA2 WILD-TYPE 
             11             305 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
             11             305 
[1] "CDK12 MUTATION ANALYSIS"
[1] 3
  CDK12 MUTATED CDK12 WILD-TYPE 
              8             308 
  CDK12 MUTATED CDK12 WILD-TYPE 
              8             308 
[1] "OR4F21 MUTATION ANALYSIS"
[1] 3
  OR4F21 MUTATED OR4F21 WILD-TYPE 
               3              313 
  OR4F21 MUTATED OR4F21 WILD-TYPE 
               3              313 
[1] "C9ORF171 MUTATION ANALYSIS"
[1] 3
  C9ORF171 MUTATED C9ORF171 WILD-TYPE 
                 5                311 
  C9ORF171 MUTATED C9ORF171 WILD-TYPE 
                 5                311 
[1] "HYDIN MUTATION ANALYSIS"
[1] 3
  HYDIN MUTATED HYDIN WILD-TYPE 
             11             305 
  HYDIN MUTATED HYDIN WILD-TYPE 
             11             305 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
            8           308 
  RB1 MUTATED RB1 WILD-TYPE 
            8           308 
[1] "GART MUTATION ANALYSIS"
[1] 3
  GART MUTATED GART WILD-TYPE 
             3            313 
  GART MUTATED GART WILD-TYPE 
             3            313 
[1] "SRC MUTATION ANALYSIS"
[1] 3
  SRC MUTATED SRC WILD-TYPE 
            4           312 
  SRC MUTATED SRC WILD-TYPE 
            4           312 
[1] "ZNF236 MUTATION ANALYSIS"
[1] 3
  ZNF236 MUTATED ZNF236 WILD-TYPE 
               7              309 
  ZNF236 MUTATED ZNF236 WILD-TYPE 
               7              309 
[1] "NBPF16 MUTATION ANALYSIS"
[1] 3
  NBPF16 MUTATED NBPF16 WILD-TYPE 
               4              312 
  NBPF16 MUTATED NBPF16 WILD-TYPE 
               4              312 
[1] "CYP11B1 MUTATION ANALYSIS"
[1] 3
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
                7               309 
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
                7               309 
[1] "SON MUTATION ANALYSIS"
[1] 3
  SON MUTATED SON WILD-TYPE 
            8           308 
  SON MUTATED SON WILD-TYPE 
            8           308 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                                      
 [2] "VITALSTATUS"                                       
 [3] "DAYSTODEATH"                                       
 [4] "DAYSTOLASTFOLLOWUP"                                
 [5] "PRIMARYSITEOFDESEASE"                              
 [6] "NEOPLASM.DISEASESTAGE"                             
 [7] "PATHOLOGY.T.STAGE"                                 
 [8] "PATHOLOGY.N.STAGE"                                 
 [9] "PATHOLOGY.M.STAGE"                                 
[10] "DCCUPLOADDATE"                                     
[11] "GENDER"                                            
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"                  
[13] "RADIATIONTHERAPY"                                  
[14] "KARNOFSKYPERFORMANCESCORE"                         
[15] "EXAMINATIONS.EXAMINATION.KARNOFSKYPERFORMANCESCORE"
[16] "HISTOLOGICALTYPE"                                  
[17] "TUMORGRADE"                                        
[18] "TUMORSTAGE"                                        
[19] "PATIENTTUMORRECURRENCESTATUS"                      
[20] "DAYSTOTUMORRECURRENCE"                             
[21] "CHEMOTHERAPY"                                      
[22] "RADIATIONS.RADIATION.REGIMENINDICATION"            
[23] "COMPLETENESS.OF.RESECTION"                         
[24] "RACE"                                              
[25] "ETHNICITY"                                         
[26] "BATCHNUMBER"                                       

Input Data has 26 rows and 316 columns.

[1] "Batch" "26"   
[1] "Last Follow UP"
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
        1224         1247         1495           NA         1418           NA 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 
          NA         1993         1919           NA           NA           NA 
TCGA-04-1356 TCGA-04-1357 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
          NA           NA          989           NA           NA         2329 
TCGA-04-1367 TCGA-04-1514 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 
        2174           NA           NA         1167           NA           NA 
TCGA-09-0366 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 
          NA           NA           NA           NA           NA           NA 
TCGA-09-1666 TCGA-09-1669 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 
        1752          928          186           NA         3419         2163 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
        1919         1209          379          788         2478          563 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 
        1011          982          356          119         1078          460 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 
         604          189          748         1355         1204           83 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 
         946          462          542         1678           76          351 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
        1036          981          869         1184         1117          873 
TCGA-13-0795 TCGA-13-0800 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
         596          247         1073          414         2097         3260 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 
        2780         2259         2028         1881         2068         2099 
TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 
        1319         1509         1748         1708         1736         1441 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
        1470         1455         1367         1128          843         1036 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 
         912          644          453          420          195          185 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
         331          201          224          184          180          208 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 
         143          128          162         1662         2648         1877 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
         895         2982          681         2154         2521         1595 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
        2237         1162         1498          129         1652         1144 
TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
        1168          999          504          128          134          145 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2060 TCGA-20-0987 TCGA-20-0990 
         127           78           94          262           NA          789 
TCGA-20-0991 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
         797         1446         1294         1233          468          816 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 
         966         1503          886          575           68         1658 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 
         139         1013         2616          130         1189         1018 
TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
        1768          759         3525         2661         2788         2342 
TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
         232          598          354          663         1264          233 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
         679         1646         1933         1442          192          194 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
         238          243          239           23          190          183 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 
         181          163          147          529          583          568 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 
        1324          260         2218          379         1373          277 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 
         105           36          676          820         1746          493 
TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 
        1721         1579         1259         1767         2692         2148 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
        1213          594         1341         1384         1451          787 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 
         312          524         2742         2688         1470         1163 
TCGA-24-2019 TCGA-24-2024 TCGA-24-2030 TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 
         148         1769         1641          857         1354         1736 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
        1100           24           11         1446          962         2143 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2298 
        1357           25         2049         1102          506         1620 
TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 
         820         1553         1126           31         1064         1977 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1324 TCGA-25-1326 TCGA-25-1328 
        1124         1033           91         1035          945         1979 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 
          90          565          548          481           11          627 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 
         239            9         1732         1843         1081         1558 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 
         396         1492           31         1157           92         1369 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
         608         1278           90          883          943          821 
TCGA-29-2427 TCGA-30-1853 TCGA-30-1862 TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 
        1900         1103          186          914          571          204 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
          67          875          885          655          695          686 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-57-1582 
         260          915          783          847          737          731 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 
         346          643          763         5481           NA         3532 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-61-1728 TCGA-61-1736 
          NA           NA           NA          165          848         1484 
TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 
        1161           61          168          441          547          122 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2088 TCGA-61-2092 
         932         1212          932           36          145         1573 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 
        2182         1875         1844         1688          197         2338 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
         629         1354         3825          676 
Variable 1:'AGE':	nDistinctValues=50,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=172,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=271,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'EXAMINATIONS.EXAMINATION.KARNOFSKYPERFORMANCESCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'TUMOR.GRADE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'TUMOR.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 19:'PATIENTTUMORRECURRENCESTATUS':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 20:'DAYSTOTUMORRECURRENCE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 21:'CHEMOTHERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 22:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 23:'COMPLETENESS.OF.RESECTION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 24:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 25:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 26:'BATCH.NUMBER':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                         "KARNOFSKY.PERFORMANCE.SCORE"
[3] "RACE"                        "ETHNICITY"                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 316 columns, 1 survival variables, and 4 non-survival variables.
AGE, nv=50, binary=FALSE, numeric=TRUE
KARNOFSKY.PERFORMANCE.SCORE, nv=4, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
D1V1, survival
                sevent
clus2              0   1
  TP53 MUTATED   119 153
  TP53 WILD-TYPE  15  28
  TP53 MUTATED TP53 WILD-TYPE 
           272             43 
  TP53 MUTATED TP53 WILD-TYPE 
           153             28 
$`TP53 MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1343 
       40.24        41.00        49.15         2.01        46.62        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1361 
       65.52        63.09        48.76        21.57        63.98        32.52 
TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 TCGA-04-1517 
       44.32        33.67        76.57        71.47        56.55        19.99 
TCGA-04-1530 TCGA-04-1542 TCGA-09-0366 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 
      119.08        84.20        57.76        35.57         9.99        38.43 
TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 TCGA-09-2044 TCGA-09-2045 
       89.33        41.62        57.60        30.51         6.12        35.15 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-10-0926 TCGA-10-0930 
      112.41        71.11        63.09        39.75        25.91        33.24 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 
       32.28        11.70         3.91        35.44        15.12        19.86 
TCGA-13-0714 TCGA-13-0720 TCGA-13-0724 TCGA-13-0726 TCGA-13-0751 TCGA-13-0760 
        6.21        44.55         2.73        31.10        55.17        11.54 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       34.06        32.25        28.57        38.93        36.72        28.70 
TCGA-13-0795 TCGA-13-0800 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
       19.59         8.12        35.28        13.61        68.94       107.18 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 
       91.40        74.27        66.67        61.84        67.99        69.01 
TCGA-13-0893 TCGA-13-0894 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 
       43.36        49.61        56.15        57.07        47.38        48.33 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
       47.84        44.94        37.08        27.72        34.06        29.98 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 
       21.17        14.89        13.81         6.41         6.08        10.88 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
        6.61         7.36         6.84         4.70         4.21         5.33 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 
       87.06        61.71        29.42        98.04        22.39        70.82 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
       82.88        52.44        73.55        38.20        49.25         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 
       54.31        37.61        38.40        32.84        16.57         4.21 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1512 TCGA-13-2060 TCGA-20-0987 TCGA-20-0990 
        4.77         4.18         3.09         8.61        23.05        25.94 
TCGA-20-0991 TCGA-23-1021 TCGA-23-1022 TCGA-23-1024 TCGA-23-1028 TCGA-23-1030 
       26.20        47.54        42.54        15.39        49.41        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
       18.90         2.24        54.51         4.57        33.30        86.01 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 
       39.09        33.47        58.13        24.95       115.89        87.48 
TCGA-23-2081 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
       77.00         7.63        19.66        11.64        21.80        41.56 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
       22.32        54.12        63.55        47.41         6.31         6.38 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 
        7.99         7.86         0.76         6.25         6.02         5.95 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
        5.36         4.83        17.39        18.67        43.53         8.55 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 
       72.92        12.46        45.14         9.11         3.45         1.18 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 TCGA-24-1551 TCGA-24-1552 
       22.22        26.96        57.40        16.21        51.91        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 
       58.09        88.50        70.62        39.88        19.53        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 
       45.50        47.70        25.87        17.23        90.15        88.37 
TCGA-24-1614 TCGA-24-1616 TCGA-24-2019 TCGA-24-2024 TCGA-24-2030 TCGA-24-2254 
       48.33        38.24         4.87        58.16        53.95        57.07 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 
       36.16         0.79         0.36        47.54        31.63        44.61 
TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-25-1313 TCGA-25-1315 
        0.82        67.36        36.23        16.64        26.96        51.06 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 
        1.02        34.98        65.00        36.95        33.96         2.99 
TCGA-25-1324 TCGA-25-1326 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 
       34.03        31.07         2.96        18.58        18.02        15.81 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
        0.36        20.61         7.86         0.30        56.94        60.59 
TCGA-25-1635 TCGA-25-2391 TCGA-25-2392 TCGA-25-2396 TCGA-25-2399 TCGA-25-2400 
       51.22        49.05         1.02         3.02        19.99        42.02 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2409 TCGA-29-2427 TCGA-30-1853 TCGA-30-1862 
        2.96        29.03        26.99        62.47        36.26         6.12 
TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 
       30.05        18.77         6.71         2.20        28.77        29.10 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1575 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 
       21.53        22.85         8.55        25.74        27.85        24.23 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 
       24.03        11.38        21.14        25.08       180.20        22.32 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 TCGA-61-1728 TCGA-61-1736 
      116.12         9.40         2.14         5.42        27.88        48.79 
TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 
       38.17         2.01         5.52        14.50        17.98         4.01 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 
       30.64        39.85         1.18         4.77        51.72        71.74 
TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       60.62        55.50         6.48        76.87        20.68        44.52 
TCGA-61-2111 TCGA-61-2113 
      125.75        22.22 

$`TP53 WILD-TYPE`
TCGA-04-1342 TCGA-04-1356 TCGA-04-1525 TCGA-09-2056 TCGA-10-0927 TCGA-10-0928 
       18.51        49.28        38.37        12.46        81.47        18.51 
TCGA-13-0717 TCGA-13-0723 TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 TCGA-13-0897 
       24.59        39.58        15.19        17.82         2.50        57.47 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1477 TCGA-13-1506 TCGA-13-1510 TCGA-23-1023 
        6.05         5.92        54.64         4.41         2.56        40.54 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1120 TCGA-23-2079 TCGA-24-0980 TCGA-24-1417 
       26.83        31.76         4.27        91.66         7.66         7.82 
TCGA-24-1431 TCGA-24-1549 TCGA-24-1565 TCGA-24-2035 TCGA-24-2038 TCGA-24-2280 
       19.17        56.58        10.26        28.18        44.52        70.45 
TCGA-24-2298 TCGA-25-1316 TCGA-25-1328 TCGA-25-1634 TCGA-25-2042 TCGA-25-2393 
       53.26        37.02        65.06        35.54        13.02        38.04 
TCGA-25-2398 TCGA-25-2408 TCGA-36-1574 TCGA-36-1576 TCGA-59-2354 TCGA-61-2012 
       45.01        31.00        22.55        30.08        34.39        30.64 
TCGA-61-2095 
       61.64 

  TP53 MUTATED TP53 WILD-TYPE 
           0.3            2.5 
  TP53 MUTATED TP53 WILD-TYPE 
        180.20          91.66 
  TP53 MUTATED TP53 WILD-TYPE 
        31.085         30.640 
[1] "0.3 - 180.2 (31.1)" "2.5 - 91.7 (30.6)" 
[1] "hr=" "1.3"
D1V2, continuous
D1V3, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TP53 MUTATED                                  1     9
  TP53 WILD-TYPE                                1     1
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED                          10   247
  TP53 WILD-TYPE                         0    39
D1V4, multiclass
                                  clus
vv                                 TP53 MUTATED TP53 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              1
  ASIAN                                       9              1
  BLACK OR AFRICAN AMERICAN                  10              0
  WHITE                                     247             39
[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"
D1V5, binary
                cls
clus               0   1
  TP53 MUTATED     4 176
  TP53 WILD-TYPE   3  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      4  176
  TP53 WILD-TYPE    3   28
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                4              3
  NOT HISPANIC OR LATINO          176             28
[1] 2 2
[1] FALSE

Clustering(2) Variable = BRCA1 MUTATION ANALYSIS
D2V1, survival
                 sevent
clus2               0   1
  BRCA1 MUTATED     4   7
  BRCA1 WILD-TYPE 130 174
  BRCA1 MUTATED BRCA1 WILD-TYPE 
             11             304 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
              7             174 
$`BRCA1 MUTATED`
TCGA-13-0730 TCGA-13-0804 TCGA-13-0887 TCGA-13-1489 TCGA-23-1026 TCGA-24-1470 
       17.82        35.28        66.67        82.88        26.83         3.45 
TCGA-24-2035 TCGA-25-1625 TCGA-25-1630 TCGA-25-1632 TCGA-29-2427 
       28.18        18.02         7.86        56.94        62.47 

$`BRCA1 WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       40.24        41.00        49.15         2.01        46.62        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 
       11.87        65.52        63.09        48.76        21.57        63.98 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       49.28        32.52        44.32        33.67        76.57        71.47 
TCGA-04-1514 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-09-0366 
       56.55        19.99        38.37       119.08        84.20        57.76 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 
       35.57         9.99        38.43        89.33        41.62        57.60 
TCGA-09-1669 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
       30.51         6.12        35.15       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       39.75        12.46        25.91        81.47        18.51        33.24 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 
       32.28        11.70         3.91        35.44        15.12        19.86 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 
        6.21        24.59        44.55        39.58         2.73        31.10 
TCGA-13-0727 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 
       15.19        55.17         2.50        11.54        34.06        32.25 
TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 
       28.57        38.93        36.72        28.70        19.59         8.12 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0889 
       13.61        68.94       107.18        91.40        74.27        61.84 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 
       67.99        69.01        43.36        49.61        57.47        56.15 
TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 
       57.07        47.38        48.33        47.84        44.94        37.08 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       27.72        34.06        29.98        21.17        14.89        13.81 
TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 
        6.41         6.08        10.88         6.61         7.36         6.05 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 
        5.92         6.84         4.70         4.21         5.33        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 
       87.06        61.71        29.42        98.04        22.39        70.82 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 
       52.44        73.55        38.20        49.25         4.24        54.31 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       37.61        38.40        32.84        16.57         4.21         4.41 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2060 TCGA-20-0987 
        4.77         4.18         2.56         3.09         8.61        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 
       25.94        26.20        47.54        42.54        40.54        15.39 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 
       31.76        49.41        29.13        18.90         2.24        54.51 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 
        4.57        33.30        86.01         4.27        39.09        33.47 
TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
       58.13        24.95       115.89        87.48        91.66        77.00 
TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        7.63        19.66        11.64        21.80        41.56         7.66 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
       22.32        54.12        63.55        47.41         6.31         6.38 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
        7.82         7.99         7.86         0.76         6.25         6.02 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 
        5.95         5.36         4.83        17.39        19.17        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 
       43.53         8.55        72.92        12.46        45.14         9.11 
TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 
        1.18        22.22        26.96        57.40        16.21        56.58 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       51.91        41.39        58.09        88.50        70.62        39.88 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 
       19.53        44.09        45.50        47.70        25.87        10.26 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-2019 
       17.23        90.15        88.37        48.33        38.24         4.87 
TCGA-24-2024 TCGA-24-2030 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 
       58.16        53.95        44.52        57.07        36.16         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
        0.36        47.54        31.63        70.45        44.61         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 
       67.36        36.23        16.64        53.26        26.96        51.06 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 
       37.02         1.02        34.98        65.00        36.95        33.96 
TCGA-25-1322 TCGA-25-1324 TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 
        2.99        34.03        31.07        65.06         2.96        18.58 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 
       15.81         0.36        20.61         0.30        60.59        35.54 
TCGA-25-1635 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 
       51.22        13.02        49.05         1.02        38.04         3.02 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 
       45.01        19.99        42.02         2.96        29.03        31.00 
TCGA-25-2409 TCGA-30-1853 TCGA-30-1862 TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 
       26.99        36.26         6.12        30.05        18.77         6.71 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
        2.20        28.77        29.10        21.53        22.85        22.55 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-57-1582 
        8.55        30.08        25.74        27.85        24.23        24.03 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 
       11.38        21.14        25.08       180.20        22.32       116.12 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-61-1728 TCGA-61-1736 
        9.40        34.39         2.14         5.42        27.88        48.79 
TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 
       38.17         2.01         5.52        14.50        17.98         4.01 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2088 TCGA-61-2092 
       30.64        39.85        30.64         1.18         4.77        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 
       71.74        61.64        60.62        55.50         6.48        76.87 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
       20.68        44.52       125.75        22.22 

