
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/423621/UCEC-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/UCEC-TP/3538590/UCEC-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ONLYSIG", "-oT=UCEC-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=UCEC-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=500, in cluster file=248, common to both=248
[1]  36 248
[1] "PPP2R1A MUTATION ANALYSIS"
[1] 3
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
               27               221 
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
               27               221 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
             132              116 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
             132              116 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              74              174 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              74              174 
[1] "PIK3R1 MUTATION ANALYSIS"
[1] 3
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              83              165 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              83              165 
[1] "PRKAR1B MUTATION ANALYSIS"
[1] 3
  PRKAR1B MUTATED PRKAR1B WILD-TYPE 
                4               244 
  PRKAR1B MUTATED PRKAR1B WILD-TYPE 
                4               244 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
           161             87 
  PTEN MUTATED PTEN WILD-TYPE 
           161             87 
[1] "RPL22 MUTATION ANALYSIS"
[1] 3
  RPL22 MUTATED RPL22 WILD-TYPE 
             31             217 
  RPL22 MUTATED RPL22 WILD-TYPE 
             31             217 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            53            195 
  KRAS MUTATED KRAS WILD-TYPE 
            53            195 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            69            179 
  TP53 MUTATED TP53 WILD-TYPE 
            69            179 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             39             209 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             39             209 
[1] "CTCF MUTATION ANALYSIS"
[1] 3
  CTCF MUTATED CTCF WILD-TYPE 
            45            203 
  CTCF MUTATED CTCF WILD-TYPE 
            45            203 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              83              165 
  ARID1A MUTATED ARID1A WILD-TYPE 
              83              165 
[1] "SPOP MUTATION ANALYSIS"
[1] 3
  SPOP MUTATED SPOP WILD-TYPE 
            21            227 
  SPOP MUTATED SPOP WILD-TYPE 
            21            227 
[1] "ARID5B MUTATION ANALYSIS"
[1] 3
  ARID5B MUTATED ARID5B WILD-TYPE 
              29              219 
  ARID5B MUTATED ARID5B WILD-TYPE 
              29              219 
[1] "FGFR2 MUTATION ANALYSIS"
[1] 3
  FGFR2 MUTATED FGFR2 WILD-TYPE 
             31             217 
  FGFR2 MUTATED FGFR2 WILD-TYPE 
             31             217 
[1] "CCND1 MUTATION ANALYSIS"
[1] 3
  CCND1 MUTATED CCND1 WILD-TYPE 
             15             233 
  CCND1 MUTATED CCND1 WILD-TYPE 
             15             233 
[1] "SMTNL2 MUTATION ANALYSIS"
[1] 3
  SMTNL2 MUTATED SMTNL2 WILD-TYPE 
               9              239 
  SMTNL2 MUTATED SMTNL2 WILD-TYPE 
               9              239 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              15              233 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              15              233 
[1] "CHD4 MUTATION ANALYSIS"
[1] 3
  CHD4 MUTATED CHD4 WILD-TYPE 
            35            213 
  CHD4 MUTATED CHD4 WILD-TYPE 
            35            213 
[1] "RBMX MUTATION ANALYSIS"
[1] 3
  RBMX MUTATED RBMX WILD-TYPE 
            13            235 
  RBMX MUTATED RBMX WILD-TYPE 
            13            235 
[1] "FAM9A MUTATION ANALYSIS"
[1] 3
  FAM9A MUTATED FAM9A WILD-TYPE 
             14             234 
  FAM9A MUTATED FAM9A WILD-TYPE 
             14             234 
[1] "HPD MUTATION ANALYSIS"
[1] 3
  HPD MUTATED HPD WILD-TYPE 
            7           241 
  HPD MUTATED HPD WILD-TYPE 
            7           241 
[1] "MORC4 MUTATION ANALYSIS"
[1] 3
  MORC4 MUTATED MORC4 WILD-TYPE 
             20             228 
  MORC4 MUTATED MORC4 WILD-TYPE 
             20             228 
[1] "CASP8 MUTATION ANALYSIS"
[1] 3
  CASP8 MUTATED CASP8 WILD-TYPE 
             17             231 
  CASP8 MUTATED CASP8 WILD-TYPE 
             17             231 
[1] "ABI1 MUTATION ANALYSIS"
[1] 3
  ABI1 MUTATED ABI1 WILD-TYPE 
             4            244 
  ABI1 MUTATED ABI1 WILD-TYPE 
             4            244 
[1] "FOXA2 MUTATION ANALYSIS"
[1] 3
  FOXA2 MUTATED FOXA2 WILD-TYPE 
             12             236 
  FOXA2 MUTATED FOXA2 WILD-TYPE 
             12             236 
[1] "BRS3 MUTATION ANALYSIS"
[1] 3
  BRS3 MUTATED BRS3 WILD-TYPE 
            15            233 
  BRS3 MUTATED BRS3 WILD-TYPE 
            15            233 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
             9            239 
  NRAS MUTATED NRAS WILD-TYPE 
             9            239 
[1] "DNER MUTATION ANALYSIS"
[1] 3
  DNER MUTATED DNER WILD-TYPE 
            18            230 
  DNER MUTATED DNER WILD-TYPE 
            18            230 
[1] "TIAL1 MUTATION ANALYSIS"
[1] 3
  TIAL1 MUTATED TIAL1 WILD-TYPE 
             11             237 
  TIAL1 MUTATED TIAL1 WILD-TYPE 
             11             237 
[1] "RPL14 MUTATION ANALYSIS"
[1] 3
  RPL14 MUTATED RPL14 WILD-TYPE 
              7             241 
  RPL14 MUTATED RPL14 WILD-TYPE 
              7             241 
[1] "SGK1 MUTATION ANALYSIS"
[1] 3
  SGK1 MUTATED SGK1 WILD-TYPE 
            15            233 
  SGK1 MUTATED SGK1 WILD-TYPE 
            15            233 
[1] "SLC48A1 MUTATION ANALYSIS"
[1] 3
  SLC48A1 MUTATED SLC48A1 WILD-TYPE 
                5               243 
  SLC48A1 MUTATED SLC48A1 WILD-TYPE 
                5               243 
[1] "BCOR MUTATION ANALYSIS"
[1] 3
  BCOR MUTATED BCOR WILD-TYPE 
            30            218 
  BCOR MUTATED BCOR WILD-TYPE 
            30            218 
[1] "ZNF263 MUTATION ANALYSIS"
[1] 3
  ZNF263 MUTATED ZNF263 WILD-TYPE 
               8              240 
  ZNF263 MUTATED ZNF263 WILD-TYPE 
               8              240 
[1] "RNF43 MUTATION ANALYSIS"
[1] 3
  RNF43 MUTATED RNF43 WILD-TYPE 
             12             236 
  RNF43 MUTATED RNF43 WILD-TYPE 
             12             236 
[1] "data2feature, selection=ALL"
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "CN_CNMF"                     "METHLYATION_CNMF"           
 [5] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [7] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [9] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[11] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 12 rows and 248 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'CN_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'RPPA_CNMF':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'RPPA_CHIERARCHICAL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MIRSEQ_MATURE_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "CN_CNMF"                     "METHLYATION_CNMF"           
 [5] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [7] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [9] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[11] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 248 columns, 0 survival variables, and 12 non-survival variables.
MRNA_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
CN_CNMF, nv=5, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=6, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=2, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=4, 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 = PPP2R1A MUTATION ANALYSIS
D1V1, multiclass
        clus
vv       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  CLUS_1               3                 9
  CLUS_2               5                13
  CLUS_3               0                11
  CLUS_4               0                10
D1V2, multiclass
        clus
vv       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  CLUS_1               4                13
  CLUS_2               0                18
  CLUS_3               4                12
D1V3, multiclass
D1V4, multiclass
        clus
vv       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  CLUS_1               9                33
  CLUS_2               1                40
  CLUS_3               5                46
D1V5, multiclass
D1V6, binary
                   cls
clus                  0   1
  PPP2R1A MUTATED     9   9
  PPP2R1A WILD-TYPE 106  62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R1A MUTATED      9    9
  PPP2R1A WILD-TYPE  106   62
        clus
vv       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  CLUS_1               9               106
  CLUS_2               9                62
D1V7, multiclass
        clus
vv       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  CLUS_1              17                62
  CLUS_2               4                76
  CLUS_3               6                76
D1V8, multiclass
        clus
vv       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  CLUS_1               2                49
  CLUS_2               3                67
  CLUS_3               5                37
  CLUS_4              17                61
D1V9, multiclass
        clus
vv       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  CLUS_1              14                57
  CLUS_2               5                86
  CLUS_3               6                72
D1V10, multiclass
        clus
vv       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  CLUS_1               7               116
  CLUS_2               3                38
  CLUS_3               0                13
  CLUS_4              15                48
D1V11, multiclass
        clus
vv       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  CLUS_1               7                30
  CLUS_2               4                50
  CLUS_3               4                20
D1V12, multiclass
        clus
vv       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  CLUS_1               3                52
  CLUS_2              11                40
  CLUS_3               1                 8

Clustering(2) Variable = PIK3CA MUTATION ANALYSIS
D2V1, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              7                5
  CLUS_2              8               10
  CLUS_3              6                5
  CLUS_4              6                4
D2V2, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             12                5
  CLUS_2              8               10
  CLUS_3              7                9
D2V3, multiclass
D2V4, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             22               20
  CLUS_2             23               18
  CLUS_3             24               27
D2V5, multiclass
D2V6, binary
                  cls
clus                0  1
  PIK3CA MUTATED   64 34
  PIK3CA WILD-TYPE 51 37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     64   34
  PIK3CA WILD-TYPE   51   37
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             64               51
  CLUS_2             34               37
D2V7, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             40               39
  CLUS_2             45               35
  CLUS_3             43               39
D2V8, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             28               23
  CLUS_2             40               30
  CLUS_3             22               20
  CLUS_4             38               40
D2V9, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             32               39
  CLUS_2             54               37
  CLUS_3             42               36
D2V10, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             69               54
  CLUS_2             24               17
  CLUS_3              5                8
  CLUS_4             30               33
D2V11, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             15               22
  CLUS_2             31               23
  CLUS_3             13               11
D2V12, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             32               23
  CLUS_2             22               29
  CLUS_3              5                4

Clustering(3) Variable = CTNNB1 MUTATION ANALYSIS
D3V1, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              0               12
  CLUS_2              3               15
  CLUS_3              4                7
  CLUS_4             10                0
D3V2, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              3               14
  CLUS_2             12                6
  CLUS_3              2               14
D3V3, multiclass
D3V4, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              4               38
  CLUS_2             14               27
  CLUS_3             19               32
D3V5, multiclass
D3V6, binary
                  cls
clus                0  1
  CTNNB1 MUTATED   45 19
  CTNNB1 WILD-TYPE 70 52
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     45   19
  CTNNB1 WILD-TYPE   70   52
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1             45               70
  CLUS_2             19               52
D3V7, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              6               73
  CLUS_2             14               66
  CLUS_3             52               30
D3V8, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1             49                2
  CLUS_2              8               62
  CLUS_3              6               36
  CLUS_4              9               69
D3V9, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              4               67
  CLUS_2             19               72
  CLUS_3             48               30
D3V10, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1             44               79
  CLUS_2             19               22
  CLUS_3              5                8
  CLUS_4              3               60
D3V11, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              4               33
  CLUS_2             15               39
  CLUS_3              8               16
D3V12, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1             16               39
  CLUS_2              9               42
  CLUS_3              2                7

Clustering(4) Variable = PIK3R1 MUTATION ANALYSIS
D4V1, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              5                7
  CLUS_2              2               16
  CLUS_3              6                5
  CLUS_4              3                7
D4V2, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              8                9
  CLUS_2              7               11
  CLUS_3              1               15
D4V3, multiclass
D4V4, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              5               37
  CLUS_2             12               29
  CLUS_3             28               23
D4V5, multiclass
D4V6, binary
                  cls
clus                0  1
  PIK3R1 MUTATED   44 26
  PIK3R1 WILD-TYPE 71 45
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED     44   26
  PIK3R1 WILD-TYPE   71   45
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1             44               71
  CLUS_2             26               45
D4V7, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1             10               69
  CLUS_2             33               47
  CLUS_3             35               47
D4V8, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1             21               30
  CLUS_2             28               42
  CLUS_3             17               25
  CLUS_4             12               66
D4V9, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1             15               56
  CLUS_2             36               55
  CLUS_3             30               48
D4V10, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1             49               74
  CLUS_2             14               27
  CLUS_3              6                7
  CLUS_4             12               51
D4V11, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              8               29
  CLUS_2             22               32
  CLUS_3              7               17
D4V12, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1             23               32
  CLUS_2             10               41
  CLUS_3              4                5

Clustering(5) Variable = PRKAR1B MUTATION ANALYSIS
D5V1, multiclass
D5V2, multiclass
D5V3, multiclass
D5V4, multiclass
        clus
vv       PRKAR1B MUTATED PRKAR1B WILD-TYPE
  CLUS_1               2                40
  CLUS_2               0                41
  CLUS_3               1                50
D5V5, multiclass
D5V6, binary
                   cls
clus                  0   1
  PRKAR1B MUTATED     3   1
  PRKAR1B WILD-TYPE 112  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRKAR1B MUTATED      3    1
  PRKAR1B WILD-TYPE  112   70
        clus
vv       PRKAR1B MUTATED PRKAR1B WILD-TYPE
  CLUS_1               3               112
  CLUS_2               1                70
D5V7, multiclass
        clus
vv       PRKAR1B MUTATED PRKAR1B WILD-TYPE
  CLUS_1               2                77
  CLUS_2               1                79
  CLUS_3               1                81
D5V8, multiclass
        clus
vv       PRKAR1B MUTATED PRKAR1B WILD-TYPE
  CLUS_1               0                51
  CLUS_2               1                69
  CLUS_3               2                40
  CLUS_4               1                77
D5V9, multiclass
        clus
vv       PRKAR1B MUTATED PRKAR1B WILD-TYPE
  CLUS_1               1                70
  CLUS_2               1                90
  CLUS_3               2                76
D5V10, multiclass
        clus
vv       PRKAR1B MUTATED PRKAR1B WILD-TYPE
  CLUS_1               1               122
  CLUS_2               1                40
  CLUS_3               1                12
  CLUS_4               1                62
D5V11, multiclass
        clus
vv       PRKAR1B MUTATED PRKAR1B WILD-TYPE
  CLUS_1               1                36
  CLUS_2               1                53
  CLUS_3               1                23
D5V12, multiclass
        clus
vv       PRKAR1B MUTATED PRKAR1B WILD-TYPE
  CLUS_1               1                54
  CLUS_2               1                50
  CLUS_3               1                 8

