
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/480583/UCEC-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/UCEC-TP/4474554/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=515, in cluster file=248, common to both=248
[1]  38 248
[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] "MORC4 MUTATION ANALYSIS"
[1] 3
  MORC4 MUTATED MORC4 WILD-TYPE 
             20             228 
  MORC4 MUTATED MORC4 WILD-TYPE 
             20             228 
[1] "HPD MUTATION ANALYSIS"
[1] 3
  HPD MUTATED HPD WILD-TYPE 
            7           241 
  HPD MUTATED HPD WILD-TYPE 
            7           241 
[1] "CASP8 MUTATION ANALYSIS"
[1] 3
  CASP8 MUTATED CASP8 WILD-TYPE 
             17             231 
  CASP8 MUTATED CASP8 WILD-TYPE 
             17             231 
[1] "FOXA2 MUTATION ANALYSIS"
[1] 3
  FOXA2 MUTATED FOXA2 WILD-TYPE 
             12             236 
  FOXA2 MUTATED FOXA2 WILD-TYPE 
             12             236 
[1] "ABI1 MUTATION ANALYSIS"
[1] 3
  ABI1 MUTATED ABI1 WILD-TYPE 
             4            244 
  ABI1 MUTATED ABI1 WILD-TYPE 
             4            244 
[1] "DNER MUTATION ANALYSIS"
[1] 3
  DNER MUTATED DNER WILD-TYPE 
            18            230 
  DNER MUTATED DNER WILD-TYPE 
            18            230 
[1] "BCOR MUTATION ANALYSIS"
[1] 3
  BCOR MUTATED BCOR WILD-TYPE 
            30            218 
  BCOR MUTATED BCOR WILD-TYPE 
            30            218 
[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] "SGK1 MUTATION ANALYSIS"
[1] 3
  SGK1 MUTATED SGK1 WILD-TYPE 
            15            233 
  SGK1 MUTATED SGK1 WILD-TYPE 
            15            233 
[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] "SIN3A MUTATION ANALYSIS"
[1] 3
  SIN3A MUTATED SIN3A WILD-TYPE 
             21             227 
  SIN3A MUTATED SIN3A WILD-TYPE 
             21             227 
[1] "SLC48A1 MUTATION ANALYSIS"
[1] 3
  SLC48A1 MUTATED SLC48A1 WILD-TYPE 
                5               243 
  SLC48A1 MUTATED SLC48A1 WILD-TYPE 
                5               243 
[1] "ZFHX3 MUTATION ANALYSIS"
[1] 3
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
             44             204 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
             44             204 
[1] "RNF43 MUTATION ANALYSIS"
[1] 3
  RNF43 MUTATED RNF43 WILD-TYPE 
             12             236 
  RNF43 MUTATED RNF43 WILD-TYPE 
             12             236 
[1] "ZNF263 MUTATION ANALYSIS"
[1] 3
  ZNF263 MUTATED ZNF263 WILD-TYPE 
               8              240 
  ZNF263 MUTATED ZNF263 WILD-TYPE 
               8              240 
[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=6,	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=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'MIRSEQ_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	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=4,	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] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "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 10 non-survival variables.
MRNA_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
CN_CNMF, nv=6, 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
MIRSEQ_CNMF, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=4, 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              10                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
D1V8, multiclass
        clus
vv       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  CLUS_1               0                10
  CLUS_2               8               128
  CLUS_3              17                77
D1V9, multiclass
        clus
vv       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  CLUS_1               9                27
  CLUS_2               4                51
  CLUS_3               3                22
D1V10, multiclass
        clus
vv       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  CLUS_1               5                17
  CLUS_2               3                54
  CLUS_3               8                19
  CLUS_4               0                10

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               21
  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
D2V8, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              4                6
  CLUS_2             76               60
  CLUS_3             48               46
D2V9, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             15               21
  CLUS_2             31               24
  CLUS_3             13               12
D2V10, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             11               11
  CLUS_2             32               25
  CLUS_3             13               14
  CLUS_4              3                7

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               39
  CLUS_2             15               26
  CLUS_3             18               33
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
D3V8, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              3                7
  CLUS_2             50               86
  CLUS_3             18               76
D3V9, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              3               33
  CLUS_2             15               40
  CLUS_3              9               16
D3V10, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              2               20
  CLUS_2             16               41
  CLUS_3              1               26
  CLUS_4              8                2

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               38
  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
D4V8, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              5                5
  CLUS_2             54               82
  CLUS_3             22               72
D4V9, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              5               31
  CLUS_2             23               32
  CLUS_3              9               16
D4V10, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              4               18
  CLUS_2             24               33
  CLUS_3              3               24
  CLUS_4              6                4

Clustering(5) Variable = PRKAR1B MUTATION ANALYSIS
D5V1, multiclass
D5V2, multiclass
D5V3, multiclass
D5V4, multiclass
        clus
vv       PRKAR1B MUTATED PRKAR1B WILD-TYPE
  CLUS_1               2                41
  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
D5V8, multiclass
        clus
vv       PRKAR1B MUTATED PRKAR1B WILD-TYPE
  CLUS_1               1                 9
  CLUS_2               1               135
  CLUS_3               2                92
D5V9, multiclass
        clus
vv       PRKAR1B MUTATED PRKAR1B WILD-TYPE
  CLUS_1               1                35
  CLUS_2               1                54
  CLUS_3               1                24
D5V10, multiclass
        clus
vv       PRKAR1B MUTATED PRKAR1B WILD-TYPE
  CLUS_1               1                21
  CLUS_2               1                56
  CLUS_3               1                26
  CLUS_4               0                10

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             36
  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
D6V8, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            9              1
  CLUS_2          113             23
  CLUS_3           36             58
D6V9, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           10             26
  CLUS_2           49              6
  CLUS_3           11             14
D6V10, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            6             16
  CLUS_2           52              5
  CLUS_3            5             22
  CLUS_4            7              3