  BRCA1 MUTATED BRCA1 WILD-TYPE 
           3.45            0.30 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
          82.88          180.20 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
         28.180          31.035 
[1] "3.5 - 82.9 (28.2)"  "0.3 - 180.2 (31.0)"
[1] "hr=" "1"  
D2V2, continuous
D2V3, continuous
[1] "Remove cluster labels:" "BRCA1 MUTATED"         
clus
  BRCA1 MUTATED BRCA1 WILD-TYPE 
              2              54 
     TCGA-04-1346      TCGA-04-1347      TCGA-04-1356      TCGA-04-1367 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-10-0926      TCGA-13-0714      TCGA-13-0720      TCGA-13-0724 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-0755      TCGA-13-0760      TCGA-13-0762      TCGA-13-0791 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-0792      TCGA-13-0793      TCGA-13-0795      TCGA-13-0885 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-0889      TCGA-13-0891      TCGA-13-0894      TCGA-13-0897 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-0900      TCGA-13-0903      TCGA-13-0904      TCGA-13-0905 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-0906      TCGA-13-0910      TCGA-13-0911      TCGA-13-0912 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-0913      TCGA-13-0919      TCGA-13-1404      TCGA-13-1405 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-1409      TCGA-13-1410      TCGA-13-1412      TCGA-13-1482 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-1483      TCGA-13-1484      TCGA-13-1488      TCGA-13-1491 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-1492      TCGA-13-1495      TCGA-13-1497      TCGA-13-1498 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-1499      TCGA-13-1501      TCGA-13-1504      TCGA-13-1506 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-13-1507      TCGA-13-1509      TCGA-13-1512      TCGA-13-2060 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-24-1614      TCGA-61-2101 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BRCA1 MUTATED                                  0     0
  BRCA1 WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BRCA1 MUTATED                           0    11
  BRCA1 WILD-TYPE                        10   275
D2V4, multiclass
                                  clus
vv                                 BRCA1 MUTATED BRCA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              10
  WHITE                                       11             275
[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"
D2V5, binary
                 cls
clus                0   1
  BRCA1 MUTATED     0   8
  BRCA1 WILD-TYPE   7 196
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA1 MUTATED      0    8
  BRCA1 WILD-TYPE    7  196
                        clus
vv                       BRCA1 MUTATED BRCA1 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             8             196
[1] 2 2
[1] FALSE

Clustering(3) Variable = FAM86B2 MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  FAM86B2 MUTATED     4   2
  FAM86B2 WILD-TYPE 130 179
  FAM86B2 MUTATED FAM86B2 WILD-TYPE 
                6               309 
  FAM86B2 MUTATED FAM86B2 WILD-TYPE 
                2               179 
$`FAM86B2 MUTATED`
TCGA-04-1356 TCGA-13-1409 TCGA-13-1494 TCGA-23-1116 TCGA-25-2401 TCGA-31-1950 
       49.28         6.84        38.20         4.57         2.96        18.77 

$`FAM86B2 WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       40.24        41.00        49.15         2.01        46.62        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 
       11.87        65.52        63.09        48.76        21.57        63.98 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 
       32.52        44.32        33.67        76.57        71.47        56.55 
TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-09-0366 TCGA-09-0369 
       19.99        38.37       119.08        84.20        57.76        35.57 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 
        9.99        38.43        89.33        41.62        57.60        30.51 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 
        6.12        35.15       112.41        71.11        63.09        39.75 
TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       12.46        25.91        81.47        18.51        33.24        32.28 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
       11.70         3.91        35.44        15.12        19.86         6.21 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 
       24.59        44.55        39.58         2.73        31.10        15.19 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 
       17.82        55.17         2.50        11.54        34.06        32.25 
TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 
       28.57        38.93        36.72        28.70        19.59         8.12 
TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 
       35.28        13.61        68.94       107.18        91.40        74.27 
TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 
       66.67        61.84        67.99        69.01        43.36        49.61 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       57.47        56.15        57.07        47.38        48.33        47.84 
TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       44.94        37.08        27.72        34.06        29.98        21.17 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 
       14.89        13.81         6.41         6.08        10.88         6.61 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
        7.36         6.05         5.92         4.70         4.21         5.33 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 
       54.64        87.06        61.71        29.42        98.04        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1495 TCGA-13-1496 
       70.82        82.88        52.44        73.55        49.25         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 
       54.31        37.61        38.40        32.84        16.57         4.21 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2060 
        4.41         4.77         4.18         2.56         3.09         8.61 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 
       23.05        25.94        26.20        47.54        42.54        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 
       15.39        26.83        31.76        49.41        29.13        18.90 
TCGA-23-1032 TCGA-23-1110 TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 TCGA-23-1122 
        2.24        54.51        33.30        86.01         4.27        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 
       33.47        58.13        24.95       115.89        87.48        91.66 
TCGA-23-2081 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
       77.00         7.63        19.66        11.64        21.80        41.56 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 
        7.66        22.32        54.12        63.55        47.41         6.31 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 
        6.38         7.82         7.99         7.86         0.76         6.25 
TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 
        6.02         5.95         5.36         4.83        17.39        19.17 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 
       18.67        43.53         8.55        72.92        12.46        45.14 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 
        9.11         3.45         1.18        22.22        26.96        57.40 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       16.21        56.58        51.91        41.39        58.09        88.50 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       70.62        39.88        19.53        44.09        45.50        47.70 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 
       25.87        10.26        17.23        90.15        88.37        48.33 
TCGA-24-1616 TCGA-24-2019 TCGA-24-2024 TCGA-24-2030 TCGA-24-2035 TCGA-24-2038 
       38.24         4.87        58.16        53.95        28.18        44.52 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 
       57.07        36.16         0.79         0.36        47.54        31.63 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 
       70.45        44.61         0.82        67.36        36.23        16.64 
TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
       53.26        26.96        51.06        37.02         1.02        34.98 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1324 TCGA-25-1326 
       65.00        36.95        33.96         2.99        34.03        31.07 
TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 
       65.06         2.96        18.58        18.02        15.81         0.36 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
       20.61         7.86         0.30        56.94        60.59        35.54 
TCGA-25-1635 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 
       51.22        13.02        49.05         1.02        38.04         3.02 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       45.01        19.99        42.02        29.03        31.00        26.99 
TCGA-29-2427 TCGA-30-1853 TCGA-30-1862 TCGA-30-1891 TCGA-31-1953 TCGA-31-1959 
       62.47        36.26         6.12        30.05         6.71         2.20 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 
       28.77        29.10        21.53        22.85        22.55         8.55 
TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-57-1582 TCGA-57-1583 
       30.08        25.74        27.85        24.23        24.03        11.38 
TCGA-57-1584 TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       21.14        25.08       180.20        22.32       116.12         9.40 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-61-1728 TCGA-61-1736 TCGA-61-1919 
       34.39         2.14         5.42        27.88        48.79        38.17 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 
        2.01         5.52        14.50        17.98         4.01        30.64 
TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 
       39.85        30.64         1.18         4.77        51.72        71.74 
TCGA-61-2095 TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       61.64        60.62        55.50         6.48        76.87        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
       44.52       125.75        22.22 

  FAM86B2 MUTATED FAM86B2 WILD-TYPE 
             2.96              0.30 
  FAM86B2 MUTATED FAM86B2 WILD-TYPE 
            49.28            180.20 
  FAM86B2 MUTATED FAM86B2 WILD-TYPE 
           12.805            31.070 
[1] "3.0 - 49.3 (12.8)"  "0.3 - 180.2 (31.1)"
[1] "hr=" "1.1"
D3V2, continuous
D3V3, continuous
[1] "Remove cluster labels:" "FAM86B2 MUTATED"       
clus
  FAM86B2 MUTATED FAM86B2 WILD-TYPE 
                2                54 
       TCGA-04-1346        TCGA-04-1347        TCGA-04-1367        TCGA-10-0926 
"FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" 
       TCGA-13-0714        TCGA-13-0720        TCGA-13-0724        TCGA-13-0755 
"FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" 
       TCGA-13-0760        TCGA-13-0762        TCGA-13-0791        TCGA-13-0792 
"FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" 
       TCGA-13-0793        TCGA-13-0795        TCGA-13-0885        TCGA-13-0887 
"FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" 
       TCGA-13-0889        TCGA-13-0891        TCGA-13-0894        TCGA-13-0897 
"FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" 
       TCGA-13-0900        TCGA-13-0903        TCGA-13-0904        TCGA-13-0905 
"FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" 
       TCGA-13-0906        TCGA-13-0910        TCGA-13-0911        TCGA-13-0912 
"FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" 
       TCGA-13-0913        TCGA-13-0919        TCGA-13-1404        TCGA-13-1405 
"FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" 
       TCGA-13-1410        TCGA-13-1412        TCGA-13-1482        TCGA-13-1483 
"FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" 
       TCGA-13-1484        TCGA-13-1488        TCGA-13-1489        TCGA-13-1491 
"FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" 
       TCGA-13-1492        TCGA-13-1495        TCGA-13-1497        TCGA-13-1498 
"FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" 
       TCGA-13-1499        TCGA-13-1501        TCGA-13-1504        TCGA-13-1506 
"FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" 
       TCGA-13-1507        TCGA-13-1509        TCGA-13-1512        TCGA-13-2060 
"FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" 
       TCGA-24-1614        TCGA-61-2101 
"FAM86B2 WILD-TYPE" "FAM86B2 WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM86B2 MUTATED                                  0     0
  FAM86B2 WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM86B2 MUTATED                           0     6
  FAM86B2 WILD-TYPE                        10   280
D3V4, multiclass
                                  clus
vv                                 FAM86B2 MUTATED FAM86B2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                10
  WHITE                                          6               280
[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"
D3V5, binary
                   cls
clus                  0   1
  FAM86B2 MUTATED     1   5
  FAM86B2 WILD-TYPE   6 199
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM86B2 MUTATED      1    5
  FAM86B2 WILD-TYPE    6  199
                        clus
vv                       FAM86B2 MUTATED FAM86B2 WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO               5               199
[1] 2 2
[1] FALSE

Clustering(4) Variable = TBP MUTATION ANALYSIS
D4V1, survival
               sevent
clus2             0   1
  TBP MUTATED     2   2
  TBP WILD-TYPE 132 179
  TBP MUTATED TBP WILD-TYPE 
            4           311 
  TBP MUTATED TBP WILD-TYPE 
            2           179 
$`TBP MUTATED`
TCGA-23-2078 TCGA-24-2038 TCGA-29-2427 TCGA-59-2350 
       87.48        44.52        62.47        22.32 

$`TBP WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       40.24        41.00        49.15         2.01        46.62        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 
       11.87        65.52        63.09        48.76        21.57        63.98 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       49.28        32.52        44.32        33.67        76.57        71.47 
TCGA-04-1514 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-09-0366 
       56.55        19.99        38.37       119.08        84.20        57.76 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 
       35.57         9.99        38.43        89.33        41.62        57.60 
TCGA-09-1669 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
       30.51         6.12        35.15       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       39.75        12.46        25.91        81.47        18.51        33.24 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 
       32.28        11.70         3.91        35.44        15.12        19.86 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 
        6.21        24.59        44.55        39.58         2.73        31.10 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 
       15.19        17.82        55.17         2.50        11.54        34.06 
TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 
       32.25        28.57        38.93        36.72        28.70        19.59 
TCGA-13-0800 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 
        8.12        35.28        13.61        68.94       107.18        91.40 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
       74.27        66.67        61.84        67.99        69.01        43.36 
TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 
       49.61        57.47        56.15        57.07        47.38        48.33 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
       47.84        44.94        37.08        27.72        34.06        29.98 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 
       21.17        14.89        13.81         6.41         6.08        10.88 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
        6.61         7.36         6.05         5.92         6.84         4.70 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
        4.21         5.33        54.64        87.06        61.71        29.42 
TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
       98.04        22.39        70.82        82.88        52.44        73.55 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 
       38.20        49.25         4.24        54.31        37.61        38.40 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       32.84        16.57         4.21         4.41         4.77         4.18 
TCGA-13-1510 TCGA-13-1512 TCGA-13-2060 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
        2.56         3.09         8.61        23.05        25.94        26.20 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
       47.54        42.54        40.54        15.39        26.83        31.76 
TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1116 
       49.41        29.13        18.90         2.24        54.51         4.57 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 
       33.30        86.01         4.27        39.09        33.47        58.13 
TCGA-23-2072 TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-24-0966 TCGA-24-0968 
       24.95       115.89        91.66        77.00         7.63        19.66 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 
       11.64        21.80        41.56         7.66        22.32        54.12 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 
       63.55        47.41         6.31         6.38         7.82         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 
        7.86         0.76         6.25         6.02         5.95         5.36 
TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
        4.83        17.39        19.17        18.67        43.53         8.55 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 
       72.92        12.46        45.14         9.11         3.45         1.18 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 
       22.22        26.96        57.40        16.21        56.58        51.91 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 
       41.39        58.09        88.50        70.62        39.88        19.53 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 
       44.09        45.50        47.70        25.87        10.26        17.23 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-2019 TCGA-24-2024 
       90.15        88.37        48.33        38.24         4.87        58.16 
TCGA-24-2030 TCGA-24-2035 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 
       53.95        28.18        57.07        36.16         0.79         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 
       47.54        31.63        70.45        44.61         0.82        67.36 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 
       36.23        16.64        53.26        26.96        51.06        37.02 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 
        1.02        34.98        65.00        36.95        33.96         2.99 
TCGA-25-1324 TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       34.03        31.07        65.06         2.96        18.58        18.02 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 
       15.81         0.36        20.61         7.86         0.30        56.94 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 
       60.59        35.54        51.22        13.02        49.05         1.02 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 
       38.04         3.02        45.01        19.99        42.02         2.96 
TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-30-1853 TCGA-30-1862 TCGA-30-1891 
       29.03        31.00        26.99        36.26         6.12        30.05 
TCGA-31-1950 TCGA-31-1953 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
       18.77         6.71         2.20        28.77        29.10        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 
       22.85        22.55         8.55        30.08        25.74        27.85 
TCGA-36-1580 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1993 TCGA-59-2348 
       24.23        24.03        11.38        21.14        25.08       180.20 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-61-1728 
      116.12         9.40        34.39         2.14         5.42        27.88 
TCGA-61-1736 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       48.79        38.17         2.01         5.52        14.50        17.98 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2088 
        4.01        30.64        39.85        30.64         1.18         4.77 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 
       51.72        71.74        61.64        60.62        55.50         6.48 
TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
       76.87        20.68        44.52       125.75        22.22 

  TBP MUTATED TBP WILD-TYPE 
        22.32          0.30 
  TBP MUTATED TBP WILD-TYPE 
        87.48        180.20 
  TBP MUTATED TBP WILD-TYPE 
       53.495        30.640 
[1] "22.3 - 87.5 (53.5)" "0.3 - 180.2 (30.6)"
[1] "hr=" "2"  
D4V2, continuous
D4V3, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TBP MUTATED                                  0     0
  TBP WILD-TYPE                                2    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  TBP MUTATED                           0     3
  TBP WILD-TYPE                        10   283
D4V4, multiclass
                                  clus
vv                                 TBP MUTATED TBP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  0            10
  WHITE                                      3           283
[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"
D4V5, binary
               cls
clus              0   1
  TBP MUTATED     0   1
  TBP WILD-TYPE   7 203
[1] "tbl2"
               cls
clus            [,1] [,2]
  TBP MUTATED      0    1
  TBP WILD-TYPE    7  203
                        clus
vv                       TBP MUTATED TBP WILD-TYPE
  HISPANIC OR LATINO               0             7
  NOT HISPANIC OR LATINO           1           203
[1] 2 2
[1] FALSE

Clustering(5) Variable = NBPF10 MUTATION ANALYSIS
D5V1, survival
                  sevent
clus2                0   1
  NBPF10 MUTATED     2   2
  NBPF10 WILD-TYPE 132 179
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               4              311 
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               2              179 
$`NBPF10 MUTATED`
TCGA-13-0913 TCGA-13-1494 TCGA-25-2391 TCGA-25-2396 
       29.98        38.20        49.05         3.02 

