
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Cluster_mutation_onlysig.3.4048/Clusters2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Cluster_mutation_onlysig.3.4048/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/397994/OV-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/OV-TP/3148251/1.GDAC_mergedClustering.Finished/OV-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ONLYSIG", "-oT=OV-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"       "-oT=OV-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=586, in cluster file=316, common to both=316
[1]   8 316
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           276             40 
  TP53 MUTATED TP53 WILD-TYPE 
           276             40 
[1] "SRC MUTATION ANALYSIS"
[1] 3
  SRC MUTATED SRC WILD-TYPE 
            4           312 
  SRC MUTATED SRC WILD-TYPE 
            4           312 
[1] "TBP MUTATION ANALYSIS"
[1] 3
  TBP MUTATED TBP WILD-TYPE 
            4           312 
  TBP MUTATED TBP WILD-TYPE 
            4           312 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
            9           307 
  RB1 MUTATED RB1 WILD-TYPE 
            9           307 
[1] "GABRA6 MUTATION ANALYSIS"
[1] 3
  GABRA6 MUTATED GABRA6 WILD-TYPE 
               6              310 
  GABRA6 MUTATED GABRA6 WILD-TYPE 
               6              310 
[1] "BRCA1 MUTATION ANALYSIS"
[1] 3
  BRCA1 MUTATED BRCA1 WILD-TYPE 
             12             304 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
             12             304 
[1] "CSMD3 MUTATION ANALYSIS"
[1] 3
  CSMD3 MUTATED CSMD3 WILD-TYPE 
             18             298 
  CSMD3 MUTATED CSMD3 WILD-TYPE 
             18             298 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           14           302 
  NF1 MUTATED NF1 WILD-TYPE 
           14           302 
[1] "data2feature, selection=ALL"
 [1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "MIR_CNMF"             
 [4] "MIR_CHIERARCHICAL"     "CN_CNMF"               "METHLYATION_CNMF"     
 [7] "RPPA_CNMF"             "RPPA_CHIERARCHICAL"    "MRNASEQ_CNMF"         
[10] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 

Input Data has 12 rows and 316 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MIR_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MIR_CHIERARCHICAL':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'RPPA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'RPPA_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "MIR_CNMF"             
 [4] "MIR_CHIERARCHICAL"     "CN_CNMF"               "METHLYATION_CNMF"     
 [7] "RPPA_CNMF"             "RPPA_CHIERARCHICAL"    "MRNASEQ_CNMF"         
[10] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 316 columns, 0 survival variables, and 12 non-survival variables.
MRNA_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIR_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIR_CHIERARCHICAL, nv=6, binary=FALSE, numeric=FALSE
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
D1V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1          106             13
  CLUS_2           98             14
  CLUS_3           72             13
D1V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1          104             20
  CLUS_2           96             11
  CLUS_3           76              9
D1V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           83              9
  CLUS_2           81             15
  CLUS_3          112             16
D1V4, multiclass
D1V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           94             13
  CLUS_2           91             11
  CLUS_3           87             15
D1V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           78             10
  CLUS_2           91             16
  CLUS_3          107             14
D1V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           65             11
  CLUS_2           88              8
  CLUS_3           33              5
D1V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           28              2
  CLUS_2           41              4
  CLUS_3           48              4
  CLUS_4           69             14
D1V9, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           60             10
  CLUS_2           36              4
  CLUS_3           46              5
D1V10, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           61              7
  CLUS_2           57              9
  CLUS_3           24              3
D1V11, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           65             14
  CLUS_2          106             13
  CLUS_3           79             10
D1V12, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            3              1
  CLUS_2          154             27
  CLUS_3           93              9

Clustering(2) Variable = SRC MUTATION ANALYSIS
D2V1, multiclass
        clus
vv       SRC MUTATED SRC WILD-TYPE
  CLUS_1           1           118
  CLUS_2           2           110
  CLUS_3           1            84
D2V2, multiclass
        clus
vv       SRC MUTATED SRC WILD-TYPE
  CLUS_1           1           123
  CLUS_2           1           106
  CLUS_3           2            83
D2V3, multiclass
        clus
vv       SRC MUTATED SRC WILD-TYPE
  CLUS_1           0            92
  CLUS_2           2            94
  CLUS_3           2           126
D2V4, multiclass
D2V5, multiclass
        clus
vv       SRC MUTATED SRC WILD-TYPE
  CLUS_1           0           107
  CLUS_2           3            99
  CLUS_3           1           101
D2V6, multiclass
        clus
vv       SRC MUTATED SRC WILD-TYPE
  CLUS_1           0            88