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              41
  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
D7V8, multiclass
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  CLUS_1             4               6
  CLUS_2            15             121
  CLUS_3            12              82
D7V9, multiclass
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  CLUS_1             2              34
  CLUS_2             8              47
  CLUS_3             5              20
D7V10, multiclass
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  CLUS_1             4              18
  CLUS_2             7              50
  CLUS_3             3              24
  CLUS_4             1               9

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             37
  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
D8V8, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            2              8
  CLUS_2           31            105
  CLUS_3           19             75
D8V9, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            3             33
  CLUS_2           14             41
  CLUS_3            8             17
D8V10, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            6             16
  CLUS_2           15             42
  CLUS_3            4             23
  CLUS_4            0             10

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           31             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
D9V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            6              4
  CLUS_2           10            126
  CLUS_3           48             46
D9V9, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           25             11
  CLUS_2            5             50
  CLUS_3            6             19
D9V10, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            9             13
  CLUS_2            5             52
  CLUS_3           20              7
  CLUS_4            2              8

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              32
  CLUS_2             3              38
  CLUS_3             8              43
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
D10V8, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             2               8
  CLUS_2            15             121
  CLUS_3            18              76
D10V9, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             8              28
  CLUS_2             6              49
  CLUS_3             4              21
D10V10, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             4              18
  CLUS_2             6              51
  CLUS_3             8              19
  CLUS_4             0              10

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             40
  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
D11V8, multiclass
        clus
vv       CTCF MUTATED CTCF WILD-TYPE
  CLUS_1            2              8
  CLUS_2           35            101
  CLUS_3            8             86
D11V9, multiclass
        clus
vv       CTCF MUTATED CTCF WILD-TYPE
  CLUS_1            1             35
  CLUS_2           12             43
  CLUS_3            1             24
D11V10, multiclass
        clus
vv       CTCF MUTATED CTCF WILD-TYPE
  CLUS_1            1             21
  CLUS_2           11             46
  CLUS_3            1             26
  CLUS_4            1              9

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               33
  CLUS_2             16               25
  CLUS_3             19               32
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
D12V8, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              5                5
  CLUS_2             54               82
  CLUS_3             21               73
D12V9, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              6               30
  CLUS_2             24               31
  CLUS_3             10               15
D12V10, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              7               15
  CLUS_2             25               32
  CLUS_3              5               22
  CLUS_4              3                7

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             39
  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
D13V8, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            0             10
  CLUS_2           11            125
  CLUS_3           10             84
D13V9, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            4             32
  CLUS_2            3             52
  CLUS_3            2             23
D13V10, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            2             20
  CLUS_2            4             53
  CLUS_3            3             24
  CLUS_4            0             10

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               42
  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
D14V8, multiclass
        clus
vv       ARID5B MUTATED ARID5B WILD-TYPE
  CLUS_1              2                8
  CLUS_2             16              120
  CLUS_3              9               85
D14V9, multiclass
        clus
vv       ARID5B MUTATED ARID5B WILD-TYPE
  CLUS_1              1               35
  CLUS_2              5               50
  CLUS_3              0               25
D14V10, multiclass
        clus
vv       ARID5B MUTATED ARID5B WILD-TYPE
  CLUS_1              0               22
  CLUS_2              5               52
  CLUS_3              1               26
  CLUS_4              0               10

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              38
  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
D15V8, multiclass
        clus
vv       FGFR2 MUTATED FGFR2 WILD-TYPE
  CLUS_1             4               6
  CLUS_2            16             120
  CLUS_3            10              84
D15V9, multiclass
        clus
vv       FGFR2 MUTATED FGFR2 WILD-TYPE
  CLUS_1             6              30
  CLUS_2             8              47
  CLUS_3             2              23
D15V10, multiclass
        clus
vv       FGFR2 MUTATED FGFR2 WILD-TYPE
  CLUS_1             3              19
  CLUS_2             8              49
  CLUS_3             4              23
  CLUS_4             1               9

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              42
  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
D16V8, multiclass
        clus
vv       CCND1 MUTATED CCND1 WILD-TYPE
  CLUS_1             1               9
  CLUS_2            11             125
  CLUS_3             3              91
D16V9, multiclass
        clus
vv       CCND1 MUTATED CCND1 WILD-TYPE
  CLUS_1             0              36
  CLUS_2             3              52
  CLUS_3             1              24
D16V10, multiclass
        clus
vv       CCND1 MUTATED CCND1 WILD-TYPE
  CLUS_1             1              21
  CLUS_2             3              54
  CLUS_3             0              27
  CLUS_4             0              10

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               42
  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
D17V8, multiclass
        clus
vv       SMTNL2 MUTATED SMTNL2 WILD-TYPE
  CLUS_1              2                8
  CLUS_2              6              130
  CLUS_3              1               93
D17V9, multiclass
        clus
vv       SMTNL2 MUTATED SMTNL2 WILD-TYPE
  CLUS_1              1               35
  CLUS_2              1               54
  CLUS_3              1               24
D17V10, multiclass
        clus
vv       SMTNL2 MUTATED SMTNL2 WILD-TYPE
  CLUS_1              0               22
  CLUS_2              2               55
  CLUS_3              1               26
  CLUS_4              0               10

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               42
  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
D18V8, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              1                9
  CLUS_2              9              127
  CLUS_3              5               89
D18V9, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              1               35
  CLUS_2              5               50
  CLUS_3              0               25
D18V10, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              0               22
  CLUS_2              5               52
  CLUS_3              1               26
  CLUS_4              0               10

