
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/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/Correlate_Genomic_Events.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-tTRUE", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/OV-TP/6068732/transformed.cor.cli.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/OV-TP/6185328/OV-TP.transferedmergedcluster.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ALL", "-oT=OV-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "terrence_modification_tag"
[1] TRUE
[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" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/OV-TP/6185328/OV-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/OV-TP/6068732/transformed.cor.cli.txt"

nPatients in clinical file=586, in cluster file=316, common to both=316
[1] "Reduce the number of clustering variables from 4 to 3."
[1]   3 316
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           276             40 
  TP53 MUTATED TP53 WILD-TYPE 
           276             40 
[1] "TBP MUTATION ANALYSIS"
[1] 3
  TBP MUTATED TBP WILD-TYPE 
            4           312 
  TBP MUTATED TBP WILD-TYPE 
            4           312 
[1] "SRC MUTATION ANALYSIS"
[1] 3
  SRC MUTATED SRC WILD-TYPE 
            4           312 
  SRC MUTATED SRC WILD-TYPE 
            4           312 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "MIR_CNMF"                    "MIR_CHIERARCHICAL"          
 [5] "CN_CNMF"                     "METHLYATION_CNMF"           
 [7] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [9] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
[11] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[13] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 14 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.
Variable 13:'MIRSEQ_MATURE_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "MIR_CNMF"                    "MIR_CHIERARCHICAL"          
 [5] "CN_CNMF"                     "METHLYATION_CNMF"           
 [7] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [9] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
[11] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[13] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 316 columns, 0 survival variables, and 14 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
MIRSEQ_MATURE_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED      105    101     70
  TP53 WILD-TYPE     14     14     12
D1V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1          105             14
  CLUS_2          101             14
  CLUS_3           70             12
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       71    106     99
  TP53 WILD-TYPE     14     12     14
D1V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           71             14
  CLUS_2          106             12
  CLUS_3           99             14
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       83     81    112
  TP53 WILD-TYPE      9     15     16
D1V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           83              9
  CLUS_2           81             15
  CLUS_3          112             16
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  TP53 MUTATED       29     67     68     50     24     38
  TP53 WILD-TYPE      3      9      7      7      3     11
D1V4, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       97     93     82
  TP53 WILD-TYPE     15     10     14
D1V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           97             15
  CLUS_2           93             10
  CLUS_3           82             14
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       80     90    106
  TP53 WILD-TYPE     10     15     15
D1V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           80             10
  CLUS_2           90             15
  CLUS_3          106             15
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       65     88     33
  TP53 WILD-TYPE     11      8      5
D1V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           65             11
  CLUS_2           88              8
  CLUS_3           33              5
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED       28     41     48     69
  TP53 WILD-TYPE      2      4      4     14
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
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       60     36     46
  TP53 WILD-TYPE     10      4      5
D1V9, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           60             10
  CLUS_2           36              4
  CLUS_3           46              5
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       61     57     24
  TP53 WILD-TYPE      7      9      3
D1V10, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           61              7
  CLUS_2           57              9
  CLUS_3           24              3
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       65    106     79
  TP53 WILD-TYPE     14     13     10
D1V11, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           65             14
  CLUS_2          106             13
  CLUS_3           79             10
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        3    154     93
  TP53 WILD-TYPE      1     27      9
D1V12, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            3              1
  CLUS_2          154             27
  CLUS_3           93              9
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       51    111     88
  TP53 WILD-TYPE     13     13     11
D1V13, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           51             13
  CLUS_2          111             13
  CLUS_3           88             11
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       89      5    156
  TP53 WILD-TYPE     11      0     26
D1V14, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           89             11
  CLUS_2            5              0
  CLUS_3          156             26