  CLUS_2           1           106
  CLUS_3           3           118
D2V7, multiclass
[1] "Remove cluster labels:" "SRC MUTATED"           
clus
  SRC MUTATED SRC WILD-TYPE 
            2           208 
   TCGA-04-1336    TCGA-04-1338    TCGA-04-1342    TCGA-04-1343    TCGA-04-1348 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-04-1349    TCGA-04-1356    TCGA-04-1357    TCGA-04-1361    TCGA-04-1362 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-04-1514    TCGA-04-1517    TCGA-04-1542    TCGA-09-1662    TCGA-09-1665 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-09-1666    TCGA-09-2044    TCGA-09-2045    TCGA-09-2049    TCGA-09-2051 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-09-2056    TCGA-10-0926    TCGA-10-0931    TCGA-10-0933    TCGA-13-0720 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-0793    TCGA-13-0800    TCGA-13-0804    TCGA-13-0884    TCGA-13-0886 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-0887    TCGA-13-0891    TCGA-13-0894    TCGA-13-0897    TCGA-13-0899 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-0903    TCGA-13-0906    TCGA-13-0910    TCGA-13-0911    TCGA-13-0913 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-0916    TCGA-13-0920    TCGA-13-1404    TCGA-13-1405    TCGA-13-1408 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1409    TCGA-13-1410    TCGA-13-1411    TCGA-13-1412    TCGA-13-1477 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1481    TCGA-13-1482    TCGA-13-1483    TCGA-13-1484    TCGA-13-1487 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1488    TCGA-13-1489    TCGA-13-1491    TCGA-13-1492    TCGA-13-1494 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1495    TCGA-13-1496    TCGA-13-1498    TCGA-13-1499    TCGA-13-1501 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1504    TCGA-13-1505    TCGA-13-1506    TCGA-13-1507    TCGA-13-1509 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1512    TCGA-13-2060    TCGA-23-1110    TCGA-23-1122    TCGA-23-1123 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-23-1124    TCGA-23-2077    TCGA-23-2078    TCGA-23-2079    TCGA-23-2081 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-0966    TCGA-24-0970    TCGA-24-0979    TCGA-24-0980    TCGA-24-0982 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1103    TCGA-24-1104    TCGA-24-1105    TCGA-24-1416    TCGA-24-1417 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1419    TCGA-24-1422    TCGA-24-1423    TCGA-24-1424    TCGA-24-1427 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1428    TCGA-24-1431    TCGA-24-1434    TCGA-24-1435    TCGA-24-1436 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1463    TCGA-24-1464    TCGA-24-1466    TCGA-24-1469    TCGA-24-1470 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1471    TCGA-24-1474    TCGA-24-1544    TCGA-24-1545    TCGA-24-1548 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1549    TCGA-24-1551    TCGA-24-1552    TCGA-24-1553    TCGA-24-1555 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1556    TCGA-24-1557    TCGA-24-1558    TCGA-24-1560    TCGA-24-1562 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1563    TCGA-24-1564    TCGA-24-1565    TCGA-24-1567    TCGA-24-1603 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1604    TCGA-24-1614    TCGA-24-1616    TCGA-24-2024    TCGA-24-2030 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-2038    TCGA-24-2254    TCGA-24-2260    TCGA-24-2261    TCGA-24-2262 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-2267    TCGA-24-2271    TCGA-24-2281    TCGA-24-2288    TCGA-24-2289 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-2290    TCGA-24-2293    TCGA-24-2298    TCGA-25-1313    TCGA-25-1315 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1316    TCGA-25-1319    TCGA-25-1320    TCGA-25-1321    TCGA-25-1322 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1326    TCGA-25-1328    TCGA-25-1329    TCGA-25-1623    TCGA-25-1625 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1626    TCGA-25-1627    TCGA-25-1628    TCGA-25-1630    TCGA-25-1631 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1632    TCGA-25-1633    TCGA-25-1635    TCGA-25-2042    TCGA-25-2391 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-2393    TCGA-25-2396    TCGA-25-2398    TCGA-25-2399    TCGA-25-2400 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-2401    TCGA-25-2404    TCGA-25-2408    TCGA-25-2409    TCGA-29-2427 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-30-1891    TCGA-31-1950    TCGA-36-1568    TCGA-36-1569    TCGA-36-1570 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-36-1571    TCGA-36-1575    TCGA-36-1576    TCGA-36-1577    TCGA-36-1578 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-36-1580    TCGA-59-2348    TCGA-59-2351    TCGA-59-2352    TCGA-59-2354 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-59-2363    TCGA-61-1736    TCGA-61-1919    TCGA-61-1995    TCGA-61-2000 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-61-2003    TCGA-61-2009    TCGA-61-2012    TCGA-61-2088    TCGA-61-2092 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-61-2094    TCGA-61-2095    TCGA-61-2101    TCGA-61-2102    TCGA-61-2104 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-61-2109    TCGA-61-2111    TCGA-61-2113 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
D2V8, multiclass
[1] "Remove cluster labels:" "SRC MUTATED"           
clus
  SRC MUTATED SRC WILD-TYPE 
            2           208 