$`NBPF10 WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       40.24        41.00        49.15         2.01        46.62        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 
       11.87        65.52        63.09        48.76        21.57        63.98 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       49.28        32.52        44.32        33.67        76.57        71.47 
TCGA-04-1514 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-09-0366 
       56.55        19.99        38.37       119.08        84.20        57.76 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 
       35.57         9.99        38.43        89.33        41.62        57.60 
TCGA-09-1669 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
       30.51         6.12        35.15       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       39.75        12.46        25.91        81.47        18.51        33.24 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 
       32.28        11.70         3.91        35.44        15.12        19.86 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 
        6.21        24.59        44.55        39.58         2.73        31.10 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 
       15.19        17.82        55.17         2.50        11.54        34.06 
TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 
       32.25        28.57        38.93        36.72        28.70        19.59 
TCGA-13-0800 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 
        8.12        35.28        13.61        68.94       107.18        91.40 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
       74.27        66.67        61.84        67.99        69.01        43.36 
TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 
       49.61        57.47        56.15        57.07        47.38        48.33 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 
       47.84        44.94        37.08        27.72        34.06        21.17 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 
       14.89        13.81         6.41         6.08        10.88         6.61 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
        7.36         6.05         5.92         6.84         4.70         4.21 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
        5.33        54.64        87.06        61.71        29.42        98.04 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1495 
       22.39        70.82        82.88        52.44        73.55        49.25 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 
        4.24        54.31        37.61        38.40        32.84        16.57 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 
        4.21         4.41         4.77         4.18         2.56         3.09 
TCGA-13-2060 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-23-1021 TCGA-23-1022 
        8.61        23.05        25.94        26.20        47.54        42.54 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1030 
       40.54        15.39        26.83        31.76        49.41        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
       18.90         2.24        54.51         4.57        33.30        86.01 
TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 
        4.27        39.09        33.47        58.13        24.95       115.89 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 
       87.48        91.66        77.00         7.63        19.66        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 
       21.80        41.56         7.66        22.32        54.12        63.55 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       47.41         6.31         6.38         7.82         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        0.76         6.25         6.02         5.95         5.36         4.83 
TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 
       17.39        19.17        18.67        43.53         8.55        72.92 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 
       12.46        45.14         9.11         3.45         1.18        22.22 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 
       26.96        57.40        16.21        56.58        51.91        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 
       58.09        88.50        70.62        39.88        19.53        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       45.50        47.70        25.87        10.26        17.23        90.15 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-2019 TCGA-24-2024 TCGA-24-2030 
       88.37        48.33        38.24         4.87        58.16        53.95 
TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 
       28.18        44.52        57.07        36.16         0.79         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 
       47.54        31.63        70.45        44.61         0.82        67.36 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 
       36.23        16.64        53.26        26.96        51.06        37.02 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 
        1.02        34.98        65.00        36.95        33.96         2.99 
TCGA-25-1324 TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       34.03        31.07        65.06         2.96        18.58        18.02 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 
       15.81         0.36        20.61         7.86         0.30        56.94 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-2042 TCGA-25-2392 TCGA-25-2393 
       60.59        35.54        51.22        13.02         1.02        38.04 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 
       45.01        19.99        42.02         2.96        29.03        31.00 
TCGA-25-2409 TCGA-29-2427 TCGA-30-1853 TCGA-30-1862 TCGA-30-1891 TCGA-31-1950 
       26.99        62.47        36.26         6.12        30.05        18.77 
TCGA-31-1953 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 
        6.71         2.20        28.77        29.10        21.53        22.85 
TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 
       22.55         8.55        30.08        25.74        27.85        24.23 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 
       24.03        11.38        21.14        25.08       180.20        22.32 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-61-1728 
      116.12         9.40        34.39         2.14         5.42        27.88 
TCGA-61-1736 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       48.79        38.17         2.01         5.52        14.50        17.98 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2088 
        4.01        30.64        39.85        30.64         1.18         4.77 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 
       51.72        71.74        61.64        60.62        55.50         6.48 
TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
       76.87        20.68        44.52       125.75        22.22 

  NBPF10 MUTATED NBPF10 WILD-TYPE 
            3.02             0.30 
  NBPF10 MUTATED NBPF10 WILD-TYPE 
           49.05           180.20 
  NBPF10 MUTATED NBPF10 WILD-TYPE 
           34.09            31.00 
[1] "3.0 - 49.0 (34.1)"  "0.3 - 180.2 (31.0)"
[1] "hr=" "1.1"
D5V2, continuous
D5V3, continuous
[1] "Remove cluster labels:" "NBPF10 MUTATED"        
clus
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               1               55 
      TCGA-04-1346       TCGA-04-1347       TCGA-04-1356       TCGA-04-1367 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-10-0926       TCGA-13-0714       TCGA-13-0720       TCGA-13-0724 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-13-0755       TCGA-13-0760       TCGA-13-0762       TCGA-13-0791 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-13-0792       TCGA-13-0793       TCGA-13-0795       TCGA-13-0885 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-13-0887       TCGA-13-0889       TCGA-13-0891       TCGA-13-0894 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-13-0897       TCGA-13-0900       TCGA-13-0903       TCGA-13-0904 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-13-0905       TCGA-13-0906       TCGA-13-0910       TCGA-13-0911 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-13-0912       TCGA-13-0919       TCGA-13-1404       TCGA-13-1405 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-13-1409       TCGA-13-1410       TCGA-13-1412       TCGA-13-1482 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-13-1483       TCGA-13-1484       TCGA-13-1488       TCGA-13-1489 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-13-1491       TCGA-13-1492       TCGA-13-1495       TCGA-13-1497 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-13-1498       TCGA-13-1499       TCGA-13-1501       TCGA-13-1504 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-13-1506       TCGA-13-1507       TCGA-13-1509       TCGA-13-1512 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-13-2060       TCGA-24-1614       TCGA-61-2101 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NBPF10 MUTATED                                  0     0
  NBPF10 WILD-TYPE                                2    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NBPF10 MUTATED                           0     4
  NBPF10 WILD-TYPE                        10   282
D5V4, multiclass
                                  clus
vv                                 NBPF10 MUTATED NBPF10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               10
  WHITE                                         4              282
[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"
D5V5, binary
                  cls
clus                 0   1
  NBPF10 MUTATED     0   4
  NBPF10 WILD-TYPE   7 200
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF10 MUTATED      0    4
  NBPF10 WILD-TYPE    7  200
                        clus
vv                       NBPF10 MUTATED NBPF10 WILD-TYPE
  HISPANIC OR LATINO                  0                7
  NOT HISPANIC OR LATINO              4              200
[1] 2 2
[1] FALSE

Clustering(6) Variable = NF1 MUTATION ANALYSIS
D6V1, survival
               sevent
clus2             0   1
  NF1 MUTATED     7   7
  NF1 WILD-TYPE 127 174
  NF1 MUTATED NF1 WILD-TYPE 
           14           301 
  NF1 MUTATED NF1 WILD-TYPE 
            7           174 
$`NF1 MUTATED`
TCGA-04-1331 TCGA-04-1367 TCGA-09-2053 TCGA-13-1483 TCGA-23-1027 TCGA-23-1028 
       40.24        71.47        39.75        29.42        31.76        49.41 
TCGA-23-2078 TCGA-24-1463 TCGA-24-1470 TCGA-24-1562 TCGA-25-1633 TCGA-30-1862 
       87.48        72.92         3.45        45.50        60.59         6.12 
TCGA-59-2363 TCGA-61-2094 
        5.42        71.74 

$`NF1 WILD-TYPE`
TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 TCGA-04-1343 
       41.00        49.15         2.01        46.62        18.51        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 
       65.52        63.09        48.76        21.57        63.98        49.28 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1514 TCGA-04-1517 
       32.52        44.32        33.67        76.57        56.55        19.99 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-09-0366 TCGA-09-0369 TCGA-09-1659 
       38.37       119.08        84.20        57.76        35.57         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 TCGA-09-2044 
       38.43        89.33        41.62        57.60        30.51         6.12 
TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2056 TCGA-10-0926 
       35.15       112.41        71.11        63.09        12.46        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       81.47        18.51        33.24        32.28        11.70         3.91 
TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
       35.44        15.12        19.86         6.21        24.59        44.55 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
       39.58         2.73        31.10        15.19        17.82        55.17 
TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 
        2.50        11.54        34.06        32.25        28.57        38.93 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 TCGA-13-0804 TCGA-13-0807 
       36.72        28.70        19.59         8.12        35.28        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 
       68.94       107.18        91.40        74.27        66.67        61.84 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 
       67.99        69.01        43.36        49.61        57.47        56.15 
TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 
       57.07        47.38        48.33        47.84        44.94        37.08 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       27.72        34.06        29.98        21.17        14.89        13.81 
TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 
        6.41         6.08        10.88         6.61         7.36         6.05 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 
        5.92         6.84         4.70         4.21         5.33        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 
       87.06        61.71        98.04        22.39        70.82        82.88 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 
       52.44        73.55        38.20        49.25         4.24        54.31 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       37.61        38.40        32.84        16.57         4.21         4.41 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2060 TCGA-20-0987 
        4.77         4.18         2.56         3.09         8.61        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 
       25.94        26.20        47.54        42.54        40.54        15.39 
TCGA-23-1026 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1116 
       26.83        29.13        18.90         2.24        54.51         4.57 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 
       33.30        86.01         4.27        39.09        33.47        58.13 
TCGA-23-2072 TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-24-0966 TCGA-24-0968 
       24.95       115.89        91.66        77.00         7.63        19.66 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 
       11.64        21.80        41.56         7.66        22.32        54.12 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 
       63.55        47.41         6.31         6.38         7.82         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 
        7.86         0.76         6.25         6.02         5.95         5.36 
TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
        4.83        17.39        19.17        18.67        43.53         8.55 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
       12.46        45.14         9.11         1.18        22.22        26.96 
TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 
       57.40        16.21        56.58        51.91        41.39        58.09 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1563 
       88.50        70.62        39.88        19.53        44.09        47.70 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 
       25.87        10.26        17.23        90.15        88.37        48.33 
TCGA-24-1616 TCGA-24-2019 TCGA-24-2024 TCGA-24-2030 TCGA-24-2035 TCGA-24-2038 
       38.24         4.87        58.16        53.95        28.18        44.52 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 
       57.07        36.16         0.79         0.36        47.54        31.63 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 
       70.45        44.61         0.82        67.36        36.23        16.64 
TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
       53.26        26.96        51.06        37.02         1.02        34.98 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1324 TCGA-25-1326 
       65.00        36.95        33.96         2.99        34.03        31.07 
TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 
       65.06         2.96        18.58        18.02        15.81         0.36 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1634 TCGA-25-1635 
       20.61         7.86         0.30        56.94        35.54        51.22 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 
       13.02        49.05         1.02        38.04         3.02        45.01 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       19.99        42.02         2.96        29.03        31.00        26.99 
TCGA-29-2427 TCGA-30-1853 TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 TCGA-31-1959 
       62.47        36.26        30.05        18.77         6.71         2.20 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 
       28.77        29.10        21.53        22.85        22.55         8.55 
TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-57-1582 TCGA-57-1583 
       30.08        25.74        27.85        24.23        24.03        11.38 
TCGA-57-1584 TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       21.14        25.08       180.20        22.32       116.12         9.40 
TCGA-59-2354 TCGA-59-2355 TCGA-61-1728 TCGA-61-1736 TCGA-61-1919 TCGA-61-1995 
       34.39         2.14        27.88        48.79        38.17         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 
        5.52        14.50        17.98         4.01        30.64        39.85 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2088 TCGA-61-2092 TCGA-61-2095 TCGA-61-2097 
       30.64         1.18         4.77        51.72        61.64        60.62 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       55.50         6.48        76.87        20.68        44.52       125.75 
TCGA-61-2113 
       22.22 

  NF1 MUTATED NF1 WILD-TYPE 
         3.45          0.30 
  NF1 MUTATED NF1 WILD-TYPE 
        87.48        180.20 
  NF1 MUTATED NF1 WILD-TYPE 
        42.87         30.51 
[1] "3.5 - 87.5 (42.9)"  "0.3 - 180.2 (30.5)"
[1] "hr=" "1.6"
D6V2, continuous
D6V3, continuous
[1] "Remove cluster labels:" "NF1 MUTATED"           
clus
  NF1 MUTATED NF1 WILD-TYPE 
            2            54 
   TCGA-04-1346    TCGA-04-1347    TCGA-04-1356    TCGA-10-0926    TCGA-13-0714 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-13-0720    TCGA-13-0724    TCGA-13-0755    TCGA-13-0760    TCGA-13-0762 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-13-0791    TCGA-13-0792    TCGA-13-0793    TCGA-13-0795    TCGA-13-0885 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-13-0887    TCGA-13-0889    TCGA-13-0891    TCGA-13-0894    TCGA-13-0897 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-13-0900    TCGA-13-0903    TCGA-13-0904    TCGA-13-0905    TCGA-13-0906 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-13-0910    TCGA-13-0911    TCGA-13-0912    TCGA-13-0913    TCGA-13-0919 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-13-1404    TCGA-13-1405    TCGA-13-1409    TCGA-13-1410    TCGA-13-1412 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-13-1482    TCGA-13-1484    TCGA-13-1488    TCGA-13-1489    TCGA-13-1491 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-13-1492    TCGA-13-1495    TCGA-13-1497    TCGA-13-1498    TCGA-13-1499 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-13-1501    TCGA-13-1504    TCGA-13-1506    TCGA-13-1507    TCGA-13-1509 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-13-1512    TCGA-13-2060    TCGA-24-1614    TCGA-61-2101 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NF1 MUTATED                                  0     1
  NF1 WILD-TYPE                                2     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NF1 MUTATED                           0    13
  NF1 WILD-TYPE                        10   273
D6V4, multiclass
                                  clus
vv                                 NF1 MUTATED NF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      1             9
  BLACK OR AFRICAN AMERICAN                  0            10
  WHITE                                     13           273
[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"
D6V5, binary
               cls
clus              0   1
  NF1 MUTATED     1  11
  NF1 WILD-TYPE   6 193
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      1   11
  NF1 WILD-TYPE    6  193
                        clus
vv                       NF1 MUTATED NF1 WILD-TYPE
  HISPANIC OR LATINO               1             6
  NOT HISPANIC OR LATINO          11           193
[1] 2 2
[1] FALSE

Clustering(7) Variable = C10ORF140 MUTATION ANALYSIS
D7V1, survival
                     sevent
clus2                   0   1
  C10ORF140 MUTATED     3   2
  C10ORF140 WILD-TYPE 131 179
  C10ORF140 MUTATED C10ORF140 WILD-TYPE 
                  5                 310 
  C10ORF140 MUTATED C10ORF140 WILD-TYPE 
                  2                 179 
$`C10ORF140 MUTATED`
TCGA-13-0916 TCGA-23-1116 TCGA-24-2262 TCGA-24-2280 TCGA-25-2042 
       21.17         4.57         0.36        70.45        13.02 

$`C10ORF140 WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       40.24        41.00        49.15         2.01        46.62        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 
       11.87        65.52        63.09        48.76        21.57        63.98 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       49.28        32.52        44.32        33.67        76.57        71.47 
TCGA-04-1514 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-09-0366 
       56.55        19.99        38.37       119.08        84.20        57.76 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 
       35.57         9.99        38.43        89.33        41.62        57.60 
TCGA-09-1669 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
       30.51         6.12        35.15       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       39.75        12.46        25.91        81.47        18.51        33.24 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 
       32.28        11.70         3.91        35.44        15.12        19.86 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 
        6.21        24.59        44.55        39.58         2.73        31.10 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 
       15.19        17.82        55.17         2.50        11.54        34.06 
TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 
       32.25        28.57        38.93        36.72        28.70        19.59 
TCGA-13-0800 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 
        8.12        35.28        13.61        68.94       107.18        91.40 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
       74.27        66.67        61.84        67.99        69.01        43.36 
TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 
       49.61        57.47        56.15        57.07        47.38        48.33 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
       47.84        44.94        37.08        27.72        34.06        29.98 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 
       14.89        13.81         6.41         6.08        10.88         6.61 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
        7.36         6.05         5.92         6.84         4.70         4.21 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
        5.33        54.64        87.06        61.71        29.42        98.04 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       22.39        70.82        82.88        52.44        73.55        38.20 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 
       49.25         4.24        54.31        37.61        38.40        32.84 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 
       16.57         4.21         4.41         4.77         4.18         2.56 
TCGA-13-1512 TCGA-13-2060 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-23-1021 
        3.09         8.61        23.05        25.94        26.20        47.54 
TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       42.54        40.54        15.39        26.83        31.76        49.41 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1117 TCGA-23-1118 
       29.13        18.90         2.24        54.51        33.30        86.01 
TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 
        4.27        39.09        33.47        58.13        24.95       115.89 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 
       87.48        91.66        77.00         7.63        19.66        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 
       21.80        41.56         7.66        22.32        54.12        63.55 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       47.41         6.31         6.38         7.82         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        0.76         6.25         6.02         5.95         5.36         4.83 
TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 
       17.39        19.17        18.67        43.53         8.55        72.92 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 
       12.46        45.14         9.11         3.45         1.18        22.22 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 
       26.96        57.40        16.21        56.58        51.91        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 
       58.09        88.50        70.62        39.88        19.53        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       45.50        47.70        25.87        10.26        17.23        90.15 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-2019 TCGA-24-2024 TCGA-24-2030 
       88.37        48.33        38.24         4.87        58.16        53.95 
TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 
       28.18        44.52        57.07        36.16         0.79        47.54 
TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 
       31.63        44.61         0.82        67.36        36.23        16.64 
TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
       53.26        26.96        51.06        37.02         1.02        34.98 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1324 TCGA-25-1326 
       65.00        36.95        33.96         2.99        34.03        31.07 
TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 
       65.06         2.96        18.58        18.02        15.81         0.36 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
       20.61         7.86         0.30        56.94        60.59        35.54 
TCGA-25-1635 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 
       51.22        49.05         1.02        38.04         3.02        45.01 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       19.99        42.02         2.96        29.03        31.00        26.99 
TCGA-29-2427 TCGA-30-1853 TCGA-30-1862 TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 
       62.47        36.26         6.12        30.05        18.77         6.71 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
        2.20        28.77        29.10        21.53        22.85        22.55 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-57-1582 
        8.55        30.08        25.74        27.85        24.23        24.03 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 
       11.38        21.14        25.08       180.20        22.32       116.12 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-61-1728 TCGA-61-1736 
        9.40        34.39         2.14         5.42        27.88        48.79 
TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 
       38.17         2.01         5.52        14.50        17.98         4.01 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2088 TCGA-61-2092 
       30.64        39.85        30.64         1.18         4.77        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 
       71.74        61.64        60.62        55.50         6.48        76.87 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
       20.68        44.52       125.75        22.22 