Clustering(6) Variable = PTEN MUTATION ANALYSIS
D6V1, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           11              1
  CLUS_2            6             12
  CLUS_3            9              2
  CLUS_4            7              3
D6V2, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           15              2
  CLUS_2           14              4
  CLUS_3            4             12
D6V3, multiclass
D6V4, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            7             35
  CLUS_2           30             11
  CLUS_3           44              7
D6V5, multiclass
D6V6, binary
                cls
clus              0  1
  PTEN MUTATED   86 46
  PTEN WILD-TYPE 29 25
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     86   46
  PTEN WILD-TYPE   29   25
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           86             29
  CLUS_2           46             25
D6V7, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           18             61
  CLUS_2           74              6
  CLUS_3           63             19
D6V8, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           38             13
  CLUS_2           64              6
  CLUS_3           31             11
  CLUS_4           22             56
D6V9, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           21             50
  CLUS_2           80             11
  CLUS_3           57             21
D6V10, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1          106             17
  CLUS_2           27             14
  CLUS_3           10              3
  CLUS_4           15             48
D6V11, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           13             24
  CLUS_2           48              6
  CLUS_3            9             15
D6V12, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           50              5
  CLUS_2           15             36
  CLUS_3            5              4

Clustering(7) Variable = RPL22 MUTATION ANALYSIS
D7V1, multiclass
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  CLUS_1             5               7
  CLUS_2             2              16
  CLUS_3             1              10
  CLUS_4             0              10
D7V2, multiclass
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  CLUS_1             5              12
  CLUS_2             1              17
  CLUS_3             2              14
D7V3, multiclass
D7V4, multiclass
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  CLUS_1             2              40
  CLUS_2             2              39
  CLUS_3            12              39
D7V5, multiclass
D7V6, binary
                 cls
clus                0   1
  RPL22 MUTATED    12  12
  RPL22 WILD-TYPE 103  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPL22 MUTATED     12   12
  RPL22 WILD-TYPE  103   59
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  CLUS_1            12             103
  CLUS_2            12              59
D7V7, multiclass
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  CLUS_1             7              72
  CLUS_2            10              70
  CLUS_3            13              69
D7V8, multiclass
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  CLUS_1             2              49
  CLUS_2             9              61
  CLUS_3             8              34
  CLUS_4            11              67
D7V9, multiclass
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  CLUS_1             6              65
  CLUS_2            12              79
  CLUS_3            13              65
D7V10, multiclass
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  CLUS_1            13             110
  CLUS_2            10              31
  CLUS_3             4               9
  CLUS_4             4              59
D7V11, multiclass
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  CLUS_1             3              34
  CLUS_2             8              46
  CLUS_3             4              20
D7V12, multiclass
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  CLUS_1             8              47
  CLUS_2             5              46
  CLUS_3             2               7

Clustering(8) Variable = KRAS MUTATION ANALYSIS
D8V1, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            5              7
  CLUS_2            2             16
  CLUS_3            3              8
  CLUS_4            1              9
D8V2, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            9              8
  CLUS_2            1             17
  CLUS_3            1             15
D8V3, multiclass
D8V4, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            6             36
  CLUS_2            8             33
  CLUS_3           16             35
D8V5, multiclass
D8V6, binary
                cls
clus              0  1
  KRAS MUTATED   24 16
  KRAS WILD-TYPE 91 55
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     24   16
  KRAS WILD-TYPE   91   55
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           24             91
  CLUS_2           16             55
D8V7, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           14             65
  CLUS_2           20             60
  CLUS_3           17             65
D8V8, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            3             48
  CLUS_2           20             50
  CLUS_3           16             26
  CLUS_4           12             66
D8V9, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           10             61
  CLUS_2           25             66
  CLUS_3           17             61
D8V10, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           29             94
  CLUS_2           14             27
  CLUS_3            2             11
  CLUS_4            7             56
D8V11, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            4             33
  CLUS_2           14             40
  CLUS_3            7             17
D8V12, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           15             40
  CLUS_2            9             42
  CLUS_3            1              8

Clustering(9) Variable = TP53 MUTATION ANALYSIS
D9V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2             10
  CLUS_2           13              5
  CLUS_3            1             10
  CLUS_4            0             10
D9V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            3             14
  CLUS_2            0             18
  CLUS_3           13              3
D9V3, multiclass
D9V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           30             12
  CLUS_2            4             37
  CLUS_3            5             46
D9V5, multiclass
D9V6, binary
                cls
clus              0  1
  TP53 MUTATED   18 26
  TP53 WILD-TYPE 97 45
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     18   26
  TP53 WILD-TYPE   97   45
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           18             97
  CLUS_2           26             45
D9V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           57             22
  CLUS_2            3             77
  CLUS_3            8             74
D9V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            0             51
  CLUS_2            2             68
  CLUS_3           10             32
  CLUS_4           56             22
D9V9, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           47             24
  CLUS_2            8             83
  CLUS_3            9             69
D9V10, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            7            116
  CLUS_2            5             36
  CLUS_3            7              6
  CLUS_4           45             18
D9V11, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           24             13
  CLUS_2            3             51
  CLUS_3            8             16
D9V12, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            3             52
  CLUS_2           28             23
  CLUS_3            4              5

Clustering(10) Variable = FBXW7 MUTATION ANALYSIS
D10V1, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             3               9
  CLUS_2             4              14
  CLUS_3             4               7
  CLUS_4             0              10
D10V2, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             5              12
  CLUS_2             3              15
  CLUS_3             3              13
D10V3, multiclass
D10V4, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1            11              31
  CLUS_2             4              37
  CLUS_3             7              44
D10V5, multiclass
D10V6, binary
                 cls
clus                0   1
  FBXW7 MUTATED    15  16
  FBXW7 WILD-TYPE 100  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     15   16
  FBXW7 WILD-TYPE  100   55
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1            15             100
  CLUS_2            16              55
D10V7, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1            19              60
  CLUS_2            11              69
  CLUS_3             9              73
D10V8, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             0              51
  CLUS_2            10              60
  CLUS_3            10              32
  CLUS_4            19              59
D10V9, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1            12              59
  CLUS_2            12              79
  CLUS_3            11              67
D10V10, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1            13             110
  CLUS_2             6              35
  CLUS_3             2              11
  CLUS_4            14              49
D10V11, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             9              28
  CLUS_2             5              49
  CLUS_3             4              20
D10V12, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             5              50
  CLUS_2            12              39
  CLUS_3             1               8

Clustering(11) Variable = CTCF MUTATION ANALYSIS
D11V1, multiclass
        clus
vv       CTCF MUTATED CTCF WILD-TYPE
  CLUS_1            3              9
  CLUS_2            1             17
  CLUS_3            4              7
  CLUS_4            1              9
D11V2, multiclass
        clus
vv       CTCF MUTATED CTCF WILD-TYPE
  CLUS_1            4             13
  CLUS_2            4             14
  CLUS_3            1             15
D11V3, multiclass
D11V4, multiclass
        clus
vv       CTCF MUTATED CTCF WILD-TYPE
  CLUS_1            3             39
  CLUS_2           11             30
  CLUS_3            7             44
D11V5, multiclass
D11V6, binary
                cls
clus              0  1
  CTCF MUTATED   21 14
  CTCF WILD-TYPE 94 57
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED     21   14
  CTCF WILD-TYPE   94   57
        clus
vv       CTCF MUTATED CTCF WILD-TYPE
  CLUS_1           21             94
  CLUS_2           14             57
D11V7, multiclass
        clus
vv       CTCF MUTATED CTCF WILD-TYPE
  CLUS_1            4             75
  CLUS_2           21             59
  CLUS_3           19             63
D11V8, multiclass
        clus
vv       CTCF MUTATED CTCF WILD-TYPE
  CLUS_1           11             40
  CLUS_2           19             51
  CLUS_3           11             31
  CLUS_4            3             75
D11V9, multiclass
        clus
vv       CTCF MUTATED CTCF WILD-TYPE
  CLUS_1            5             66
  CLUS_2           23             68
  CLUS_3           17             61
D11V10, multiclass
        clus
vv       CTCF MUTATED CTCF WILD-TYPE
  CLUS_1           33             90
  CLUS_2            5             36
  CLUS_3            2             11
  CLUS_4            5             58
D11V11, multiclass
        clus
vv       CTCF MUTATED CTCF WILD-TYPE
  CLUS_1            1             36
  CLUS_2           12             42
  CLUS_3            1             23
D11V12, multiclass
        clus
vv       CTCF MUTATED CTCF WILD-TYPE
  CLUS_1           11             44
  CLUS_2            2             49
  CLUS_3            1              8

Clustering(12) Variable = ARID1A MUTATION ANALYSIS
D12V1, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              5                7
  CLUS_2              3               15
  CLUS_3              4                7
  CLUS_4              5                5
D12V2, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              9                8
  CLUS_2              7               11
  CLUS_3              1               15
D12V3, multiclass
D12V4, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1             10               32
  CLUS_2             17               24
  CLUS_3             18               33
D12V5, multiclass
D12V6, binary
                  cls
clus                0  1
  ARID1A MUTATED   41 25
  ARID1A WILD-TYPE 74 46
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     41   25
  ARID1A WILD-TYPE   74   46
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1             41               74
  CLUS_2             25               46
D12V7, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1             18               61
  CLUS_2             31               49
  CLUS_3             32               50
D12V8, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1             20               31
  CLUS_2             29               41
  CLUS_3             14               28
  CLUS_4             18               60
D12V9, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1             16               55
  CLUS_2             38               53
  CLUS_3             26               52
D12V10, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1             48               75
  CLUS_2             15               26
  CLUS_3              6                7
  CLUS_4             11               52
D12V11, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              8               29
  CLUS_2             25               29
  CLUS_3              7               17
D12V12, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1             26               29
  CLUS_2             14               37
  CLUS_3              0                9

Clustering(13) Variable = SPOP MUTATION ANALYSIS
D13V1, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            2             10
  CLUS_2            1             17
  CLUS_3            0             11
  CLUS_4            2              8
D13V2, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            2             15
  CLUS_2            2             16
  CLUS_3            1             15
D13V3, multiclass
D13V4, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            4             38
  CLUS_2            1             40
  CLUS_3            5             46
D13V5, multiclass
D13V6, binary
                cls
clus               0   1
  SPOP MUTATED    11   4
  SPOP WILD-TYPE 104  67
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPOP MUTATED     11    4
  SPOP WILD-TYPE  104   67
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1           11            104
  CLUS_2            4             67
D13V7, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            6             73
  CLUS_2            6             74
  CLUS_3            9             73
D13V8, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            4             47
  CLUS_2            6             64
  CLUS_3            4             38
  CLUS_4            7             71
D13V9, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            7             64
  CLUS_2            8             83
  CLUS_3            6             72
D13V10, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            9            114
  CLUS_2            5             36
  CLUS_3            1             12
  CLUS_4            6             57
D13V11, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            4             33
  CLUS_2            3             51
  CLUS_3            2             22
D13V12, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            4             51
  CLUS_2            5             46
  CLUS_3            0              9

Clustering(14) Variable = ARID5B MUTATION ANALYSIS
D14V1, multiclass
        clus
vv       ARID5B MUTATED ARID5B WILD-TYPE
  CLUS_1              3                9
  CLUS_2              3               15
  CLUS_3              2                9
  CLUS_4              2                8
D14V2, multiclass
        clus
vv       ARID5B MUTATED ARID5B WILD-TYPE
  CLUS_1              5               12
  CLUS_2              3               15
  CLUS_3              2               14
D14V3, multiclass
D14V4, multiclass
        clus
vv       ARID5B MUTATED ARID5B WILD-TYPE
  CLUS_1              1               41
  CLUS_2              1               40
  CLUS_3              6               45
D14V5, multiclass
D14V6, binary
                  cls
clus                0  1
  ARID5B MUTATED   18  6
  ARID5B WILD-TYPE 97 65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID5B MUTATED     18    6
  ARID5B WILD-TYPE   97   65
        clus
vv       ARID5B MUTATED ARID5B WILD-TYPE
  CLUS_1             18               97
  CLUS_2              6               65
D14V7, multiclass
        clus
vv       ARID5B MUTATED ARID5B WILD-TYPE
  CLUS_1              6               73
  CLUS_2             11               69
  CLUS_3             12               70
D14V8, multiclass
        clus
vv       ARID5B MUTATED ARID5B WILD-TYPE
  CLUS_1              3               48
  CLUS_2             11               59
  CLUS_3              9               33
  CLUS_4              6               72
D14V9, multiclass
        clus
vv       ARID5B MUTATED ARID5B WILD-TYPE
  CLUS_1              5               66
  CLUS_2             13               78
  CLUS_3              9               69
D14V10, multiclass
        clus
vv       ARID5B MUTATED ARID5B WILD-TYPE
  CLUS_1             16              107
  CLUS_2              6               35
  CLUS_3              2               11
  CLUS_4              3               60
D14V11, multiclass
        clus
vv       ARID5B MUTATED ARID5B WILD-TYPE
  CLUS_1              1               36
  CLUS_2              4               50
  CLUS_3              1               23
D14V12, multiclass
        clus
vv       ARID5B MUTATED ARID5B WILD-TYPE
  CLUS_1              4               51
  CLUS_2              1               50
  CLUS_3              1                8