   TCGA-04-1336    TCGA-04-1338    TCGA-04-1342    TCGA-04-1343    TCGA-04-1348 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-04-1349    TCGA-04-1356    TCGA-04-1357    TCGA-04-1361    TCGA-04-1362 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-04-1514    TCGA-04-1517    TCGA-04-1542    TCGA-09-1662    TCGA-09-1665 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-09-1666    TCGA-09-2044    TCGA-09-2045    TCGA-09-2049    TCGA-09-2051 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-09-2056    TCGA-10-0926    TCGA-10-0931    TCGA-10-0933    TCGA-13-0720 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-0793    TCGA-13-0800    TCGA-13-0804    TCGA-13-0884    TCGA-13-0886 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-0887    TCGA-13-0891    TCGA-13-0894    TCGA-13-0897    TCGA-13-0899 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-0903    TCGA-13-0906    TCGA-13-0910    TCGA-13-0911    TCGA-13-0913 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-0916    TCGA-13-0920    TCGA-13-1404    TCGA-13-1405    TCGA-13-1408 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1409    TCGA-13-1410    TCGA-13-1411    TCGA-13-1412    TCGA-13-1477 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1481    TCGA-13-1482    TCGA-13-1483    TCGA-13-1484    TCGA-13-1487 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1488    TCGA-13-1489    TCGA-13-1491    TCGA-13-1492    TCGA-13-1494 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1495    TCGA-13-1496    TCGA-13-1498    TCGA-13-1499    TCGA-13-1501 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1504    TCGA-13-1505    TCGA-13-1506    TCGA-13-1507    TCGA-13-1509 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1512    TCGA-13-2060    TCGA-23-1110    TCGA-23-1122    TCGA-23-1123 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-23-1124    TCGA-23-2077    TCGA-23-2078    TCGA-23-2079    TCGA-23-2081 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-0966    TCGA-24-0970    TCGA-24-0979    TCGA-24-0980    TCGA-24-0982 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1103    TCGA-24-1104    TCGA-24-1105    TCGA-24-1416    TCGA-24-1417 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1419    TCGA-24-1422    TCGA-24-1423    TCGA-24-1424    TCGA-24-1427 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1428    TCGA-24-1431    TCGA-24-1434    TCGA-24-1435    TCGA-24-1436 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1463    TCGA-24-1464    TCGA-24-1466    TCGA-24-1469    TCGA-24-1470 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1471    TCGA-24-1474    TCGA-24-1544    TCGA-24-1545    TCGA-24-1548 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1549    TCGA-24-1551    TCGA-24-1552    TCGA-24-1553    TCGA-24-1555 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1556    TCGA-24-1557    TCGA-24-1558    TCGA-24-1560    TCGA-24-1562 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1563    TCGA-24-1564    TCGA-24-1565    TCGA-24-1567    TCGA-24-1603 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1604    TCGA-24-1614    TCGA-24-1616    TCGA-24-2024    TCGA-24-2030 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-2038    TCGA-24-2254    TCGA-24-2260    TCGA-24-2261    TCGA-24-2262 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-2267    TCGA-24-2271    TCGA-24-2281    TCGA-24-2288    TCGA-24-2289 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-2290    TCGA-24-2293    TCGA-24-2298    TCGA-25-1313    TCGA-25-1315 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1316    TCGA-25-1319    TCGA-25-1320    TCGA-25-1321    TCGA-25-1322 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1326    TCGA-25-1328    TCGA-25-1329    TCGA-25-1623    TCGA-25-1625 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1626    TCGA-25-1627    TCGA-25-1628    TCGA-25-1630    TCGA-25-1631 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1632    TCGA-25-1633    TCGA-25-1635    TCGA-25-2042    TCGA-25-2391 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-2393    TCGA-25-2396    TCGA-25-2398    TCGA-25-2399    TCGA-25-2400 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-2401    TCGA-25-2404    TCGA-25-2408    TCGA-25-2409    TCGA-29-2427 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-30-1891    TCGA-31-1950    TCGA-36-1568    TCGA-36-1569    TCGA-36-1570 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-36-1571    TCGA-36-1575    TCGA-36-1576    TCGA-36-1577    TCGA-36-1578 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-36-1580    TCGA-59-2348    TCGA-59-2351    TCGA-59-2352    TCGA-59-2354 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-59-2363    TCGA-61-1736    TCGA-61-1919    TCGA-61-1995    TCGA-61-2000 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-61-2003    TCGA-61-2009    TCGA-61-2012    TCGA-61-2088    TCGA-61-2092 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-61-2094    TCGA-61-2095    TCGA-61-2101    TCGA-61-2102    TCGA-61-2104 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-61-2109    TCGA-61-2111    TCGA-61-2113 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
D2V9, multiclass
[1] "Remove cluster labels:" "SRC MUTATED"           
clus
  SRC MUTATED SRC WILD-TYPE 
            2           159 