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             36
  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
D19V8, multiclass
        clus
vv       CHD4 MUTATED CHD4 WILD-TYPE
  CLUS_1            2              8
  CLUS_2           17            119
  CLUS_3           11             83
D19V9, multiclass
        clus
vv       CHD4 MUTATED CHD4 WILD-TYPE
  CLUS_1            4             32
  CLUS_2           10             45
  CLUS_3            2             23
D19V10, multiclass
        clus
vv       CHD4 MUTATED CHD4 WILD-TYPE
  CLUS_1            2             20
  CLUS_2            9             48
  CLUS_3            4             23
  CLUS_4            1              9

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             42
  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
D20V8, multiclass
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  CLUS_1            1              9
  CLUS_2            4            132
  CLUS_3            8             86
D20V9, multiclass
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  CLUS_1            1             35
  CLUS_2            3             52
  CLUS_3            0             25
D20V10, multiclass
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  CLUS_1            0             22
  CLUS_2            3             54
  CLUS_3            1             26
  CLUS_4            0             10

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              38
  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
D21V8, multiclass
        clus
vv       FAM9A MUTATED FAM9A WILD-TYPE
  CLUS_1             2               8
  CLUS_2             4             132
  CLUS_3             8              86
D21V9, multiclass
        clus
vv       FAM9A MUTATED FAM9A WILD-TYPE
  CLUS_1             6              30
  CLUS_2             2              53
  CLUS_3             0              25
D21V10, multiclass
        clus
vv       FAM9A MUTATED FAM9A WILD-TYPE
  CLUS_1             2              20
  CLUS_2             2              55
  CLUS_3             4              23
  CLUS_4             0              10

Clustering(22) Variable = MORC4 MUTATION ANALYSIS
D22V1, multiclass
        clus
vv       MORC4 MUTATED MORC4 WILD-TYPE
  CLUS_1             1              11
  CLUS_2             3              15
  CLUS_3             0              11
  CLUS_4             1               9
D22V2, multiclass
        clus
vv       MORC4 MUTATED MORC4 WILD-TYPE
  CLUS_1             3              14
  CLUS_2             0              18
  CLUS_3             2              14
D22V3, multiclass
D22V4, multiclass
        clus
vv       MORC4 MUTATED MORC4 WILD-TYPE
  CLUS_1             2              41
  CLUS_2             6              35
  CLUS_3             4              47
D22V5, multiclass
D22V6, 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
D22V7, multiclass
D22V8, multiclass
        clus
vv       MORC4 MUTATED MORC4 WILD-TYPE
  CLUS_1             1               9
  CLUS_2             7             129
  CLUS_3            11              83
D22V9, multiclass
        clus
vv       MORC4 MUTATED MORC4 WILD-TYPE
  CLUS_1             2              34
  CLUS_2             3              52
  CLUS_3             4              21
D22V10, multiclass
        clus
vv       MORC4 MUTATED MORC4 WILD-TYPE
  CLUS_1             3              19
  CLUS_2             4              53
  CLUS_3             1              26
  CLUS_4             1               9

Clustering(23) Variable = HPD MUTATION ANALYSIS
D23V1, 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" 
D23V2, 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" 
D23V3, multiclass
D23V4, multiclass
        clus
vv       HPD MUTATED HPD WILD-TYPE
  CLUS_1           1            42
  CLUS_2           0            41
  CLUS_3           2            49
D23V5, multiclass
D23V6, 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
D23V7, multiclass
D23V8, multiclass
        clus
vv       HPD MUTATED HPD WILD-TYPE
  CLUS_1           0            10
  CLUS_2           3           133
  CLUS_3           4            90
D23V9, multiclass
        clus
vv       HPD MUTATED HPD WILD-TYPE
  CLUS_1           1            35
  CLUS_2           2            53
  CLUS_3           1            24
D23V10, multiclass
        clus
vv       HPD MUTATED HPD WILD-TYPE
  CLUS_1           1            21
  CLUS_2           2            55
  CLUS_3           1            26
  CLUS_4           0            10

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              41
  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
D24V8, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             3               7
  CLUS_2             7             129
  CLUS_3             6              88
D24V9, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             3              33
  CLUS_2             4              51
  CLUS_3             0              25
D24V10, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             1              21
  CLUS_2             4              53
  CLUS_3             2              25
  CLUS_4             0              10

Clustering(25) Variable = FOXA2 MUTATION ANALYSIS
D25V1, 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" 
D25V2, 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" 
D25V3, multiclass
D25V4, multiclass
        clus
vv       FOXA2 MUTATED FOXA2 WILD-TYPE
  CLUS_1             2              41
  CLUS_2             3              38
  CLUS_3             2              49
D25V5, multiclass
D25V6, 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
D25V7, multiclass
D25V8, multiclass
        clus
vv       FOXA2 MUTATED FOXA2 WILD-TYPE
  CLUS_1             0              10
  CLUS_2             7             129
  CLUS_3             4              90
D25V9, multiclass
        clus
vv       FOXA2 MUTATED FOXA2 WILD-TYPE
  CLUS_1             1              35
  CLUS_2             4              51
  CLUS_3             2              23
D25V10, multiclass
        clus
vv       FOXA2 MUTATED FOXA2 WILD-TYPE
  CLUS_1             1              21
  CLUS_2             4              53
  CLUS_3             1              26
  CLUS_4             1               9