Clustering(15) Variable = FGFR2 MUTATION ANALYSIS
D15V1, multiclass
        clus
vv       FGFR2 MUTATED FGFR2 WILD-TYPE
  CLUS_1             3               9
  CLUS_2             2              16
  CLUS_3             1              10
  CLUS_4             0              10
D15V2, multiclass
        clus
vv       FGFR2 MUTATED FGFR2 WILD-TYPE
  CLUS_1             4              13
  CLUS_2             1              17
  CLUS_3             1              15
D15V3, multiclass
D15V4, multiclass
        clus
vv       FGFR2 MUTATED FGFR2 WILD-TYPE
  CLUS_1             5              37
  CLUS_2             6              35
  CLUS_3             6              45
D15V5, multiclass
D15V6, binary
                 cls
clus                0   1
  FGFR2 MUTATED    15  10
  FGFR2 WILD-TYPE 100  61
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR2 MUTATED     15   10
  FGFR2 WILD-TYPE  100   61
        clus
vv       FGFR2 MUTATED FGFR2 WILD-TYPE
  CLUS_1            15             100
  CLUS_2            10              61
D15V7, multiclass
        clus
vv       FGFR2 MUTATED FGFR2 WILD-TYPE
  CLUS_1             9              70
  CLUS_2            11              69
  CLUS_3            10              72
D15V8, multiclass
        clus
vv       FGFR2 MUTATED FGFR2 WILD-TYPE
  CLUS_1             2              49
  CLUS_2            10              60
  CLUS_3             9              33
  CLUS_4             9              69
D15V9, multiclass
        clus
vv       FGFR2 MUTATED FGFR2 WILD-TYPE
  CLUS_1             6              65
  CLUS_2            12              79
  CLUS_3            12              66
D15V10, multiclass
        clus
vv       FGFR2 MUTATED FGFR2 WILD-TYPE
  CLUS_1            15             108
  CLUS_2             5              36
  CLUS_3             4               9
  CLUS_4             6              57
D15V11, multiclass
        clus
vv       FGFR2 MUTATED FGFR2 WILD-TYPE
  CLUS_1             6              31
  CLUS_2             8              46
  CLUS_3             2              22
D15V12, multiclass
        clus
vv       FGFR2 MUTATED FGFR2 WILD-TYPE
  CLUS_1             8              47
  CLUS_2             7              44
  CLUS_3             1               8

Clustering(16) Variable = CCND1 MUTATION ANALYSIS
D16V1, multiclass
        clus
vv       CCND1 MUTATED CCND1 WILD-TYPE
  CLUS_1             2              10
  CLUS_2             1              17
  CLUS_3             0              11
  CLUS_4             1               9
D16V2, multiclass
        clus
vv       CCND1 MUTATED CCND1 WILD-TYPE
  CLUS_1             2              15
  CLUS_2             1              17
  CLUS_3             1              15
D16V3, multiclass
D16V4, multiclass
        clus
vv       CCND1 MUTATED CCND1 WILD-TYPE
  CLUS_1             1              41
  CLUS_2             2              39
  CLUS_3             4              47
D16V5, multiclass
D16V6, binary
                 cls
clus                0   1
  CCND1 MUTATED     5   6
  CCND1 WILD-TYPE 110  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCND1 MUTATED      5    6
  CCND1 WILD-TYPE  110   65
        clus
vv       CCND1 MUTATED CCND1 WILD-TYPE
  CLUS_1             5             110
  CLUS_2             6              65
D16V7, multiclass
        clus
vv       CCND1 MUTATED CCND1 WILD-TYPE
  CLUS_1             3              76
  CLUS_2             5              75
  CLUS_3             7              75
D16V8, multiclass
        clus
vv       CCND1 MUTATED CCND1 WILD-TYPE
  CLUS_1             2              49
  CLUS_2             5              65
  CLUS_3             5              37
  CLUS_4             3              75
D16V9, multiclass
        clus
vv       CCND1 MUTATED CCND1 WILD-TYPE
  CLUS_1             2              69
  CLUS_2             5              86
  CLUS_3             8              70
D16V10, multiclass
        clus
vv       CCND1 MUTATED CCND1 WILD-TYPE
  CLUS_1            10             113
  CLUS_2             2              39
  CLUS_3             2              11
  CLUS_4             1              62
D16V11, multiclass
        clus
vv       CCND1 MUTATED CCND1 WILD-TYPE
  CLUS_1             0              37
  CLUS_2             3              51
  CLUS_3             1              23
D16V12, multiclass
        clus
vv       CCND1 MUTATED CCND1 WILD-TYPE
  CLUS_1             3              52
  CLUS_2             1              50
  CLUS_3             0               9

Clustering(17) Variable = SMTNL2 MUTATION ANALYSIS
D17V1, multiclass
[1] "Remove cluster labels:" "SMTNL2 MUTATED"        
clus
  SMTNL2 MUTATED SMTNL2 WILD-TYPE 
               1               50 
      TCGA-A5-A0G3       TCGA-A5-A0G5       TCGA-A5-A0GA       TCGA-A5-A0GB 
"SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" 
      TCGA-A5-A0GE       TCGA-A5-A0GH       TCGA-A5-A0GM       TCGA-A5-A0GP 
"SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" 
      TCGA-A5-A0GU       TCGA-AP-A052       TCGA-AP-A053       TCGA-AP-A054 
"SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" 
      TCGA-AP-A056       TCGA-AP-A05A       TCGA-AP-A05D       TCGA-AP-A05H 
"SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" 
      TCGA-AP-A05J       TCGA-AP-A05N       TCGA-AP-A05P       TCGA-AP-A0L8 
"SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" 
      TCGA-AP-A0L9       TCGA-AP-A0LD       TCGA-AP-A0LG       TCGA-AP-A0LH 
"SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" 
      TCGA-AP-A0LJ       TCGA-AP-A0LN       TCGA-AP-A0LT       TCGA-AP-A0LV 
"SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" 
      TCGA-AX-A05S       TCGA-AX-A05T       TCGA-AX-A05U       TCGA-AX-A05W 
"SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" 
      TCGA-AX-A05Y       TCGA-AX-A05Z       TCGA-AX-A060       TCGA-AX-A062 
"SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" 
      TCGA-AX-A063       TCGA-AX-A064       TCGA-AX-A06B       TCGA-AX-A0IW 
"SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" 
      TCGA-AX-A0J1       TCGA-B5-A0JR       TCGA-B5-A0JZ       TCGA-B5-A0K0 
"SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" 
      TCGA-B5-A0K1       TCGA-B5-A0K4       TCGA-BG-A0LW       TCGA-BG-A0MI 
"SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" 
      TCGA-BK-A0C9       TCGA-BK-A0CC 
"SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" 
D17V2, multiclass
[1] "Remove cluster labels:" "SMTNL2 MUTATED"        
clus
  SMTNL2 MUTATED SMTNL2 WILD-TYPE 
               1               50 
      TCGA-A5-A0G3       TCGA-A5-A0G5       TCGA-A5-A0GA       TCGA-A5-A0GB 
"SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" 
      TCGA-A5-A0GE       TCGA-A5-A0GH       TCGA-A5-A0GM       TCGA-A5-A0GP 
"SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" 
      TCGA-A5-A0GU       TCGA-AP-A052       TCGA-AP-A053       TCGA-AP-A054 
"SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" 
      TCGA-AP-A056       TCGA-AP-A05A       TCGA-AP-A05D       TCGA-AP-A05H 
"SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" 
      TCGA-AP-A05J       TCGA-AP-A05N       TCGA-AP-A05P       TCGA-AP-A0L8 
"SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" 
      TCGA-AP-A0L9       TCGA-AP-A0LD       TCGA-AP-A0LG       TCGA-AP-A0LH 
"SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" 
      TCGA-AP-A0LJ       TCGA-AP-A0LN       TCGA-AP-A0LT       TCGA-AP-A0LV 
"SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" 
      TCGA-AX-A05S       TCGA-AX-A05T       TCGA-AX-A05U       TCGA-AX-A05W 
"SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" 
      TCGA-AX-A05Y       TCGA-AX-A05Z       TCGA-AX-A060       TCGA-AX-A062 
"SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" 
      TCGA-AX-A063       TCGA-AX-A064       TCGA-AX-A06B       TCGA-AX-A0IW 
"SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" 
      TCGA-AX-A0J1       TCGA-B5-A0JR       TCGA-B5-A0JZ       TCGA-B5-A0K0 
"SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" 
      TCGA-B5-A0K1       TCGA-B5-A0K4       TCGA-BG-A0LW       TCGA-BG-A0MI 
"SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" 
      TCGA-BK-A0C9       TCGA-BK-A0CC 
"SMTNL2 WILD-TYPE" "SMTNL2 WILD-TYPE" 
D17V3, multiclass
D17V4, multiclass
        clus
vv       SMTNL2 MUTATED SMTNL2 WILD-TYPE
  CLUS_1              1               41
  CLUS_2              3               38
  CLUS_3              2               49
D17V5, multiclass
D17V6, binary
                  cls
clus                 0   1
  SMTNL2 MUTATED     3   2
  SMTNL2 WILD-TYPE 112  69
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SMTNL2 MUTATED      3    2
  SMTNL2 WILD-TYPE  112   69
        clus
vv       SMTNL2 MUTATED SMTNL2 WILD-TYPE
  CLUS_1              3              112
  CLUS_2              2               69
D17V7, multiclass
        clus
vv       SMTNL2 MUTATED SMTNL2 WILD-TYPE
  CLUS_1              2               77
  CLUS_2              4               76
  CLUS_3              3               79
D17V8, multiclass
        clus
vv       SMTNL2 MUTATED SMTNL2 WILD-TYPE
  CLUS_1              2               49
  CLUS_2              3               67
  CLUS_3              1               41
  CLUS_4              3               75
D17V9, multiclass
        clus
vv       SMTNL2 MUTATED SMTNL2 WILD-TYPE
  CLUS_1              2               69
  CLUS_2              4               87
  CLUS_3              3               75
D17V10, multiclass
        clus
vv       SMTNL2 MUTATED SMTNL2 WILD-TYPE
  CLUS_1              5              118
  CLUS_2              1               40
  CLUS_3              2               11
  CLUS_4              1               62
D17V11, multiclass
        clus
vv       SMTNL2 MUTATED SMTNL2 WILD-TYPE
  CLUS_1              1               36
  CLUS_2              1               53
  CLUS_3              1               23
D17V12, multiclass
        clus
vv       SMTNL2 MUTATED SMTNL2 WILD-TYPE
  CLUS_1              2               53
  CLUS_2              1               50
  CLUS_3              0                9

Clustering(18) Variable = NFE2L2 MUTATION ANALYSIS
D18V1, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              0               12
  CLUS_2              1               17
  CLUS_3              3                8
  CLUS_4              0               10
D18V2, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              2               15
  CLUS_2              1               17
  CLUS_3              1               15
D18V3, multiclass
D18V4, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              1               41
  CLUS_2              3               38
  CLUS_3              3               48
D18V5, multiclass
D18V6, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     8   5
  NFE2L2 WILD-TYPE 107  66
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      8    5
  NFE2L2 WILD-TYPE  107   66
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              8              107
  CLUS_2              5               66
D18V7, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              2               77
  CLUS_2              9               71
  CLUS_3              2               80
D18V8, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              0               51
  CLUS_2              8               62
  CLUS_3              4               38
  CLUS_4              1               77
D18V9, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              3               68
  CLUS_2              8               83
  CLUS_3              4               74
D18V10, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              9              114
  CLUS_2              2               39
  CLUS_3              1               12
  CLUS_4              3               60
D18V11, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              1               36
  CLUS_2              5               49
  CLUS_3              0               24
D18V12, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              5               50
  CLUS_2              1               50
  CLUS_3              0                9

Clustering(19) Variable = CHD4 MUTATION ANALYSIS
D19V1, multiclass
        clus
vv       CHD4 MUTATED CHD4 WILD-TYPE
  CLUS_1            1             11
  CLUS_2            6             12
  CLUS_3            0             11
  CLUS_4            2              8
D19V2, multiclass
        clus
vv       CHD4 MUTATED CHD4 WILD-TYPE
  CLUS_1            2             15
  CLUS_2            2             16
  CLUS_3            5             11
D19V3, multiclass
D19V4, multiclass
        clus
vv       CHD4 MUTATED CHD4 WILD-TYPE
  CLUS_1            7             35
  CLUS_2            5             36
  CLUS_3            7             44
D19V5, multiclass
D19V6, binary
                cls
clus               0   1
  CHD4 MUTATED    14  13
  CHD4 WILD-TYPE 101  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD4 MUTATED     14   13
  CHD4 WILD-TYPE  101   58
        clus
vv       CHD4 MUTATED CHD4 WILD-TYPE
  CLUS_1           14            101
  CLUS_2           13             58
D19V7, multiclass
        clus
vv       CHD4 MUTATED CHD4 WILD-TYPE
  CLUS_1           14             65
  CLUS_2           10             70
  CLUS_3           11             71
D19V8, multiclass
        clus
vv       CHD4 MUTATED CHD4 WILD-TYPE
  CLUS_1            5             46
  CLUS_2            9             61
  CLUS_3            6             36
  CLUS_4           15             63
D19V9, multiclass
        clus
vv       CHD4 MUTATED CHD4 WILD-TYPE
  CLUS_1           10             61
  CLUS_2            8             83
  CLUS_3           12             66
D19V10, multiclass
        clus
vv       CHD4 MUTATED CHD4 WILD-TYPE
  CLUS_1           15            108
  CLUS_2            3             38
  CLUS_3            2             11
  CLUS_4           10             53
D19V11, multiclass
        clus
vv       CHD4 MUTATED CHD4 WILD-TYPE
  CLUS_1            4             33
  CLUS_2            9             45
  CLUS_3            3             21
D19V12, multiclass
        clus
vv       CHD4 MUTATED CHD4 WILD-TYPE
  CLUS_1            8             47
  CLUS_2            6             45
  CLUS_3            2              7