   TCGA-04-1348    TCGA-04-1357    TCGA-04-1362    TCGA-04-1364    TCGA-04-1365 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-04-1514    TCGA-09-0366    TCGA-09-0369    TCGA-09-1662    TCGA-09-1666 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-09-1669    TCGA-09-2044    TCGA-09-2045    TCGA-09-2051    TCGA-09-2056 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-10-0928    TCGA-13-0730    TCGA-13-0800    TCGA-13-0890    TCGA-13-0893 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-0897    TCGA-13-0899    TCGA-13-0913    TCGA-13-0916    TCGA-13-0920 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-0924    TCGA-13-1403    TCGA-13-1405    TCGA-13-1410    TCGA-13-1481 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1497    TCGA-13-1498    TCGA-13-1505    TCGA-13-1506    TCGA-13-1507 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1512    TCGA-13-2060    TCGA-23-1023    TCGA-23-1026    TCGA-23-1027 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-23-1120    TCGA-23-1122    TCGA-23-1123    TCGA-23-2077    TCGA-23-2081 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-0975    TCGA-24-1103    TCGA-24-1413    TCGA-24-1416    TCGA-24-1417 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1418    TCGA-24-1419    TCGA-24-1423    TCGA-24-1424    TCGA-24-1427 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1428    TCGA-24-1436    TCGA-24-1469    TCGA-24-1474    TCGA-24-1544 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1548    TCGA-24-1549    TCGA-24-1551    TCGA-24-1552    TCGA-24-1553 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1555    TCGA-24-1556    TCGA-24-1557    TCGA-24-1558    TCGA-24-1560 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1562    TCGA-24-1563    TCGA-24-1564    TCGA-24-1567    TCGA-24-1603 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1604    TCGA-24-1616    TCGA-24-2019    TCGA-24-2024    TCGA-24-2035 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-2038    TCGA-24-2254    TCGA-24-2261    TCGA-24-2262    TCGA-24-2267 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-2271    TCGA-24-2281    TCGA-24-2288    TCGA-24-2290    TCGA-24-2298 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1313    TCGA-25-1315    TCGA-25-1316    TCGA-25-1317    TCGA-25-1319 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1321    TCGA-25-1322    TCGA-25-1324    TCGA-25-1326    TCGA-25-1328 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1329    TCGA-25-1623    TCGA-25-1625    TCGA-25-1627    TCGA-25-1630 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1631    TCGA-25-1632    TCGA-25-1633    TCGA-25-1634    TCGA-25-1635 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-2391    TCGA-25-2393    TCGA-25-2396    TCGA-25-2399    TCGA-25-2400 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-2404    TCGA-25-2409    TCGA-29-2427    TCGA-30-1862    TCGA-30-1891 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-31-1953    TCGA-36-1568    TCGA-36-1570    TCGA-36-1571    TCGA-36-1574 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-36-1575    TCGA-36-1577    TCGA-36-1578    TCGA-36-1580    TCGA-57-1582 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-57-1583    TCGA-57-1584    TCGA-57-1993    TCGA-59-2348    TCGA-59-2350 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-59-2351    TCGA-59-2352    TCGA-59-2355    TCGA-59-2363    TCGA-61-1728 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-61-1736    TCGA-61-1919    TCGA-61-1995    TCGA-61-1998    TCGA-61-2000 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-61-2008    TCGA-61-2009    TCGA-61-2012    TCGA-61-2016    TCGA-61-2088 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-61-2092    TCGA-61-2094    TCGA-61-2097    TCGA-61-2102    TCGA-61-2104 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-61-2109    TCGA-61-2110    TCGA-61-2111    TCGA-61-2113 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
D2V10, multiclass
[1] "Remove cluster labels:" "SRC MUTATED"           
clus
  SRC MUTATED SRC WILD-TYPE 
            2           159 
   TCGA-04-1348    TCGA-04-1357    TCGA-04-1362    TCGA-04-1364    TCGA-04-1365 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-04-1514    TCGA-09-0366    TCGA-09-0369    TCGA-09-1662    TCGA-09-1666 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-09-1669    TCGA-09-2044    TCGA-09-2045    TCGA-09-2051    TCGA-09-2056 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-10-0928    TCGA-13-0730    TCGA-13-0800    TCGA-13-0890    TCGA-13-0893 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-0897    TCGA-13-0899    TCGA-13-0913    TCGA-13-0916    TCGA-13-0920 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-0924    TCGA-13-1403    TCGA-13-1405    TCGA-13-1410    TCGA-13-1481 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1497    TCGA-13-1498    TCGA-13-1505    TCGA-13-1506    TCGA-13-1507 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-13-1512    TCGA-13-2060    TCGA-23-1023    TCGA-23-1026    TCGA-23-1027 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-23-1120    TCGA-23-1122    TCGA-23-1123    TCGA-23-2077    TCGA-23-2081 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-0975    TCGA-24-1103    TCGA-24-1413    TCGA-24-1416    TCGA-24-1417 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1418    TCGA-24-1419    TCGA-24-1423    TCGA-24-1424    TCGA-24-1427 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1428    TCGA-24-1436    TCGA-24-1469    TCGA-24-1474    TCGA-24-1544 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1548    TCGA-24-1549    TCGA-24-1551    TCGA-24-1552    TCGA-24-1553 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1555    TCGA-24-1556    TCGA-24-1557    TCGA-24-1558    TCGA-24-1560 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1562    TCGA-24-1563    TCGA-24-1564    TCGA-24-1567    TCGA-24-1603 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-1604    TCGA-24-1616    TCGA-24-2019    TCGA-24-2024    TCGA-24-2035 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-2038    TCGA-24-2254    TCGA-24-2261    TCGA-24-2262    TCGA-24-2267 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-24-2271    TCGA-24-2281    