Clustering(26) Variable = ABI1 MUTATION ANALYSIS
D26V1, 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" 
D26V2, 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" 
D26V3, multiclass
D26V4, multiclass
[1] "Remove cluster labels:" "ABI1 MUTATED"          
clus
  ABI1 MUTATED ABI1 WILD-TYPE 
             2            133 
    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-A0CC 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BK-A139     TCGA-BK-A13C     TCGA-BS-A0T9     TCGA-BS-A0U5 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BS-A0U9     TCGA-BS-A0UA     TCGA-BS-A0UL     TCGA-BS-A0V6 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BS-A0V7     TCGA-BS-A0V8     TCGA-BS-A0WQ     TCGA-D1-A0ZN 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A0ZO     TCGA-D1-A0ZP     TCGA-D1-A0ZQ     TCGA-D1-A0ZR 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A0ZS     TCGA-D1-A0ZU     TCGA-D1-A0ZV     TCGA-D1-A0ZZ 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A101     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" 
D26V5, multiclass
D26V6, 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
D26V7, multiclass
D26V8, multiclass
        clus
vv       ABI1 MUTATED ABI1 WILD-TYPE
  CLUS_1            0             10
  CLUS_2            3            133
  CLUS_3            1             93
D26V9, multiclass
[1] "Remove cluster labels:" "ABI1 MUTATED"          
clus
  ABI1 MUTATED ABI1 WILD-TYPE 
             2            114 
    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-A0CC     TCGA-BK-A139 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BK-A13C     TCGA-BS-A0T9     TCGA-BS-A0UA     TCGA-BS-A0V6 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BS-A0V7     TCGA-BS-A0V8     TCGA-D1-A0ZN     TCGA-D1-A0ZO 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A0ZQ     TCGA-D1-A0ZS     TCGA-D1-A102     TCGA-D1-A103 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A15V     TCGA-D1-A15W     TCGA-D1-A15X     TCGA-D1-A15Z 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A160     TCGA-D1-A161     TCGA-D1-A163     TCGA-D1-A165 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A167     TCGA-D1-A168     TCGA-D1-A169     TCGA-D1-A16B 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A16D     TCGA-D1-A16E     TCGA-D1-A16F     TCGA-D1-A16G 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A16I     TCGA-D1-A16J     TCGA-D1-A16N     TCGA-D1-A16O 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A16Q     TCGA-D1-A16R     TCGA-D1-A16S     TCGA-D1-A16Y 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A174     TCGA-D1-A176     TCGA-D1-A177     TCGA-D1-A17A 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A17B     TCGA-D1-A17C     TCGA-D1-A17D     TCGA-D1-A17F 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A17H     TCGA-D1-A17K     TCGA-D1-A17L     TCGA-D1-A17M 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A17N     TCGA-D1-A17R     TCGA-D1-A17S     TCGA-D1-A17T 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A17U     TCGA-D1-A1NU     TCGA-D1-A1NX     TCGA-DI-A0WH 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-DI-A1NN     TCGA-E6-A1LZ     TCGA-EO-A1Y5     TCGA-EO-A1Y8 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-EY-A1GS     TCGA-EY-A212     TCGA-FI-A2D2     TCGA-FI-A2EW 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-FI-A2EX     TCGA-FI-A2F8 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
D26V10, multiclass
[1] "Remove cluster labels:" "ABI1 MUTATED"          
clus
  ABI1 MUTATED ABI1 WILD-TYPE 
             2            114 
    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-A0CC     TCGA-BK-A139 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BK-A13C     TCGA-BS-A0T9     TCGA-BS-A0UA     TCGA-BS-A0V6 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BS-A0V7     TCGA-BS-A0V8     TCGA-D1-A0ZN     TCGA-D1-A0ZO 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A0ZQ     TCGA-D1-A0ZS     TCGA-D1-A102     TCGA-D1-A103 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A15V     TCGA-D1-A15W     TCGA-D1-A15X     TCGA-D1-A15Z 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A160     TCGA-D1-A161     TCGA-D1-A163     TCGA-D1-A165 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A167     TCGA-D1-A168     TCGA-D1-A169     TCGA-D1-A16B 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A16D     TCGA-D1-A16E     TCGA-D1-A16F     TCGA-D1-A16G 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A16I     TCGA-D1-A16J     TCGA-D1-A16N     TCGA-D1-A16O 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A16Q     TCGA-D1-A16R     TCGA-D1-A16S     TCGA-D1-A16Y 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A174     TCGA-D1-A176     TCGA-D1-A177     TCGA-D1-A17A 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A17B     TCGA-D1-A17C     TCGA-D1-A17D     TCGA-D1-A17F 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A17H     TCGA-D1-A17K     TCGA-D1-A17L     TCGA-D1-A17M 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A17N     TCGA-D1-A17R     TCGA-D1-A17S     TCGA-D1-A17T 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A17U     TCGA-D1-A1NU     TCGA-D1-A1NX     TCGA-DI-A0WH 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-DI-A1NN     TCGA-E6-A1LZ     TCGA-EO-A1Y5     TCGA-EO-A1Y8 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-EY-A1GS     TCGA-EY-A212     TCGA-FI-A2D2     TCGA-FI-A2EW 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-FI-A2EX     TCGA-FI-A2F8 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 

Clustering(27) Variable = DNER MUTATION ANALYSIS
D27V1, multiclass
        clus
vv       DNER MUTATED DNER WILD-TYPE
  CLUS_1            3              9
  CLUS_2            2             16
  CLUS_3            0             11
  CLUS_4            0             10
D27V2, multiclass
        clus
vv       DNER MUTATED DNER WILD-TYPE
  CLUS_1            4             13
  CLUS_2            0             18
  CLUS_3            1             15
D27V3, multiclass
D27V4, multiclass
        clus
vv       DNER MUTATED DNER WILD-TYPE
  CLUS_1            3             40
  CLUS_2            1             40
  CLUS_3            4             47
D27V5, multiclass
D27V6, 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
D27V7, multiclass
D27V8, multiclass
        clus
vv       DNER MUTATED DNER WILD-TYPE
  CLUS_1            3              7
  CLUS_2            6            130
  CLUS_3            8             86
D27V9, multiclass
        clus
vv       DNER MUTATED DNER WILD-TYPE
  CLUS_1            2             34
  CLUS_2            4             51
  CLUS_3            1             24
D27V10, multiclass
        clus
vv       DNER MUTATED DNER WILD-TYPE
  CLUS_1            2             20
  CLUS_2            4             53
  CLUS_3            1             26
  CLUS_4            0             10