Clustering(20) Variable = RBMX MUTATION ANALYSIS
D20V1, multiclass
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  CLUS_1            3              9
  CLUS_2            2             16
  CLUS_3            0             11
  CLUS_4            0             10
D20V2, multiclass
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  CLUS_1            3             14
  CLUS_2            0             18
  CLUS_3            2             14
D20V3, multiclass
D20V4, multiclass
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  CLUS_1            1             41
  CLUS_2            0             41
  CLUS_3            3             48
D20V5, multiclass
D20V6, binary
                cls
clus               0   1
  RBMX MUTATED     7   4
  RBMX WILD-TYPE 108  67
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      7    4
  RBMX WILD-TYPE  108   67
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  CLUS_1            7            108
  CLUS_2            4             67
D20V7, multiclass
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  CLUS_1            3             76
  CLUS_2            5             75
  CLUS_3            5             77
D20V8, multiclass
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  CLUS_1            0             51
  CLUS_2            4             66
  CLUS_3            6             36
  CLUS_4            3             75
D20V9, multiclass
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  CLUS_1            4             67
  CLUS_2            5             86
  CLUS_3            4             74
D20V10, multiclass
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  CLUS_1            4            119
  CLUS_2            5             36
  CLUS_3            1             12
  CLUS_4            3             60
D20V11, multiclass
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  CLUS_1            1             36
  CLUS_2            3             51
  CLUS_3            0             24
D20V12, multiclass
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  CLUS_1            3             52
  CLUS_2            1             50
  CLUS_3            0              9

Clustering(21) Variable = FAM9A MUTATION ANALYSIS
D21V1, multiclass
[1] "Remove cluster labels:" "FAM9A MUTATED"         
clus
  FAM9A MUTATED FAM9A WILD-TYPE 
              1              50 
     TCGA-A5-A0G3      TCGA-A5-A0G5      TCGA-A5-A0GA      TCGA-A5-A0GB 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-A5-A0GE      TCGA-A5-A0GH      TCGA-A5-A0GM      TCGA-A5-A0GP 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-A5-A0GU      TCGA-AP-A051      TCGA-AP-A052      TCGA-AP-A053 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AP-A054      TCGA-AP-A056      TCGA-AP-A05A      TCGA-AP-A05D 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AP-A05H      TCGA-AP-A05J      TCGA-AP-A05N      TCGA-AP-A05P 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AP-A0L8      TCGA-AP-A0L9      TCGA-AP-A0LD      TCGA-AP-A0LG 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AP-A0LH      TCGA-AP-A0LJ      TCGA-AP-A0LN      TCGA-AP-A0LT 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AP-A0LV      TCGA-AX-A05S      TCGA-AX-A05T      TCGA-AX-A05U 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AX-A05W      TCGA-AX-A05Y      TCGA-AX-A05Z      TCGA-AX-A060 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AX-A062      TCGA-AX-A063      TCGA-AX-A064      TCGA-AX-A06B 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AX-A0IW      TCGA-AX-A0J1      TCGA-B5-A0JR      TCGA-B5-A0JZ 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-B5-A0K0      TCGA-B5-A0K4      TCGA-BG-A0LW      TCGA-BG-A0MI 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-BK-A0C9      TCGA-BK-A0CC 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
D21V2, multiclass
[1] "Remove cluster labels:" "FAM9A MUTATED"         
clus
  FAM9A MUTATED FAM9A WILD-TYPE 
              1              50 
     TCGA-A5-A0G3      TCGA-A5-A0G5      TCGA-A5-A0GA      TCGA-A5-A0GB 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-A5-A0GE      TCGA-A5-A0GH      TCGA-A5-A0GM      TCGA-A5-A0GP 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-A5-A0GU      TCGA-AP-A051      TCGA-AP-A052      TCGA-AP-A053 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AP-A054      TCGA-AP-A056      TCGA-AP-A05A      TCGA-AP-A05D 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AP-A05H      TCGA-AP-A05J      TCGA-AP-A05N      TCGA-AP-A05P 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AP-A0L8      TCGA-AP-A0L9      TCGA-AP-A0LD      TCGA-AP-A0LG 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AP-A0LH      TCGA-AP-A0LJ      TCGA-AP-A0LN      TCGA-AP-A0LT 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AP-A0LV      TCGA-AX-A05S      TCGA-AX-A05T      TCGA-AX-A05U 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AX-A05W      TCGA-AX-A05Y      TCGA-AX-A05Z      TCGA-AX-A060 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AX-A062      TCGA-AX-A063      TCGA-AX-A064      TCGA-AX-A06B 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AX-A0IW      TCGA-AX-A0J1      TCGA-B5-A0JR      TCGA-B5-A0JZ 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-B5-A0K0      TCGA-B5-A0K4      TCGA-BG-A0LW      TCGA-BG-A0MI 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-BK-A0C9      TCGA-BK-A0CC 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
D21V3, multiclass
D21V4, multiclass
        clus
vv       FAM9A MUTATED FAM9A WILD-TYPE
  CLUS_1             5              37
  CLUS_2             1              40
  CLUS_3             4              47
D21V5, multiclass
D21V6, binary
                 cls
clus                0   1
  FAM9A MUTATED     3   8
  FAM9A WILD-TYPE 112  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAM9A MUTATED      3    8
  FAM9A WILD-TYPE  112   63
        clus
vv       FAM9A MUTATED FAM9A WILD-TYPE
  CLUS_1             3             112
  CLUS_2             8              63
D21V7, multiclass
        clus
vv       FAM9A MUTATED FAM9A WILD-TYPE
  CLUS_1             6              73
  CLUS_2             2              78
  CLUS_3             6              76
D21V8, multiclass
        clus
vv       FAM9A MUTATED FAM9A WILD-TYPE
  CLUS_1             1              50
  CLUS_2             2              68
  CLUS_3             4              38
  CLUS_4             7              71
D21V9, multiclass
        clus
vv       FAM9A MUTATED FAM9A WILD-TYPE
  CLUS_1             5              66
  CLUS_2             4              87
  CLUS_3             5              73
D21V10, multiclass
        clus
vv       FAM9A MUTATED FAM9A WILD-TYPE
  CLUS_1             4             119
  CLUS_2             2              39
  CLUS_3             2              11
  CLUS_4             6              57
D21V11, multiclass
        clus
vv       FAM9A MUTATED FAM9A WILD-TYPE
  CLUS_1             6              31
  CLUS_2             1              53
  CLUS_3             1              23
D21V12, multiclass
        clus
vv       FAM9A MUTATED FAM9A WILD-TYPE
  CLUS_1             1              54
  CLUS_2             6              45
  CLUS_3             1               8

Clustering(22) Variable = HPD MUTATION ANALYSIS
D22V1, multiclass
[1] "Remove cluster labels:" "HPD MUTATED"           
clus
  HPD MUTATED HPD WILD-TYPE 
            2            49 
   TCGA-A5-A0G3    TCGA-A5-A0G5    TCGA-A5-A0GA    TCGA-A5-A0GB    TCGA-A5-A0GE 
"HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" 
   TCGA-A5-A0GH    TCGA-A5-A0GM    TCGA-A5-A0GP    TCGA-A5-A0GU    TCGA-AP-A051 
"HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" 
   TCGA-AP-A052    TCGA-AP-A053    TCGA-AP-A054    TCGA-AP-A056    TCGA-AP-A05A 
"HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" 
   TCGA-AP-A05D    TCGA-AP-A05H    TCGA-AP-A05J    TCGA-AP-A05N    TCGA-AP-A05P 
"HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" 
   TCGA-AP-A0L8    TCGA-AP-A0L9    TCGA-AP-A0LD    TCGA-AP-A0LG    TCGA-AP-A0LH 
"HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" 
   TCGA-AP-A0LJ    TCGA-AP-A0LN    TCGA-AP-A0LT    TCGA-AP-A0LV    TCGA-AX-A05S 
"HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" 
   TCGA-AX-A05T    TCGA-AX-A05U    TCGA-AX-A05W    TCGA-AX-A05Y    TCGA-AX-A05Z 
"HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" 
   TCGA-AX-A060    TCGA-AX-A062    TCGA-AX-A063    TCGA-AX-A064    TCGA-AX-A06B 
"HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" 
   TCGA-AX-A0IW    TCGA-B5-A0JZ    TCGA-B5-A0K0    TCGA-B5-A0K1    TCGA-B5-A0K4 
"HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" 
   TCGA-BG-A0LW    TCGA-BG-A0MI    TCGA-BK-A0C9    TCGA-BK-A0CC 
"HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" 
D22V2, multiclass
[1] "Remove cluster labels:" "HPD MUTATED"           
clus
  HPD MUTATED HPD WILD-TYPE 
            2            49 
   TCGA-A5-A0G3    TCGA-A5-A0G5    TCGA-A5-A0GA    TCGA-A5-A0GB    TCGA-A5-A0GE 
"HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" 
   TCGA-A5-A0GH    TCGA-A5-A0GM    TCGA-A5-A0GP    TCGA-A5-A0GU    TCGA-AP-A051 
"HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" 
   TCGA-AP-A052    TCGA-AP-A053    TCGA-AP-A054    TCGA-AP-A056    TCGA-AP-A05A 
"HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" 
   TCGA-AP-A05D    TCGA-AP-A05H    TCGA-AP-A05J    TCGA-AP-A05N    TCGA-AP-A05P 
"HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" 
   TCGA-AP-A0L8    TCGA-AP-A0L9    TCGA-AP-A0LD    TCGA-AP-A0LG    TCGA-AP-A0LH 
"HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" 
   TCGA-AP-A0LJ    TCGA-AP-A0LN    TCGA-AP-A0LT    TCGA-AP-A0LV    TCGA-AX-A05S 
"HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" 
   TCGA-AX-A05T    TCGA-AX-A05U    TCGA-AX-A05W    TCGA-AX-A05Y    TCGA-AX-A05Z 
"HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" 
   TCGA-AX-A060    TCGA-AX-A062    TCGA-AX-A063    TCGA-AX-A064    TCGA-AX-A06B 
"HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" 
   TCGA-AX-A0IW    TCGA-B5-A0JZ    TCGA-B5-A0K0    TCGA-B5-A0K1    TCGA-B5-A0K4 
"HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" 
   TCGA-BG-A0LW    TCGA-BG-A0MI    TCGA-BK-A0C9    TCGA-BK-A0CC 
"HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" "HPD WILD-TYPE" 
D22V3, multiclass
D22V4, multiclass
        clus
vv       HPD MUTATED HPD WILD-TYPE
  CLUS_1           1            41
  CLUS_2           0            41
  CLUS_3           2            49
D22V5, multiclass
D22V6, binary
               cls
clus              0   1
  HPD MUTATED     4   1
  HPD WILD-TYPE 111  70
[1] "tbl2"
               cls
clus            [,1] [,2]
  HPD MUTATED      4    1
  HPD WILD-TYPE  111   70
        clus
vv       HPD MUTATED HPD WILD-TYPE
  CLUS_1           4           111
  CLUS_2           1            70
D22V7, multiclass
        clus
vv       HPD MUTATED HPD WILD-TYPE
  CLUS_1           1            78
  CLUS_2           1            79
  CLUS_3           4            78
D22V8, multiclass
        clus
vv       HPD MUTATED HPD WILD-TYPE
  CLUS_1           1            50
  CLUS_2           1            69
  CLUS_3           4            38
  CLUS_4           0            78
D22V9, multiclass
        clus
vv       HPD MUTATED HPD WILD-TYPE
  CLUS_1           1            70
  CLUS_2           2            89
  CLUS_3           4            74
D22V10, multiclass
        clus
vv       HPD MUTATED HPD WILD-TYPE
  CLUS_1           2           121
  CLUS_2           3            38
  CLUS_3           0            13
  CLUS_4           2            61
D22V11, multiclass
        clus
vv       HPD MUTATED HPD WILD-TYPE
  CLUS_1           2            35
  CLUS_2           2            52
  CLUS_3           0            24
D22V12, multiclass
        clus
vv       HPD MUTATED HPD WILD-TYPE
  CLUS_1           2            53
  CLUS_2           2            49
  CLUS_3           0             9

Clustering(23) Variable = MORC4 MUTATION ANALYSIS
D23V1, multiclass
        clus
vv       MORC4 MUTATED MORC4 WILD-TYPE
  CLUS_1             1              11
  CLUS_2             3              15
  CLUS_3             0              11
  CLUS_4             1               9
D23V2, multiclass
        clus
vv       MORC4 MUTATED MORC4 WILD-TYPE
  CLUS_1             3              14
  CLUS_2             0              18
  CLUS_3             2              14
D23V3, multiclass
D23V4, multiclass
        clus
vv       MORC4 MUTATED MORC4 WILD-TYPE
  CLUS_1             2              40
  CLUS_2             6              35
  CLUS_3             4              47
D23V5, multiclass
D23V6, binary
                 cls
clus                0   1
  MORC4 MUTATED     6  11
  MORC4 WILD-TYPE 109  60
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC4 MUTATED      6   11
  MORC4 WILD-TYPE  109   60
        clus
vv       MORC4 MUTATED MORC4 WILD-TYPE
  CLUS_1             6             109
  CLUS_2            11              60
D23V7, multiclass
        clus
vv       MORC4 MUTATED MORC4 WILD-TYPE
  CLUS_1             5              74
  CLUS_2             3              77
  CLUS_3            11              71
D23V8, multiclass
        clus
vv       MORC4 MUTATED MORC4 WILD-TYPE
  CLUS_1             4              47
  CLUS_2             3              67
  CLUS_3             6              36
  CLUS_4             6              72
D23V9, multiclass
        clus
vv       MORC4 MUTATED MORC4 WILD-TYPE
  CLUS_1             3              68
  CLUS_2             4              87
  CLUS_3            12              66
D23V10, multiclass
        clus
vv       MORC4 MUTATED MORC4 WILD-TYPE
  CLUS_1             7             116
  CLUS_2             6              35
  CLUS_3             1              12
  CLUS_4             5              58
D23V11, multiclass
        clus
vv       MORC4 MUTATED MORC4 WILD-TYPE
  CLUS_1             2              35
  CLUS_2             3              51
  CLUS_3             4              20
D23V12, multiclass
        clus
vv       MORC4 MUTATED MORC4 WILD-TYPE
  CLUS_1             4              51
  CLUS_2             5              46
  CLUS_3             0               9

