
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/397949/UCEC-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/UCEC-TP/3148122/1.GDAC_mergedClustering.Finished/UCEC-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ONLYSIG", "-oT=UCEC-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=UCEC-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=500, in cluster file=248, common to both=248
[1]  43 248
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
           161             87 
  PTEN MUTATED PTEN WILD-TYPE 
           161             87 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              74              174 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              74              174 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             39             209 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             39             209 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            53            195 
  KRAS MUTATED KRAS WILD-TYPE 
            53            195 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
             132              116 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
             132              116 
[1] "PIK3R1 MUTATION ANALYSIS"
[1] 3
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              83              165 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              83              165 
[1] "PPP2R1A MUTATION ANALYSIS"
[1] 3
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
               27               221 
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
               27               221 
[1] "PRKAR1B MUTATION ANALYSIS"
[1] 3
  PRKAR1B MUTATED PRKAR1B WILD-TYPE 
                4               244 
  PRKAR1B MUTATED PRKAR1B WILD-TYPE 
                4               244 
[1] "RPL22 MUTATION ANALYSIS"
[1] 3
  RPL22 MUTATED RPL22 WILD-TYPE 
             31             217 
  RPL22 MUTATED RPL22 WILD-TYPE 
             31             217 
[1] "SPOP MUTATION ANALYSIS"
[1] 3
  SPOP MUTATED SPOP WILD-TYPE 
            21            227 
  SPOP MUTATED SPOP WILD-TYPE 
            21            227 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            69            179 
  TP53 MUTATED TP53 WILD-TYPE 
            69            179 
[1] "CTCF MUTATION ANALYSIS"
[1] 3
  CTCF MUTATED CTCF WILD-TYPE 
            45            203 
  CTCF MUTATED CTCF WILD-TYPE 
            45            203 
[1] "FGFR2 MUTATION ANALYSIS"
[1] 3
  FGFR2 MUTATED FGFR2 WILD-TYPE 
             31             217 
  FGFR2 MUTATED FGFR2 WILD-TYPE 
             31             217 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              83              165 
  ARID1A MUTATED ARID1A WILD-TYPE 
              83              165 
[1] "P2RY11 MUTATION ANALYSIS"
[1] 3
  P2RY11 MUTATED P2RY11 WILD-TYPE 
               7              241 
  P2RY11 MUTATED P2RY11 WILD-TYPE 
               7              241 
[1] "CCND1 MUTATION ANALYSIS"
[1] 3
  CCND1 MUTATED CCND1 WILD-TYPE 
             15             233 
  CCND1 MUTATED CCND1 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] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              15              233 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              15              233 
[1] "SOX17 MUTATION ANALYSIS"
[1] 3
  SOX17 MUTATED SOX17 WILD-TYPE 
              7             241 
  SOX17 MUTATED SOX17 WILD-TYPE 
              7             241 
[1] "FOXA2 MUTATION ANALYSIS"
[1] 3
  FOXA2 MUTATED FOXA2 WILD-TYPE 
             12             236 
  FOXA2 MUTATED FOXA2 WILD-TYPE 
             12             236 
[1] "FAM9A MUTATION ANALYSIS"
[1] 3
  FAM9A MUTATED FAM9A WILD-TYPE 
             14             234 
  FAM9A MUTATED FAM9A WILD-TYPE 
             14             234 
[1] "SMTNL2 MUTATION ANALYSIS"
[1] 3
  SMTNL2 MUTATED SMTNL2 WILD-TYPE 
               9              239 
  SMTNL2 MUTATED SMTNL2 WILD-TYPE 
               9              239 
[1] "RBMX MUTATION ANALYSIS"
[1] 3
  RBMX MUTATED RBMX WILD-TYPE 
            13            235 
  RBMX MUTATED RBMX WILD-TYPE 
            13            235 
[1] "MAX MUTATION ANALYSIS"
[1] 3
  MAX MUTATED MAX WILD-TYPE 
           11           237 
  MAX MUTATED MAX WILD-TYPE 
           11           237 
[1] "ING1 MUTATION ANALYSIS"
[1] 3
  ING1 MUTATED ING1 WILD-TYPE 
            13            235 
  ING1 MUTATED ING1 WILD-TYPE 
            13            235 
[1] "ABI1 MUTATION ANALYSIS"
[1] 3
  ABI1 MUTATED ABI1 WILD-TYPE 
             4            244 
  ABI1 MUTATED ABI1 WILD-TYPE 
             4            244 
[1] "RPL14 MUTATION ANALYSIS"
[1] 3
  RPL14 MUTATED RPL14 WILD-TYPE 
              7             241 
  RPL14 MUTATED RPL14 WILD-TYPE 
              7             241 
[1] "DNER MUTATION ANALYSIS"
[1] 3
  DNER MUTATED DNER WILD-TYPE 
            18            230 
  DNER MUTATED DNER WILD-TYPE 
            18            230 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
             9            239 
  NRAS MUTATED NRAS WILD-TYPE 
             9            239 
[1] "HPD MUTATION ANALYSIS"
[1] 3
  HPD MUTATED HPD WILD-TYPE 
            7           241 
  HPD MUTATED HPD WILD-TYPE 
            7           241 
[1] "RASA1 MUTATION ANALYSIS"
[1] 3
  RASA1 MUTATED RASA1 WILD-TYPE 
             22             226 
  RASA1 MUTATED RASA1 WILD-TYPE 
             22             226 
[1] "ZNF267 MUTATION ANALYSIS"
[1] 3
  ZNF267 MUTATED ZNF267 WILD-TYPE 
              16              232 
  ZNF267 MUTATED ZNF267 WILD-TYPE 
              16              232 
[1] "SGK1 MUTATION ANALYSIS"
[1] 3
  SGK1 MUTATED SGK1 WILD-TYPE 
            15            233 
  SGK1 MUTATED SGK1 WILD-TYPE 
            15            233 
[1] "ARID5B MUTATION ANALYSIS"
[1] 3
  ARID5B MUTATED ARID5B WILD-TYPE 
              29              219 
  ARID5B MUTATED ARID5B WILD-TYPE 
              29              219 
[1] "CYLC1 MUTATION ANALYSIS"
[1] 3
  CYLC1 MUTATED CYLC1 WILD-TYPE 
             18             230 
  CYLC1 MUTATED CYLC1 WILD-TYPE 
             18             230 
[1] "DYRK1A MUTATION ANALYSIS"
[1] 3
  DYRK1A MUTATED DYRK1A WILD-TYPE 
              12              236 
  DYRK1A MUTATED DYRK1A WILD-TYPE 
              12              236 
[1] "METTL14 MUTATION ANALYSIS"
[1] 3
  METTL14 MUTATED METTL14 WILD-TYPE 
               10               238 
  METTL14 MUTATED METTL14 WILD-TYPE 
               10               238 
[1] "TPTE MUTATION ANALYSIS"
[1] 3
  TPTE MUTATED TPTE WILD-TYPE 
            15            233 
  TPTE MUTATED TPTE WILD-TYPE 
            15            233 
[1] "UPF3B MUTATION ANALYSIS"
[1] 3
  UPF3B MUTATED UPF3B WILD-TYPE 
             16             232 
  UPF3B MUTATED UPF3B WILD-TYPE 
             16             232 
[1] "UBE2QL1 MUTATION ANALYSIS"
[1] 3
  UBE2QL1 MUTATED UBE2QL1 WILD-TYPE 
                5               243 
  UBE2QL1 MUTATED UBE2QL1 WILD-TYPE 
                5               243 
[1] "ZNF286A MUTATION ANALYSIS"
[1] 3
  ZNF286A MUTATED ZNF286A WILD-TYPE 
               12               236 
  ZNF286A MUTATED ZNF286A 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] "TAB3 MUTATION ANALYSIS"
[1] 3
  TAB3 MUTATED TAB3 WILD-TYPE 
            18            230 
  TAB3 MUTATED TAB3 WILD-TYPE 
            18            230 
[1] "data2feature, selection=ALL"
 [1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "CN_CNMF"              
 [4] "METHLYATION_CNMF"      "RPPA_CNMF"             "RPPA_CHIERARCHICAL"   
 [7] "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"          
[10] "MIRSEQ_CHIERARCHICAL" 