  C10ORF140 MUTATED C10ORF140 WILD-TYPE 
               0.36                0.30 
  C10ORF140 MUTATED C10ORF140 WILD-TYPE 
              70.45              180.20 
  C10ORF140 MUTATED C10ORF140 WILD-TYPE 
             13.020              31.085 
[1] "0.4 - 70.5 (13.0)"  "0.3 - 180.2 (31.1)"
[1] "hr=" "1.1"
D7V2, continuous
D7V3, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C10ORF140 MUTATED                                  1     0
  C10ORF140 WILD-TYPE                                1    10
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  C10ORF140 MUTATED                           0     4
  C10ORF140 WILD-TYPE                        10   282
D7V4, multiclass
                                  clus
vv                                 C10ORF140 MUTATED C10ORF140 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 1                   1
  ASIAN                                            0                  10
  BLACK OR AFRICAN AMERICAN                        0                  10
  WHITE                                            4                 282
[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"
D7V5, binary
                     cls
clus                    0   1
  C10ORF140 MUTATED     0   3
  C10ORF140 WILD-TYPE   7 201
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C10ORF140 MUTATED      0    3
  C10ORF140 WILD-TYPE    7  201
                        clus
vv                       C10ORF140 MUTATED C10ORF140 WILD-TYPE
  HISPANIC OR LATINO                     0                   7
  NOT HISPANIC OR LATINO                 3                 201
[1] 2 2
[1] FALSE

Clustering(8) Variable = BRCA2 MUTATION ANALYSIS
D8V1, survival
                 sevent
clus2               0   1
  BRCA2 MUTATED     5   6
  BRCA2 WILD-TYPE 129 175
  BRCA2 MUTATED BRCA2 WILD-TYPE 
             11             304 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
              6             175 
$`BRCA2 MUTATED`
TCGA-04-1331 TCGA-09-2050 TCGA-13-0726 TCGA-13-0885 TCGA-13-0890 TCGA-13-1481 
       40.24        71.11        31.10        91.40        67.99        87.06 
TCGA-23-1030 TCGA-23-1120 TCGA-24-1103 TCGA-24-1555 TCGA-24-1562 
       29.13         4.27        54.12        88.50        45.50 

$`BRCA2 WILD-TYPE`
TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 TCGA-04-1343 
       41.00        49.15         2.01        46.62        18.51        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 
       65.52        63.09        48.76        21.57        63.98        49.28 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 
       32.52        44.32        33.67        76.57        71.47        56.55 
TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-09-0366 TCGA-09-0369 
       19.99        38.37       119.08        84.20        57.76        35.57 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 
        9.99        38.43        89.33        41.62        57.60        30.51 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 
        6.12        35.15       112.41        63.09        39.75        12.46 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 
       25.91        81.47        18.51        33.24        32.28        11.70 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
        3.91        35.44        15.12        19.86         6.21        24.59 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
       44.55        39.58         2.73        15.19        17.82        55.17 
TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 
        2.50        11.54        34.06        32.25        28.57        38.93 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 TCGA-13-0804 TCGA-13-0807 
       36.72        28.70        19.59         8.12        35.28        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0891 
       68.94       107.18        74.27        66.67        61.84        69.01 
TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 
       43.36        49.61        57.47        56.15        57.07        47.38 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       48.33        47.84        44.94        37.08        27.72        34.06 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 
       29.98        21.17        14.89        13.81         6.41         6.08 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
       10.88         6.61         7.36         6.05         5.92         6.84 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 
        4.70         4.21         5.33        54.64        61.71        29.42 
TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
       98.04        22.39        70.82        82.88        52.44        73.55 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 
       38.20        49.25         4.24        54.31        37.61        38.40 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       32.84        16.57         4.21         4.41         4.77         4.18 
TCGA-13-1510 TCGA-13-1512 TCGA-13-2060 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
        2.56         3.09         8.61        23.05        25.94        26.20 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
       47.54        42.54        40.54        15.39        26.83        31.76 
TCGA-23-1028 TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1116 TCGA-23-1117 
       49.41        18.90         2.24        54.51         4.57        33.30 
TCGA-23-1118 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 
       86.01        39.09        33.47        58.13        24.95       115.89 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 
       87.48        91.66        77.00         7.63        19.66        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1104 TCGA-24-1105 
       21.80        41.56         7.66        22.32        63.55        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 
        6.31         6.38         7.82         7.99         7.86         0.76 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        6.25         6.02         5.95         5.36         4.83        17.39 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 
       19.17        18.67        43.53         8.55        72.92        12.46 
TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
       45.14         9.11         3.45         1.18        22.22        26.96 
TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 
       57.40        16.21        56.58        51.91        41.39        58.09 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1563 TCGA-24-1564 
       70.62        39.88        19.53        44.09        47.70        25.87 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 
       10.26        17.23        90.15        88.37        48.33        38.24 
TCGA-24-2019 TCGA-24-2024 TCGA-24-2030 TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 
        4.87        58.16        53.95        28.18        44.52        57.07 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       36.16         0.79         0.36        47.54        31.63        70.45 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2298 
       44.61         0.82        67.36        36.23        16.64        53.26 
TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 
       26.96        51.06        37.02         1.02        34.98        65.00 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1324 TCGA-25-1326 TCGA-25-1328 
       36.95        33.96         2.99        34.03        31.07        65.06 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 
        2.96        18.58        18.02        15.81         0.36        20.61 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 
        7.86         0.30        56.94        60.59        35.54        51.22 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 
       13.02        49.05         1.02        38.04         3.02        45.01 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       19.99        42.02         2.96        29.03        31.00        26.99 
TCGA-29-2427 TCGA-30-1853 TCGA-30-1862 TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 
       62.47        36.26         6.12        30.05        18.77         6.71 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
        2.20        28.77        29.10        21.53        22.85        22.55 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-57-1582 
        8.55        30.08        25.74        27.85        24.23        24.03 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 
       11.38        21.14        25.08       180.20        22.32       116.12 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-61-1728 TCGA-61-1736 
        9.40        34.39         2.14         5.42        27.88        48.79 
TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 
       38.17         2.01         5.52        14.50        17.98         4.01 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2088 TCGA-61-2092 
       30.64        39.85        30.64         1.18         4.77        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 
       71.74        61.64        60.62        55.50         6.48        76.87 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
       20.68        44.52       125.75        22.22 

  BRCA2 MUTATED BRCA2 WILD-TYPE 
           4.27            0.30 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
           91.4           180.2 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
         54.120          30.295 
[1] "4.3 - 91.4 (54.1)"  "0.3 - 180.2 (30.3)"
[1] "hr=" "2"  
D8V2, continuous
D8V3, continuous
[1] "Remove cluster labels:" "BRCA2 MUTATED"         
clus
  BRCA2 MUTATED BRCA2 WILD-TYPE 
              1              55 
     TCGA-04-1346      TCGA-04-1347      TCGA-04-1356      TCGA-04-1367 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-10-0926      TCGA-13-0714      TCGA-13-0720      TCGA-13-0724 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-0755      TCGA-13-0760      TCGA-13-0762      TCGA-13-0791 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-0792      TCGA-13-0793      TCGA-13-0795      TCGA-13-0887 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-0889      TCGA-13-0891      TCGA-13-0894      TCGA-13-0897 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-0900      TCGA-13-0903      TCGA-13-0904      TCGA-13-0905 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-0906      TCGA-13-0910      TCGA-13-0911      TCGA-13-0912 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-0913      TCGA-13-0919      TCGA-13-1404      TCGA-13-1405 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-1409      TCGA-13-1410      TCGA-13-1412      TCGA-13-1482 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-1483      TCGA-13-1484      TCGA-13-1488      TCGA-13-1489 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-1491      TCGA-13-1492      TCGA-13-1495      TCGA-13-1497 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-1498      TCGA-13-1499      TCGA-13-1501      TCGA-13-1504 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-1506      TCGA-13-1507      TCGA-13-1509      TCGA-13-1512 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-13-2060      TCGA-24-1614      TCGA-61-2101 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BRCA2 MUTATED                                  0     0
  BRCA2 WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BRCA2 MUTATED                           1    10
  BRCA2 WILD-TYPE                         9   276
D8V4, multiclass
                                  clus
vv                                 BRCA2 MUTATED BRCA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1               9
  WHITE                                       10             276
[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"
D8V5, binary
                 cls
clus                0   1
  BRCA2 MUTATED     0   8
  BRCA2 WILD-TYPE   7 196
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA2 MUTATED      0    8
  BRCA2 WILD-TYPE    7  196
                        clus
vv                       BRCA2 MUTATED BRCA2 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             8             196
[1] 2 2
[1] FALSE

Clustering(9) Variable = CDK12 MUTATION ANALYSIS
D9V1, survival
                 sevent
clus2               0   1
  CDK12 MUTATED     4   4
  CDK12 WILD-TYPE 130 177
  CDK12 MUTATED CDK12 WILD-TYPE 
              8             307 
  CDK12 MUTATED CDK12 WILD-TYPE 
              4             177 
$`CDK12 MUTATED`
TCGA-13-0891 TCGA-13-1495 TCGA-20-0987 TCGA-24-1466 TCGA-25-1322 TCGA-25-2392 
       69.01        49.25        23.05        45.14         2.99         1.02 
TCGA-31-1953 TCGA-59-2351 
        6.71       116.12 

$`CDK12 WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       40.24        41.00        49.15         2.01        46.62        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 
       11.87        65.52        63.09        48.76        21.57        63.98 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       49.28        32.52        44.32        33.67        76.57        71.47 
TCGA-04-1514 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-09-0366 
       56.55        19.99        38.37       119.08        84.20        57.76 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 
       35.57         9.99        38.43        89.33        41.62        57.60 
TCGA-09-1669 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
       30.51         6.12        35.15       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       39.75        12.46        25.91        81.47        18.51        33.24 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 
       32.28        11.70         3.91        35.44        15.12        19.86 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 
        6.21        24.59        44.55        39.58         2.73        31.10 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 
       15.19        17.82        55.17         2.50        11.54        34.06 
TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 
       32.25        28.57        38.93        36.72        28.70        19.59 
TCGA-13-0800 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 
        8.12        35.28        13.61        68.94       107.18        91.40 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0893 TCGA-13-0894 
       74.27        66.67        61.84        67.99        43.36        49.61 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       57.47        56.15        57.07        47.38        48.33        47.84 
TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       44.94        37.08        27.72        34.06        29.98        21.17 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 
       14.89        13.81         6.41         6.08        10.88         6.61 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
        7.36         6.05         5.92         6.84         4.70         4.21 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
        5.33        54.64        87.06        61.71        29.42        98.04 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       22.39        70.82        82.88        52.44        73.55        38.20 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 
        4.24        54.31        37.61        38.40        32.84        16.57 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 
        4.21         4.41         4.77         4.18         2.56         3.09 
TCGA-13-2060 TCGA-20-0990 TCGA-20-0991 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 
        8.61        25.94        26.20        47.54        42.54        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 
       15.39        26.83        31.76        49.41        29.13        18.90 
TCGA-23-1032 TCGA-23-1110 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 
        2.24        54.51         4.57        33.30        86.01         4.27 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 
       39.09        33.47        58.13        24.95       115.89        87.48 
TCGA-23-2079 TCGA-23-2081 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 
       91.66        77.00         7.63        19.66        11.64        21.80 
TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 
       41.56         7.66        22.32        54.12        63.55        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 
        6.31         6.38         7.82         7.99         7.86         0.76 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        6.25         6.02         5.95         5.36         4.83        17.39 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 
       19.17        18.67        43.53         8.55        72.92        12.46 
TCGA-24-1469 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-24-1549 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       16.21        56.58        51.91        41.39        58.09        88.50 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       70.62        39.88        19.53        44.09        45.50        47.70 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 
       25.87        10.26        17.23        90.15        88.37        48.33 
TCGA-24-1616 TCGA-24-2019 TCGA-24-2024 TCGA-24-2030 TCGA-24-2035 TCGA-24-2038 
       38.24         4.87        58.16        53.95        28.18        44.52 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 
       57.07        36.16         0.79         0.36        47.54        31.63 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 
       70.45        44.61         0.82        67.36        36.23        16.64 
TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
       53.26        26.96        51.06        37.02         1.02        34.98 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1324 TCGA-25-1326 TCGA-25-1328 
       65.00        36.95        33.96        34.03        31.07        65.06 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 
        2.96        18.58        18.02        15.81         0.36        20.61 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 
        7.86         0.30        56.94        60.59        35.54        51.22 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 
       13.02        49.05        38.04         3.02        45.01        19.99 
TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-2427 
       42.02         2.96        29.03        31.00        26.99        62.47 
TCGA-30-1853 TCGA-30-1862 TCGA-30-1891 TCGA-31-1950 TCGA-31-1959 TCGA-36-1568 
       36.26         6.12        30.05        18.77         2.20        28.77 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 
       29.10        21.53        22.85        22.55         8.55        30.08 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 
       25.74        27.85        24.23        24.03        11.38        21.14 
TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 
       25.08       180.20        22.32         9.40        34.39         2.14 
TCGA-59-2363 TCGA-61-1728 TCGA-61-1736 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
        5.42        27.88        48.79        38.17         2.01         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 
       14.50        17.98         4.01        30.64        39.85        30.64 
TCGA-61-2016 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 
        1.18         4.77        51.72        71.74        61.64        60.62 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       55.50         6.48        76.87        20.68        44.52       125.75 
TCGA-61-2113 
       22.22 

  CDK12 MUTATED CDK12 WILD-TYPE 
           1.02            0.30 
  CDK12 MUTATED CDK12 WILD-TYPE 
         116.12          180.20 
  CDK12 MUTATED CDK12 WILD-TYPE 
         34.095          31.000 
[1] "1.0 - 116.1 (34.1)" "0.3 - 180.2 (31.0)"
[1] "hr=" "1.4"
D9V2, continuous
D9V3, continuous
[1] "Remove cluster labels:" "CDK12 MUTATED"         
clus
  CDK12 MUTATED CDK12 WILD-TYPE 
              2              54 
     TCGA-04-1346      TCGA-04-1347      TCGA-04-1356      TCGA-04-1367 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-10-0926      TCGA-13-0714      TCGA-13-0720      TCGA-13-0724 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-13-0755      TCGA-13-0760      TCGA-13-0762      TCGA-13-0791 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-13-0792      TCGA-13-0793      TCGA-13-0795      TCGA-13-0885 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-13-0887      TCGA-13-0889      TCGA-13-0894      TCGA-13-0897 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-13-0900      TCGA-13-0903      TCGA-13-0904      TCGA-13-0905 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-13-0906      TCGA-13-0910      TCGA-13-0911      TCGA-13-0912 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-13-0913      TCGA-13-0919      TCGA-13-1404      TCGA-13-1405 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-13-1409      TCGA-13-1410      TCGA-13-1412      TCGA-13-1482 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-13-1483      TCGA-13-1484      TCGA-13-1488      TCGA-13-1489 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-13-1491      TCGA-13-1492      TCGA-13-1497      TCGA-13-1498 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-13-1499      TCGA-13-1501      TCGA-13-1504      TCGA-13-1506 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-13-1507      TCGA-13-1509      TCGA-13-1512      TCGA-13-2060 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-24-1614      TCGA-61-2101 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDK12 MUTATED                                  0     1
  CDK12 WILD-TYPE                                2     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CDK12 MUTATED                           0     7
  CDK12 WILD-TYPE                        10   279
D9V4, multiclass
                                  clus
vv                                 CDK12 MUTATED CDK12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    0              10
  WHITE                                        7             279
[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"
D9V5, binary
                 cls
clus                0   1
  CDK12 MUTATED     0   7
  CDK12 WILD-TYPE   7 197
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED      0    7
  CDK12 WILD-TYPE    7  197
                        clus
vv                       CDK12 MUTATED CDK12 WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             7             197
[1] 2 2
[1] FALSE

Clustering(10) Variable = OR4F21 MUTATION ANALYSIS
D10V1, survival
                  sevent
clus2                0   1
  OR4F21 MUTATED     2   1
  OR4F21 WILD-TYPE 132 180
  OR4F21 MUTATED OR4F21 WILD-TYPE 
               3              312 
  OR4F21 MUTATED OR4F21 WILD-TYPE 
               1              180 
$`OR4F21 MUTATED`
TCGA-24-2030 TCGA-59-2351 TCGA-61-2000 
       53.95       116.12        14.50 