Clustering(24) Variable = CASP8 MUTATION ANALYSIS
D24V1, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             2              10
  CLUS_2             1              17
  CLUS_3             0              11
  CLUS_4             0              10
D24V2, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             3              14
  CLUS_2             0              18
  CLUS_3             0              16
D24V3, multiclass
D24V4, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             2              40
  CLUS_2             2              39
  CLUS_3             5              46
D24V5, multiclass
D24V6, binary
                 cls
clus                0   1
  CASP8 MUTATED     7   8
  CASP8 WILD-TYPE 108  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      7    8
  CASP8 WILD-TYPE  108   63
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             7             108
  CLUS_2             8              63
D24V7, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             7              72
  CLUS_2             5              75
  CLUS_3             5              77
D24V8, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             1              50
  CLUS_2             4              66
  CLUS_3             4              38
  CLUS_4             8              70
D24V9, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             7              64
  CLUS_2             5              86
  CLUS_3             4              74
D24V10, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             7             116
  CLUS_2             0              41
  CLUS_3             3              10
  CLUS_4             6              57
D24V11, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             3              34
  CLUS_2             3              51
  CLUS_3             1              23
D24V12, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             3              52
  CLUS_2             3              48
  CLUS_3             1               8

Clustering(25) Variable = ABI1 MUTATION ANALYSIS
D25V1, multiclass
[1] "Remove cluster labels:" "ABI1 MUTATED"          
clus
  ABI1 MUTATED ABI1 WILD-TYPE 
             1             50 
    TCGA-A5-A0G3     TCGA-A5-A0G5     TCGA-A5-A0GA     TCGA-A5-A0GB 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-A5-A0GE     TCGA-A5-A0GH     TCGA-A5-A0GM     TCGA-A5-A0GP 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-A5-A0GU     TCGA-AP-A051     TCGA-AP-A052     TCGA-AP-A053 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-AP-A054     TCGA-AP-A056     TCGA-AP-A05A     TCGA-AP-A05D 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-AP-A05H     TCGA-AP-A05J     TCGA-AP-A05N     TCGA-AP-A05P 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-AP-A0L8     TCGA-AP-A0L9     TCGA-AP-A0LD     TCGA-AP-A0LG 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-AP-A0LH     TCGA-AP-A0LJ     TCGA-AP-A0LN     TCGA-AP-A0LT 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-AP-A0LV     TCGA-AX-A05S     TCGA-AX-A05T     TCGA-AX-A05U 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-AX-A05W     TCGA-AX-A05Y     TCGA-AX-A060     TCGA-AX-A062 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-AX-A063     TCGA-AX-A064     TCGA-AX-A06B     TCGA-AX-A0IW 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-AX-A0J1     TCGA-B5-A0JR     TCGA-B5-A0JZ     TCGA-B5-A0K0 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-B5-A0K1     TCGA-B5-A0K4     TCGA-BG-A0LW     TCGA-BG-A0MI 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BK-A0C9     TCGA-BK-A0CC 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
D25V2, multiclass
[1] "Remove cluster labels:" "ABI1 MUTATED"          
clus
  ABI1 MUTATED ABI1 WILD-TYPE 
             1             50 
    TCGA-A5-A0G3     TCGA-A5-A0G5     TCGA-A5-A0GA     TCGA-A5-A0GB 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-A5-A0GE     TCGA-A5-A0GH     TCGA-A5-A0GM     TCGA-A5-A0GP 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-A5-A0GU     TCGA-AP-A051     TCGA-AP-A052     TCGA-AP-A053 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-AP-A054     TCGA-AP-A056     TCGA-AP-A05A     TCGA-AP-A05D 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-AP-A05H     TCGA-AP-A05J     TCGA-AP-A05N     TCGA-AP-A05P 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-AP-A0L8     TCGA-AP-A0L9     TCGA-AP-A0LD     TCGA-AP-A0LG 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-AP-A0LH     TCGA-AP-A0LJ     TCGA-AP-A0LN     TCGA-AP-A0LT 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-AP-A0LV     TCGA-AX-A05S     TCGA-AX-A05T     TCGA-AX-A05U 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-AX-A05W     TCGA-AX-A05Y     TCGA-AX-A060     TCGA-AX-A062 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-AX-A063     TCGA-AX-A064     TCGA-AX-A06B     TCGA-AX-A0IW 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-AX-A0J1     TCGA-B5-A0JR     TCGA-B5-A0JZ     TCGA-B5-A0K0 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-B5-A0K1     TCGA-B5-A0K4     TCGA-BG-A0LW     TCGA-BG-A0MI 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BK-A0C9     TCGA-BK-A0CC 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
D25V3, multiclass
D25V4, multiclass
[1] "Remove cluster labels:" "ABI1 MUTATED"          
clus
  ABI1 MUTATED ABI1 WILD-TYPE 
             2            132 
    TCGA-A5-A0GQ     TCGA-A5-A0VO     TCGA-AJ-A23M     TCGA-AP-A059 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-AP-A0LF     TCGA-AP-A0LM     TCGA-AP-A1DQ     TCGA-AX-A06H 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-AX-A06L     TCGA-AX-A0IS     TCGA-AX-A0J0     TCGA-AX-A1C7 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-AX-A1C8     TCGA-AX-A1CP     TCGA-AX-A2H5     TCGA-AX-A2HF 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-B5-A0JT     TCGA-B5-A0K8     TCGA-B5-A11E     TCGA-B5-A11F 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-B5-A11G     TCGA-B5-A11H     TCGA-B5-A11I     TCGA-B5-A11J 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-B5-A11M     TCGA-B5-A11N     TCGA-B5-A11O     TCGA-B5-A11Q 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-B5-A11R     TCGA-B5-A11S     TCGA-B5-A11U     TCGA-B5-A11V 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-B5-A11W     TCGA-B5-A11X     TCGA-B5-A11Y     TCGA-B5-A11Z 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-B5-A121     TCGA-B5-A1MU     TCGA-B5-A1MY     TCGA-BG-A0VT 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BG-A0VV     TCGA-BG-A0VW     TCGA-BG-A0VX     TCGA-BG-A0VZ 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BG-A0W1     TCGA-BG-A0W2     TCGA-BG-A0YU     TCGA-BG-A0YV 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BG-A186     TCGA-BG-A187     TCGA-BG-A18A     TCGA-BG-A18B 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BG-A18C     TCGA-BG-A2AE     TCGA-BK-A0CA     TCGA-BK-A139 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BK-A13C     TCGA-BS-A0T9     TCGA-BS-A0U5     TCGA-BS-A0U9 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BS-A0UA     TCGA-BS-A0UL     TCGA-BS-A0V6     TCGA-BS-A0V7 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BS-A0V8     TCGA-BS-A0WQ     TCGA-D1-A0ZN     TCGA-D1-A0ZO 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A0ZP     TCGA-D1-A0ZQ     TCGA-D1-A0ZR     TCGA-D1-A0ZS 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A0ZU     TCGA-D1-A0ZV     TCGA-D1-A0ZZ     TCGA-D1-A101 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A102     TCGA-D1-A103     TCGA-D1-A15V     TCGA-D1-A15W 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A15X     TCGA-D1-A15Z     TCGA-D1-A160     TCGA-D1-A161 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A163     TCGA-D1-A165     TCGA-D1-A167     TCGA-D1-A168 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A169     TCGA-D1-A16B     TCGA-D1-A16D     TCGA-D1-A16E 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A16F     TCGA-D1-A16G     TCGA-D1-A16I     TCGA-D1-A16J 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A16N     TCGA-D1-A16O     TCGA-D1-A16Q     TCGA-D1-A16R 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A16S     TCGA-D1-A16Y     TCGA-D1-A174     TCGA-D1-A176 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A177     TCGA-D1-A17A     TCGA-D1-A17B     TCGA-D1-A17C 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A17D     TCGA-D1-A17F     TCGA-D1-A17H     TCGA-D1-A17K 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A17L     TCGA-D1-A17M     TCGA-D1-A17N     TCGA-D1-A17R 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A17S     TCGA-D1-A17T     TCGA-D1-A17U     TCGA-D1-A1NU 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A1NX     TCGA-DI-A0WH     TCGA-DI-A1NN     TCGA-E6-A1LZ 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-EO-A1Y5     TCGA-EO-A1Y8     TCGA-EY-A1GS     TCGA-EY-A212 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-FI-A2D2     TCGA-FI-A2EW     TCGA-FI-A2EX     TCGA-FI-A2F8 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
D25V5, multiclass
D25V6, binary
                cls
clus               0   1
  ABI1 MUTATED     2   2
  ABI1 WILD-TYPE 113  69
[1] "tbl2"
                cls
clus             [,1] [,2]
  ABI1 MUTATED      2    2
  ABI1 WILD-TYPE  113   69
        clus
vv       ABI1 MUTATED ABI1 WILD-TYPE
  CLUS_1            2            113
  CLUS_2            2             69
D25V7, multiclass
        clus
vv       ABI1 MUTATED ABI1 WILD-TYPE
  CLUS_1            0             79
  CLUS_2            2             78
  CLUS_3            2             80
D25V8, multiclass
        clus
vv       ABI1 MUTATED ABI1 WILD-TYPE
  CLUS_1            0             51
  CLUS_2            2             68
  CLUS_3            1             41
  CLUS_4            1             77
D25V9, multiclass
        clus
vv       ABI1 MUTATED ABI1 WILD-TYPE
  CLUS_1            0             71
  CLUS_2            2             89
  CLUS_3            2             76
D25V10, multiclass
        clus
vv       ABI1 MUTATED ABI1 WILD-TYPE
  CLUS_1            3            120
  CLUS_2            1             40
  CLUS_3            0             13
  CLUS_4            0             63
D25V11, multiclass
[1] "Remove cluster labels:" "ABI1 MUTATED"          
clus
  ABI1 MUTATED ABI1 WILD-TYPE 
             2            113 
    TCGA-A5-A0GB     TCGA-A5-A0GN     TCGA-A5-A0GQ     TCGA-AJ-A23M 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-AP-A059     TCGA-AP-A0LF     TCGA-AP-A0LM     TCGA-AP-A0LO 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-AP-A1DQ     TCGA-AX-A064     TCGA-AX-A06H     TCGA-AX-A06L 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-AX-A1C7     TCGA-AX-A1C8     TCGA-AX-A1CP     TCGA-AX-A2H5 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-AX-A2HF     TCGA-B5-A0JR     TCGA-B5-A0JT     TCGA-B5-A0K8 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-B5-A11G     TCGA-B5-A11H     TCGA-B5-A11J     TCGA-B5-A11M 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-B5-A11N     TCGA-B5-A11O     TCGA-B5-A11Q     TCGA-B5-A11R 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-B5-A11S     TCGA-B5-A11U     TCGA-B5-A11W     TCGA-B5-A11Z 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-B5-A121     TCGA-B5-A1MU     TCGA-B5-A1MY     TCGA-BG-A0VV 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BG-A0VW     TCGA-BG-A0VX     TCGA-BG-A0YV     TCGA-BG-A186 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BG-A187     TCGA-BG-A18A     TCGA-BG-A18B     TCGA-BG-A18C 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BG-A2AE     TCGA-BK-A0CA     TCGA-BK-A139     TCGA-BK-A13C 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BS-A0T9     TCGA-BS-A0UA     TCGA-BS-A0V6     TCGA-BS-A0V7 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BS-A0V8     TCGA-D1-A0ZN     TCGA-D1-A0ZO     TCGA-D1-A0ZQ 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A0ZS     TCGA-D1-A102     TCGA-D1-A103     TCGA-D1-A15V 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A15W     TCGA-D1-A15X     TCGA-D1-A15Z     TCGA-D1-A160 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A161     TCGA-D1-A163     TCGA-D1-A165     TCGA-D1-A167 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A168     TCGA-D1-A169     TCGA-D1-A16B     TCGA-D1-A16D 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A16E     TCGA-D1-A16F     TCGA-D1-A16G     TCGA-D1-A16I 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A16J     TCGA-D1-A16N     TCGA-D1-A16O     TCGA-D1-A16Q 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A16R     TCGA-D1-A16S     TCGA-D1-A16Y     TCGA-D1-A174 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A176     TCGA-D1-A177     TCGA-D1-A17A     TCGA-D1-A17B 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A17C     TCGA-D1-A17D     TCGA-D1-A17F     TCGA-D1-A17H 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A17K     TCGA-D1-A17L     TCGA-D1-A17M     TCGA-D1-A17N 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A17R     TCGA-D1-A17S     TCGA-D1-A17T     TCGA-D1-A17U 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A1NU     TCGA-D1-A1NX     TCGA-DI-A0WH     TCGA-DI-A1NN 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-E6-A1LZ     TCGA-EO-A1Y5     TCGA-EO-A1Y8     TCGA-EY-A1GS 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-EY-A212     TCGA-FI-A2D2     TCGA-FI-A2EW     TCGA-FI-A2EX 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-FI-A2F8 
"ABI1 WILD-TYPE" 
D25V12, multiclass
[1] "Remove cluster labels:" "ABI1 MUTATED"          
clus
  ABI1 MUTATED ABI1 WILD-TYPE 
             2            113 
    TCGA-A5-A0GB     TCGA-A5-A0GN     TCGA-A5-A0GQ     TCGA-AJ-A23M 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-AP-A059     TCGA-AP-A0LF     TCGA-AP-A0LM     TCGA-AP-A0LO 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-AP-A1DQ     TCGA-AX-A064     TCGA-AX-A06H     TCGA-AX-A06L 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-AX-A1C7     TCGA-AX-A1C8     TCGA-AX-A1CP     TCGA-AX-A2H5 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-AX-A2HF     TCGA-B5-A0JR     TCGA-B5-A0JT     TCGA-B5-A0K8 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-B5-A11G     TCGA-B5-A11H     TCGA-B5-A11J     TCGA-B5-A11M 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-B5-A11N     TCGA-B5-A11O     TCGA-B5-A11Q     TCGA-B5-A11R 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-B5-A11S     TCGA-B5-A11U     TCGA-B5-A11W     TCGA-B5-A11Z 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-B5-A121     TCGA-B5-A1MU     TCGA-B5-A1MY     TCGA-BG-A0VV 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BG-A0VW     TCGA-BG-A0VX     TCGA-BG-A0YV     TCGA-BG-A186 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BG-A187     TCGA-BG-A18A     TCGA-BG-A18B     TCGA-BG-A18C 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BG-A2AE     TCGA-BK-A0CA     TCGA-BK-A139     TCGA-BK-A13C 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BS-A0T9     TCGA-BS-A0UA     TCGA-BS-A0V6     TCGA-BS-A0V7 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BS-A0V8     TCGA-D1-A0ZN     TCGA-D1-A0ZO     TCGA-D1-A0ZQ 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A0ZS     TCGA-D1-A102     TCGA-D1-A103     TCGA-D1-A15V 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A15W     TCGA-D1-A15X     TCGA-D1-A15Z     TCGA-D1-A160 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A161     TCGA-D1-A163     TCGA-D1-A165     TCGA-D1-A167 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A168     TCGA-D1-A169     TCGA-D1-A16B     TCGA-D1-A16D 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A16E     TCGA-D1-A16F     TCGA-D1-A16G     TCGA-D1-A16I 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A16J     TCGA-D1-A16N     TCGA-D1-A16O     TCGA-D1-A16Q 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A16R     TCGA-D1-A16S     TCGA-D1-A16Y     TCGA-D1-A174 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A176     TCGA-D1-A177     TCGA-D1-A17A     TCGA-D1-A17B 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A17C     TCGA-D1-A17D     TCGA-D1-A17F     TCGA-D1-A17H 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A17K     TCGA-D1-A17L     TCGA-D1-A17M     TCGA-D1-A17N 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A17R     TCGA-D1-A17S     TCGA-D1-A17T     TCGA-D1-A17U 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A1NU     TCGA-D1-A1NX     TCGA-DI-A0WH     TCGA-DI-A1NN 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-E6-A1LZ     TCGA-EO-A1Y5     TCGA-EO-A1Y8     TCGA-EY-A1GS 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-EY-A212     TCGA-FI-A2D2     TCGA-FI-A2EW     TCGA-FI-A2EX 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-FI-A2F8 
"ABI1 WILD-TYPE" 