TCGA-24-2288    TCGA-24-2290    TCGA-24-2298 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1313    TCGA-25-1315    TCGA-25-1316    TCGA-25-1317    TCGA-25-1319 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1321    TCGA-25-1322    TCGA-25-1324    TCGA-25-1326    TCGA-25-1328 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1329    TCGA-25-1623    TCGA-25-1625    TCGA-25-1627    TCGA-25-1630 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-1631    TCGA-25-1632    TCGA-25-1633    TCGA-25-1634    TCGA-25-1635 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-2391    TCGA-25-2393    TCGA-25-2396    TCGA-25-2399    TCGA-25-2400 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-25-2404    TCGA-25-2409    TCGA-29-2427    TCGA-30-1862    TCGA-30-1891 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-31-1953    TCGA-36-1568    TCGA-36-1570    TCGA-36-1571    TCGA-36-1574 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-36-1575    TCGA-36-1577    TCGA-36-1578    TCGA-36-1580    TCGA-57-1582 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-57-1583    TCGA-57-1584    TCGA-57-1993    TCGA-59-2348    TCGA-59-2350 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-59-2351    TCGA-59-2352    TCGA-59-2355    TCGA-59-2363    TCGA-61-1728 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-61-1736    TCGA-61-1919    TCGA-61-1995    TCGA-61-1998    TCGA-61-2000 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-61-2008    TCGA-61-2009    TCGA-61-2012    TCGA-61-2016    TCGA-61-2088 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-61-2092    TCGA-61-2094    TCGA-61-2097    TCGA-61-2102    TCGA-61-2104 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
   TCGA-61-2109    TCGA-61-2110    TCGA-61-2111    TCGA-61-2113 
"SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" "SRC WILD-TYPE" 
D2V11, multiclass
        clus
vv       SRC MUTATED SRC WILD-TYPE
  CLUS_1           0            79
  CLUS_2           1           118
  CLUS_3           2            87
D2V12, multiclass
        clus
vv       SRC MUTATED SRC WILD-TYPE
  CLUS_1           0             4
  CLUS_2           1           180
  CLUS_3           2           100

Clustering(3) Variable = TBP MUTATION ANALYSIS
D3V1, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           2           117
  CLUS_2           1           111
  CLUS_3           1            84
D3V2, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           2           122
  CLUS_2           1           106
  CLUS_3           1            84
D3V3, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           2            90
  CLUS_2           1            95
  CLUS_3           1           127
D3V4, multiclass
D3V5, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           4           103
  CLUS_2           0           102
  CLUS_3           0           102
D3V6, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           0            88
  CLUS_2           4           103
  CLUS_3           0           121
D3V7, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           3            73
  CLUS_2           0            96
  CLUS_3           0            38
D3V8, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           0            30
  CLUS_2           0            45
  CLUS_3           1            51
  CLUS_4           2            81
D3V9, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           1            69
  CLUS_2           1            39
  CLUS_3           1            50
D3V10, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           2            66
  CLUS_2           1            65
  CLUS_3           0            27
D3V11, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           2            77
  CLUS_2           1           118
  CLUS_3           1            88
D3V12, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           0             4
  CLUS_2           3           178
  CLUS_3           1           101

Clustering(4) Variable = RB1 MUTATION ANALYSIS
D4V1, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           4           115
  CLUS_2           2           110
  CLUS_3           3            82
D4V2, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           4           120
  CLUS_2           5           102
  CLUS_3           0            85
D4V3, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           3            89
  CLUS_2           1            95
  CLUS_3           5           123
D4V4, multiclass
D4V5, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           3           104
  CLUS_2           2           100
  CLUS_3           4            98
D4V6, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           4            84
  CLUS_2           4           103
  CLUS_3           1           120
D4V7, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           3            73
  CLUS_2           3            93
  CLUS_3           2            36
D4V8, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           2            28
  CLUS_2           1            44
  CLUS_3           2            50
  CLUS_4           3            80
D4V9, multiclass
[1] "Remove cluster labels:" "RB1 MUTATED"           
clus
  RB1 MUTATED RB1 WILD-TYPE 
            2           159 