$`OR4F21 WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       40.24        41.00        49.15         2.01        46.62        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 
       11.87        65.52        63.09        48.76        21.57        63.98 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       49.28        32.52        44.32        33.67        76.57        71.47 
TCGA-04-1514 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-09-0366 
       56.55        19.99        38.37       119.08        84.20        57.76 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 
       35.57         9.99        38.43        89.33        41.62        57.60 
TCGA-09-1669 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
       30.51         6.12        35.15       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       39.75        12.46        25.91        81.47        18.51        33.24 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 
       32.28        11.70         3.91        35.44        15.12        19.86 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 
        6.21        24.59        44.55        39.58         2.73        31.10 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 
       15.19        17.82        55.17         2.50        11.54        34.06 
TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 
       32.25        28.57        38.93        36.72        28.70        19.59 
TCGA-13-0800 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 
        8.12        35.28        13.61        68.94       107.18        91.40 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
       74.27        66.67        61.84        67.99        69.01        43.36 
TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 
       49.61        57.47        56.15        57.07        47.38        48.33 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
       47.84        44.94        37.08        27.72        34.06        29.98 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 
       21.17        14.89        13.81         6.41         6.08        10.88 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
        6.61         7.36         6.05         5.92         6.84         4.70 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
        4.21         5.33        54.64        87.06        61.71        29.42 
TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
       98.04        22.39        70.82        82.88        52.44        73.55 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 
       38.20        49.25         4.24        54.31        37.61        38.40 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       32.84        16.57         4.21         4.41         4.77         4.18 
TCGA-13-1510 TCGA-13-1512 TCGA-13-2060 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
        2.56         3.09         8.61        23.05        25.94        26.20 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
       47.54        42.54        40.54        15.39        26.83        31.76 
TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1116 
       49.41        29.13        18.90         2.24        54.51         4.57 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 
       33.30        86.01         4.27        39.09        33.47        58.13 
TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-24-0966 
       24.95       115.89        87.48        91.66        77.00         7.63 
TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
       19.66        11.64        21.80        41.56         7.66        22.32 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 
       54.12        63.55        47.41         6.31         6.38         7.82 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 
        7.99         7.86         0.76         6.25         6.02         5.95 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 
        5.36         4.83        17.39        19.17        18.67        43.53 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 
        8.55        72.92        12.46        45.14         9.11         3.45 
TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 
        1.18        22.22        26.96        57.40        16.21        56.58 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       51.91        41.39        58.09        88.50        70.62        39.88 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 
       19.53        44.09        45.50        47.70        25.87        10.26 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-2019 
       17.23        90.15        88.37        48.33        38.24         4.87 
TCGA-24-2024 TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 
       58.16        28.18        44.52        57.07        36.16         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
        0.36        47.54        31.63        70.45        44.61         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 
       67.36        36.23        16.64        53.26        26.96        51.06 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 
       37.02         1.02        34.98        65.00        36.95        33.96 
TCGA-25-1322 TCGA-25-1324 TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 
        2.99        34.03        31.07        65.06         2.96        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
       18.02        15.81         0.36        20.61         7.86         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-2042 TCGA-25-2391 
       56.94        60.59        35.54        51.22        13.02        49.05 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 
        1.02        38.04         3.02        45.01        19.99        42.02 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-2427 TCGA-30-1853 
        2.96        29.03        31.00        26.99        62.47        36.26 
TCGA-30-1862 TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 TCGA-31-1959 TCGA-36-1568 
        6.12        30.05        18.77         6.71         2.20        28.77 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 
       29.10        21.53        22.85        22.55         8.55        30.08 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 
       25.74        27.85        24.23        24.03        11.38        21.14 
TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 
       25.08       180.20        22.32         9.40        34.39         2.14 
TCGA-59-2363 TCGA-61-1728 TCGA-61-1736 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
        5.42        27.88        48.79        38.17         2.01         5.52 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 
       17.98         4.01        30.64        39.85        30.64         1.18 
TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 TCGA-61-2101 
        4.77        51.72        71.74        61.64        60.62        55.50 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
        6.48        76.87        20.68        44.52       125.75        22.22 

  OR4F21 MUTATED OR4F21 WILD-TYPE 
            14.5              0.3 
  OR4F21 MUTATED OR4F21 WILD-TYPE 
          116.12           180.20 
  OR4F21 MUTATED OR4F21 WILD-TYPE 
           53.95            30.82 
[1] "14.5 - 116.1 (54.0)" "0.3 - 180.2 (30.8)" 
[1] "hr=" "3.4"
D10V2, continuous
[1] "Remove cluster labels:" "OR4F21 MUTATED"        
clus
  OR4F21 MUTATED OR4F21 WILD-TYPE 
               2              306 
      TCGA-04-1331       TCGA-04-1332       TCGA-04-1336       TCGA-04-1337 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-04-1338       TCGA-04-1342       TCGA-04-1343       TCGA-04-1346 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-04-1347       TCGA-04-1348       TCGA-04-1349       TCGA-04-1350 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-04-1356       TCGA-04-1357       TCGA-04-1361       TCGA-04-1362 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-04-1364       TCGA-04-1365       TCGA-04-1367       TCGA-04-1514 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-04-1517       TCGA-04-1525       TCGA-04-1530       TCGA-04-1542 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-09-0366       TCGA-09-0369       TCGA-09-1659       TCGA-09-1661 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-09-1662       TCGA-09-1665       TCGA-09-1666       TCGA-09-1669 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-09-2044       TCGA-09-2045       TCGA-09-2049       TCGA-09-2050 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-09-2051       TCGA-09-2053       TCGA-09-2056       TCGA-10-0926 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-10-0927       TCGA-10-0928       TCGA-10-0930       TCGA-10-0931 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-10-0933       TCGA-10-0934       TCGA-10-0935       TCGA-10-0937 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-10-0938       TCGA-13-0714       TCGA-13-0717       TCGA-13-0720 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-0723       TCGA-13-0724       TCGA-13-0726       TCGA-13-0727 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-0730       TCGA-13-0751       TCGA-13-0755       TCGA-13-0760 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-0761       TCGA-13-0762       TCGA-13-0765       TCGA-13-0791 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-0792       TCGA-13-0793       TCGA-13-0795       TCGA-13-0800 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-0804       TCGA-13-0807       TCGA-13-0883       TCGA-13-0884 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-0885       TCGA-13-0886       TCGA-13-0887       TCGA-13-0889 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-0890       TCGA-13-0891       TCGA-13-0893       TCGA-13-0894 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-0897       TCGA-13-0899       TCGA-13-0900       TCGA-13-0903 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-0904       TCGA-13-0905       TCGA-13-0906       TCGA-13-0910 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-0911       TCGA-13-0912       TCGA-13-0913       TCGA-13-0916 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-0919       TCGA-13-0920       TCGA-13-0923       TCGA-13-0924 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-1403       TCGA-13-1404       TCGA-13-1405       TCGA-13-1407 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-1408       TCGA-13-1409       TCGA-13-1410       TCGA-13-1411 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-1412       TCGA-13-1477       TCGA-13-1481       TCGA-13-1482 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-1483       TCGA-13-1484       TCGA-13-1487       TCGA-13-1488 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-1489       TCGA-13-1491       TCGA-13-1492       TCGA-13-1494 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-1495       TCGA-13-1496       TCGA-13-1497       TCGA-13-1498 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-1499       TCGA-13-1501       TCGA-13-1504       TCGA-13-1505 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-1506       TCGA-13-1507       TCGA-13-1509       TCGA-13-1510 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-13-1512       TCGA-13-2060       TCGA-20-0987       TCGA-20-0990 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-20-0991       TCGA-23-1021       TCGA-23-1022       TCGA-23-1023 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-23-1024       TCGA-23-1026       TCGA-23-1027       TCGA-23-1028 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-23-1030       TCGA-23-1031       TCGA-23-1032       TCGA-23-1110 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-23-1116       TCGA-23-1117       TCGA-23-1118       TCGA-23-1120 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-23-1122       TCGA-23-1123       TCGA-23-1124       TCGA-23-2072 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-23-2077       TCGA-23-2078       TCGA-23-2079       TCGA-23-2081 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-0966       TCGA-24-0968       TCGA-24-0970       TCGA-24-0975 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-0979       TCGA-24-0980       TCGA-24-0982       TCGA-24-1103 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-1104       TCGA-24-1105       TCGA-24-1413       TCGA-24-1416 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-1417       TCGA-24-1418       TCGA-24-1419       TCGA-24-1422 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-1423       TCGA-24-1424       TCGA-24-1425       TCGA-24-1426 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-1427       TCGA-24-1428       TCGA-24-1431       TCGA-24-1434 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-1435       TCGA-24-1436       TCGA-24-1463       TCGA-24-1464 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-1466       TCGA-24-1469       TCGA-24-1470       TCGA-24-1471 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-1474       TCGA-24-1544       TCGA-24-1545       TCGA-24-1548 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-1549       TCGA-24-1551       TCGA-24-1552       TCGA-24-1553 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-1555       TCGA-24-1556       TCGA-24-1557       TCGA-24-1558 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-1560       TCGA-24-1562       TCGA-24-1563       TCGA-24-1564 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-1565       TCGA-24-1567       TCGA-24-1603       TCGA-24-1604 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-1614       TCGA-24-1616       TCGA-24-2019       TCGA-24-2024 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-2035       TCGA-24-2038       TCGA-24-2254       TCGA-24-2260 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-2261       TCGA-24-2262       TCGA-24-2267       TCGA-24-2271 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-2280       TCGA-24-2281       TCGA-24-2288       TCGA-24-2289 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-24-2290       TCGA-24-2293       TCGA-24-2298       TCGA-25-1313 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-25-1315       TCGA-25-1316       TCGA-25-1317       TCGA-25-1318 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-25-1319       TCGA-25-1320       TCGA-25-1321       TCGA-25-1322 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-25-1324       TCGA-25-1326       TCGA-25-1328       TCGA-25-1329 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-25-1623       TCGA-25-1625       TCGA-25-1626       TCGA-25-1627 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-25-1628       TCGA-25-1630       TCGA-25-1631       TCGA-25-1632 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-25-1633       TCGA-25-1634       TCGA-25-1635       TCGA-25-2042 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-25-2391       TCGA-25-2392       TCGA-25-2393       TCGA-25-2396 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-25-2398       TCGA-25-2399       TCGA-25-2400       TCGA-25-2401 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-25-2404       TCGA-25-2408       TCGA-25-2409       TCGA-29-2427 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-30-1853       TCGA-30-1862       TCGA-30-1891       TCGA-31-1950 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-31-1953       TCGA-31-1959       TCGA-36-1568       TCGA-36-1569 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-36-1570       TCGA-36-1571       TCGA-36-1574       TCGA-36-1575 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-36-1576       TCGA-36-1577       TCGA-36-1578       TCGA-36-1580 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-57-1583       TCGA-57-1584       TCGA-57-1993       TCGA-61-1728 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-61-1736       TCGA-61-1919       TCGA-61-1995       TCGA-61-1998 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-61-2002       TCGA-61-2003       TCGA-61-2008       TCGA-61-2009 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-61-2012       TCGA-61-2016       TCGA-61-2088       TCGA-61-2092 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-61-2094       TCGA-61-2095       TCGA-61-2097       TCGA-61-2101 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-61-2102       TCGA-61-2104       TCGA-61-2109       TCGA-61-2110 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
      TCGA-61-2111       TCGA-61-2113 
"OR4F21 WILD-TYPE" "OR4F21 WILD-TYPE" 
D10V3, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR4F21 MUTATED                                  0     0
  OR4F21 WILD-TYPE                                2    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR4F21 MUTATED                           0     3
  OR4F21 WILD-TYPE                        10   283
D10V4, multiclass
                                  clus
vv                                 OR4F21 MUTATED OR4F21 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               10
  WHITE                                         3              283
[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"
D10V5, binary
                  cls
clus                 0   1
  OR4F21 MUTATED     0   2
  OR4F21 WILD-TYPE   7 202
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4F21 MUTATED      0    2
  OR4F21 WILD-TYPE    7  202
                        clus
vv                       OR4F21 MUTATED OR4F21 WILD-TYPE
  HISPANIC OR LATINO                  0                7
  NOT HISPANIC OR LATINO              2              202
[1] 2 2
[1] FALSE

Clustering(11) Variable = C9ORF171 MUTATION ANALYSIS
D11V1, survival
                    sevent
clus2                  0   1
  C9ORF171 MUTATED     4   1
  C9ORF171 WILD-TYPE 130 180
  C9ORF171 MUTATED C9ORF171 WILD-TYPE 
                 5                310 
  C9ORF171 MUTATED C9ORF171 WILD-TYPE 
                 1                180 
$`C9ORF171 MUTATED`
TCGA-13-0793 TCGA-13-1404 TCGA-13-1408 TCGA-13-1412 TCGA-24-2035 
       28.70         6.61         5.92         5.33        28.18 

$`C9ORF171 WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       40.24        41.00        49.15         2.01        46.62        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 
       11.87        65.52        63.09        48.76        21.57        63.98 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       49.28        32.52        44.32        33.67        76.57        71.47 
TCGA-04-1514 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-09-0366 
       56.55        19.99        38.37       119.08        84.20        57.76 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 
       35.57         9.99        38.43        89.33        41.62        57.60 
TCGA-09-1669 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
       30.51         6.12        35.15       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       39.75        12.46        25.91        81.47        18.51        33.24 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 
       32.28        11.70         3.91        35.44        15.12        19.86 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 
        6.21        24.59        44.55        39.58         2.73        31.10 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 
       15.19        17.82        55.17         2.50        11.54        34.06 
TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0795 TCGA-13-0800 
       32.25        28.57        38.93        36.72        19.59         8.12 
TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 
       35.28        13.61        68.94       107.18        91.40        74.27 
TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 
       66.67        61.84        67.99        69.01        43.36        49.61 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       57.47        56.15        57.07        47.38        48.33        47.84 
TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       44.94        37.08        27.72        34.06        29.98        21.17 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1405 
       14.89        13.81         6.41         6.08        10.88         7.36 
TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1477 TCGA-13-1481 
        6.05         6.84         4.70         4.21        54.64        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 
       61.71        29.42        98.04        22.39        70.82        82.88 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 
       52.44        73.55        38.20        49.25         4.24        54.31 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       37.61        38.40        32.84        16.57         4.21         4.41 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2060 TCGA-20-0987 
        4.77         4.18         2.56         3.09         8.61        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 
       25.94        26.20        47.54        42.54        40.54        15.39 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       26.83        31.76        49.41        29.13        18.90         2.24 
TCGA-23-1110 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 TCGA-23-1122 
       54.51         4.57        33.30        86.01         4.27        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 
       33.47        58.13        24.95       115.89        87.48        91.66 
TCGA-23-2081 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
       77.00         7.63        19.66        11.64        21.80        41.56 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 
        7.66        22.32        54.12        63.55        47.41         6.31 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 
        6.38         7.82         7.99         7.86         0.76         6.25 
TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 
        6.02         5.95         5.36         4.83        17.39        19.17 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 
       18.67        43.53         8.55        72.92        12.46        45.14 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 
        9.11         3.45         1.18        22.22        26.96        57.40 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       16.21        56.58        51.91        41.39        58.09        88.50 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       70.62        39.88        19.53        44.09        45.50        47.70 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 
       25.87        10.26        17.23        90.15        88.37        48.33 
TCGA-24-1616 TCGA-24-2019 TCGA-24-2024 TCGA-24-2030 TCGA-24-2038 TCGA-24-2254 
       38.24         4.87        58.16        53.95        44.52        57.07 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       36.16         0.79         0.36        47.54        31.63        70.45 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2298 
       44.61         0.82        67.36        36.23        16.64        53.26 
TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 
       26.96        51.06        37.02         1.02        34.98        65.00 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1324 TCGA-25-1326 TCGA-25-1328 
       36.95        33.96         2.99        34.03        31.07        65.06 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 
        2.96        18.58        18.02        15.81         0.36        20.61 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 
        7.86         0.30        56.94        60.59        35.54        51.22 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 
       13.02        49.05         1.02        38.04         3.02        45.01 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       19.99        42.02         2.96        29.03        31.00        26.99 
TCGA-29-2427 TCGA-30-1853 TCGA-30-1862 TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 
       62.47        36.26         6.12        30.05        18.77         6.71 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
        2.20        28.77        29.10        21.53        22.85        22.55 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-57-1582 
        8.55        30.08        25.74        27.85        24.23        24.03 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 
       11.38        21.14        25.08       180.20        22.32       116.12 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-61-1728 TCGA-61-1736 
        9.40        34.39         2.14         5.42        27.88        48.79 
TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 
       38.17         2.01         5.52        14.50        17.98         4.01 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2088 TCGA-61-2092 
       30.64        39.85        30.64         1.18         4.77        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 
       71.74        61.64        60.62        55.50         6.48        76.87 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
       20.68        44.52       125.75        22.22 

  C9ORF171 MUTATED C9ORF171 WILD-TYPE 
              5.33               0.30 
  C9ORF171 MUTATED C9ORF171 WILD-TYPE 
              28.7              180.2 
  C9ORF171 MUTATED C9ORF171 WILD-TYPE 
             6.610             31.365 
[1] "5.3 - 28.7 (6.6)"   "0.3 - 180.2 (31.4)"
[1] "hr=" "1.1"
D11V2, continuous
D11V3, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C9ORF171 MUTATED                                  0     0
  C9ORF171 WILD-TYPE                                2    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C9ORF171 MUTATED                           0     5
  C9ORF171 WILD-TYPE                        10   281
D11V4, multiclass
                                  clus
vv                                 C9ORF171 MUTATED C9ORF171 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 10
  WHITE                                           5                281
[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"
D11V5, binary
                    cls
clus                   0   1
  C9ORF171 MUTATED     0   4
  C9ORF171 WILD-TYPE   7 200
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF171 MUTATED      0    4
  C9ORF171 WILD-TYPE    7  200
                        clus
vv                       C9ORF171 MUTATED C9ORF171 WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO                4                200
[1] 2 2
[1] FALSE

Clustering(12) Variable = HYDIN MUTATION ANALYSIS
D12V1, survival
                 sevent
clus2               0   1
  HYDIN MUTATED     2   9
  HYDIN WILD-TYPE 132 172
  HYDIN MUTATED HYDIN WILD-TYPE 
             11             304 
  HYDIN MUTATED HYDIN WILD-TYPE 
              9             172 
$`HYDIN MUTATED`
TCGA-04-1350 TCGA-10-0928 TCGA-13-0762 TCGA-13-0883 TCGA-13-1487 TCGA-13-1496 
       63.98        18.51        32.25        68.94        22.39         4.24 
TCGA-23-1022 TCGA-23-1118 TCGA-23-2081 TCGA-25-1318 TCGA-25-2398 
       42.54        86.01        77.00        34.98        45.01 