Input Data has 10 rows and 248 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'CN_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'RPPA_CNMF':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'RPPA_CHIERARCHICAL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "CN_CNMF"              
 [4] "METHLYATION_CNMF"      "RPPA_CNMF"             "RPPA_CHIERARCHICAL"   
 [7] "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"          
[10] "MIRSEQ_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=5, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=6, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=2, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = PTEN MUTATION ANALYSIS
D1V1, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           11              0
  CLUS_2            6             13
  CLUS_3           11              2
  CLUS_4            5              3
D1V2, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           15              4
  CLUS_2           12              1
  CLUS_3            6             13
D1V3, multiclass
D1V4, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            7             35
  CLUS_2           31             11
  CLUS_3           43              7
D1V5, multiclass
D1V6, 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
D1V7, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           18             61
  CLUS_2           74              6
  CLUS_3           63             19
D1V8, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           38             13
  CLUS_2           64              6
  CLUS_3           31             11
  CLUS_4           22             56
D1V9, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           21             50
  CLUS_2           80             11
  CLUS_3           57             21
D1V10, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1          106             17
  CLUS_2           27             14
  CLUS_3           10              3
  CLUS_4           15             48

Clustering(2) Variable = CTNNB1 MUTATION ANALYSIS
D2V1, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              0               11
  CLUS_2              3               16
  CLUS_3              6                7
  CLUS_4              8                0
D2V2, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1             14                5
  CLUS_2              1               12
  CLUS_3              2               17
D2V3, multiclass
D2V4, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              4               38
  CLUS_2             15               27
  CLUS_3             18               32
D2V5, multiclass
D2V6, 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
D2V7, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              6               73
  CLUS_2             14               66
  CLUS_3             52               30
D2V8, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1             49                2
  CLUS_2              8               62
  CLUS_3              6               36
  CLUS_4              9               69
D2V9, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              4               67
  CLUS_2             19               72
  CLUS_3             48               30
D2V10, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1             44               79
  CLUS_2             19               22
  CLUS_3              5                8
  CLUS_4              3               60

Clustering(3) Variable = FBXW7 MUTATION ANALYSIS
D3V1, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             3               8
  CLUS_2             4              15
  CLUS_3             4               9
  CLUS_4             0               8
D3V2, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             1              18
  CLUS_2             5               8
  CLUS_3             5              14
D3V3, multiclass
D3V4, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1            11              31
  CLUS_2             4              38
  CLUS_3             7              43
D3V5, multiclass
D3V6, 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
D3V7, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1            19              60
  CLUS_2            11              69
  CLUS_3             9              73
D3V8, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             0              51
  CLUS_2            10              60
  CLUS_3            10              32
  CLUS_4            19              59
D3V9, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1            12              59
  CLUS_2            12              79
  CLUS_3            11              67
D3V10, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1            13             110
  CLUS_2             6              35
  CLUS_3             2              11
  CLUS_4            14              49

Clustering(4) Variable = KRAS MUTATION ANALYSIS
D4V1, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            5              6
  CLUS_2            2             17
  CLUS_3            3             10
  CLUS_4            1              7
D4V2, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            2             17
  CLUS_2            7              6
  CLUS_3            2             17
D4V3, multiclass
D4V4, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            6             36
  CLUS_2            8             34
  CLUS_3           16             34
D4V5, multiclass
D4V6, 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
D4V7, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           14             65
  CLUS_2           20             60
  CLUS_3           17             65
D4V8, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            3             48
  CLUS_2           20             50
  CLUS_3           16             26
  CLUS_4           12             66
D4V9, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           10             61
  CLUS_2           25             66
  CLUS_3           17             61
D4V10, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           29             94
  CLUS_2           14             27
  CLUS_3            2             11
  CLUS_4            7             56