   TCGA-04-1348    TCGA-04-1357    TCGA-04-1362    TCGA-04-1364    TCGA-04-1365 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-04-1514    TCGA-09-0366    TCGA-09-0369    TCGA-09-1662    TCGA-09-1666 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-09-1669    TCGA-09-2044    TCGA-09-2045    TCGA-09-2051    TCGA-09-2056 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-10-0928    TCGA-13-0730    TCGA-13-0800    TCGA-13-0890    TCGA-13-0893 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-0897    TCGA-13-0899    TCGA-13-0913    TCGA-13-0916    TCGA-13-0920 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-0924    TCGA-13-1403    TCGA-13-1405    TCGA-13-1410    TCGA-13-1481 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-1497    TCGA-13-1498    TCGA-13-1505    TCGA-13-1506    TCGA-13-1507 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-1512    TCGA-13-2060    TCGA-23-1023    TCGA-23-1026    TCGA-23-1027 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-23-1120    TCGA-23-1122    TCGA-23-1123    TCGA-23-2077    TCGA-23-2081 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-0975    TCGA-24-1103    TCGA-24-1413    TCGA-24-1416    TCGA-24-1417 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-1418    TCGA-24-1419    TCGA-24-1423    TCGA-24-1424    TCGA-24-1427 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-1428    TCGA-24-1436    TCGA-24-1474    TCGA-24-1544    TCGA-24-1548 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-1549    TCGA-24-1551    TCGA-24-1552    TCGA-24-1553    TCGA-24-1555 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-1556    TCGA-24-1557    TCGA-24-1558    TCGA-24-1560    TCGA-24-1562 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-1563    TCGA-24-1564    TCGA-24-1567    TCGA-24-1603    TCGA-24-1604 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-1616    TCGA-24-2019    TCGA-24-2024    TCGA-24-2035    TCGA-24-2038 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-2254    TCGA-24-2261    TCGA-24-2262    TCGA-24-2267    TCGA-24-2271 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-2281    TCGA-24-2288    TCGA-24-2290    TCGA-24-2298    TCGA-25-1313 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-25-1315    TCGA-25-1316    TCGA-25-1317    TCGA-25-1318    TCGA-25-1319 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-25-1321    TCGA-25-1322    TCGA-25-1324    TCGA-25-1326    TCGA-25-1328 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-25-1329    TCGA-25-1623    TCGA-25-1625    TCGA-25-1627    TCGA-25-1630 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-25-1631    TCGA-25-1632    TCGA-25-1633    TCGA-25-1634    TCGA-25-2391 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-25-2392    TCGA-25-2393    TCGA-25-2396    TCGA-25-2399    TCGA-25-2400 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-25-2404    TCGA-25-2409    TCGA-29-2427    TCGA-30-1862    TCGA-30-1891 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-31-1953    TCGA-36-1568    TCGA-36-1570    TCGA-36-1571    TCGA-36-1574 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-36-1575    TCGA-36-1577    TCGA-36-1578    TCGA-36-1580    TCGA-57-1582 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-57-1583    TCGA-57-1584    TCGA-57-1993    TCGA-59-2348    TCGA-59-2350 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-59-2351    TCGA-59-2352    TCGA-59-2355    TCGA-59-2363    TCGA-61-1728 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-61-1736    TCGA-61-1919    TCGA-61-1995    TCGA-61-1998    TCGA-61-2000 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-61-2008    TCGA-61-2009    TCGA-61-2012    TCGA-61-2016    TCGA-61-2088 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-61-2092    TCGA-61-2094    TCGA-61-2097    TCGA-61-2102    TCGA-61-2104 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-61-2109    TCGA-61-2110    TCGA-61-2111    TCGA-61-2113 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
D4V10, multiclass
[1] "Remove cluster labels:" "RB1 MUTATED"           
clus
  RB1 MUTATED RB1 WILD-TYPE 
            2           159 
   TCGA-04-1348    TCGA-04-1357    TCGA-04-1362    TCGA-04-1364    TCGA-04-1365 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-04-1514    TCGA-09-0366    TCGA-09-0369    TCGA-09-1662    TCGA-09-1666 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-09-1669    TCGA-09-2044    TCGA-09-2045    TCGA-09-2051    TCGA-09-2056 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-10-0928    TCGA-13-0730    TCGA-13-0800    TCGA-13-0890    TCGA-13-0893 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-0897    TCGA-13-0899    TCGA-13-0913    TCGA-13-0916    TCGA-13-0920 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-0924    TCGA-13-1403    TCGA-13-1405    TCGA-13-1410    TCGA-13-1481 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-1497    TCGA-13-1498    TCGA-13-1505    TCGA-13-1506    TCGA-13-1507 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-13-1512    TCGA-13-2060    TCGA-23-1023    TCGA-23-1026    TCGA-23-1027 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-23-1120    TCGA-23-1122    TCGA-23-1123    TCGA-23-2077    TCGA-23-2081 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-0975    TCGA-24-1103    TCGA-24-1413    TCGA-24-1416    TCGA-24-1417 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-1418    TCGA-24-1419    TCGA-24-1423    TCGA-24-1424    TCGA-24-1427 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-1428    TCGA-24-1436    TCGA-24-1474    TCGA-24-1544    TCGA-24-1548 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-1549    TCGA-24-1551    TCGA-24-1552    TCGA-24-1553    TCGA-24-1555 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-1556    TCGA-24-1557    TCGA-24-1558    TCGA-24-1560    TCGA-24-1562 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-1563    TCGA-24-1564    TCGA-24-1567    TCGA-24-1603    TCGA-24-1604 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-1616    TCGA-24-2019    TCGA-24-2024    TCGA-24-2035    