Clustering(28) Variable = BCOR MUTATION ANALYSIS
D28V1, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            1             11
  CLUS_2            2             16
  CLUS_3            0             11
  CLUS_4            0             10
D28V2, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            2             15
  CLUS_2            0             18
  CLUS_3            1             15
D28V3, multiclass
D28V4, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            1             42
  CLUS_2            4             37
  CLUS_3           10             41
D28V5, multiclass
D28V6, 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
D28V7, multiclass
D28V8, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            4              6
  CLUS_2           15            121
  CLUS_3           10             84
D28V9, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            3             33
  CLUS_2            7             48
  CLUS_3            3             22
D28V10, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            1             21
  CLUS_2            8             49
  CLUS_3            2             25
  CLUS_4            2              8

Clustering(29) Variable = BRS3 MUTATION ANALYSIS
D29V1, multiclass
        clus
vv       BRS3 MUTATED BRS3 WILD-TYPE
  CLUS_1            2             10
  CLUS_2            2             16
  CLUS_3            0             11
  CLUS_4            0             10
D29V2, multiclass
        clus
vv       BRS3 MUTATED BRS3 WILD-TYPE
  CLUS_1            3             14
  CLUS_2            0             18
  CLUS_3            1             15
D29V3, multiclass
D29V4, multiclass
        clus
vv       BRS3 MUTATED BRS3 WILD-TYPE
  CLUS_1            3             40
  CLUS_2            1             40
  CLUS_3            1             50
D29V5, multiclass
D29V6, 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
D29V7, multiclass
D29V8, multiclass
        clus
vv       BRS3 MUTATED BRS3 WILD-TYPE
  CLUS_1            2              8
  CLUS_2            4            132
  CLUS_3            8             86
D29V9, multiclass
        clus
vv       BRS3 MUTATED BRS3 WILD-TYPE
  CLUS_1            2             34
  CLUS_2            1             54
  CLUS_3            1             24
D29V10, multiclass
        clus
vv       BRS3 MUTATED BRS3 WILD-TYPE
  CLUS_1            1             21
  CLUS_2            1             56
  CLUS_3            2             25
  CLUS_4            0             10

Clustering(30) Variable = NRAS MUTATION ANALYSIS
D30V1, 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" 
D30V2, 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" 
D30V3, multiclass
D30V4, multiclass
[1] "Remove cluster labels:" "NRAS MUTATED"          
clus
  NRAS MUTATED NRAS WILD-TYPE 
             2            133 
    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-A0CC     TCGA-BK-A139 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BK-A13C     TCGA-BS-A0T9     TCGA-BS-A0U5     TCGA-BS-A0U9 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BS-A0UA     TCGA-BS-A0UL     TCGA-BS-A0V6     TCGA-BS-A0V7 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BS-A0V8     TCGA-BS-A0WQ     TCGA-D1-A0ZN     TCGA-D1-A0ZO 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A0ZP     TCGA-D1-A0ZQ     TCGA-D1-A0ZR     TCGA-D1-A0ZS 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A0ZU     TCGA-D1-A0ZV     TCGA-D1-A0ZZ     TCGA-D1-A101 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A102     TCGA-D1-A103     TCGA-D1-A15V     TCGA-D1-A15W 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A15X     TCGA-D1-A15Z     TCGA-D1-A160     TCGA-D1-A161 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A163     TCGA-D1-A165     TCGA-D1-A167     TCGA-D1-A168 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A169     TCGA-D1-A16B     TCGA-D1-A16D     TCGA-D1-A16E 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A16F     TCGA-D1-A16G     TCGA-D1-A16I     TCGA-D1-A16J 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A16N     TCGA-D1-A16O     TCGA-D1-A16Q     TCGA-D1-A16R 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A16S     TCGA-D1-A16X     TCGA-D1-A16Y     TCGA-D1-A174 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A176     TCGA-D1-A177     TCGA-D1-A17A     TCGA-D1-A17B 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A17C     TCGA-D1-A17D     TCGA-D1-A17H     TCGA-D1-A17K 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A17L     TCGA-D1-A17M     TCGA-D1-A17N     TCGA-D1-A17Q 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A17R     TCGA-D1-A17S     TCGA-D1-A17T     TCGA-D1-A17U 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A1NU     TCGA-D1-A1NX     TCGA-DI-A0WH     TCGA-DI-A1NN 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-E6-A1LZ     TCGA-EO-A1Y5     TCGA-EO-A1Y8     TCGA-EY-A1GS 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-EY-A212     TCGA-FI-A2D2     TCGA-FI-A2EW     TCGA-FI-A2EX 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-FI-A2F8 
"NRAS WILD-TYPE" 
D30V5, multiclass
D30V6, 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
D30V7, multiclass
D30V8, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            1              9
  CLUS_2            4            132
  CLUS_3            4             90
D30V9, multiclass
[1] "Remove cluster labels:" "NRAS MUTATED"          
clus
  NRAS MUTATED NRAS WILD-TYPE 
             1            115 
    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-A0CC     TCGA-BK-A139 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BK-A13C     TCGA-BS-A0T9     TCGA-BS-A0UA     TCGA-BS-A0V6 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BS-A0V7     TCGA-BS-A0V8     TCGA-D1-A0ZN     TCGA-D1-A0ZO 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A0ZQ     TCGA-D1-A0ZS     TCGA-D1-A102     TCGA-D1-A103 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A15V     TCGA-D1-A15W     TCGA-D1-A15X     TCGA-D1-A15Z 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A160     TCGA-D1-A161     TCGA-D1-A163     TCGA-D1-A165 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A167     TCGA-D1-A168     TCGA-D1-A169     TCGA-D1-A16B 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A16D     TCGA-D1-A16E     TCGA-D1-A16F     TCGA-D1-A16G 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A16I     TCGA-D1-A16J     TCGA-D1-A16N     TCGA-D1-A16O 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A16Q     TCGA-D1-A16R     TCGA-D1-A16S     TCGA-D1-A16X 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A16Y     TCGA-D1-A174     TCGA-D1-A176     TCGA-D1-A177 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A17A     TCGA-D1-A17B     TCGA-D1-A17C     TCGA-D1-A17D 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A17H     TCGA-D1-A17K     TCGA-D1-A17L     TCGA-D1-A17M 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A17N     TCGA-D1-A17Q     TCGA-D1-A17R     TCGA-D1-A17S 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A17T     TCGA-D1-A17U     TCGA-D1-A1NU     TCGA-D1-A1NX 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-DI-A0WH     TCGA-DI-A1NN     TCGA-E6-A1LZ     TCGA-EO-A1Y5 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-EO-A1Y8     TCGA-EY-A1GS     TCGA-EY-A212     TCGA-FI-A2D2 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-FI-A2EW     TCGA-FI-A2EX     TCGA-FI-A2F8 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
D30V10, multiclass
[1] "Remove cluster labels:" "NRAS MUTATED"          
clus
  NRAS MUTATED NRAS WILD-TYPE 
             1            115 
    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-A0CC     TCGA-BK-A139 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BK-A13C     TCGA-BS-A0T9     TCGA-BS-A0UA     TCGA-BS-A0V6 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BS-A0V7     TCGA-BS-A0V8     TCGA-D1-A0ZN     TCGA-D1-A0ZO 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A0ZQ     TCGA-D1-A0ZS     TCGA-D1-A102     TCGA-D1-A103 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A15V     TCGA-D1-A15W     TCGA-D1-A15X     TCGA-D1-A15Z 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A160     TCGA-D1-A161     TCGA-D1-A163     TCGA-D1-A165 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A167     TCGA-D1-A168     TCGA-D1-A169     TCGA-D1-A16B 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A16D     TCGA-D1-A16E     TCGA-D1-A16F     TCGA-D1-A16G 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A16I     TCGA-D1-A16J     TCGA-D1-A16N     TCGA-D1-A16O 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A16Q     TCGA-D1-A16R     TCGA-D1-A16S     TCGA-D1-A16X 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A16Y     TCGA-D1-A174     TCGA-D1-A176     TCGA-D1-A177 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A17A     TCGA-D1-A17B     TCGA-D1-A17C     TCGA-D1-A17D 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A17H     TCGA-D1-A17K     TCGA-D1-A17L     TCGA-D1-A17M 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A17N     TCGA-D1-A17Q     TCGA-D1-A17R     TCGA-D1-A17S 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A17T     TCGA-D1-A17U     TCGA-D1-A1NU     TCGA-D1-A1NX 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-DI-A0WH     TCGA-DI-A1NN     TCGA-E6-A1LZ     TCGA-EO-A1Y5 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-EO-A1Y8     TCGA-EY-A1GS     TCGA-EY-A212     TCGA-FI-A2D2 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-FI-A2EW     TCGA-FI-A2EX     TCGA-FI-A2F8 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 