$`HYDIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       40.24        41.00        49.15         2.01        46.62        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1356 
       11.87        65.52        63.09        48.76        21.57        49.28 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 
       32.52        44.32        33.67        76.57        71.47        56.55 
TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-09-0366 TCGA-09-0369 
       19.99        38.37       119.08        84.20        57.76        35.57 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 
        9.99        38.43        89.33        41.62        57.60        30.51 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 
        6.12        35.15       112.41        71.11        63.09        39.75 
TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 
       12.46        25.91        81.47        33.24        32.28        11.70 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
        3.91        35.44        15.12        19.86         6.21        24.59 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 
       44.55        39.58         2.73        31.10        15.19        17.82 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 TCGA-13-0765 TCGA-13-0791 
       55.17         2.50        11.54        34.06        28.57        38.93 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 TCGA-13-0804 TCGA-13-0807 
       36.72        28.70        19.59         8.12        35.28        13.61 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 
      107.18        91.40        74.27        66.67        61.84        67.99 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       69.01        43.36        49.61        57.47        56.15        57.07 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 
       47.38        48.33        47.84        44.94        37.08        27.72 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 
       34.06        29.98        21.17        14.89        13.81         6.41 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 
        6.08        10.88         6.61         7.36         6.05         5.92 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
        6.84         4.70         4.21         5.33        54.64        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
       61.71        29.42        98.04        70.82        82.88        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 
       73.55        38.20        49.25        54.31        37.61        38.40 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       32.84        16.57         4.21         4.41         4.77         4.18 
TCGA-13-1510 TCGA-13-1512 TCGA-13-2060 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
        2.56         3.09         8.61        23.05        25.94        26.20 
TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       47.54        40.54        15.39        26.83        31.76        49.41 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1116 TCGA-23-1117 
       29.13        18.90         2.24        54.51         4.57        33.30 
TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 
        4.27        39.09        33.47        58.13        24.95       115.89 
TCGA-23-2078 TCGA-23-2079 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 
       87.48        91.66         7.63        19.66        11.64        21.80 
TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 
       41.56         7.66        22.32        54.12        63.55        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 
        6.31         6.38         7.82         7.99         7.86         0.76 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        6.25         6.02         5.95         5.36         4.83        17.39 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 
       19.17        18.67        43.53         8.55        72.92        12.46 
TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
       45.14         9.11         3.45         1.18        22.22        26.96 
TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 
       57.40        16.21        56.58        51.91        41.39        58.09 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 
       88.50        70.62        39.88        19.53        44.09        45.50 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 
       47.70        25.87        10.26        17.23        90.15        88.37 
TCGA-24-1614 TCGA-24-1616 TCGA-24-2019 TCGA-24-2024 TCGA-24-2030 TCGA-24-2035 
       48.33        38.24         4.87        58.16        53.95        28.18 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 
       44.52        57.07        36.16         0.79         0.36        47.54 
TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 
       31.63        70.45        44.61         0.82        67.36        36.23 
TCGA-24-2293 TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
       16.64        53.26        26.96        51.06        37.02         1.02 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1324 TCGA-25-1326 
       65.00        36.95        33.96         2.99        34.03        31.07 
TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 
       65.06         2.96        18.58        18.02        15.81         0.36 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
       20.61         7.86         0.30        56.94        60.59        35.54 
TCGA-25-1635 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 
       51.22        13.02        49.05         1.02        38.04         3.02 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       19.99        42.02         2.96        29.03        31.00        26.99 
TCGA-29-2427 TCGA-30-1853 TCGA-30-1862 TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 
       62.47        36.26         6.12        30.05        18.77         6.71 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
        2.20        28.77        29.10        21.53        22.85        22.55 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-57-1582 
        8.55        30.08        25.74        27.85        24.23        24.03 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 
       11.38        21.14        25.08       180.20        22.32       116.12 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-61-1728 TCGA-61-1736 
        9.40        34.39         2.14         5.42        27.88        48.79 
TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 
       38.17         2.01         5.52        14.50        17.98         4.01 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2088 TCGA-61-2092 
       30.64        39.85        30.64         1.18         4.77        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 
       71.74        61.64        60.62        55.50         6.48        76.87 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
       20.68        44.52       125.75        22.22 

  HYDIN MUTATED HYDIN WILD-TYPE 
           4.24            0.30 
  HYDIN MUTATED HYDIN WILD-TYPE 
          86.01          180.20 
  HYDIN MUTATED HYDIN WILD-TYPE 
         42.540          30.575 
[1] "4.2 - 86.0 (42.5)"  "0.3 - 180.2 (30.6)"
[1] "hr=" "1"  
D12V2, continuous
D12V3, continuous
[1] "Remove cluster labels:" "HYDIN MUTATED"         
clus
  HYDIN MUTATED HYDIN WILD-TYPE 
              1              55 
     TCGA-04-1346      TCGA-04-1347      TCGA-04-1356      TCGA-04-1367 
"HYDIN WILD-TYPE" "HYDIN WILD-TYPE" "HYDIN WILD-TYPE" "HYDIN WILD-TYPE" 
     TCGA-10-0926      TCGA-13-0714      TCGA-13-0720      TCGA-13-0724 
"HYDIN WILD-TYPE" "HYDIN WILD-TYPE" "HYDIN WILD-TYPE" "HYDIN WILD-TYPE" 
     TCGA-13-0755      TCGA-13-0760      TCGA-13-0791      TCGA-13-0792 
"HYDIN WILD-TYPE" "HYDIN WILD-TYPE" "HYDIN WILD-TYPE" "HYDIN WILD-TYPE" 
     TCGA-13-0793      TCGA-13-0795      TCGA-13-0885      TCGA-13-0887 
"HYDIN WILD-TYPE" "HYDIN WILD-TYPE" "HYDIN WILD-TYPE" "HYDIN WILD-TYPE" 
     TCGA-13-0889      TCGA-13-0891      TCGA-13-0894      TCGA-13-0897 
"HYDIN WILD-TYPE" "HYDIN WILD-TYPE" "HYDIN WILD-TYPE" "HYDIN WILD-TYPE" 
     TCGA-13-0900      TCGA-13-0903      TCGA-13-0904      TCGA-13-0905 
"HYDIN WILD-TYPE" "HYDIN WILD-TYPE" "HYDIN WILD-TYPE" "HYDIN WILD-TYPE" 
     TCGA-13-0906      TCGA-13-0910      TCGA-13-0911      TCGA-13-0912 
"HYDIN WILD-TYPE" "HYDIN WILD-TYPE" "HYDIN WILD-TYPE" "HYDIN WILD-TYPE" 
     TCGA-13-0913      TCGA-13-0919      TCGA-13-1404      TCGA-13-1405 
"HYDIN WILD-TYPE" "HYDIN WILD-TYPE" "HYDIN WILD-TYPE" "HYDIN WILD-TYPE" 
     TCGA-13-1409      TCGA-13-1410      TCGA-13-1412      TCGA-13-1482 
"HYDIN WILD-TYPE" "HYDIN WILD-TYPE" "HYDIN WILD-TYPE" "HYDIN WILD-TYPE" 
     TCGA-13-1483      TCGA-13-1484      TCGA-13-1488      TCGA-13-1489 
"HYDIN WILD-TYPE" "HYDIN WILD-TYPE" "HYDIN WILD-TYPE" "HYDIN WILD-TYPE" 
     TCGA-13-1491      TCGA-13-1492      TCGA-13-1495      TCGA-13-1497 
"HYDIN WILD-TYPE" "HYDIN WILD-TYPE" "HYDIN WILD-TYPE" "HYDIN WILD-TYPE" 
     TCGA-13-1498      TCGA-13-1499      TCGA-13-1501      TCGA-13-1504 
"HYDIN WILD-TYPE" "HYDIN WILD-TYPE" "HYDIN WILD-TYPE" "HYDIN WILD-TYPE" 
     TCGA-13-1506      TCGA-13-1507      TCGA-13-1509      TCGA-13-1512 
"HYDIN WILD-TYPE" "HYDIN WILD-TYPE" "HYDIN WILD-TYPE" "HYDIN WILD-TYPE" 
     TCGA-13-2060      TCGA-24-1614      TCGA-61-2101 
"HYDIN WILD-TYPE" "HYDIN WILD-TYPE" "HYDIN WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HYDIN MUTATED                                  0     0
  HYDIN WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HYDIN MUTATED                           0    11
  HYDIN WILD-TYPE                        10   275
D12V4, multiclass
                                  clus
vv                                 HYDIN MUTATED HYDIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              10
  WHITE                                       11             275
[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"
D12V5, binary
                 cls
clus                0   1
  HYDIN MUTATED     0   9
  HYDIN WILD-TYPE   7 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HYDIN MUTATED      0    9
  HYDIN WILD-TYPE    7  195
                        clus
vv                       HYDIN MUTATED HYDIN WILD-TYPE
  HISPANIC OR LATINO                 0               7
  NOT HISPANIC OR LATINO             9             195
[1] 2 2
[1] FALSE

Clustering(13) Variable = RB1 MUTATION ANALYSIS
D13V1, survival
               sevent
clus2             0   1
  RB1 MUTATED     3   5
  RB1 WILD-TYPE 131 176
  RB1 MUTATED RB1 WILD-TYPE 
            8           307 
  RB1 MUTATED RB1 WILD-TYPE 
            5           176 
$`RB1 MUTATED`
TCGA-04-1350 TCGA-09-1665 TCGA-10-0933 TCGA-13-1489 TCGA-23-2079 TCGA-24-1463 
       63.98        41.62        11.70        82.88        91.66        72.92 
TCGA-24-1469 TCGA-25-1635 
        9.11        51.22 

$`RB1 WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       40.24        41.00        49.15         2.01        46.62        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1356 
       11.87        65.52        63.09        48.76        21.57        49.28 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 
       32.52        44.32        33.67        76.57        71.47        56.55 
TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-09-0366 TCGA-09-0369 
       19.99        38.37       119.08        84.20        57.76        35.57 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1666 TCGA-09-1669 TCGA-09-2044 
        9.99        38.43        89.33        57.60        30.51         6.12 
TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 
       35.15       112.41        71.11        63.09        39.75        12.46 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 
       25.91        81.47        18.51        33.24        32.28         3.91 
TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
       35.44        15.12        19.86         6.21        24.59        44.55 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
       39.58         2.73        31.10        15.19        17.82        55.17 
TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 
        2.50        11.54        34.06        32.25        28.57        38.93 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 TCGA-13-0804 TCGA-13-0807 
       36.72        28.70        19.59         8.12        35.28        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 
       68.94       107.18        91.40        74.27        66.67        61.84 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 
       67.99        69.01        43.36        49.61        57.47        56.15 
TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 
       57.07        47.38        48.33        47.84        44.94        37.08 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       27.72        34.06        29.98        21.17        14.89        13.81 
TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 
        6.41         6.08        10.88         6.61         7.36         6.05 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 
        5.92         6.84         4.70         4.21         5.33        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 
       87.06        61.71        29.42        98.04        22.39        70.82 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 
       52.44        73.55        38.20        49.25         4.24        54.31 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       37.61        38.40        32.84        16.57         4.21         4.41 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2060 TCGA-20-0987 
        4.77         4.18         2.56         3.09         8.61        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 
       25.94        26.20        47.54        42.54        40.54        15.39 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       26.83        31.76        49.41        29.13        18.90         2.24 
TCGA-23-1110 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 TCGA-23-1122 
       54.51         4.57        33.30        86.01         4.27        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2081 
       33.47        58.13        24.95       115.89        87.48        77.00 
TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        7.63        19.66        11.64        21.80        41.56         7.66 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
       22.32        54.12        63.55        47.41         6.31         6.38 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
        7.82         7.99         7.86         0.76         6.25         6.02 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 
        5.95         5.36         4.83        17.39        19.17        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 TCGA-24-1470 TCGA-24-1471 
       43.53         8.55        12.46        45.14         3.45         1.18 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 
       22.22        26.96        57.40        16.21        56.58        51.91 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 
       41.39        58.09        88.50        70.62        39.88        19.53 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 
       44.09        45.50        47.70        25.87        10.26        17.23 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-2019 TCGA-24-2024 
       90.15        88.37        48.33        38.24         4.87        58.16 
TCGA-24-2030 TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 
       53.95        28.18        44.52        57.07        36.16         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
        0.36        47.54        31.63        70.45        44.61         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 
       67.36        36.23        16.64        53.26        26.96        51.06 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 
       37.02         1.02        34.98        65.00        36.95        33.96 
TCGA-25-1322 TCGA-25-1324 TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 
        2.99        34.03        31.07        65.06         2.96        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
       18.02        15.81         0.36        20.61         7.86         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 
       56.94        60.59        35.54        13.02        49.05         1.02 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 
       38.04         3.02        45.01        19.99        42.02         2.96 
TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-2427 TCGA-30-1853 TCGA-30-1862 
       29.03        31.00        26.99        62.47        36.26         6.12 
TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 
       30.05        18.77         6.71         2.20        28.77        29.10 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 
       21.53        22.85        22.55         8.55        30.08        25.74 
TCGA-36-1578 TCGA-36-1580 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1993 
       27.85        24.23        24.03        11.38        21.14        25.08 
TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 
      180.20        22.32       116.12         9.40        34.39         2.14 
TCGA-59-2363 TCGA-61-1728 TCGA-61-1736 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
        5.42        27.88        48.79        38.17         2.01         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 
       14.50        17.98         4.01        30.64        39.85        30.64 
TCGA-61-2016 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 
        1.18         4.77        51.72        71.74        61.64        60.62 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       55.50         6.48        76.87        20.68        44.52       125.75 
TCGA-61-2113 
       22.22 

  RB1 MUTATED RB1 WILD-TYPE 
         9.11          0.30 
  RB1 MUTATED RB1 WILD-TYPE 
        91.66        180.20 
  RB1 MUTATED RB1 WILD-TYPE 
        57.60         30.64 
[1] "9.1 - 91.7 (57.6)"  "0.3 - 180.2 (30.6)"
[1] "hr=" "1.7"
D13V2, continuous
D13V3, continuous
[1] "Remove cluster labels:" "RB1 MUTATED"           
clus
  RB1 MUTATED RB1 WILD-TYPE 
            1            55 
   TCGA-04-1346    TCGA-04-1347    TCGA-04-1356    TCGA-04-1367    TCGA-10-0926 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-0714    TCGA-13-0720    TCGA-13-0724    TCGA-13-0755    TCGA-13-0760 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-0762    TCGA-13-0791    TCGA-13-0792    TCGA-13-0793    TCGA-13-0795 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-0885    TCGA-13-0887    TCGA-13-0889    TCGA-13-0891    TCGA-13-0894 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-0897    TCGA-13-0900    TCGA-13-0903    TCGA-13-0904    TCGA-13-0905 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-0906    TCGA-13-0910    TCGA-13-0911    TCGA-13-0912    TCGA-13-0913 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-0919    TCGA-13-1404    TCGA-13-1405    TCGA-13-1409    TCGA-13-1410 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-1412    TCGA-13-1482    TCGA-13-1483    TCGA-13-1484    TCGA-13-1488 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-1491    TCGA-13-1492    TCGA-13-1495    TCGA-13-1497    TCGA-13-1498 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-1499    TCGA-13-1501    TCGA-13-1504    TCGA-13-1506    TCGA-13-1507 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-1509    TCGA-13-1512    TCGA-13-2060    TCGA-24-1614    TCGA-61-2101 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RB1 MUTATED                                  0     0
  RB1 WILD-TYPE                                2    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  RB1 MUTATED                           0     8
  RB1 WILD-TYPE                        10   278
D13V4, multiclass
                                  clus
vv                                 RB1 MUTATED RB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  0            10
  WHITE                                      8           278
[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"
D13V5, binary
               cls
clus              0   1
  RB1 MUTATED     0   6
  RB1 WILD-TYPE   7 198
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      0    6
  RB1 WILD-TYPE    7  198
                        clus
vv                       RB1 MUTATED RB1 WILD-TYPE
  HISPANIC OR LATINO               0             7
  NOT HISPANIC OR LATINO           6           198
[1] 2 2
[1] FALSE

Clustering(14) Variable = GART MUTATION ANALYSIS
D14V1, survival
                sevent
clus2              0   1
  GART MUTATED     2   1
  GART WILD-TYPE 132 180
  GART MUTATED GART WILD-TYPE 
             3            312 
  GART MUTATED GART WILD-TYPE 
             1            180 
$`GART MUTATED`
TCGA-04-1338 TCGA-04-1365 TCGA-25-1632 
       46.62        76.57        56.94 

$`GART WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 
       40.24        41.00        49.15         2.01        18.51        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 
       65.52        63.09        48.76        21.57        63.98        49.28 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1367 TCGA-04-1514 TCGA-04-1517 
       32.52        44.32        33.67        71.47        56.55        19.99 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-09-0366 TCGA-09-0369 TCGA-09-1659 
       38.37       119.08        84.20        57.76        35.57         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 TCGA-09-2044 
       38.43        89.33        41.62        57.60        30.51         6.12 
TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 
       35.15       112.41        71.11        63.09        39.75        12.46 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 
       25.91        81.47        18.51        33.24        32.28        11.70 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
        3.91        35.44        15.12        19.86         6.21        24.59 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 
       44.55        39.58         2.73        31.10        15.19        17.82 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0765 
       55.17         2.50        11.54        34.06        32.25        28.57 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 TCGA-13-0804 
       38.93        36.72        28.70        19.59         8.12        35.28 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
       13.61        68.94       107.18        91.40        74.27        66.67 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 
       61.84        67.99        69.01        43.36        49.61        57.47 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
       56.15        57.07        47.38        48.33        47.84        44.94 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
       37.08        27.72        34.06        29.98        21.17        14.89 
TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
       13.81         6.41         6.08        10.88         6.61         7.36 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
        6.05         5.92         6.84         4.70         4.21         5.33 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 
       54.64        87.06        61.71        29.42        98.04        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       70.82        82.88        52.44        73.55        38.20        49.25 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 
        4.24        54.31        37.61        38.40        32.84        16.57 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 
        4.21         4.41         4.77         4.18         2.56         3.09 
TCGA-13-2060 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-23-1021 TCGA-23-1022 
        8.61        23.05        25.94        26.20        47.54        42.54 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1030 
       40.54        15.39        26.83        31.76        49.41        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
       18.90         2.24        54.51         4.57        33.30        86.01 
TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 
        4.27        39.09        33.47        58.13        24.95       115.89 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 
       87.48        91.66        77.00         7.63        19.66        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 
       21.80        41.56         7.66        22.32        54.12        63.55 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       47.41         6.31         6.38         7.82         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        0.76         6.25         6.02         5.95         5.36         4.83 
TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 
       17.39        19.17        18.67        43.53         8.55        72.92 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 
       12.46        45.14         9.11         3.45         1.18        22.22 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 
       26.96        57.40        16.21        56.58        51.91        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 
       58.09        88.50        70.62        39.88        19.53        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       45.50        47.70        25.87        10.26        17.23        90.15 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-2019 TCGA-24-2024 TCGA-24-2030 
       88.37        48.33        38.24         4.87        58.16        53.95 
TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 
       28.18        44.52        57.07        36.16         0.79         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 
       47.54        31.63        70.45        44.61         0.82        67.36 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 
       36.23        16.64        53.26        26.96        51.06        37.02 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 
        1.02        34.98        65.00        36.95        33.96         2.99 
TCGA-25-1324 TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       34.03        31.07        65.06         2.96        18.58        18.02 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1633 
       15.81         0.36        20.61         7.86         0.30        60.59 
TCGA-25-1634 TCGA-25-1635 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 
       35.54        51.22        13.02        49.05         1.02        38.04 
TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 
        3.02        45.01        19.99        42.02         2.96        29.03 
TCGA-25-2408 TCGA-25-2409 TCGA-29-2427 TCGA-30-1853 TCGA-30-1862 TCGA-30-1891 
       31.00        26.99        62.47        36.26         6.12        30.05 
TCGA-31-1950 TCGA-31-1953 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
       18.77         6.71         2.20        28.77        29.10        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 
       22.85        22.55         8.55        30.08        25.74        27.85 
TCGA-36-1580 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1993 TCGA-59-2348 
       24.23        24.03        11.38        21.14        25.08       180.20 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       22.32       116.12         9.40        34.39         2.14         5.42 
TCGA-61-1728 TCGA-61-1736 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       27.88        48.79        38.17         2.01         5.52        14.50 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 
       17.98         4.01        30.64        39.85        30.64         1.18 
TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 TCGA-61-2101 
        4.77        51.72        71.74        61.64        60.62        55.50 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
        6.48        76.87        20.68        44.52       125.75        22.22 