Clustering(2) Variable = TBP MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  TBP MUTATED        2      1      1
  TBP WILD-TYPE    117    114     81
D2V1, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           2           117
  CLUS_2           1           114
  CLUS_3           1            81
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  TBP MUTATED        1      1      2
  TBP WILD-TYPE     84    117    111
D2V2, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           1            84
  CLUS_2           1           117
  CLUS_3           2           111
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  TBP MUTATED        2      1      1
  TBP WILD-TYPE     90     95    127
D2V3, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           2            90
  CLUS_2           1            95
  CLUS_3           1           127
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  TBP MUTATED        0      1      1      2      0      0
  TBP WILD-TYPE     32     75     74     55     27     49
D2V4, multiclass
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  TBP MUTATED        4      0      0
  TBP WILD-TYPE    108    103     96
D2V5, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           4           108
  CLUS_2           0           103
  CLUS_3           0            96
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  TBP MUTATED        0      4      0
  TBP WILD-TYPE     90    101    121
D2V6, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           0            90
  CLUS_2           4           101
  CLUS_3           0           121
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  TBP MUTATED        3      0      0
  TBP WILD-TYPE     73     96     38
D2V7, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           3            73
  CLUS_2           0            96
  CLUS_3           0            38
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TBP MUTATED        0      0      1      2
  TBP WILD-TYPE     30     45     51     81
D2V8, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           0            30
  CLUS_2           0            45
  CLUS_3           1            51
  CLUS_4           2            81
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  TBP MUTATED        1      1      1
  TBP WILD-TYPE     69     39     50
D2V9, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           1            69
  CLUS_2           1            39
  CLUS_3           1            50
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  TBP MUTATED        2      1      0
  TBP WILD-TYPE     66     65     27
D2V10, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           2            66
  CLUS_2           1            65
  CLUS_3           0            27
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  TBP MUTATED        2      1      1
  TBP WILD-TYPE     77    118     88
D2V11, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           2            77
  CLUS_2           1           118
  CLUS_3           1            88
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  TBP MUTATED        0      3      1
  TBP WILD-TYPE      4    178    101
D2V12, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           0             4
  CLUS_2           3           178
  CLUS_3           1           101
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  TBP MUTATED        1      2      1
  TBP WILD-TYPE     63    122     98
D2V13, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           1            63
  CLUS_2           2           122
  CLUS_3           1            98
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  TBP MUTATED        1      0      3
  TBP WILD-TYPE     99      5    179
D2V14, multiclass
        clus
vv       TBP MUTATED TBP WILD-TYPE
  CLUS_1           1            99
  CLUS_2           0             5
  CLUS_3           3           179

Clustering(3) Variable = SRC MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  SRC MUTATED        1      2      1
  SRC WILD-TYPE    118    113     81
D3V1, multiclass
        clus
vv       SRC MUTATED SRC WILD-TYPE
  CLUS_1           1           118
  CLUS_2           2           113
  CLUS_3           1            81
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  SRC MUTATED        1      1      2
  SRC WILD-TYPE     84    117    111
D3V2, multiclass
        clus
vv       SRC MUTATED SRC WILD-TYPE
  CLUS_1           1            84
  CLUS_2           1           117
  CLUS_3           2           111
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  SRC MUTATED        0      2      2
  SRC WILD-TYPE     92     94    126
D3V3, multiclass
        clus
vv       SRC MUTATED SRC WILD-TYPE
  CLUS_1           0            92
  CLUS_2           2            94
  CLUS_3           2           126
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  SRC MUTATED        1      3      0      0      0      0
  SRC WILD-TYPE     31     73     75     57     27     49
D3V4, multiclass
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  SRC MUTATED        0      3      1
  SRC WILD-TYPE    112    100     95
D3V5, multiclass
        clus
vv       SRC MUTATED SRC WILD-TYPE
  CLUS_1           0           112
  CLUS_2           3           100
  CLUS_3           1            95
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  SRC MUTATED        0      1      3
  SRC WILD-TYPE     90    104    118
D3V6, multiclass
        clus
vv       SRC MUTATED SRC WILD-TYPE
  CLUS_1           0            90
  CLUS_2           1           104
  CLUS_3           3           118
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  SRC MUTATED        1      1      0
  SRC WILD-TYPE     75     95     38
D3V7, 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" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SRC MUTATED        0      0      1      1
  SRC WILD-TYPE     30     45     51     82
D3V8, 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" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  SRC MUTATED        1      1      0
  SRC WILD-TYPE     69     39     51
D3V9, 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" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  SRC MUTATED        0      0      2
  SRC WILD-TYPE     68     66     25
D3V10, 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" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  SRC MUTATED        0      1      2
  SRC WILD-TYPE     79    118     87
D3V11, multiclass
        clus
vv       SRC MUTATED SRC WILD-TYPE
  CLUS_1           0            79
  CLUS_2           1           118
  CLUS_3           2            87
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  SRC MUTATED        0      1      2
  SRC WILD-TYPE      4    180    100
D3V12, multiclass
        clus
vv       SRC MUTATED SRC WILD-TYPE
  CLUS_1           0             4
  CLUS_2           1           180
  CLUS_3           2           100
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  SRC MUTATED        0      1      2
  SRC WILD-TYPE     64    123     97
D3V13, multiclass
        clus
vv       SRC MUTATED SRC WILD-TYPE
  CLUS_1           0            64
  CLUS_2           1           123
  CLUS_3           2            97
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  SRC MUTATED        2      0      1
  SRC WILD-TYPE     98      5    181
D3V14, multiclass
        clus
vv       SRC MUTATED SRC WILD-TYPE
  CLUS_1           2            98
  CLUS_2           0             5
  CLUS_3           1           181
> q(save="no")