Clustering(31) Variable = SGK1 MUTATION ANALYSIS
D31V1, multiclass
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  CLUS_1            2             10
  CLUS_2            1             17
  CLUS_3            0             11
  CLUS_4            0             10
D31V2, multiclass
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  CLUS_1            3             14
  CLUS_2            0             18
  CLUS_3            0             16
D31V3, multiclass
D31V4, multiclass
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  CLUS_1            1             42
  CLUS_2            1             40
  CLUS_3            3             48
D31V5, multiclass
D31V6, 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
D31V7, multiclass
D31V8, multiclass
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  CLUS_1            1              9
  CLUS_2            8            128
  CLUS_3            5             89
D31V9, multiclass
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  CLUS_1            1             35
  CLUS_2            3             52
  CLUS_3            0             25
D31V10, multiclass
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  CLUS_1            0             22
  CLUS_2            3             54
  CLUS_3            1             26
  CLUS_4            0             10

Clustering(32) Variable = TIAL1 MUTATION ANALYSIS
D32V1, multiclass
        clus
vv       TIAL1 MUTATED TIAL1 WILD-TYPE
  CLUS_1             2              10
  CLUS_2             1              17
  CLUS_3             0              11
  CLUS_4             0              10
D32V2, multiclass
        clus
vv       TIAL1 MUTATED TIAL1 WILD-TYPE
  CLUS_1             2              15
  CLUS_2             0              18
  CLUS_3             1              15
D32V3, multiclass
D32V4, multiclass
        clus
vv       TIAL1 MUTATED TIAL1 WILD-TYPE
  CLUS_1             1              42
  CLUS_2             0              41
  CLUS_3             5              46
D32V5, multiclass
D32V6, 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
D32V7, multiclass
D32V8, multiclass
        clus
vv       TIAL1 MUTATED TIAL1 WILD-TYPE
  CLUS_1             1               9
  CLUS_2             6             130
  CLUS_3             4              90
D32V9, multiclass
        clus
vv       TIAL1 MUTATED TIAL1 WILD-TYPE
  CLUS_1             1              35
  CLUS_2             5              50
  CLUS_3             0              25
D32V10, multiclass
        clus
vv       TIAL1 MUTATED TIAL1 WILD-TYPE
  CLUS_1             0              22
  CLUS_2             4              53
  CLUS_3             2              25
  CLUS_4             0              10