Clustering(5) Variable = PIK3CA MUTATION ANALYSIS
D5V1, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              7                4
  CLUS_2              8               11
  CLUS_3              7                6
  CLUS_4              5                3
D5V2, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             12                7
  CLUS_2              8                5
  CLUS_3              7               12
D5V3, multiclass
D5V4, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             22               20
  CLUS_2             24               18
  CLUS_3             23               27
D5V5, multiclass
D5V6, 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
D5V7, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             40               39
  CLUS_2             45               35
  CLUS_3             43               39
D5V8, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             28               23
  CLUS_2             40               30
  CLUS_3             22               20
  CLUS_4             38               40
D5V9, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             32               39
  CLUS_2             54               37
  CLUS_3             42               36
D5V10, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             69               54
  CLUS_2             24               17
  CLUS_3              5                8
  CLUS_4             30               33

Clustering(6) Variable = PIK3R1 MUTATION ANALYSIS
D6V1, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              5                6
  CLUS_2              2               17
  CLUS_3              7                6
  CLUS_4              2                6
D6V2, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              8               11
  CLUS_2              6                7
  CLUS_3              2               17
D6V3, multiclass
D6V4, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              5               37
  CLUS_2             12               30
  CLUS_3             28               22
D6V5, multiclass
D6V6, 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
D6V7, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1             10               69
  CLUS_2             33               47
  CLUS_3             35               47
D6V8, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1             21               30
  CLUS_2             28               42
  CLUS_3             17               25
  CLUS_4             12               66
D6V9, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1             15               56
  CLUS_2             36               55
  CLUS_3             30               48
D6V10, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1             49               74
  CLUS_2             14               27
  CLUS_3              6                7
  CLUS_4             12               51

Clustering(7) Variable = PPP2R1A MUTATION ANALYSIS
D7V1, multiclass
        clus
vv       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  CLUS_1               2                 9
  CLUS_2               6                13
  CLUS_3               0                13
  CLUS_4               0                 8
D7V2, multiclass
        clus
vv       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  CLUS_1               0                19
  CLUS_2               4                 9
  CLUS_3               4                15
D7V3, multiclass
D7V4, multiclass
        clus
vv       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  CLUS_1               9                33
  CLUS_2               1                41
  CLUS_3               5                45
D7V5, multiclass
D7V6, 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
D7V7, multiclass
        clus
vv       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  CLUS_1              17                62
  CLUS_2               4                76
  CLUS_3               6                76
D7V8, multiclass
        clus
vv       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  CLUS_1               2                49
  CLUS_2               3                67
  CLUS_3               5                37
  CLUS_4              17                61
D7V9, multiclass
        clus
vv       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  CLUS_1              14                57
  CLUS_2               5                86
  CLUS_3               6                72
D7V10, multiclass
        clus
vv       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  CLUS_1               7               116
  CLUS_2               3                38
  CLUS_3               0                13
  CLUS_4              15                48

Clustering(8) Variable = PRKAR1B MUTATION ANALYSIS
D8V1, multiclass
D8V2, multiclass
D8V3, multiclass
D8V4, multiclass
        clus
vv       PRKAR1B MUTATED PRKAR1B WILD-TYPE
  CLUS_1               2                40
  CLUS_2               0                42
  CLUS_3               1                49
D8V5, multiclass
D8V6, 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
D8V7, multiclass
        clus
vv       PRKAR1B MUTATED PRKAR1B WILD-TYPE
  CLUS_1               2                77
  CLUS_2               1                79
  CLUS_3               1                81
D8V8, multiclass
        clus
vv       PRKAR1B MUTATED PRKAR1B WILD-TYPE
  CLUS_1               0                51
  CLUS_2               1                69
  CLUS_3               2                40
  CLUS_4               1                77
D8V9, multiclass
        clus
vv       PRKAR1B MUTATED PRKAR1B WILD-TYPE
  CLUS_1               1                70
  CLUS_2               1                90
  CLUS_3               2                76
D8V10, multiclass
        clus
vv       PRKAR1B MUTATED PRKAR1B WILD-TYPE
  CLUS_1               1               122
  CLUS_2               1                40
  CLUS_3               1                12
  CLUS_4               1                62

Clustering(9) Variable = RPL22 MUTATION ANALYSIS
D9V1, multiclass
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  CLUS_1             5               6
  CLUS_2             2              17
  CLUS_3             1              12
  CLUS_4             0               8
D9V2, multiclass
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  CLUS_1             0              19
  CLUS_2             5               8
  CLUS_3             3              16
D9V3, multiclass
D9V4, multiclass
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  CLUS_1             2              40
  CLUS_2             2              40
  CLUS_3            12              38
D9V5, multiclass
D9V6, 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
D9V7, multiclass
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  CLUS_1             7              72
  CLUS_2            10              70
  CLUS_3            13              69
D9V8, multiclass
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  CLUS_1             2              49
  CLUS_2             9              61
  CLUS_3             8              34
  CLUS_4            11              67
D9V9, multiclass
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  CLUS_1             6              65
  CLUS_2            12              79
  CLUS_3            13              65
D9V10, multiclass
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  CLUS_1            13             110
  CLUS_2            10              31
  CLUS_3             4               9
  CLUS_4             4              59