TCGA-24-2038 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-2254    TCGA-24-2261    TCGA-24-2262    TCGA-24-2267    TCGA-24-2271 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-24-2281    TCGA-24-2288    TCGA-24-2290    TCGA-24-2298    TCGA-25-1313 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-25-1315    TCGA-25-1316    TCGA-25-1317    TCGA-25-1318    TCGA-25-1319 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-25-1321    TCGA-25-1322    TCGA-25-1324    TCGA-25-1326    TCGA-25-1328 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-25-1329    TCGA-25-1623    TCGA-25-1625    TCGA-25-1627    TCGA-25-1630 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-25-1631    TCGA-25-1632    TCGA-25-1633    TCGA-25-1634    TCGA-25-2391 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-25-2392    TCGA-25-2393    TCGA-25-2396    TCGA-25-2399    TCGA-25-2400 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-25-2404    TCGA-25-2409    TCGA-29-2427    TCGA-30-1862    TCGA-30-1891 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-31-1953    TCGA-36-1568    TCGA-36-1570    TCGA-36-1571    TCGA-36-1574 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-36-1575    TCGA-36-1577    TCGA-36-1578    TCGA-36-1580    TCGA-57-1582 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-57-1583    TCGA-57-1584    TCGA-57-1993    TCGA-59-2348    TCGA-59-2350 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-59-2351    TCGA-59-2352    TCGA-59-2355    TCGA-59-2363    TCGA-61-1728 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-61-1736    TCGA-61-1919    TCGA-61-1995    TCGA-61-1998    TCGA-61-2000 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-61-2008    TCGA-61-2009    TCGA-61-2012    TCGA-61-2016    TCGA-61-2088 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-61-2092    TCGA-61-2094    TCGA-61-2097    TCGA-61-2102    TCGA-61-2104 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-61-2109    TCGA-61-2110    TCGA-61-2111    TCGA-61-2113 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
D4V11, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           1            78
  CLUS_2           6           113
  CLUS_3           2            87
D4V12, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           0             4
  CLUS_2           7           174
  CLUS_3           2           100

Clustering(5) Variable = GABRA6 MUTATION ANALYSIS
D5V1, multiclass
        clus
vv       GABRA6 MUTATED GABRA6 WILD-TYPE
  CLUS_1              3              116
  CLUS_2              2              110
  CLUS_3              1               84
D5V2, multiclass
        clus
vv       GABRA6 MUTATED GABRA6 WILD-TYPE
  CLUS_1              2              122
  CLUS_2              3              104
  CLUS_3              1               84
D5V3, multiclass
        clus
vv       GABRA6 MUTATED GABRA6 WILD-TYPE
  CLUS_1              2               90
  CLUS_2              2               94
  CLUS_3              2              126
D5V4, multiclass
D5V5, multiclass
        clus
vv       GABRA6 MUTATED GABRA6 WILD-TYPE
  CLUS_1              2              105
  CLUS_2              3               99
  CLUS_3              0              102
D5V6, multiclass
        clus
vv       GABRA6 MUTATED GABRA6 WILD-TYPE
  CLUS_1              0               88
  CLUS_2              4              103
  CLUS_3              2              119
D5V7, multiclass
        clus
vv       GABRA6 MUTATED GABRA6 WILD-TYPE
  CLUS_1              3               73
  CLUS_2              1               95
  CLUS_3              0               38
D5V8, multiclass
        clus
vv       GABRA6 MUTATED GABRA6 WILD-TYPE
  CLUS_1              0               30
  CLUS_2              1               44
  CLUS_3              1               51
  CLUS_4              2               81
D5V9, multiclass
        clus
vv       GABRA6 MUTATED GABRA6 WILD-TYPE
  CLUS_1              2               68
  CLUS_2              0               40
  CLUS_3              1               50
D5V10, multiclass
        clus
vv       GABRA6 MUTATED GABRA6 WILD-TYPE
  CLUS_1              1               67
  CLUS_2              2               64
  CLUS_3              0               27
D5V11, multiclass
        clus
vv       GABRA6 MUTATED GABRA6 WILD-TYPE
  CLUS_1              2               77
  CLUS_2              2              117
  CLUS_3              2               87
D5V12, multiclass
        clus
vv       GABRA6 MUTATED GABRA6 WILD-TYPE
  CLUS_1              0                4
  CLUS_2              4              177
  CLUS_3              2              100

Clustering(6) Variable = BRCA1 MUTATION ANALYSIS
D6V1, multiclass
        clus
vv       BRCA1 MUTATED BRCA1 WILD-TYPE
  CLUS_1             4             115
  CLUS_2             7             105
  CLUS_3             1              84
D6V2, multiclass
        clus
vv       BRCA1 MUTATED BRCA1 WILD-TYPE
  CLUS_1             5             119
  CLUS_2             3             104
  CLUS_3             4              81
D6V3, multiclass
        clus
vv       BRCA1 MUTATED BRCA1 WILD-TYPE
  CLUS_1             1              91
  CLUS_2             4              92
  CLUS_3             7             121
D6V4, multiclass
D6V5, multiclass
        clus
vv       BRCA1 MUTATED BRCA1 WILD-TYPE
  CLUS_1             5             102
  CLUS_2             5              97
  CLUS_3             2             100
D6V6, multiclass
        clus
vv       BRCA1 MUTATED BRCA1 WILD-TYPE
  CLUS_1             1              87
  CLUS_2             6             101
  CLUS_3             5             116
D6V7, multiclass
        clus
vv       BRCA1 MUTATED BRCA1 WILD-TYPE