  GART MUTATED GART WILD-TYPE 
         46.62           0.30 
  GART MUTATED GART WILD-TYPE 
         76.57         180.20 
  GART MUTATED GART WILD-TYPE 
         56.94          30.64 
[1] "46.6 - 76.6 (56.9)" "0.3 - 180.2 (30.6)"
[1] "hr=" "3.4"
D14V2, continuous
D14V3, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GART MUTATED                                  0     0
  GART WILD-TYPE                                2    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GART MUTATED                           0     3
  GART WILD-TYPE                        10   283
D14V4, multiclass
                                  clus
vv                                 GART MUTATED GART WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             10
  WHITE                                       3            283
[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"
D14V5, binary
                cls
clus               0   1
  GART MUTATED     0   3
  GART WILD-TYPE   7 201
[1] "tbl2"
                cls
clus             [,1] [,2]
  GART MUTATED      0    3
  GART WILD-TYPE    7  201
                        clus
vv                       GART MUTATED GART WILD-TYPE
  HISPANIC OR LATINO                0              7
  NOT HISPANIC OR LATINO            3            201
[1] 2 2
[1] FALSE

Clustering(15) Variable = SRC MUTATION ANALYSIS
D15V1, survival
               sevent
clus2             0   1
  SRC MUTATED     1   3
  SRC WILD-TYPE 133 178
  SRC MUTATED SRC WILD-TYPE 
            4           311 
  SRC MUTATED SRC WILD-TYPE 
            3           178 
$`SRC MUTATED`
TCGA-04-1525 TCGA-13-0761 TCGA-25-1318 TCGA-25-2392 
       38.37        34.06        34.98         1.02 

$`SRC WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       40.24        41.00        49.15         2.01        46.62        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 
       11.87        65.52        63.09        48.76        21.57        63.98 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       49.28        32.52        44.32        33.67        76.57        71.47 
TCGA-04-1514 TCGA-04-1517 TCGA-04-1530 TCGA-04-1542 TCGA-09-0366 TCGA-09-0369 
       56.55        19.99       119.08        84.20        57.76        35.57 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 
        9.99        38.43        89.33        41.62        57.60        30.51 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 
        6.12        35.15       112.41        71.11        63.09        39.75 
TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       12.46        25.91        81.47        18.51        33.24        32.28 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
       11.70         3.91        35.44        15.12        19.86         6.21 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 
       24.59        44.55        39.58         2.73        31.10        15.19 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0762 TCGA-13-0765 
       17.82        55.17         2.50        11.54        32.25        28.57 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 TCGA-13-0804 
       38.93        36.72        28.70        19.59         8.12        35.28 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
       13.61        68.94       107.18        91.40        74.27        66.67 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 
       61.84        67.99        69.01        43.36        49.61        57.47 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
       56.15        57.07        47.38        48.33        47.84        44.94 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
       37.08        27.72        34.06        29.98        21.17        14.89 
TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
       13.81         6.41         6.08        10.88         6.61         7.36 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
        6.05         5.92         6.84         4.70         4.21         5.33 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 
       54.64        87.06        61.71        29.42        98.04        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       70.82        82.88        52.44        73.55        38.20        49.25 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 
        4.24        54.31        37.61        38.40        32.84        16.57 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 
        4.21         4.41         4.77         4.18         2.56         3.09 
TCGA-13-2060 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-23-1021 TCGA-23-1022 
        8.61        23.05        25.94        26.20        47.54        42.54 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1030 
       40.54        15.39        26.83        31.76        49.41        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
       18.90         2.24        54.51         4.57        33.30        86.01 
TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 
        4.27        39.09        33.47        58.13        24.95       115.89 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 
       87.48        91.66        77.00         7.63        19.66        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 
       21.80        41.56         7.66        22.32        54.12        63.55 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       47.41         6.31         6.38         7.82         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        0.76         6.25         6.02         5.95         5.36         4.83 
TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 
       17.39        19.17        18.67        43.53         8.55        72.92 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 
       12.46        45.14         9.11         3.45         1.18        22.22 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 
       26.96        57.40        16.21        56.58        51.91        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 
       58.09        88.50        70.62        39.88        19.53        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       45.50        47.70        25.87        10.26        17.23        90.15 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-2019 TCGA-24-2024 TCGA-24-2030 
       88.37        48.33        38.24         4.87        58.16        53.95 
TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 
       28.18        44.52        57.07        36.16         0.79         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 
       47.54        31.63        70.45        44.61         0.82        67.36 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 
       36.23        16.64        53.26        26.96        51.06        37.02 
TCGA-25-1317 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1324 
        1.02        65.00        36.95        33.96         2.99        34.03 
TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 
       31.07        65.06         2.96        18.58        18.02        15.81 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
        0.36        20.61         7.86         0.30        56.94        60.59 
TCGA-25-1634 TCGA-25-1635 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 
       35.54        51.22        13.02        49.05        38.04         3.02 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 
       45.01        19.99        42.02         2.96        29.03        31.00 
TCGA-25-2409 TCGA-29-2427 TCGA-30-1853 TCGA-30-1862 TCGA-30-1891 TCGA-31-1950 
       26.99        62.47        36.26         6.12        30.05        18.77 
TCGA-31-1953 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 
        6.71         2.20        28.77        29.10        21.53        22.85 
TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 
       22.55         8.55        30.08        25.74        27.85        24.23 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 
       24.03        11.38        21.14        25.08       180.20        22.32 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-61-1728 
      116.12         9.40        34.39         2.14         5.42        27.88 
TCGA-61-1736 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       48.79        38.17         2.01         5.52        14.50        17.98 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2088 
        4.01        30.64        39.85        30.64         1.18         4.77 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 
       51.72        71.74        61.64        60.62        55.50         6.48 
TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
       76.87        20.68        44.52       125.75        22.22 

  SRC MUTATED SRC WILD-TYPE 
         1.02          0.30 
  SRC MUTATED SRC WILD-TYPE 
        38.37        180.20 
  SRC MUTATED SRC WILD-TYPE 
        34.52         30.64 
[1] "1.0 - 38.4 (34.5)"  "0.3 - 180.2 (30.6)"
[1] "hr=" "2.1"
D15V2, continuous
D15V3, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SRC MUTATED                                  0     0
  SRC WILD-TYPE                                2    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  SRC MUTATED                           0     4
  SRC WILD-TYPE                        10   282
D15V4, multiclass
                                  clus
vv                                 SRC MUTATED SRC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  0            10
  WHITE                                      4           282
[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"
D15V5, binary
               cls
clus              0   1
  SRC MUTATED     0   4
  SRC WILD-TYPE   7 200
[1] "tbl2"
               cls
clus            [,1] [,2]
  SRC MUTATED      0    4
  SRC WILD-TYPE    7  200
                        clus
vv                       SRC MUTATED SRC WILD-TYPE
  HISPANIC OR LATINO               0             7
  NOT HISPANIC OR LATINO           4           200
[1] 2 2
[1] FALSE

Clustering(16) Variable = ZNF236 MUTATION ANALYSIS
D16V1, survival
                  sevent
clus2                0   1
  ZNF236 MUTATED     3   3
  ZNF236 WILD-TYPE 131 178
  ZNF236 MUTATED ZNF236 WILD-TYPE 
               6              309 
  ZNF236 MUTATED ZNF236 WILD-TYPE 
               3              178 
$`ZNF236 MUTATED`
TCGA-09-2053 TCGA-10-0930 TCGA-20-0990 TCGA-24-0966 TCGA-25-2401 TCGA-61-1736 
       39.75        33.24        25.94         7.63         2.96        48.79 

$`ZNF236 WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       40.24        41.00        49.15         2.01        46.62        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 
       11.87        65.52        63.09        48.76        21.57        63.98 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       49.28        32.52        44.32        33.67        76.57        71.47 
TCGA-04-1514 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-09-0366 
       56.55        19.99        38.37       119.08        84.20        57.76 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 
       35.57         9.99        38.43        89.33        41.62        57.60 
TCGA-09-1669 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
       30.51         6.12        35.15       112.41        71.11        63.09 
TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0933 
       12.46        25.91        81.47        18.51        32.28        11.70 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
        3.91        35.44        15.12        19.86         6.21        24.59 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 
       44.55        39.58         2.73        31.10        15.19        17.82 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0765 
       55.17         2.50        11.54        34.06        32.25        28.57 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 TCGA-13-0804 
       38.93        36.72        28.70        19.59         8.12        35.28 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
       13.61        68.94       107.18        91.40        74.27        66.67 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 
       61.84        67.99        69.01        43.36        49.61        57.47 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
       56.15        57.07        47.38        48.33        47.84        44.94 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
       37.08        27.72        34.06        29.98        21.17        14.89 
TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
       13.81         6.41         6.08        10.88         6.61         7.36 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
        6.05         5.92         6.84         4.70         4.21         5.33 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 
       54.64        87.06        61.71        29.42        98.04        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       70.82        82.88        52.44        73.55        38.20        49.25 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 
        4.24        54.31        37.61        38.40        32.84        16.57 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 
        4.21         4.41         4.77         4.18         2.56         3.09 
TCGA-13-2060 TCGA-20-0987 TCGA-20-0991 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 
        8.61        23.05        26.20        47.54        42.54        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 
       15.39        26.83        31.76        49.41        29.13        18.90 
TCGA-23-1032 TCGA-23-1110 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 
        2.24        54.51         4.57        33.30        86.01         4.27 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 
       39.09        33.47        58.13        24.95       115.89        87.48 
TCGA-23-2079 TCGA-23-2081 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
       91.66        77.00        19.66        11.64        21.80        41.56 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 
        7.66        22.32        54.12        63.55        47.41         6.31 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 
        6.38         7.82         7.99         7.86         0.76         6.25 
TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 
        6.02         5.95         5.36         4.83        17.39        19.17 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 
       18.67        43.53         8.55        72.92        12.46        45.14 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 
        9.11         3.45         1.18        22.22        26.96        57.40 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       16.21        56.58        51.91        41.39        58.09        88.50 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       70.62        39.88        19.53        44.09        45.50        47.70 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 
       25.87        10.26        17.23        90.15        88.37        48.33 
TCGA-24-1616 TCGA-24-2019 TCGA-24-2024 TCGA-24-2030 TCGA-24-2035 TCGA-24-2038 
       38.24         4.87        58.16        53.95        28.18        44.52 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 
       57.07        36.16         0.79         0.36        47.54        31.63 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 
       70.45        44.61         0.82        67.36        36.23        16.64 
TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
       53.26        26.96        51.06        37.02         1.02        34.98 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1324 TCGA-25-1326 
       65.00        36.95        33.96         2.99        34.03        31.07 
TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 
       65.06         2.96        18.58        18.02        15.81         0.36 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
       20.61         7.86         0.30        56.94        60.59        35.54 
TCGA-25-1635 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 
       51.22        13.02        49.05         1.02        38.04         3.02 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       45.01        19.99        42.02        29.03        31.00        26.99 
TCGA-29-2427 TCGA-30-1853 TCGA-30-1862 TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 
       62.47        36.26         6.12        30.05        18.77         6.71 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
        2.20        28.77        29.10        21.53        22.85        22.55 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-57-1582 
        8.55        30.08        25.74        27.85        24.23        24.03 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 
       11.38        21.14        25.08       180.20        22.32       116.12 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-61-1728 TCGA-61-1919 
        9.40        34.39         2.14         5.42        27.88        38.17 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 
        2.01         5.52        14.50        17.98         4.01        30.64 
TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 
       39.85        30.64         1.18         4.77        51.72        71.74 
TCGA-61-2095 TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       61.64        60.62        55.50         6.48        76.87        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
       44.52       125.75        22.22 

  ZNF236 MUTATED ZNF236 WILD-TYPE 
            2.96             0.30 
  ZNF236 MUTATED ZNF236 WILD-TYPE 
           48.79           180.20 
  ZNF236 MUTATED ZNF236 WILD-TYPE 
           29.59            31.00 
[1] "3.0 - 48.8 (29.6)"  "0.3 - 180.2 (31.0)"
[1] "hr=" "1.3"
D16V2, continuous
D16V3, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF236 MUTATED                                  0     0
  ZNF236 WILD-TYPE                                2    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF236 MUTATED                           1     5
  ZNF236 WILD-TYPE                         9   281
D16V4, multiclass
                                  clus
vv                                 ZNF236 MUTATED ZNF236 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1                9
  WHITE                                         5              281
[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"
D16V5, binary
                  cls
clus                 0   1
  ZNF236 MUTATED     0   5
  ZNF236 WILD-TYPE   7 199
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF236 MUTATED      0    5
  ZNF236 WILD-TYPE    7  199
                        clus
vv                       ZNF236 MUTATED ZNF236 WILD-TYPE
  HISPANIC OR LATINO                  0                7
  NOT HISPANIC OR LATINO              5              199
[1] 2 2
[1] FALSE

Clustering(17) Variable = NBPF16 MUTATION ANALYSIS
D17V1, survival
                  sevent
clus2                0   1
  NBPF16 MUTATED     2   1
  NBPF16 WILD-TYPE 132 180
  NBPF16 MUTATED NBPF16 WILD-TYPE 
               3              312 
  NBPF16 MUTATED NBPF16 WILD-TYPE 
               1              180 
$`NBPF16 MUTATED`
TCGA-13-0911 TCGA-25-2400 TCGA-61-1998 
       27.72        42.02         5.52 

$`NBPF16 WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       40.24        41.00        49.15         2.01        46.62        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 
       11.87        65.52        63.09        48.76        21.57        63.98 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       49.28        32.52        44.32        33.67        76.57        71.47 
TCGA-04-1514 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-09-0366 
       56.55        19.99        38.37       119.08        84.20        57.76 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 
       35.57         9.99        38.43        89.33        41.62        57.60 
TCGA-09-1669 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
       30.51         6.12        35.15       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       39.75        12.46        25.91        81.47        18.51        33.24 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 
       32.28        11.70         3.91        35.44        15.12        19.86 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 
        6.21        24.59        44.55        39.58         2.73        31.10 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 
       15.19        17.82        55.17         2.50        11.54        34.06 
TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 
       32.25        28.57        38.93        36.72        28.70        19.59 
TCGA-13-0800 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 
        8.12        35.28        13.61        68.94       107.18        91.40 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
       74.27        66.67        61.84        67.99        69.01        43.36 
TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 
       49.61        57.47        56.15        57.07        47.38        48.33 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       47.84        44.94        37.08        34.06        29.98        21.17 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 
       14.89        13.81         6.41         6.08        10.88         6.61 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
        7.36         6.05         5.92         6.84         4.70         4.21 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
        5.33        54.64        87.06        61.71        29.42        98.04 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       22.39        70.82        82.88        52.44        73.55        38.20 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 
       49.25         4.24        54.31        37.61        38.40        32.84 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 
       16.57         4.21         4.41         4.77         4.18         2.56 
TCGA-13-1512 TCGA-13-2060 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-23-1021 
        3.09         8.61        23.05        25.94        26.20        47.54 
TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       42.54        40.54        15.39        26.83        31.76        49.41 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1116 TCGA-23-1117 
       29.13        18.90         2.24        54.51         4.57        33.30 
TCGA-23-1118 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 
       86.01         4.27        39.09        33.47        58.13        24.95 
TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-24-0966 TCGA-24-0968 
      115.89        87.48        91.66        77.00         7.63        19.66 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 
       11.64        21.80        41.56         7.66        22.32        54.12 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 
       63.55        47.41         6.31         6.38         7.82         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 
        7.86         0.76         6.25         6.02         5.95         5.36 
TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
        4.83        17.39        19.17        18.67        43.53         8.55 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 
       72.92        12.46        45.14         9.11         3.45         1.18 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 
       22.22        26.96        57.40        16.21        56.58        51.91 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 
       41.39        58.09        88.50        70.62        39.88        19.53 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 
       44.09        45.50        47.70        25.87        10.26        17.23 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-2019 TCGA-24-2024 
       90.15        88.37        48.33        38.24         4.87        58.16 
TCGA-24-2030 TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 
       53.95        28.18        44.52        57.07        36.16         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
        0.36        47.54        31.63        70.45        44.61         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 
       67.36        36.23        16.64        53.26        26.96        51.06 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 
       37.02         1.02        34.98        65.00        36.95        33.96 
TCGA-25-1322 TCGA-25-1324 TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 
        2.99        34.03        31.07        65.06         2.96        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
       18.02        15.81         0.36        20.61         7.86         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-2042 TCGA-25-2391 
       56.94        60.59        35.54        51.22        13.02        49.05 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2401 
        1.02        38.04         3.02        45.01        19.99         2.96 
TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-2427 TCGA-30-1853 TCGA-30-1862 
       29.03        31.00        26.99        62.47        36.26         6.12 
TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 
       30.05        18.77         6.71         2.20        28.77        29.10 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 
       21.53        22.85        22.55         8.55        30.08        25.74 
TCGA-36-1578 TCGA-36-1580 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1993 
       27.85        24.23        24.03        11.38        21.14        25.08 
TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 
      180.20        22.32       116.12         9.40        34.39         2.14 
TCGA-59-2363 TCGA-61-1728 TCGA-61-1736 TCGA-61-1919 TCGA-61-1995 TCGA-61-2000 
        5.42        27.88        48.79        38.17         2.01        14.50 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 
       17.98         4.01        30.64        39.85        30.64         1.18 
TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 TCGA-61-2101 
        4.77        51.72        71.74        61.64        60.62        55.50 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
        6.48        76.87        20.68        44.52       125.75        22.22 