Clustering(10) Variable = SPOP MUTATION ANALYSIS
D10V1, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            2              9
  CLUS_2            1             18
  CLUS_3            0             13
  CLUS_4            2              6
D10V2, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            2             17
  CLUS_2            2             11
  CLUS_3            1             18
D10V3, multiclass
D10V4, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            4             38
  CLUS_2            1             41
  CLUS_3            5             45
D10V5, multiclass
D10V6, 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
D10V7, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            6             73
  CLUS_2            6             74
  CLUS_3            9             73
D10V8, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            4             47
  CLUS_2            6             64
  CLUS_3            4             38
  CLUS_4            7             71
D10V9, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            7             64
  CLUS_2            8             83
  CLUS_3            6             72
D10V10, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            9            114
  CLUS_2            5             36
  CLUS_3            1             12
  CLUS_4            6             57

Clustering(11) Variable = TP53 MUTATION ANALYSIS
D11V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1             10
  CLUS_2           14              5
  CLUS_3            1             12
  CLUS_4            0              8
D11V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1             18
  CLUS_2            2             11
  CLUS_3           13              6
D11V3, multiclass
D11V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           30             12
  CLUS_2            4             38
  CLUS_3            5             45
D11V5, multiclass
D11V6, 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
D11V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           57             22
  CLUS_2            3             77
  CLUS_3            8             74
D11V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            0             51
  CLUS_2            2             68
  CLUS_3           10             32
  CLUS_4           56             22
D11V9, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           47             24
  CLUS_2            8             83
  CLUS_3            9             69
D11V10, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            7            116
  CLUS_2            5             36
  CLUS_3            7              6
  CLUS_4           45             18

Clustering(12) Variable = CTCF MUTATION ANALYSIS
D12V1, multiclass
        clus
vv       CTCF MUTATED CTCF WILD-TYPE
  CLUS_1            3              8
  CLUS_2            1             18
  CLUS_3            5              8
  CLUS_4            0              8
D12V2, multiclass
        clus
vv       CTCF MUTATED CTCF WILD-TYPE
  CLUS_1            3             16
  CLUS_2            4              9
  CLUS_3            2             17
D12V3, multiclass
D12V4, multiclass
        clus
vv       CTCF MUTATED CTCF WILD-TYPE
  CLUS_1            3             39
  CLUS_2           11             31
  CLUS_3            7             43
D12V5, multiclass
D12V6, 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
D12V7, multiclass
        clus
vv       CTCF MUTATED CTCF WILD-TYPE
  CLUS_1            4             75
  CLUS_2           21             59
  CLUS_3           19             63
D12V8, multiclass
        clus
vv       CTCF MUTATED CTCF WILD-TYPE
  CLUS_1           11             40
  CLUS_2           19             51
  CLUS_3           11             31
  CLUS_4            3             75
D12V9, multiclass
        clus
vv       CTCF MUTATED CTCF WILD-TYPE
  CLUS_1            5             66
  CLUS_2           23             68
  CLUS_3           17             61
D12V10, multiclass
        clus
vv       CTCF MUTATED CTCF WILD-TYPE
  CLUS_1           33             90
  CLUS_2            5             36
  CLUS_3            2             11
  CLUS_4            5             58

Clustering(13) Variable = FGFR2 MUTATION ANALYSIS
D13V1, multiclass
        clus
vv       FGFR2 MUTATED FGFR2 WILD-TYPE
  CLUS_1             3               8
  CLUS_2             2              17
  CLUS_3             1              12
  CLUS_4             0               8
D13V2, multiclass
        clus
vv       FGFR2 MUTATED FGFR2 WILD-TYPE
  CLUS_1             2              17
  CLUS_2             3              10
  CLUS_3             1              18
D13V3, multiclass
D13V4, multiclass
        clus
vv       FGFR2 MUTATED FGFR2 WILD-TYPE
  CLUS_1             5              37
  CLUS_2             6              36
  CLUS_3             6              44
D13V5, multiclass
D13V6, 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
D13V7, multiclass
        clus
vv       FGFR2 MUTATED FGFR2 WILD-TYPE
  CLUS_1             9              70
  CLUS_2            11              69
  CLUS_3            10              72
D13V8, multiclass
        clus
vv       FGFR2 MUTATED FGFR2 WILD-TYPE
  CLUS_1             2              49
  CLUS_2            10              60
  CLUS_3             9              33
  CLUS_4             9              69
D13V9, multiclass
        clus
vv       FGFR2 MUTATED FGFR2 WILD-TYPE
  CLUS_1             6              65
  CLUS_2            12              79
  CLUS_3            12              66
D13V10, multiclass
        clus
vv       FGFR2 MUTATED FGFR2 WILD-TYPE
  CLUS_1            15             108
  CLUS_2             5              36
  CLUS_3             4               9
  CLUS_4             6              57

Clustering(14) Variable = ARID1A MUTATION ANALYSIS
D14V1, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              5                6
  CLUS_2              3               16
  CLUS_3              5                8
  CLUS_4              4                4
D14V2, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              7               12
  CLUS_2              7                6
  CLUS_3              3               16
D14V3, multiclass
D14V4, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1             10               32
  CLUS_2             17               25
  CLUS_3             18               32
D14V5, multiclass
D14V6, 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
D14V7, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1             18               61
  CLUS_2             31               49
  CLUS_3             32               50
D14V8, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1             20               31
  CLUS_2             29               41
  CLUS_3             14               28
  CLUS_4             18               60
D14V9, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1             16               55
  CLUS_2             38               53
  CLUS_3             26               52
D14V10, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1             48               75
  CLUS_2             15               26
  CLUS_3              6                7
  CLUS_4             11               52