  CLUS_1             3              73
  CLUS_2             3              93
  CLUS_3             3              35
D6V8, multiclass
        clus
vv       BRCA1 MUTATED BRCA1 WILD-TYPE
  CLUS_1             2              28
  CLUS_2             2              43
  CLUS_3             4              48
  CLUS_4             1              82
D6V9, multiclass
        clus
vv       BRCA1 MUTATED BRCA1 WILD-TYPE
  CLUS_1             4              66
  CLUS_2             2              38
  CLUS_3             2              49
D6V10, multiclass
        clus
vv       BRCA1 MUTATED BRCA1 WILD-TYPE
  CLUS_1             3              65
  CLUS_2             4              62
  CLUS_3             1              26
D6V11, multiclass
        clus
vv       BRCA1 MUTATED BRCA1 WILD-TYPE
  CLUS_1             3              76
  CLUS_2             3             116
  CLUS_3             4              85
D6V12, multiclass
        clus
vv       BRCA1 MUTATED BRCA1 WILD-TYPE
  CLUS_1             0               4
  CLUS_2             6             175
  CLUS_3             4              98

Clustering(7) Variable = CSMD3 MUTATION ANALYSIS
D7V1, multiclass
        clus
vv       CSMD3 MUTATED CSMD3 WILD-TYPE
  CLUS_1             4             115
  CLUS_2             9             103
  CLUS_3             5              80
D7V2, multiclass
        clus
vv       CSMD3 MUTATED CSMD3 WILD-TYPE
  CLUS_1             9             115
  CLUS_2             5             102
  CLUS_3             4              81
D7V3, multiclass
        clus
vv       CSMD3 MUTATED CSMD3 WILD-TYPE
  CLUS_1             6              86
  CLUS_2             8              88
  CLUS_3             4             124
D7V4, multiclass
D7V5, multiclass
        clus
vv       CSMD3 MUTATED CSMD3 WILD-TYPE
  CLUS_1             4             103
  CLUS_2             7              95
  CLUS_3             7              95
D7V6, multiclass
        clus
vv       CSMD3 MUTATED CSMD3 WILD-TYPE
  CLUS_1             1              87
  CLUS_2             9              98
  CLUS_3             8             113
D7V7, multiclass
        clus
vv       CSMD3 MUTATED CSMD3 WILD-TYPE
  CLUS_1             2              74
  CLUS_2             9              87
  CLUS_3             0              38
D7V8, multiclass
        clus
vv       CSMD3 MUTATED CSMD3 WILD-TYPE
  CLUS_1             1              29
  CLUS_2             4              41
  CLUS_3             3              49
  CLUS_4             3              80
D7V9, multiclass
        clus
vv       CSMD3 MUTATED CSMD3 WILD-TYPE
  CLUS_1             6              64
  CLUS_2             2              38
  CLUS_3             3              48
D7V10, multiclass
        clus
vv       CSMD3 MUTATED CSMD3 WILD-TYPE
  CLUS_1             4              64
  CLUS_2             6              60
  CLUS_3             1              26
D7V11, multiclass
        clus
vv       CSMD3 MUTATED CSMD3 WILD-TYPE
  CLUS_1             7              72
  CLUS_2             4             115
  CLUS_3             7              82
D7V12, multiclass
        clus
vv       CSMD3 MUTATED CSMD3 WILD-TYPE
  CLUS_1             0               4
  CLUS_2            11             170
  CLUS_3             7              95

Clustering(8) Variable = NF1 MUTATION ANALYSIS
D8V1, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           4           115
  CLUS_2           4           108
  CLUS_3           6            79
D8V2, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           8           116
  CLUS_2           3           104
  CLUS_3           3            82
D8V3, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           3            89
  CLUS_2           5            91
  CLUS_3           6           122
D8V4, multiclass
D8V5, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           6           101
  CLUS_2           5            97
  CLUS_3           3            99
D8V6, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           1            87
  CLUS_2           6           101
  CLUS_3           7           114
D8V7, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           4            72
  CLUS_2           1            95
  CLUS_3           3            35
D8V8, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           1            29
  CLUS_2           0            45
  CLUS_3           0            52
  CLUS_4           7            76
D8V9, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           4            66
  CLUS_2           0            40
  CLUS_3           2            49
D8V10, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           1            67
  CLUS_2           5            61
  CLUS_3           0            27
D8V11, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           4            75
  CLUS_2           7           112
  CLUS_3           3            86
D8V12, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           0             4
  CLUS_2           9           172
  CLUS_3           5            97
                     V1                      V2                      V3 
            "MRNA_CNMF"    "MRNA_CHIERARCHICAL"              "MIR_CNMF" 
                     V4                      V5                      V6 
    "MIR_CHIERARCHICAL"               "CN_CNMF"      "METHLYATION_CNMF" 
                     V7                      V8                      V9 
            "RPPA_CNMF"    "RPPA_CHIERARCHICAL"          "MRNASEQ_CNMF" 
                    V10                     V11                     V12 
"MRNASEQ_CHIERARCHICAL"           "MIRSEQ_CNMF"  "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