  NBPF16 MUTATED NBPF16 WILD-TYPE 
            5.52             0.30 
  NBPF16 MUTATED NBPF16 WILD-TYPE 
           42.02           180.20 
  NBPF16 MUTATED NBPF16 WILD-TYPE 
          27.720           31.035 
[1] "5.5 - 42.0 (27.7)"  "0.3 - 180.2 (31.0)"
[1] "hr=" "1"  
D17V2, continuous
D17V3, continuous
[1] "Remove cluster labels:" "NBPF16 MUTATED"        
clus
  NBPF16 MUTATED NBPF16 WILD-TYPE 
               1               55 
      TCGA-04-1346       TCGA-04-1347       TCGA-04-1356       TCGA-04-1367 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
      TCGA-10-0926       TCGA-13-0714       TCGA-13-0720       TCGA-13-0724 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
      TCGA-13-0755       TCGA-13-0760       TCGA-13-0762       TCGA-13-0791 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
      TCGA-13-0792       TCGA-13-0793       TCGA-13-0795       TCGA-13-0885 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
      TCGA-13-0887       TCGA-13-0889       TCGA-13-0891       TCGA-13-0894 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
      TCGA-13-0897       TCGA-13-0900       TCGA-13-0903       TCGA-13-0904 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
      TCGA-13-0905       TCGA-13-0906       TCGA-13-0910       TCGA-13-0912 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
      TCGA-13-0913       TCGA-13-0919       TCGA-13-1404       TCGA-13-1405 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
      TCGA-13-1409       TCGA-13-1410       TCGA-13-1412       TCGA-13-1482 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
      TCGA-13-1483       TCGA-13-1484       TCGA-13-1488       TCGA-13-1489 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
      TCGA-13-1491       TCGA-13-1492       TCGA-13-1495       TCGA-13-1497 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
      TCGA-13-1498       TCGA-13-1499       TCGA-13-1501       TCGA-13-1504 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
      TCGA-13-1506       TCGA-13-1507       TCGA-13-1509       TCGA-13-1512 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
      TCGA-13-2060       TCGA-24-1614       TCGA-61-2101 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NBPF16 MUTATED                                  0     0
  NBPF16 WILD-TYPE                                2    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NBPF16 MUTATED                           0     3
  NBPF16 WILD-TYPE                        10   283
D17V4, multiclass
                                  clus
vv                                 NBPF16 MUTATED NBPF16 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               10
  WHITE                                         3              283
[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"
D17V5, binary
                  cls
clus                 0   1
  NBPF16 MUTATED     0   3
  NBPF16 WILD-TYPE   7 201
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF16 MUTATED      0    3
  NBPF16 WILD-TYPE    7  201
                        clus
vv                       NBPF16 MUTATED NBPF16 WILD-TYPE
  HISPANIC OR LATINO                  0                7
  NOT HISPANIC OR LATINO              3              201
[1] 2 2
[1] FALSE

Clustering(18) Variable = CYP11B1 MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  CYP11B1 MUTATED     1   6
  CYP11B1 WILD-TYPE 133 175
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
                7               308 
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
                6               175 
$`CYP11B1 MUTATED`
TCGA-04-1349 TCGA-09-0366 TCGA-13-0760 TCGA-13-0893 TCGA-23-1122 TCGA-59-2355 
       21.57        57.76        11.54        43.36        39.09         2.14 
TCGA-61-2012 
       30.64 

$`CYP11B1 WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       40.24        41.00        49.15         2.01        46.62        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1350 TCGA-04-1356 
       11.87        65.52        63.09        48.76        63.98        49.28 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 
       32.52        44.32        33.67        76.57        71.47        56.55 
TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-09-0369 TCGA-09-1659 
       19.99        38.37       119.08        84.20        35.57         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 TCGA-09-2044 
       38.43        89.33        41.62        57.60        30.51         6.12 
TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 
       35.15       112.41        71.11        63.09        39.75        12.46 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 
       25.91        81.47        18.51        33.24        32.28        11.70 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
        3.91        35.44        15.12        19.86         6.21        24.59 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 
       44.55        39.58         2.73        31.10        15.19        17.82 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0761 TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 
       55.17         2.50        34.06        32.25        28.57        38.93 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 TCGA-13-0804 TCGA-13-0807 
       36.72        28.70        19.59         8.12        35.28        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 
       68.94       107.18        91.40        74.27        66.67        61.84 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0894 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       67.99        69.01        49.61        57.47        56.15        57.07 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 
       47.38        48.33        47.84        44.94        37.08        27.72 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 
       34.06        29.98        21.17        14.89        13.81         6.41 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 
        6.08        10.88         6.61         7.36         6.05         5.92 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
        6.84         4.70         4.21         5.33        54.64        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 
       61.71        29.42        98.04        22.39        70.82        82.88 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 
       52.44        73.55        38.20        49.25         4.24        54.31 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       37.61        38.40        32.84        16.57         4.21         4.41 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2060 TCGA-20-0987 
        4.77         4.18         2.56         3.09         8.61        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 
       25.94        26.20        47.54        42.54        40.54        15.39 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       26.83        31.76        49.41        29.13        18.90         2.24 
TCGA-23-1110 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 TCGA-23-1123 
       54.51         4.57        33.30        86.01         4.27        33.47 
TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
       58.13        24.95       115.89        87.48        91.66        77.00 
TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        7.63        19.66        11.64        21.80        41.56         7.66 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
       22.32        54.12        63.55        47.41         6.31         6.38 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
        7.82         7.99         7.86         0.76         6.25         6.02 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 
        5.95         5.36         4.83        17.39        19.17        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 
       43.53         8.55        72.92        12.46        45.14         9.11 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 
        3.45         1.18        22.22        26.96        57.40        16.21 
TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 
       56.58        51.91        41.39        58.09        88.50        70.62 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
       39.88        19.53        44.09        45.50        47.70        25.87 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 
       10.26        17.23        90.15        88.37        48.33        38.24 
TCGA-24-2019 TCGA-24-2024 TCGA-24-2030 TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 
        4.87        58.16        53.95        28.18        44.52        57.07 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       36.16         0.79         0.36        47.54        31.63        70.45 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2298 
       44.61         0.82        67.36        36.23        16.64        53.26 
TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 
       26.96        51.06        37.02         1.02        34.98        65.00 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1324 TCGA-25-1326 TCGA-25-1328 
       36.95        33.96         2.99        34.03        31.07        65.06 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 
        2.96        18.58        18.02        15.81         0.36        20.61 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 
        7.86         0.30        56.94        60.59        35.54        51.22 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 
       13.02        49.05         1.02        38.04         3.02        45.01 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       19.99        42.02         2.96        29.03        31.00        26.99 
TCGA-29-2427 TCGA-30-1853 TCGA-30-1862 TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 
       62.47        36.26         6.12        30.05        18.77         6.71 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
        2.20        28.77        29.10        21.53        22.85        22.55 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-57-1582 
        8.55        30.08        25.74        27.85        24.23        24.03 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 
       11.38        21.14        25.08       180.20        22.32       116.12 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 TCGA-61-1728 TCGA-61-1736 TCGA-61-1919 
        9.40        34.39         5.42        27.88        48.79        38.17 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 
        2.01         5.52        14.50        17.98         4.01        30.64 
TCGA-61-2009 TCGA-61-2016 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       39.85         1.18         4.77        51.72        71.74        61.64 
TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       60.62        55.50         6.48        76.87        20.68        44.52 
TCGA-61-2111 TCGA-61-2113 
      125.75        22.22 

  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
             2.14              0.30 
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
            57.76            180.20 
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
           30.640            31.035 
[1] "2.1 - 57.8 (30.6)"  "0.3 - 180.2 (31.0)"
[1] "hr=" "2"  
D18V2, continuous
D18V3, continuous
[1] "Remove cluster labels:" "CYP11B1 MUTATED"       
clus
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
                1                55 
       TCGA-04-1346        TCGA-04-1347        TCGA-04-1356        TCGA-04-1367 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-10-0926        TCGA-13-0714        TCGA-13-0720        TCGA-13-0724 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-13-0755        TCGA-13-0762        TCGA-13-0791        TCGA-13-0792 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-13-0793        TCGA-13-0795        TCGA-13-0885        TCGA-13-0887 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-13-0889        TCGA-13-0891        TCGA-13-0894        TCGA-13-0897 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-13-0900        TCGA-13-0903        TCGA-13-0904        TCGA-13-0905 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-13-0906        TCGA-13-0910        TCGA-13-0911        TCGA-13-0912 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-13-0913        TCGA-13-0919        TCGA-13-1404        TCGA-13-1405 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-13-1409        TCGA-13-1410        TCGA-13-1412        TCGA-13-1482 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-13-1483        TCGA-13-1484        TCGA-13-1488        TCGA-13-1489 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-13-1491        TCGA-13-1492        TCGA-13-1495        TCGA-13-1497 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-13-1498        TCGA-13-1499        TCGA-13-1501        TCGA-13-1504 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-13-1506        TCGA-13-1507        TCGA-13-1509        TCGA-13-1512 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-13-2060        TCGA-24-1614        TCGA-61-2101 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYP11B1 MUTATED                                  0     0
  CYP11B1 WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CYP11B1 MUTATED                           1     6
  CYP11B1 WILD-TYPE                         9   280
D18V4, multiclass
                                  clus
vv                                 CYP11B1 MUTATED CYP11B1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                 9
  WHITE                                          6               280
[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"
D18V5, binary
                   cls
clus                  0   1
  CYP11B1 MUTATED     0   5
  CYP11B1 WILD-TYPE   7 199
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP11B1 MUTATED      0    5
  CYP11B1 WILD-TYPE    7  199
                        clus
vv                       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO               5               199
[1] 2 2
[1] FALSE

Clustering(19) Variable = SON MUTATION ANALYSIS
D19V1, survival
               sevent
clus2             0   1
  SON MUTATED     3   5
  SON WILD-TYPE 131 176
  SON MUTATED SON WILD-TYPE 
            8           307 
  SON MUTATED SON WILD-TYPE 
            5           176 
$`SON MUTATED`
TCGA-04-1362 TCGA-10-0935 TCGA-13-0724 TCGA-13-0899 TCGA-13-1487 TCGA-23-1023 
       44.32        35.44         2.73        56.15        22.39        40.54 
TCGA-24-0975 TCGA-36-1576 
       21.80        30.08 

$`SON WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       40.24        41.00        49.15         2.01        46.62        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 
       11.87        65.52        63.09        48.76        21.57        63.98 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 
       49.28        32.52        33.67        76.57        71.47        56.55 
TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-09-0366 TCGA-09-0369 
       19.99        38.37       119.08        84.20        57.76        35.57 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 
        9.99        38.43        89.33        41.62        57.60        30.51 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 
        6.12        35.15       112.41        71.11        63.09        39.75 
TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       12.46        25.91        81.47        18.51        33.24        32.28 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
       11.70         3.91        15.12        19.86         6.21        24.59 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
       44.55        39.58        31.10        15.19        17.82        55.17 
TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0765 TCGA-13-0791 
        2.50        11.54        34.06        32.25        28.57        38.93 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 TCGA-13-0804 TCGA-13-0807 
       36.72        28.70        19.59         8.12        35.28        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 
       68.94       107.18        91.40        74.27        66.67        61.84 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0894 TCGA-13-0897 TCGA-13-0900 
       67.99        69.01        43.36        49.61        57.47        57.07 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 
       47.38        48.33        47.84        44.94        37.08        27.72 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 
       34.06        29.98        21.17        14.89        13.81         6.41 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 
        6.08        10.88         6.61         7.36         6.05         5.92 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
        6.84         4.70         4.21         5.33        54.64        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
       61.71        29.42        98.04        70.82        82.88        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
       73.55        38.20        49.25         4.24        54.31        37.61 
TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
       38.40        32.84        16.57         4.21         4.41         4.77 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2060 TCGA-20-0987 TCGA-20-0990 
        4.18         2.56         3.09         8.61        23.05        25.94 
TCGA-20-0991 TCGA-23-1021 TCGA-23-1022 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
       26.20        47.54        42.54        15.39        26.83        31.76 
TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1116 
       49.41        29.13        18.90         2.24        54.51         4.57 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 
       33.30        86.01         4.27        39.09        33.47        58.13 
TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-24-0966 
       24.95       115.89        87.48        91.66        77.00         7.63 
TCGA-24-0968 TCGA-24-0970 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 
       19.66        11.64        41.56         7.66        22.32        54.12 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 
       63.55        47.41         6.31         6.38         7.82         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 
        7.86         0.76         6.25         6.02         5.95         5.36 
TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
        4.83        17.39        19.17        18.67        43.53         8.55 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 
       72.92        12.46        45.14         9.11         3.45         1.18 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 
       22.22        26.96        57.40        16.21        56.58        51.91 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 
       41.39        58.09        88.50        70.62        39.88        19.53 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 
       44.09        45.50        47.70        25.87        10.26        17.23 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-2019 TCGA-24-2024 
       90.15        88.37        48.33        38.24         4.87        58.16 
TCGA-24-2030 TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 
       53.95        28.18        44.52        57.07        36.16         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
        0.36        47.54        31.63        70.45        44.61         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 
       67.36        36.23        16.64        53.26        26.96        51.06 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 
       37.02         1.02        34.98        65.00        36.95        33.96 
TCGA-25-1322 TCGA-25-1324 TCGA-25-1326 TCGA-25-1328 TCGA-25-1329 TCGA-25-1623 
        2.99        34.03        31.07        65.06         2.96        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
       18.02        15.81         0.36        20.61         7.86         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-2042 TCGA-25-2391 
       56.94        60.59        35.54        51.22        13.02        49.05 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 
        1.02        38.04         3.02        45.01        19.99        42.02 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-2427 TCGA-30-1853 
        2.96        29.03        31.00        26.99        62.47        36.26 
TCGA-30-1862 TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 TCGA-31-1959 TCGA-36-1568 
        6.12        30.05        18.77         6.71         2.20        28.77 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 
       29.10        21.53        22.85        22.55         8.55        25.74 
TCGA-36-1578 TCGA-36-1580 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1993 
       27.85        24.23        24.03        11.38        21.14        25.08 
TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 
      180.20        22.32       116.12         9.40        34.39         2.14 
TCGA-59-2363 TCGA-61-1728 TCGA-61-1736 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
        5.42        27.88        48.79        38.17         2.01         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 
       14.50        17.98         4.01        30.64        39.85        30.64 
TCGA-61-2016 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 
        1.18         4.77        51.72        71.74        61.64        60.62 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       55.50         6.48        76.87        20.68        44.52       125.75 
TCGA-61-2113 
       22.22 

  SON MUTATED SON WILD-TYPE 
         2.73          0.30 
  SON MUTATED SON WILD-TYPE 
        56.15        180.20 
  SON MUTATED SON WILD-TYPE 
        32.76         31.00 
[1] "2.7 - 56.1 (32.8)"  "0.3 - 180.2 (31.0)"
[1] "hr=" "1.4"
D19V2, continuous
D19V3, continuous
[1] "Remove cluster labels:" "SON MUTATED"           
clus
  SON MUTATED SON WILD-TYPE 
            1            55 
   TCGA-04-1346    TCGA-04-1347    TCGA-04-1356    TCGA-04-1367    TCGA-10-0926 
"SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" 
   TCGA-13-0714    TCGA-13-0720    TCGA-13-0755    TCGA-13-0760    TCGA-13-0762 
"SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" 
   TCGA-13-0791    TCGA-13-0792    TCGA-13-0793    TCGA-13-0795    TCGA-13-0885 
"SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" 
   TCGA-13-0887    TCGA-13-0889    TCGA-13-0891    TCGA-13-0894    TCGA-13-0897 
"SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" 
   TCGA-13-0900    TCGA-13-0903    TCGA-13-0904    TCGA-13-0905    TCGA-13-0906 
"SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" 
   TCGA-13-0910    TCGA-13-0911    TCGA-13-0912    TCGA-13-0913    TCGA-13-0919 
"SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" 
   TCGA-13-1404    TCGA-13-1405    TCGA-13-1409    TCGA-13-1410    TCGA-13-1412 
"SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" 
   TCGA-13-1482    TCGA-13-1483    TCGA-13-1484    TCGA-13-1488    TCGA-13-1489 
"SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" 
   TCGA-13-1491    TCGA-13-1492    TCGA-13-1495    TCGA-13-1497    TCGA-13-1498 
"SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" 
   TCGA-13-1499    TCGA-13-1501    TCGA-13-1504    TCGA-13-1506    TCGA-13-1507 
"SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" 
   TCGA-13-1509    TCGA-13-1512    TCGA-13-2060    TCGA-24-1614    TCGA-61-2101 
"SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" "SON WILD-TYPE" 
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SON MUTATED                                  0     0
  SON WILD-TYPE                                2    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  SON MUTATED                           0     7
  SON WILD-TYPE                        10   279
D19V4, multiclass
                                  clus
vv                                 SON MUTATED SON WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  0            10
  WHITE                                      7           279
[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"
D19V5, binary
               cls
clus              0   1
  SON MUTATED     1   4
  SON WILD-TYPE   6 200
[1] "tbl2"
               cls
clus            [,1] [,2]
  SON MUTATED      1    4
  SON WILD-TYPE    6  200
                        clus
vv                       SON MUTATED SON WILD-TYPE
  HISPANIC OR LATINO               1             6
  NOT HISPANIC OR LATINO           4           200
[1] 2 2
[1] FALSE