Clustering(15) Variable = P2RY11 MUTATION ANALYSIS
D15V1, multiclass
[1] "Remove cluster labels:" "P2RY11 MUTATED"        
clus
  P2RY11 MUTATED P2RY11 WILD-TYPE 
               1               50 
      TCGA-A5-A0G3       TCGA-A5-A0G5       TCGA-A5-A0GA       TCGA-A5-A0GB 
"P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" 
      TCGA-A5-A0GE       TCGA-A5-A0GH       TCGA-A5-A0GM       TCGA-A5-A0GP 
"P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" 
      TCGA-A5-A0GU       TCGA-AP-A051       TCGA-AP-A052       TCGA-AP-A053 
"P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" 
      TCGA-AP-A054       TCGA-AP-A056       TCGA-AP-A05A       TCGA-AP-A05D 
"P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" 
      TCGA-AP-A05J       TCGA-AP-A05N       TCGA-AP-A05P       TCGA-AP-A0L8 
"P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" 
      TCGA-AP-A0L9       TCGA-AP-A0LD       TCGA-AP-A0LG       TCGA-AP-A0LH 
"P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" 
      TCGA-AP-A0LJ       TCGA-AP-A0LN       TCGA-AP-A0LT       TCGA-AP-A0LV 
"P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" 
      TCGA-AX-A05S       TCGA-AX-A05T       TCGA-AX-A05U       TCGA-AX-A05W 
"P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" 
      TCGA-AX-A05Y       TCGA-AX-A05Z       TCGA-AX-A060       TCGA-AX-A062 
"P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" 
      TCGA-AX-A063       TCGA-AX-A064       TCGA-AX-A06B       TCGA-AX-A0IW 
"P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" 
      TCGA-AX-A0J1       TCGA-B5-A0JR       TCGA-B5-A0JZ       TCGA-B5-A0K0 
"P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" 
      TCGA-B5-A0K1       TCGA-B5-A0K4       TCGA-BG-A0LW       TCGA-BG-A0MI 
"P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" 
      TCGA-BK-A0C9       TCGA-BK-A0CC 
"P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" 
D15V2, multiclass
[1] "Remove cluster labels:" "P2RY11 MUTATED"        
clus
  P2RY11 MUTATED P2RY11 WILD-TYPE 
               1               50 
      TCGA-A5-A0G3       TCGA-A5-A0G5       TCGA-A5-A0GA       TCGA-A5-A0GB 
"P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" 
      TCGA-A5-A0GE       TCGA-A5-A0GH       TCGA-A5-A0GM       TCGA-A5-A0GP 
"P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" 
      TCGA-A5-A0GU       TCGA-AP-A051       TCGA-AP-A052       TCGA-AP-A053 
"P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" 
      TCGA-AP-A054       TCGA-AP-A056       TCGA-AP-A05A       TCGA-AP-A05D 
"P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" 
      TCGA-AP-A05J       TCGA-AP-A05N       TCGA-AP-A05P       TCGA-AP-A0L8 
"P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" 
      TCGA-AP-A0L9       TCGA-AP-A0LD       TCGA-AP-A0LG       TCGA-AP-A0LH 
"P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" 
      TCGA-AP-A0LJ       TCGA-AP-A0LN       TCGA-AP-A0LT       TCGA-AP-A0LV 
"P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" 
      TCGA-AX-A05S       TCGA-AX-A05T       TCGA-AX-A05U       TCGA-AX-A05W 
"P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" 
      TCGA-AX-A05Y       TCGA-AX-A05Z       TCGA-AX-A060       TCGA-AX-A062 
"P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" 
      TCGA-AX-A063       TCGA-AX-A064       TCGA-AX-A06B       TCGA-AX-A0IW 
"P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" 
      TCGA-AX-A0J1       TCGA-B5-A0JR       TCGA-B5-A0JZ       TCGA-B5-A0K0 
"P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" 
      TCGA-B5-A0K1       TCGA-B5-A0K4       TCGA-BG-A0LW       TCGA-BG-A0MI 
"P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" 
      TCGA-BK-A0C9       TCGA-BK-A0CC 
"P2RY11 WILD-TYPE" "P2RY11 WILD-TYPE" 
D15V3, multiclass
D15V4, multiclass
        clus
vv       P2RY11 MUTATED P2RY11 WILD-TYPE
  CLUS_1              1               41
  CLUS_2              3               39
  CLUS_3              1               49
D15V5, multiclass
D15V6, binary
                  cls
clus                 0   1
  P2RY11 MUTATED     2   4
  P2RY11 WILD-TYPE 113  67
[1] "tbl2"
                  cls
clus               [,1] [,2]
  P2RY11 MUTATED      2    4
  P2RY11 WILD-TYPE  113   67
        clus
vv       P2RY11 MUTATED P2RY11 WILD-TYPE
  CLUS_1              2              113
  CLUS_2              4               67
D15V7, multiclass
        clus
vv       P2RY11 MUTATED P2RY11 WILD-TYPE
  CLUS_1              4               75
  CLUS_2              3               77
  CLUS_3              0               82
D15V8, multiclass
        clus
vv       P2RY11 MUTATED P2RY11 WILD-TYPE
  CLUS_1              0               51
  CLUS_2              3               67
  CLUS_3              1               41
  CLUS_4              3               75
D15V9, multiclass
        clus
vv       P2RY11 MUTATED P2RY11 WILD-TYPE
  CLUS_1              3               68
  CLUS_2              2               89
  CLUS_3              1               77
D15V10, multiclass
        clus
vv       P2RY11 MUTATED P2RY11 WILD-TYPE
  CLUS_1              3              120
  CLUS_2              0               41
  CLUS_3              1               12
  CLUS_4              2               61