Clustering(26) Variable = FOXA2 MUTATION ANALYSIS
D26V1, multiclass
[1] "Remove cluster labels:" "FOXA2 MUTATED"         
clus
  FOXA2 MUTATED FOXA2 WILD-TYPE 
              2              49 
     TCGA-A5-A0G3      TCGA-A5-A0G5      TCGA-A5-A0GA      TCGA-A5-A0GB 
"FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" 
     TCGA-A5-A0GE      TCGA-A5-A0GH      TCGA-A5-A0GM      TCGA-A5-A0GP 
"FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" 
     TCGA-A5-A0GU      TCGA-AP-A051      TCGA-AP-A052      TCGA-AP-A053 
"FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" 
     TCGA-AP-A054      TCGA-AP-A056      TCGA-AP-A05A      TCGA-AP-A05H 
"FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" 
     TCGA-AP-A05J      TCGA-AP-A05N      TCGA-AP-A05P      TCGA-AP-A0L8 
"FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" 
     TCGA-AP-A0L9      TCGA-AP-A0LD      TCGA-AP-A0LG      TCGA-AP-A0LH 
"FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" 
     TCGA-AP-A0LJ      TCGA-AP-A0LN      TCGA-AP-A0LT      TCGA-AP-A0LV 
"FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" 
     TCGA-AX-A05S      TCGA-AX-A05T      TCGA-AX-A05U      TCGA-AX-A05W 
"FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" 
     TCGA-AX-A05Y      TCGA-AX-A05Z      TCGA-AX-A060      TCGA-AX-A062 
"FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" 
     TCGA-AX-A063      TCGA-AX-A064      TCGA-AX-A06B      TCGA-AX-A0IW 
"FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" 
     TCGA-AX-A0J1      TCGA-B5-A0JR      TCGA-B5-A0JZ      TCGA-B5-A0K0 
"FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" 
     TCGA-B5-A0K1      TCGA-B5-A0K4      TCGA-BG-A0LW      TCGA-BG-A0MI 
"FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" 
     TCGA-BK-A0CC 
"FOXA2 WILD-TYPE" 
D26V2, multiclass
[1] "Remove cluster labels:" "FOXA2 MUTATED"         
clus
  FOXA2 MUTATED FOXA2 WILD-TYPE 
              2              49 
     TCGA-A5-A0G3      TCGA-A5-A0G5      TCGA-A5-A0GA      TCGA-A5-A0GB 
"FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" 
     TCGA-A5-A0GE      TCGA-A5-A0GH      TCGA-A5-A0GM      TCGA-A5-A0GP 
"FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" 
     TCGA-A5-A0GU      TCGA-AP-A051      TCGA-AP-A052      TCGA-AP-A053 
"FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" 
     TCGA-AP-A054      TCGA-AP-A056      TCGA-AP-A05A      TCGA-AP-A05H 
"FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" 
     TCGA-AP-A05J      TCGA-AP-A05N      TCGA-AP-A05P      TCGA-AP-A0L8 
"FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" 
     TCGA-AP-A0L9      TCGA-AP-A0LD      TCGA-AP-A0LG      TCGA-AP-A0LH 
"FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" 
     TCGA-AP-A0LJ      TCGA-AP-A0LN      TCGA-AP-A0LT      TCGA-AP-A0LV 
"FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" 
     TCGA-AX-A05S      TCGA-AX-A05T      TCGA-AX-A05U      TCGA-AX-A05W 
"FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" 
     TCGA-AX-A05Y      TCGA-AX-A05Z      TCGA-AX-A060      TCGA-AX-A062 
"FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" 
     TCGA-AX-A063      TCGA-AX-A064      TCGA-AX-A06B      TCGA-AX-A0IW 
"FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" 
     TCGA-AX-A0J1      TCGA-B5-A0JR      TCGA-B5-A0JZ      TCGA-B5-A0K0 
"FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" 
     TCGA-B5-A0K1      TCGA-B5-A0K4      TCGA-BG-A0LW      TCGA-BG-A0MI 
"FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" "FOXA2 WILD-TYPE" 
     TCGA-BK-A0CC 
"FOXA2 WILD-TYPE" 
D26V3, multiclass
D26V4, multiclass
        clus
vv       FOXA2 MUTATED FOXA2 WILD-TYPE
  CLUS_1             2              40
  CLUS_2             3              38
  CLUS_3             2              49
D26V5, multiclass
D26V6, binary
                 cls
clus                0   1
  FOXA2 MUTATED     7   3
  FOXA2 WILD-TYPE 108  68
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXA2 MUTATED      7    3
  FOXA2 WILD-TYPE  108   68
        clus
vv       FOXA2 MUTATED FOXA2 WILD-TYPE
  CLUS_1             7             108
  CLUS_2             3              68
D26V7, multiclass
        clus
vv       FOXA2 MUTATED FOXA2 WILD-TYPE
  CLUS_1             3              76
  CLUS_2             5              75
  CLUS_3             4              78
D26V8, multiclass
        clus
vv       FOXA2 MUTATED FOXA2 WILD-TYPE
  CLUS_1             3              48
  CLUS_2             5              65
  CLUS_3             0              42
  CLUS_4             4              74
D26V9, multiclass
        clus
vv       FOXA2 MUTATED FOXA2 WILD-TYPE
  CLUS_1             1              70
  CLUS_2             4              87
  CLUS_3             6              72
D26V10, multiclass
        clus
vv       FOXA2 MUTATED FOXA2 WILD-TYPE
  CLUS_1             7             116
  CLUS_2             2              39
  CLUS_3             0              13
  CLUS_4             2              61
D26V11, multiclass
        clus
vv       FOXA2 MUTATED FOXA2 WILD-TYPE
  CLUS_1             3              34
  CLUS_2             4              50
  CLUS_3             0              24
D26V12, multiclass
        clus
vv       FOXA2 MUTATED FOXA2 WILD-TYPE
  CLUS_1             4              51
  CLUS_2             2              49
  CLUS_3             1               8

Clustering(27) Variable = BRS3 MUTATION ANALYSIS
D27V1, multiclass
        clus
vv       BRS3 MUTATED BRS3 WILD-TYPE
  CLUS_1            2             10
  CLUS_2            2             16
  CLUS_3            0             11
  CLUS_4            0             10
D27V2, multiclass
        clus
vv       BRS3 MUTATED BRS3 WILD-TYPE
  CLUS_1            3             14
  CLUS_2            0             18
  CLUS_3            1             15
D27V3, multiclass
D27V4, multiclass
        clus
vv       BRS3 MUTATED BRS3 WILD-TYPE
  CLUS_1            3             39
  CLUS_2            1             40
  CLUS_3            1             50
D27V5, multiclass
D27V6, binary
                cls
clus               0   1
  BRS3 MUTATED     6   6
  BRS3 WILD-TYPE 109  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRS3 MUTATED      6    6
  BRS3 WILD-TYPE  109   65
        clus
vv       BRS3 MUTATED BRS3 WILD-TYPE
  CLUS_1            6            109
  CLUS_2            6             65
D27V7, multiclass
        clus
vv       BRS3 MUTATED BRS3 WILD-TYPE
  CLUS_1            5             74
  CLUS_2            1             79
  CLUS_3            8             74
D27V8, multiclass
        clus
vv       BRS3 MUTATED BRS3 WILD-TYPE
  CLUS_1            0             51
  CLUS_2            1             69
  CLUS_3            6             36
  CLUS_4            7             71
D27V9, multiclass
        clus
vv       BRS3 MUTATED BRS3 WILD-TYPE
  CLUS_1            4             67
  CLUS_2            3             88
  CLUS_3            7             71
D27V10, multiclass
        clus
vv       BRS3 MUTATED BRS3 WILD-TYPE
  CLUS_1            3            120
  CLUS_2            4             37
  CLUS_3            2             11
  CLUS_4            5             58
D27V11, multiclass
        clus
vv       BRS3 MUTATED BRS3 WILD-TYPE
  CLUS_1            2             35
  CLUS_2            1             53
  CLUS_3            1             23
D27V12, multiclass
        clus
vv       BRS3 MUTATED BRS3 WILD-TYPE
  CLUS_1            1             54
  CLUS_2            3             48
  CLUS_3            0              9