Clustering(33) Variable = RPL14 MUTATION ANALYSIS
D33V1, multiclass
D33V2, multiclass
D33V3, multiclass
D33V4, multiclass
        clus
vv       RPL14 MUTATED RPL14 WILD-TYPE
  CLUS_1             2              41
  CLUS_2             1              40
  CLUS_3             3              48
D33V5, multiclass
D33V6, 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
D33V7, multiclass
D33V8, multiclass
        clus
vv       RPL14 MUTATED RPL14 WILD-TYPE
  CLUS_1             0              10
  CLUS_2             4             132
  CLUS_3             2              92
D33V9, multiclass
        clus
vv       RPL14 MUTATED RPL14 WILD-TYPE
  CLUS_1             1              35
  CLUS_2             3              52
  CLUS_3             1              24
D33V10, multiclass
        clus
vv       RPL14 MUTATED RPL14 WILD-TYPE
  CLUS_1             1              21
  CLUS_2             3              54
  CLUS_3             1              26
  CLUS_4             0              10

Clustering(34) Variable = SIN3A MUTATION ANALYSIS
D34V1, multiclass
[1] "Remove cluster labels:" "SIN3A MUTATED"         
clus
  SIN3A MUTATED SIN3A WILD-TYPE 
              2              49 
     TCGA-A5-A0G3      TCGA-A5-A0G5      TCGA-A5-A0GA      TCGA-A5-A0GB 
"SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" 
     TCGA-A5-A0GE      TCGA-A5-A0GH      TCGA-A5-A0GM      TCGA-A5-A0GP 
"SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" 
     TCGA-A5-A0GU      TCGA-AP-A051      TCGA-AP-A052      TCGA-AP-A053 
"SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" 
     TCGA-AP-A054      TCGA-AP-A056      TCGA-AP-A05A      TCGA-AP-A05D 
"SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" 
     TCGA-AP-A05H      TCGA-AP-A05J      TCGA-AP-A05N      TCGA-AP-A05P 
"SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" 
     TCGA-AP-A0L8      TCGA-AP-A0L9      TCGA-AP-A0LD      TCGA-AP-A0LG 
"SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" 
     TCGA-AP-A0LH      TCGA-AP-A0LJ      TCGA-AP-A0LN      TCGA-AP-A0LT 
"SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" 
     TCGA-AP-A0LV      TCGA-AX-A05S      TCGA-AX-A05T      TCGA-AX-A05U 
"SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" 
     TCGA-AX-A05W      TCGA-AX-A05Y      TCGA-AX-A05Z      TCGA-AX-A062 
"SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" 
     TCGA-AX-A063      TCGA-AX-A064      TCGA-AX-A06B      TCGA-AX-A0IW 
"SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" 
     TCGA-B5-A0JR      TCGA-B5-A0JZ      TCGA-B5-A0K0      TCGA-B5-A0K1 
"SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" 
     TCGA-B5-A0K4      TCGA-BG-A0LW      TCGA-BG-A0MI      TCGA-BK-A0C9 
"SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" 
     TCGA-BK-A0CC 
"SIN3A WILD-TYPE" 
D34V2, multiclass
[1] "Remove cluster labels:" "SIN3A MUTATED"         
clus
  SIN3A MUTATED SIN3A WILD-TYPE 
              2              49 
     TCGA-A5-A0G3      TCGA-A5-A0G5      TCGA-A5-A0GA      TCGA-A5-A0GB 
"SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" 
     TCGA-A5-A0GE      TCGA-A5-A0GH      TCGA-A5-A0GM      TCGA-A5-A0GP 
"SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" 
     TCGA-A5-A0GU      TCGA-AP-A051      TCGA-AP-A052      TCGA-AP-A053 
"SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" 
     TCGA-AP-A054      TCGA-AP-A056      TCGA-AP-A05A      TCGA-AP-A05D 
"SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" 
     TCGA-AP-A05H      TCGA-AP-A05J      TCGA-AP-A05N      TCGA-AP-A05P 
"SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" 
     TCGA-AP-A0L8      TCGA-AP-A0L9      TCGA-AP-A0LD      TCGA-AP-A0LG 
"SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" 
     TCGA-AP-A0LH      TCGA-AP-A0LJ      TCGA-AP-A0LN      TCGA-AP-A0LT 
"SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" 
     TCGA-AP-A0LV      TCGA-AX-A05S      TCGA-AX-A05T      TCGA-AX-A05U 
"SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" 
     TCGA-AX-A05W      TCGA-AX-A05Y      TCGA-AX-A05Z      TCGA-AX-A062 
"SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" 
     TCGA-AX-A063      TCGA-AX-A064      TCGA-AX-A06B      TCGA-AX-A0IW 
"SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" 
     TCGA-B5-A0JR      TCGA-B5-A0JZ      TCGA-B5-A0K0      TCGA-B5-A0K1 
"SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" 
     TCGA-B5-A0K4      TCGA-BG-A0LW      TCGA-BG-A0MI      TCGA-BK-A0C9 
"SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" "SIN3A WILD-TYPE" 
     TCGA-BK-A0CC 
"SIN3A WILD-TYPE" 
D34V3, multiclass
D34V4, multiclass
        clus
vv       SIN3A MUTATED SIN3A WILD-TYPE
  CLUS_1             4              39
  CLUS_2             3              38
  CLUS_3             7              44
D34V5, multiclass
D34V6, binary
                 cls
clus                0   1
  SIN3A MUTATED     8  10
  SIN3A WILD-TYPE 107  61
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIN3A MUTATED      8   10
  SIN3A WILD-TYPE  107   61
        clus
vv       SIN3A MUTATED SIN3A WILD-TYPE
  CLUS_1             8             107
  CLUS_2            10              61
D34V7, multiclass
D34V8, multiclass
        clus
vv       SIN3A MUTATED SIN3A WILD-TYPE
  CLUS_1             4               6
  CLUS_2             4             132
  CLUS_3            13              81
D34V9, multiclass
        clus
vv       SIN3A MUTATED SIN3A WILD-TYPE
  CLUS_1             4              32
  CLUS_2             3              52
  CLUS_3             3              22
D34V10, multiclass
        clus
vv       SIN3A MUTATED SIN3A WILD-TYPE
  CLUS_1             3              19
  CLUS_2             3              54
  CLUS_3             3              24
  CLUS_4             1               9