Clustering(16) Variable = CCND1 MUTATION ANALYSIS
D16V1, multiclass
        clus
vv       CCND1 MUTATED CCND1 WILD-TYPE
  CLUS_1             2               9
  CLUS_2             1              18
  CLUS_3             0              13
  CLUS_4             1               7
D16V2, multiclass
        clus
vv       CCND1 MUTATED CCND1 WILD-TYPE
  CLUS_1             1              18
  CLUS_2             2              11
  CLUS_3             1              18
D16V3, multiclass
D16V4, multiclass
        clus
vv       CCND1 MUTATED CCND1 WILD-TYPE
  CLUS_1             1              41
  CLUS_2             2              40
  CLUS_3             4              46
D16V5, multiclass
D16V6, binary
                 cls
clus                0   1
  CCND1 MUTATED     5   6
  CCND1 WILD-TYPE 110  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCND1 MUTATED      5    6
  CCND1 WILD-TYPE  110   65
        clus
vv       CCND1 MUTATED CCND1 WILD-TYPE
  CLUS_1             5             110
  CLUS_2             6              65
D16V7, multiclass
        clus
vv       CCND1 MUTATED CCND1 WILD-TYPE
  CLUS_1             3              76
  CLUS_2             5              75
  CLUS_3             7              75
D16V8, multiclass
        clus
vv       CCND1 MUTATED CCND1 WILD-TYPE
  CLUS_1             2              49
  CLUS_2             5              65
  CLUS_3             5              37
  CLUS_4             3              75
D16V9, multiclass
        clus
vv       CCND1 MUTATED CCND1 WILD-TYPE
  CLUS_1             2              69
  CLUS_2             5              86
  CLUS_3             8              70
D16V10, multiclass
        clus
vv       CCND1 MUTATED CCND1 WILD-TYPE
  CLUS_1            10             113
  CLUS_2             2              39
  CLUS_3             2              11
  CLUS_4             1              62

Clustering(17) Variable = CHD4 MUTATION ANALYSIS
D17V1, multiclass
        clus
vv       CHD4 MUTATED CHD4 WILD-TYPE
  CLUS_1            1             10
  CLUS_2            6             13
  CLUS_3            0             13
  CLUS_4            2              6
D17V2, multiclass
        clus
vv       CHD4 MUTATED CHD4 WILD-TYPE
  CLUS_1            2             17
  CLUS_2            2             11
  CLUS_3            5             14
D17V3, multiclass
D17V4, multiclass
        clus
vv       CHD4 MUTATED CHD4 WILD-TYPE
  CLUS_1            7             35
  CLUS_2            5             37
  CLUS_3            7             43
D17V5, multiclass
D17V6, 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
D17V7, multiclass
        clus
vv       CHD4 MUTATED CHD4 WILD-TYPE
  CLUS_1           14             65
  CLUS_2           10             70
  CLUS_3           11             71
D17V8, multiclass
        clus
vv       CHD4 MUTATED CHD4 WILD-TYPE
  CLUS_1            5             46
  CLUS_2            9             61
  CLUS_3            6             36
  CLUS_4           15             63
D17V9, multiclass
        clus
vv       CHD4 MUTATED CHD4 WILD-TYPE
  CLUS_1           10             61
  CLUS_2            8             83
  CLUS_3           12             66
D17V10, multiclass
        clus
vv       CHD4 MUTATED CHD4 WILD-TYPE
  CLUS_1           15            108
  CLUS_2            3             38
  CLUS_3            2             11
  CLUS_4           10             53

Clustering(18) Variable = NFE2L2 MUTATION ANALYSIS
D18V1, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              0               11
  CLUS_2              1               18
  CLUS_3              3               10
  CLUS_4              0                8
D18V2, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              2               17
  CLUS_2              1               12
  CLUS_3              1               18
D18V3, multiclass
D18V4, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              1               41
  CLUS_2              3               39
  CLUS_3              3               47
D18V5, multiclass
D18V6, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     8   5
  NFE2L2 WILD-TYPE 107  66
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      8    5
  NFE2L2 WILD-TYPE  107   66
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              8              107
  CLUS_2              5               66
D18V7, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              2               77
  CLUS_2              9               71
  CLUS_3              2               80
D18V8, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              0               51
  CLUS_2              8               62
  CLUS_3              4               38
  CLUS_4              1               77
D18V9, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              3               68
  CLUS_2              8               83
  CLUS_3              4               74
D18V10, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              9              114
  CLUS_2              2               39
  CLUS_3              1               12
  CLUS_4              3               60