Clustering(28) Variable = NRAS MUTATION ANALYSIS
D28V1, multiclass
[1] "Remove cluster labels:" "NRAS MUTATED"          
clus
  NRAS MUTATED NRAS WILD-TYPE 
             2             49 
    TCGA-A5-A0G3     TCGA-A5-A0G5     TCGA-A5-A0GA     TCGA-A5-A0GB 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-A5-A0GE     TCGA-A5-A0GM     TCGA-A5-A0GP     TCGA-A5-A0GU 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AP-A051     TCGA-AP-A052     TCGA-AP-A053     TCGA-AP-A054 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AP-A056     TCGA-AP-A05A     TCGA-AP-A05D     TCGA-AP-A05H 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AP-A05J     TCGA-AP-A05N     TCGA-AP-A05P     TCGA-AP-A0L8 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AP-A0LD     TCGA-AP-A0LG     TCGA-AP-A0LH     TCGA-AP-A0LJ 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AP-A0LN     TCGA-AP-A0LT     TCGA-AP-A0LV     TCGA-AX-A05S 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AX-A05T     TCGA-AX-A05U     TCGA-AX-A05W     TCGA-AX-A05Y 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AX-A05Z     TCGA-AX-A060     TCGA-AX-A062     TCGA-AX-A063 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AX-A064     TCGA-AX-A06B     TCGA-AX-A0IW     TCGA-AX-A0J1 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-B5-A0JR     TCGA-B5-A0JZ     TCGA-B5-A0K0     TCGA-B5-A0K1 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-B5-A0K4     TCGA-BG-A0LW     TCGA-BG-A0MI     TCGA-BK-A0C9 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BK-A0CC 
"NRAS WILD-TYPE" 
D28V2, multiclass
[1] "Remove cluster labels:" "NRAS MUTATED"          
clus
  NRAS MUTATED NRAS WILD-TYPE 
             2             49 
    TCGA-A5-A0G3     TCGA-A5-A0G5     TCGA-A5-A0GA     TCGA-A5-A0GB 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-A5-A0GE     TCGA-A5-A0GM     TCGA-A5-A0GP     TCGA-A5-A0GU 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AP-A051     TCGA-AP-A052     TCGA-AP-A053     TCGA-AP-A054 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AP-A056     TCGA-AP-A05A     TCGA-AP-A05D     TCGA-AP-A05H 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AP-A05J     TCGA-AP-A05N     TCGA-AP-A05P     TCGA-AP-A0L8 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AP-A0LD     TCGA-AP-A0LG     TCGA-AP-A0LH     TCGA-AP-A0LJ 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AP-A0LN     TCGA-AP-A0LT     TCGA-AP-A0LV     TCGA-AX-A05S 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AX-A05T     TCGA-AX-A05U     TCGA-AX-A05W     TCGA-AX-A05Y 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AX-A05Z     TCGA-AX-A060     TCGA-AX-A062     TCGA-AX-A063 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AX-A064     TCGA-AX-A06B     TCGA-AX-A0IW     TCGA-AX-A0J1 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-B5-A0JR     TCGA-B5-A0JZ     TCGA-B5-A0K0     TCGA-B5-A0K1 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-B5-A0K4     TCGA-BG-A0LW     TCGA-BG-A0MI     TCGA-BK-A0C9 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BK-A0CC 
"NRAS WILD-TYPE" 
D28V3, multiclass
D28V4, multiclass
[1] "Remove cluster labels:" "NRAS MUTATED"          
clus
  NRAS MUTATED NRAS WILD-TYPE 
             2            132 
    TCGA-A5-A0GQ     TCGA-A5-A0VO     TCGA-AJ-A23M     TCGA-AP-A059 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AP-A0LF     TCGA-AP-A0LM     TCGA-AP-A1DQ     TCGA-AX-A06H 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AX-A06L     TCGA-AX-A0IS     TCGA-AX-A1C7     TCGA-AX-A1C8 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AX-A1CP     TCGA-AX-A2H5     TCGA-AX-A2HF     TCGA-B5-A0JT 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-B5-A0K8     TCGA-B5-A11E     TCGA-B5-A11F     TCGA-B5-A11G 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-B5-A11H     TCGA-B5-A11I     TCGA-B5-A11J     TCGA-B5-A11M 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-B5-A11N     TCGA-B5-A11O     TCGA-B5-A11Q     TCGA-B5-A11R 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-B5-A11S     TCGA-B5-A11U     TCGA-B5-A11V     TCGA-B5-A11W 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-B5-A11X     TCGA-B5-A11Y     TCGA-B5-A11Z     TCGA-B5-A121 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-B5-A1MU     TCGA-B5-A1MY     TCGA-BG-A0VT     TCGA-BG-A0VV 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BG-A0VW     TCGA-BG-A0VX     TCGA-BG-A0VZ     TCGA-BG-A0W1 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BG-A0W2     TCGA-BG-A0YU     TCGA-BG-A0YV     TCGA-BG-A186 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BG-A187     TCGA-BG-A18A     TCGA-BG-A18B     TCGA-BG-A18C 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BG-A2AE     TCGA-BK-A0CA     TCGA-BK-A139     TCGA-BK-A13C 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BS-A0T9     TCGA-BS-A0U5     TCGA-BS-A0U9     TCGA-BS-A0UA 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BS-A0UL     TCGA-BS-A0V6     TCGA-BS-A0V7     TCGA-BS-A0V8 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BS-A0WQ     TCGA-D1-A0ZN     TCGA-D1-A0ZO     TCGA-D1-A0ZP 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A0ZQ     TCGA-D1-A0ZR     TCGA-D1-A0ZS     TCGA-D1-A0ZU 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A0ZV     TCGA-D1-A0ZZ     TCGA-D1-A101     TCGA-D1-A102 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A103     TCGA-D1-A15V     TCGA-D1-A15W     TCGA-D1-A15X 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A15Z     TCGA-D1-A160     TCGA-D1-A161     TCGA-D1-A163 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A165     TCGA-D1-A167     TCGA-D1-A168     TCGA-D1-A169 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A16B     TCGA-D1-A16D     TCGA-D1-A16E     TCGA-D1-A16F 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A16G     TCGA-D1-A16I     TCGA-D1-A16J     TCGA-D1-A16N 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A16O     TCGA-D1-A16Q     TCGA-D1-A16R     TCGA-D1-A16S 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A16X     TCGA-D1-A16Y     TCGA-D1-A174     TCGA-D1-A176 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A177     TCGA-D1-A17A     TCGA-D1-A17B     TCGA-D1-A17C 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A17D     TCGA-D1-A17H     TCGA-D1-A17K     TCGA-D1-A17L 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A17M     TCGA-D1-A17N     TCGA-D1-A17Q     TCGA-D1-A17R 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A17S     TCGA-D1-A17T     TCGA-D1-A17U     TCGA-D1-A1NU 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A1NX     TCGA-DI-A0WH     TCGA-DI-A1NN     TCGA-E6-A1LZ 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-EO-A1Y5     TCGA-EO-A1Y8     TCGA-EY-A1GS     TCGA-EY-A212 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-FI-A2D2     TCGA-FI-A2EW     TCGA-FI-A2EX     TCGA-FI-A2F8 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
D28V5, multiclass
D28V6, binary
                cls
clus               0   1
  NRAS MUTATED     4   2
  NRAS WILD-TYPE 111  69
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      4    2
  NRAS WILD-TYPE  111   69
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            4            111
  CLUS_2            2             69
D28V7, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            3             76
  CLUS_2            2             78
  CLUS_3            4             78
D28V8, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            2             49
  CLUS_2            2             68
  CLUS_3            2             40
  CLUS_4            3             75
D28V9, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            3             68
  CLUS_2            2             89
  CLUS_3            4             74
D28V10, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            4            119
  CLUS_2            1             40
  CLUS_3            1             12
  CLUS_4            3             60
D28V11, multiclass
[1] "Remove cluster labels:" "NRAS MUTATED"          
clus
  NRAS MUTATED NRAS WILD-TYPE 
             1            114 
    TCGA-A5-A0GB     TCGA-A5-A0GN     TCGA-A5-A0GQ     TCGA-AJ-A23M 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AP-A059     TCGA-AP-A0LF     TCGA-AP-A0LM     TCGA-AP-A0LO 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AP-A1DQ     TCGA-AX-A064     TCGA-AX-A06H     TCGA-AX-A06L 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AX-A1C7     TCGA-AX-A1C8     TCGA-AX-A1CP     TCGA-AX-A2H5 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AX-A2HF     TCGA-B5-A0JR     TCGA-B5-A0JT     TCGA-B5-A0K8 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-B5-A11G     TCGA-B5-A11H     TCGA-B5-A11J     TCGA-B5-A11M 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-B5-A11N     TCGA-B5-A11O     TCGA-B5-A11Q     TCGA-B5-A11R 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-B5-A11S     TCGA-B5-A11U     TCGA-B5-A11W     TCGA-B5-A11Z 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-B5-A121     TCGA-B5-A1MU     TCGA-B5-A1MY     TCGA-BG-A0VV 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BG-A0VW     TCGA-BG-A0VX     TCGA-BG-A0YV     TCGA-BG-A186 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BG-A187     TCGA-BG-A18A     TCGA-BG-A18B     TCGA-BG-A18C 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BG-A2AE     TCGA-BK-A0CA     TCGA-BK-A139     TCGA-BK-A13C 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BS-A0T9     TCGA-BS-A0UA     TCGA-BS-A0V6     TCGA-BS-A0V7 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BS-A0V8     TCGA-D1-A0ZN     TCGA-D1-A0ZO     TCGA-D1-A0ZQ 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A0ZS     TCGA-D1-A102     TCGA-D1-A103     TCGA-D1-A15V 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A15W     TCGA-D1-A15X     TCGA-D1-A15Z     TCGA-D1-A160 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A161     TCGA-D1-A163     TCGA-D1-A165     TCGA-D1-A167 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A168     TCGA-D1-A169     TCGA-D1-A16B     TCGA-D1-A16D 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A16E     TCGA-D1-A16F     TCGA-D1-A16G     TCGA-D1-A16I 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A16J     TCGA-D1-A16N     TCGA-D1-A16O     TCGA-D1-A16Q 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A16R     TCGA-D1-A16S     TCGA-D1-A16X     TCGA-D1-A16Y 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A174     TCGA-D1-A176     TCGA-D1-A177     TCGA-D1-A17A 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A17B     TCGA-D1-A17C     TCGA-D1-A17D     TCGA-D1-A17H 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A17K     TCGA-D1-A17L     TCGA-D1-A17M     TCGA-D1-A17N 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A17Q     TCGA-D1-A17R     TCGA-D1-A17S     TCGA-D1-A17T 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A17U     TCGA-D1-A1NU     TCGA-D1-A1NX     TCGA-DI-A0WH 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-DI-A1NN     TCGA-E6-A1LZ     TCGA-EO-A1Y5     TCGA-EO-A1Y8 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-EY-A1GS     TCGA-EY-A212     TCGA-FI-A2D2     TCGA-FI-A2EW 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-FI-A2EX     TCGA-FI-A2F8 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" 
D28V12, multiclass
[1] "Remove cluster labels:" "NRAS MUTATED"          
clus
  NRAS MUTATED NRAS WILD-TYPE 
             1            114 
    TCGA-A5-A0GB     TCGA-A5-A0GN     TCGA-A5-A0GQ     TCGA-AJ-A23M 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AP-A059     TCGA-AP-A0LF     TCGA-AP-A0LM     TCGA-AP-A0LO 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AP-A1DQ     TCGA-AX-A064     TCGA-AX-A06H     TCGA-AX-A06L 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AX-A1C7     TCGA-AX-A1C8     TCGA-AX-A1CP     TCGA-AX-A2H5 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AX-A2HF     TCGA-B5-A0JR     TCGA-B5-A0JT     TCGA-B5-A0K8 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-B5-A11G     TCGA-B5-A11H     TCGA-B5-A11J     TCGA-B5-A11M 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-B5-A11N     TCGA-B5-A11O     TCGA-B5-A11Q     TCGA-B5-A11R 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-B5-A11S     TCGA-B5-A11U     TCGA-B5-A11W     TCGA-B5-A11Z 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-B5-A121     TCGA-B5-A1MU     TCGA-B5-A1MY     TCGA-BG-A0VV 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BG-A0VW     TCGA-BG-A0VX     TCGA-BG-A0YV     TCGA-BG-A186 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BG-A187     TCGA-BG-A18A     TCGA-BG-A18B     TCGA-BG-A18C 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BG-A2AE     TCGA-BK-A0CA     TCGA-BK-A139     TCGA-BK-A13C 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BS-A0T9     TCGA-BS-A0UA     TCGA-BS-A0V6     TCGA-BS-A0V7 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BS-A0V8     TCGA-D1-A0ZN     TCGA-D1-A0ZO     TCGA-D1-A0ZQ 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A0ZS     TCGA-D1-A102     TCGA-D1-A103     TCGA-D1-A15V 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A15W     TCGA-D1-A15X     TCGA-D1-A15Z     TCGA-D1-A160 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A161     TCGA-D1-A163     TCGA-D1-A165     TCGA-D1-A167 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A168     TCGA-D1-A169     TCGA-D1-A16B     TCGA-D1-A16D 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A16E     TCGA-D1-A16F     TCGA-D1-A16G     TCGA-D1-A16I 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A16J     TCGA-D1-A16N     TCGA-D1-A16O     TCGA-D1-A16Q 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A16R     TCGA-D1-A16S     TCGA-D1-A16X     TCGA-D1-A16Y 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A174     TCGA-D1-A176     TCGA-D1-A177     TCGA-D1-A17A 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A17B     TCGA-D1-A17C     TCGA-D1-A17D     TCGA-D1-A17H 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A17K     TCGA-D1-A17L     TCGA-D1-A17M     TCGA-D1-A17N 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A17Q     TCGA-D1-A17R     TCGA-D1-A17S     TCGA-D1-A17T 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A17U     TCGA-D1-A1NU     TCGA-D1-A1NX     TCGA-DI-A0WH 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-DI-A1NN     TCGA-E6-A1LZ     TCGA-EO-A1Y5     TCGA-EO-A1Y8 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-EY-A1GS     TCGA-EY-A212     TCGA-FI-A2D2     TCGA-FI-A2EW 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-FI-A2EX     TCGA-FI-A2F8 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" 

Clustering(29) Variable = DNER MUTATION ANALYSIS
D29V1, multiclass
        clus
vv       DNER MUTATED DNER WILD-TYPE
  CLUS_1            3              9
  CLUS_2            2             16
  CLUS_3            0             11
  CLUS_4            0             10
D29V2, multiclass
        clus
vv       DNER MUTATED DNER WILD-TYPE
  CLUS_1            4             13
  CLUS_2            0             18
  CLUS_3            1             15
D29V3, multiclass
D29V4, multiclass
        clus
vv       DNER MUTATED DNER WILD-TYPE
  CLUS_1            3             39
  CLUS_2            1             40
  CLUS_3            4             47
D29V5, multiclass
D29V6, binary
                cls
clus               0   1
  DNER MUTATED     8   7
  DNER WILD-TYPE 107  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  DNER MUTATED      8    7
  DNER WILD-TYPE  107   64
        clus
vv       DNER MUTATED DNER WILD-TYPE
  CLUS_1            8            107
  CLUS_2            7             64
D29V7, multiclass
        clus
vv       DNER MUTATED DNER WILD-TYPE
  CLUS_1            7             72
  CLUS_2            4             76
  CLUS_3            6             76
D29V8, multiclass
        clus
vv       DNER MUTATED DNER WILD-TYPE
  CLUS_1            0             51
  CLUS_2            4             66
  CLUS_3            7             35
  CLUS_4            6             72
D29V9, multiclass
        clus
vv       DNER MUTATED DNER WILD-TYPE
  CLUS_1            5             66
  CLUS_2            5             86
  CLUS_3            7             71
D29V10, multiclass
        clus
vv       DNER MUTATED DNER WILD-TYPE
  CLUS_1            6            117
  CLUS_2            3             38
  CLUS_3            3             10
  CLUS_4            5             58
D29V11, multiclass
        clus
vv       DNER MUTATED DNER WILD-TYPE
  CLUS_1            1             36
  CLUS_2            4             50
  CLUS_3            2             22
D29V12, multiclass
        clus
vv       DNER MUTATED DNER WILD-TYPE
  CLUS_1            4             51
  CLUS_2            3             48
  CLUS_3            0              9