Clustering(35) Variable = SLC48A1 MUTATION ANALYSIS
D35V1, multiclass
D35V2, multiclass
D35V3, multiclass
D35V4, multiclass
        clus
vv       SLC48A1 MUTATED SLC48A1 WILD-TYPE
  CLUS_1               0                43
  CLUS_2               1                40
  CLUS_3               2                49
D35V5, multiclass
D35V6, 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
D35V7, multiclass
D35V8, multiclass
        clus
vv       SLC48A1 MUTATED SLC48A1 WILD-TYPE
  CLUS_1               0                10
  CLUS_2               2               134
  CLUS_3               3                91
D35V9, multiclass
        clus
vv       SLC48A1 MUTATED SLC48A1 WILD-TYPE
  CLUS_1               1                35
  CLUS_2               1                54
  CLUS_3               1                24
D35V10, multiclass
        clus
vv       SLC48A1 MUTATED SLC48A1 WILD-TYPE
  CLUS_1               1                21
  CLUS_2               1                56
  CLUS_3               1                26
  CLUS_4               0                10

Clustering(36) Variable = ZFHX3 MUTATION ANALYSIS
D36V1, multiclass
        clus
vv       ZFHX3 MUTATED ZFHX3 WILD-TYPE
  CLUS_1             6               6
  CLUS_2             6              12
  CLUS_3             2               9
  CLUS_4             2               8
D36V2, multiclass
        clus
vv       ZFHX3 MUTATED ZFHX3 WILD-TYPE
  CLUS_1             9               8
  CLUS_2             2              16
  CLUS_3             5              11
D36V3, multiclass
D36V4, multiclass
        clus
vv       ZFHX3 MUTATED ZFHX3 WILD-TYPE
  CLUS_1             5              38
  CLUS_2             2              39
  CLUS_3            11              40
D36V5, multiclass
D36V6, binary
                 cls
clus               0  1
  ZFHX3 MUTATED   18 17
  ZFHX3 WILD-TYPE 97 54
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX3 MUTATED     18   17
  ZFHX3 WILD-TYPE   97   54
        clus
vv       ZFHX3 MUTATED ZFHX3 WILD-TYPE
  CLUS_1            18              97
  CLUS_2            17              54
D36V7, multiclass
D36V8, multiclass
        clus
vv       ZFHX3 MUTATED ZFHX3 WILD-TYPE
  CLUS_1             2               8
  CLUS_2            22             114
  CLUS_3            17              77
D36V9, multiclass
        clus
vv       ZFHX3 MUTATED ZFHX3 WILD-TYPE
  CLUS_1             3              33
  CLUS_2             9              46
  CLUS_3             4              21
D36V10, multiclass
        clus
vv       ZFHX3 MUTATED ZFHX3 WILD-TYPE
  CLUS_1             3              19
  CLUS_2             9              48
  CLUS_3             3              24
  CLUS_4             1               9

Clustering(37) Variable = RNF43 MUTATION ANALYSIS
D37V1, multiclass
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  CLUS_1             3               9
  CLUS_2             1              17
  CLUS_3             0              11
  CLUS_4             0              10
D37V2, multiclass
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  CLUS_1             3              14
  CLUS_2             0              18
  CLUS_3             1              15
D37V3, multiclass
D37V4, multiclass
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  CLUS_1             2              41
  CLUS_2             0              41
  CLUS_3             3              48
D37V5, multiclass
D37V6, 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
D37V7, multiclass
D37V8, multiclass
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  CLUS_1             2               8
  CLUS_2             4             132
  CLUS_3             6              88
D37V9, multiclass
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  CLUS_1             1              35
  CLUS_2             1              54
  CLUS_3             2              23
D37V10, multiclass
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  CLUS_1             1              21
  CLUS_2             1              56
  CLUS_3             1              26
  CLUS_4             1               9

Clustering(38) Variable = ZNF263 MUTATION ANALYSIS
D38V1, multiclass
        clus
vv       ZNF263 MUTATED ZNF263 WILD-TYPE
  CLUS_1              3                9
  CLUS_2              0               18
  CLUS_3              0               11
  CLUS_4              0               10
D38V2, multiclass
        clus
vv       ZNF263 MUTATED ZNF263 WILD-TYPE
  CLUS_1              3               14
  CLUS_2              0               18
  CLUS_3              0               16
D38V3, multiclass
D38V4, multiclass
        clus
vv       ZNF263 MUTATED ZNF263 WILD-TYPE
  CLUS_1              1               42
  CLUS_2              0               41
  CLUS_3              3               48
D38V5, multiclass
D38V6, 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
D38V7, multiclass
D38V8, multiclass
        clus
vv       ZNF263 MUTATED ZNF263 WILD-TYPE
  CLUS_1              0               10
  CLUS_2              5              131
  CLUS_3              3               91
D38V9, multiclass
        clus
vv       ZNF263 MUTATED ZNF263 WILD-TYPE
  CLUS_1              0               36
  CLUS_2              3               52
  CLUS_3              1               24
D38V10, multiclass
        clus
vv       ZNF263 MUTATED ZNF263 WILD-TYPE
  CLUS_1              1               21
  CLUS_2              1               56
  CLUS_3              2               25
  CLUS_4              0               10
                           V1                            V2 
                  "MRNA_CNMF"          "MRNA_CHIERARCHICAL" 
                           V3                            V4 
                    "CN_CNMF"            "METHLYATION_CNMF" 
                           V5                            V6 
                  "RPPA_CNMF"          "RPPA_CHIERARCHICAL" 
                           V7                            V8 
                "MIRSEQ_CNMF"        "MIRSEQ_CHIERARCHICAL" 
                           V9                           V10 
         "MIRSEQ_MATURE_CNMF" "MIRSEQ_MATURE_CHIERARCHICAL" 
> q(save="no")