Clustering(19) Variable = SOX17 MUTATION ANALYSIS
D19V1, multiclass
[1] "Remove cluster labels:" "SOX17 MUTATED"         
clus
  SOX17 MUTATED SOX17 WILD-TYPE 
              2              49 
     TCGA-A5-A0G3      TCGA-A5-A0G5      TCGA-A5-A0GA      TCGA-A5-A0GB 
"SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" 
     TCGA-A5-A0GE      TCGA-A5-A0GH      TCGA-A5-A0GM      TCGA-A5-A0GP 
"SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" 
     TCGA-A5-A0GU      TCGA-AP-A051      TCGA-AP-A052      TCGA-AP-A053 
"SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" 
     TCGA-AP-A054      TCGA-AP-A056      TCGA-AP-A05A      TCGA-AP-A05D 
"SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" 
     TCGA-AP-A05H      TCGA-AP-A05J      TCGA-AP-A05N      TCGA-AP-A0L8 
"SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" 
     TCGA-AP-A0L9      TCGA-AP-A0LD      TCGA-AP-A0LG      TCGA-AP-A0LH 
"SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" 
     TCGA-AP-A0LJ      TCGA-AP-A0LN      TCGA-AP-A0LT      TCGA-AP-A0LV 
"SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" 
     TCGA-AX-A05S      TCGA-AX-A05T      TCGA-AX-A05U      TCGA-AX-A05W 
"SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" 
     TCGA-AX-A05Y      TCGA-AX-A05Z      TCGA-AX-A060      TCGA-AX-A062 
"SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" 
     TCGA-AX-A063      TCGA-AX-A064      TCGA-AX-A06B      TCGA-AX-A0IW 
"SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" 
     TCGA-AX-A0J1      TCGA-B5-A0JR      TCGA-B5-A0JZ      TCGA-B5-A0K0 
"SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" 
     TCGA-B5-A0K1      TCGA-BG-A0LW      TCGA-BG-A0MI      TCGA-BK-A0C9 
"SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" 
     TCGA-BK-A0CC 
"SOX17 WILD-TYPE" 
D19V2, multiclass
[1] "Remove cluster labels:" "SOX17 MUTATED"         
clus
  SOX17 MUTATED SOX17 WILD-TYPE 
              2              49 
     TCGA-A5-A0G3      TCGA-A5-A0G5      TCGA-A5-A0GA      TCGA-A5-A0GB 
"SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" 
     TCGA-A5-A0GE      TCGA-A5-A0GH      TCGA-A5-A0GM      TCGA-A5-A0GP 
"SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" 
     TCGA-A5-A0GU      TCGA-AP-A051      TCGA-AP-A052      TCGA-AP-A053 
"SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" 
     TCGA-AP-A054      TCGA-AP-A056      TCGA-AP-A05A      TCGA-AP-A05D 
"SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" 
     TCGA-AP-A05H      TCGA-AP-A05J      TCGA-AP-A05N      TCGA-AP-A0L8 
"SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" 
     TCGA-AP-A0L9      TCGA-AP-A0LD      TCGA-AP-A0LG      TCGA-AP-A0LH 
"SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" 
     TCGA-AP-A0LJ      TCGA-AP-A0LN      TCGA-AP-A0LT      TCGA-AP-A0LV 
"SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" 
     TCGA-AX-A05S      TCGA-AX-A05T      TCGA-AX-A05U      TCGA-AX-A05W 
"SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" 
     TCGA-AX-A05Y      TCGA-AX-A05Z      TCGA-AX-A060      TCGA-AX-A062 
"SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" 
     TCGA-AX-A063      TCGA-AX-A064      TCGA-AX-A06B      TCGA-AX-A0IW 
"SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" 
     TCGA-AX-A0J1      TCGA-B5-A0JR      TCGA-B5-A0JZ      TCGA-B5-A0K0 
"SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" 
     TCGA-B5-A0K1      TCGA-BG-A0LW      TCGA-BG-A0MI      TCGA-BK-A0C9 
"SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" "SOX17 WILD-TYPE" 
     TCGA-BK-A0CC 
"SOX17 WILD-TYPE" 
D19V3, multiclass
D19V4, multiclass
        clus
vv       SOX17 MUTATED SOX17 WILD-TYPE
  CLUS_1             0              42
  CLUS_2             3              39
  CLUS_3             1              49
D19V5, multiclass
D19V6, binary
                 cls
clus                0   1
  SOX17 MUTATED     5   1
  SOX17 WILD-TYPE 110  70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SOX17 MUTATED      5    1
  SOX17 WILD-TYPE  110   70
        clus
vv       SOX17 MUTATED SOX17 WILD-TYPE
  CLUS_1             5             110
  CLUS_2             1              70
D19V7, multiclass
        clus
vv       SOX17 MUTATED SOX17 WILD-TYPE
  CLUS_1             2              77
  CLUS_2             4              76
  CLUS_3             1              81
D19V8, multiclass
        clus
vv       SOX17 MUTATED SOX17 WILD-TYPE
  CLUS_1             1              50
  CLUS_2             4              66
  CLUS_3             0              42
  CLUS_4             2              76
D19V9, multiclass
        clus
vv       SOX17 MUTATED SOX17 WILD-TYPE
  CLUS_1             1              70
  CLUS_2             3              88
  CLUS_3             3              75
D19V10, multiclass
        clus
vv       SOX17 MUTATED SOX17 WILD-TYPE
  CLUS_1             5             118
  CLUS_2             1              40
  CLUS_3             1              12
  CLUS_4             0              63

Clustering(20) Variable = FOXA2 MUTATION ANALYSIS
D20V1, 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" 
D20V2, 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" 
D20V3, multiclass
D20V4, multiclass
        clus
vv       FOXA2 MUTATED FOXA2 WILD-TYPE
  CLUS_1             2              40
  CLUS_2             3              39
  CLUS_3             2              48
D20V5, multiclass
D20V6, 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
D20V7, multiclass
        clus
vv       FOXA2 MUTATED FOXA2 WILD-TYPE
  CLUS_1             3              76
  CLUS_2             5              75
  CLUS_3             4              78
D20V8, multiclass
        clus
vv       FOXA2 MUTATED FOXA2 WILD-TYPE
  CLUS_1             3              48
  CLUS_2             5              65
  CLUS_3             0              42
  CLUS_4             4              74
D20V9, multiclass
        clus
vv       FOXA2 MUTATED FOXA2 WILD-TYPE
  CLUS_1             1              70
  CLUS_2             4              87
  CLUS_3             6              72
D20V10, multiclass
        clus
vv       FOXA2 MUTATED FOXA2 WILD-TYPE
  CLUS_1             7             116
  CLUS_2             2              39
  CLUS_3             0              13
  CLUS_4             2              61