Clustering(30) Variable = TIAL1 MUTATION ANALYSIS
D30V1, multiclass
        clus
vv       TIAL1 MUTATED TIAL1 WILD-TYPE
  CLUS_1             2              10
  CLUS_2             1              17
  CLUS_3             0              11
  CLUS_4             0              10
D30V2, multiclass
        clus
vv       TIAL1 MUTATED TIAL1 WILD-TYPE
  CLUS_1             2              15
  CLUS_2             0              18
  CLUS_3             1              15
D30V3, multiclass
D30V4, multiclass
        clus
vv       TIAL1 MUTATED TIAL1 WILD-TYPE
  CLUS_1             1              41
  CLUS_2             0              41
  CLUS_3             5              46
D30V5, multiclass
D30V6, binary
                 cls
clus                0   1
  TIAL1 MUTATED     7   3
  TIAL1 WILD-TYPE 108  68
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIAL1 MUTATED      7    3
  TIAL1 WILD-TYPE  108   68
        clus
vv       TIAL1 MUTATED TIAL1 WILD-TYPE
  CLUS_1             7             108
  CLUS_2             3              68
D30V7, multiclass
        clus
vv       TIAL1 MUTATED TIAL1 WILD-TYPE
  CLUS_1             2              77
  CLUS_2             2              78
  CLUS_3             7              75
D30V8, multiclass
        clus
vv       TIAL1 MUTATED TIAL1 WILD-TYPE
  CLUS_1             0              51
  CLUS_2             2              68
  CLUS_3             5              37
  CLUS_4             4              74
D30V9, multiclass
        clus
vv       TIAL1 MUTATED TIAL1 WILD-TYPE
  CLUS_1             2              69
  CLUS_2             5              86
  CLUS_3             4              74
D30V10, multiclass
        clus
vv       TIAL1 MUTATED TIAL1 WILD-TYPE
  CLUS_1             5             118
  CLUS_2             2              39
  CLUS_3             1              12
  CLUS_4             3              60
D30V11, multiclass
        clus
vv       TIAL1 MUTATED TIAL1 WILD-TYPE
  CLUS_1             1              36
  CLUS_2             4              50
  CLUS_3             1              23
D30V12, multiclass
        clus
vv       TIAL1 MUTATED TIAL1 WILD-TYPE
  CLUS_1             4              51
  CLUS_2             1              50
  CLUS_3             1               8

Clustering(31) Variable = RPL14 MUTATION ANALYSIS
D31V1, multiclass
D31V2, multiclass
D31V3, multiclass
D31V4, multiclass
        clus
vv       RPL14 MUTATED RPL14 WILD-TYPE
  CLUS_1             2              40
  CLUS_2             1              40
  CLUS_3             3              48
D31V5, multiclass
D31V6, binary
                 cls
clus                0   1
  RPL14 MUTATED     3   2
  RPL14 WILD-TYPE 112  69
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPL14 MUTATED      3    2
  RPL14 WILD-TYPE  112   69
        clus
vv       RPL14 MUTATED RPL14 WILD-TYPE
  CLUS_1             3             112
  CLUS_2             2              69
D31V7, multiclass
        clus
vv       RPL14 MUTATED RPL14 WILD-TYPE
  CLUS_1             2              77
  CLUS_2             3              77
  CLUS_3             2              80
D31V8, multiclass
        clus
vv       RPL14 MUTATED RPL14 WILD-TYPE
  CLUS_1             1              50
  CLUS_2             3              67
  CLUS_3             2              40
  CLUS_4             1              77
D31V9, multiclass
        clus
vv       RPL14 MUTATED RPL14 WILD-TYPE
  CLUS_1             1              70
  CLUS_2             4              87
  CLUS_3             1              77
D31V10, multiclass
        clus
vv       RPL14 MUTATED RPL14 WILD-TYPE
  CLUS_1             4             119
  CLUS_2             1              40
  CLUS_3             0              13
  CLUS_4             1              62
D31V11, multiclass
        clus
vv       RPL14 MUTATED RPL14 WILD-TYPE
  CLUS_1             1              36
  CLUS_2             3              51
  CLUS_3             1              23
D31V12, multiclass
        clus
vv       RPL14 MUTATED RPL14 WILD-TYPE
  CLUS_1             3              52
  CLUS_2             2              49
  CLUS_3             0               9

Clustering(32) Variable = SGK1 MUTATION ANALYSIS
D32V1, multiclass
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  CLUS_1            2             10
  CLUS_2            1             17
  CLUS_3            0             11
  CLUS_4            0             10
D32V2, multiclass
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  CLUS_1            3             14
  CLUS_2            0             18
  CLUS_3            0             16
D32V3, multiclass
D32V4, multiclass
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  CLUS_1            1             41
  CLUS_2            1             40
  CLUS_3            3             48
D32V5, multiclass
D32V6, binary
                cls
clus               0   1
  SGK1 MUTATED     6   9
  SGK1 WILD-TYPE 109  62
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGK1 MUTATED      6    9
  SGK1 WILD-TYPE  109   62
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  CLUS_1            6            109
  CLUS_2            9             62
D32V7, multiclass
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  CLUS_1            4             75
  CLUS_2            6             74
  CLUS_3            5             77
D32V8, multiclass
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  CLUS_1            3             48
  CLUS_2            4             66
  CLUS_3            4             38
  CLUS_4            4             74
D32V9, multiclass
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  CLUS_1            2             69
  CLUS_2            5             86
  CLUS_3            7             71
D32V10, multiclass
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  CLUS_1            7            116
  CLUS_2            2             39
  CLUS_3            2             11
  CLUS_4            3             60
D32V11, multiclass
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  CLUS_1            1             36
  CLUS_2            3             51
  CLUS_3            0             24
D32V12, multiclass
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  CLUS_1            3             52
  CLUS_2            1             50
  CLUS_3            0              9

Clustering(33) Variable = SLC48A1 MUTATION ANALYSIS
D33V1, multiclass
D33V2, multiclass
D33V3, multiclass
D33V4, multiclass
        clus
vv       SLC48A1 MUTATED SLC48A1 WILD-TYPE
  CLUS_1               0                42
  CLUS_2               1                40
  CLUS_3               2                49
D33V5, multiclass
D33V6, binary
                   cls
clus                  0   1
  SLC48A1 MUTATED     2   3
  SLC48A1 WILD-TYPE 113  68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC48A1 MUTATED      2    3
  SLC48A1 WILD-TYPE  113   68
        clus
vv       SLC48A1 MUTATED SLC48A1 WILD-TYPE
  CLUS_1               2               113
  CLUS_2               3                68
D33V7, multiclass
        clus
vv       SLC48A1 MUTATED SLC48A1 WILD-TYPE
  CLUS_1               1                78
  CLUS_2               1                79
  CLUS_3               3                79
D33V8, multiclass
        clus
vv       SLC48A1 MUTATED SLC48A1 WILD-TYPE
  CLUS_1               1                50
  CLUS_2               1                69
  CLUS_3               1                41
  CLUS_4               2                76
D33V9, multiclass
        clus
vv       SLC48A1 MUTATED SLC48A1 WILD-TYPE
  CLUS_1               1                70
  CLUS_2               1                90
  CLUS_3               3                75
D33V10, multiclass
        clus
vv       SLC48A1 MUTATED SLC48A1 WILD-TYPE
  CLUS_1               2               121
  CLUS_2               2                39
  CLUS_3               0                13
  CLUS_4               1                62
D33V11, multiclass
        clus
vv       SLC48A1 MUTATED SLC48A1 WILD-TYPE
  CLUS_1               1                36
  CLUS_2               1                53
  CLUS_3               1                23
D33V12, multiclass
        clus
vv       SLC48A1 MUTATED SLC48A1 WILD-TYPE
  CLUS_1               1                54
  CLUS_2               2                49
  CLUS_3               0                 9

Clustering(34) Variable = BCOR MUTATION ANALYSIS
D34V1, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            1             11
  CLUS_2            2             16
  CLUS_3            0             11
  CLUS_4            0             10
D34V2, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            2             15
  CLUS_2            0             18
  CLUS_3            1             15
D34V3, multiclass
D34V4, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            1             41
  CLUS_2            4             37
  CLUS_3           10             41
D34V5, multiclass
D34V6, binary
                cls
clus               0   1
  BCOR MUTATED    13  11
  BCOR WILD-TYPE 102  60
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED     13   11
  BCOR WILD-TYPE  102   60
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1           13            102
  CLUS_2           11             60
D34V7, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            6             73
  CLUS_2            8             72
  CLUS_3           15             67
D34V8, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            6             45
  CLUS_2            6             64
  CLUS_3            9             33
  CLUS_4            8             70
D34V9, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            9             62
  CLUS_2           10             81
  CLUS_3           10             68
D34V10, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1           13            110
  CLUS_2            4             37
  CLUS_3            4              9
  CLUS_4            8             55
D34V11, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            3             34
  CLUS_2            6             48
  CLUS_3            4             20
D34V12, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            7             48
  CLUS_2            4             47
  CLUS_3            2              7

Clustering(35) Variable = ZNF263 MUTATION ANALYSIS
D35V1, multiclass
        clus
vv       ZNF263 MUTATED ZNF263 WILD-TYPE
  CLUS_1              3                9
  CLUS_2              0               18
  CLUS_3              0               11
  CLUS_4              0               10
D35V2, multiclass
        clus
vv       ZNF263 MUTATED ZNF263 WILD-TYPE
  CLUS_1              3               14
  CLUS_2              0               18
  CLUS_3              0               16
D35V3, multiclass
D35V4, multiclass
        clus
vv       ZNF263 MUTATED ZNF263 WILD-TYPE
  CLUS_1              1               41
  CLUS_2              0               41
  CLUS_3              3               48
D35V5, multiclass
D35V6, binary
                  cls
clus                 0   1
  ZNF263 MUTATED     5   3
  ZNF263 WILD-TYPE 110  68
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF263 MUTATED      5    3
  ZNF263 WILD-TYPE  110   68
        clus
vv       ZNF263 MUTATED ZNF263 WILD-TYPE
  CLUS_1              5              110
  CLUS_2              3               68
D35V7, multiclass
        clus
vv       ZNF263 MUTATED ZNF263 WILD-TYPE
  CLUS_1              1               78
  CLUS_2              2               78
  CLUS_3              5               77
D35V8, multiclass
        clus
vv       ZNF263 MUTATED ZNF263 WILD-TYPE
  CLUS_1              0               51
  CLUS_2              2               68
  CLUS_3              4               38
  CLUS_4              2               76
D35V9, multiclass
        clus
vv       ZNF263 MUTATED ZNF263 WILD-TYPE
  CLUS_1              0               71
  CLUS_2              4               87
  CLUS_3              4               74
D35V10, multiclass
        clus
vv       ZNF263 MUTATED ZNF263 WILD-TYPE
  CLUS_1              4              119
  CLUS_2              4               37
  CLUS_3              0               13
  CLUS_4              0               63
D35V11, multiclass
        clus
vv       ZNF263 MUTATED ZNF263 WILD-TYPE
  CLUS_1              0               37
  CLUS_2              3               51
  CLUS_3              1               23
D35V12, multiclass
        clus
vv       ZNF263 MUTATED ZNF263 WILD-TYPE
  CLUS_1              2               53
  CLUS_2              1               50
  CLUS_3              1                8

Clustering(36) Variable = RNF43 MUTATION ANALYSIS
D36V1, multiclass
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  CLUS_1             3               9
  CLUS_2             1              17
  CLUS_3             0              11
  CLUS_4             0              10
D36V2, multiclass
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  CLUS_1             3              14
  CLUS_2             0              18
  CLUS_3             1              15
D36V3, multiclass
D36V4, multiclass
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  CLUS_1             2              40
  CLUS_2             0              41
  CLUS_3             3              48
D36V5, multiclass
D36V6, binary
                 cls
clus                0   1
  RNF43 MUTATED     8   4
  RNF43 WILD-TYPE 107  67
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED      8    4
  RNF43 WILD-TYPE  107   67
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  CLUS_1             8             107
  CLUS_2             4              67
D36V7, multiclass
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  CLUS_1             3              76
  CLUS_2             1              79
  CLUS_3             8              74
D36V8, multiclass
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  CLUS_1             1              50
  CLUS_2             1              69
  CLUS_3             9              33
  CLUS_4             1              77
D36V9, multiclass
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  CLUS_1             2              69
  CLUS_2             2              89
  CLUS_3             8              70
D36V10, multiclass
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  CLUS_1             3             120
  CLUS_2             5              36
  CLUS_3             2              11
  CLUS_4             2              61
D36V11, multiclass
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  CLUS_1             2              35
  CLUS_2             0              54
  CLUS_3             2              22
D36V12, multiclass
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  CLUS_1             0              55
  CLUS_2             3              48
  CLUS_3             1               8
                           V1                            V2 
                  "MRNA_CNMF"          "MRNA_CHIERARCHICAL" 
                           V3                            V4 
                    "CN_CNMF"            "METHLYATION_CNMF" 
                           V5                            V6 
                  "RPPA_CNMF"          "RPPA_CHIERARCHICAL" 
                           V7                            V8 
               "MRNASEQ_CNMF"       "MRNASEQ_CHIERARCHICAL" 
                           V9                           V10 
                "MIRSEQ_CNMF"        "MIRSEQ_CHIERARCHICAL" 
                          V11                           V12 
         "MIRSEQ_MATURE_CNMF" "MIRSEQ_MATURE_CHIERARCHICAL" 
> q(save="no")