Clustering(21) Variable = FAM9A MUTATION ANALYSIS
D21V1, multiclass
[1] "Remove cluster labels:" "FAM9A MUTATED"         
clus
  FAM9A MUTATED FAM9A WILD-TYPE 
              1              50 
     TCGA-A5-A0G3      TCGA-A5-A0G5      TCGA-A5-A0GA      TCGA-A5-A0GB 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-A5-A0GE      TCGA-A5-A0GH      TCGA-A5-A0GM      TCGA-A5-A0GP 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-A5-A0GU      TCGA-AP-A051      TCGA-AP-A052      TCGA-AP-A053 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AP-A054      TCGA-AP-A056      TCGA-AP-A05A      TCGA-AP-A05D 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AP-A05H      TCGA-AP-A05J      TCGA-AP-A05N      TCGA-AP-A05P 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AP-A0L8      TCGA-AP-A0L9      TCGA-AP-A0LD      TCGA-AP-A0LG 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AP-A0LH      TCGA-AP-A0LJ      TCGA-AP-A0LN      TCGA-AP-A0LT 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AP-A0LV      TCGA-AX-A05S      TCGA-AX-A05T      TCGA-AX-A05U 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AX-A05W      TCGA-AX-A05Y      TCGA-AX-A05Z      TCGA-AX-A060 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AX-A062      TCGA-AX-A063      TCGA-AX-A064      TCGA-AX-A06B 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AX-A0IW      TCGA-AX-A0J1      TCGA-B5-A0JR      TCGA-B5-A0JZ 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-B5-A0K0      TCGA-B5-A0K4      TCGA-BG-A0LW      TCGA-BG-A0MI 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-BK-A0C9      TCGA-BK-A0CC 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
D21V2, multiclass
[1] "Remove cluster labels:" "FAM9A MUTATED"         
clus
  FAM9A MUTATED FAM9A WILD-TYPE 
              1              50 
     TCGA-A5-A0G3      TCGA-A5-A0G5      TCGA-A5-A0GA      TCGA-A5-A0GB 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-A5-A0GE      TCGA-A5-A0GH      TCGA-A5-A0GM      TCGA-A5-A0GP 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-A5-A0GU      TCGA-AP-A051      TCGA-AP-A052      TCGA-AP-A053 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AP-A054      TCGA-AP-A056      TCGA-AP-A05A      TCGA-AP-A05D 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AP-A05H      TCGA-AP-A05J      TCGA-AP-A05N      TCGA-AP-A05P 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AP-A0L8      TCGA-AP-A0L9      TCGA-AP-A0LD      TCGA-AP-A0LG 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AP-A0LH      TCGA-AP-A0LJ      TCGA-AP-A0LN      TCGA-AP-A0LT 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AP-A0LV      TCGA-AX-A05S      TCGA-AX-A05T      TCGA-AX-A05U 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AX-A05W      TCGA-AX-A05Y      TCGA-AX-A05Z      TCGA-AX-A060 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AX-A062      TCGA-AX-A063      TCGA-AX-A064      TCGA-AX-A06B 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-AX-A0IW      TCGA-AX-A0J1      TCGA-B5-A0JR      TCGA-B5-A0JZ 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-B5-A0K0      TCGA-B5-A0K4      TCGA-BG-A0LW      TCGA-BG-A0MI 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-BK-A0C9      TCGA-BK-A0CC 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
D21V3, multiclass
D21V4, multiclass
        clus
vv       FAM9A MUTATED FAM9A WILD-TYPE
  CLUS_1             5              37
  CLUS_2             1              41
  CLUS_3             4              46
D21V5, multiclass
D21V6, binary
                 cls
clus                0   1
  FAM9A MUTATED     3   8
  FAM9A WILD-TYPE 112  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAM9A MUTATED      3    8
  FAM9A WILD-TYPE  112   63
        clus
vv       FAM9A MUTATED FAM9A WILD-TYPE
  CLUS_1             3             112
  CLUS_2             8              63
D21V7, multiclass
        clus
vv       FAM9A MUTATED FAM9A WILD-TYPE
  CLUS_1             6              73
  CLUS_2             2              78
  CLUS_3             6              76
D21V8, multiclass
        clus
vv       FAM9A MUTATED FAM9A WILD-TYPE
  CLUS_1             1              50
  CLUS_2             2              68
  CLUS_3             4              38
  CLUS_4             7              71
D21V9, multiclass
        clus
vv       FAM9A MUTATED FAM9A WILD-TYPE
  CLUS_1             5              66
  CLUS_2             4              87
  CLUS_3             5              73
D21V10, multiclass
        clus
vv       FAM9A MUTATED FAM9A WILD-TYPE
  CLUS_1             4             119
  CLUS_2             2              39
  CLUS_3             2              11
  CLUS_4             6              57

Clustering(22) Variable = SMTNL2 MUTATION ANALYSIS
D22V1, 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" 
D22V2, 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" 
D22V3, multiclass
D22V4, multiclass
        clus
vv       SMTNL2 MUTATED SMTNL2 WILD-TYPE
  CLUS_1              1               41
  CLUS_2              3               39
  CLUS_3              2               48
D22V5, multiclass
D22V6, 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
D22V7, multiclass
        clus
vv       SMTNL2 MUTATED SMTNL2 WILD-TYPE
  CLUS_1              2               77
  CLUS_2              4               76
  CLUS_3              3               79
D22V8, multiclass
        clus
vv       SMTNL2 MUTATED SMTNL2 WILD-TYPE
  CLUS_1              2               49
  CLUS_2              3               67
  CLUS_3              1               41
  CLUS_4              3               75
D22V9, multiclass
        clus
vv       SMTNL2 MUTATED SMTNL2 WILD-TYPE
  CLUS_1              2               69
  CLUS_2              4               87
  CLUS_3              3               75
D22V10, multiclass
        clus
vv       SMTNL2 MUTATED SMTNL2 WILD-TYPE
  CLUS_1              5              118
  CLUS_2              1               40
  CLUS_3              2               11
  CLUS_4              1               62

Clustering(23) Variable = RBMX MUTATION ANALYSIS
D23V1, multiclass
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  CLUS_1            3              8
  CLUS_2            2             17
  CLUS_3            0             13
  CLUS_4            0              8
D23V2, multiclass
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  CLUS_1            0             19
  CLUS_2            3             10
  CLUS_3            2             17
D23V3, multiclass
D23V4, multiclass
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  CLUS_1            1             41
  CLUS_2            0             42
  CLUS_3            3             47
D23V5, multiclass
D23V6, 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
D23V7, multiclass
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  CLUS_1            3             76
  CLUS_2            5             75
  CLUS_3            5             77
D23V8, multiclass
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  CLUS_1            0             51
  CLUS_2            4             66
  CLUS_3            6             36
  CLUS_4            3             75
D23V9, multiclass
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  CLUS_1            4             67
  CLUS_2            5             86
  CLUS_3            4             74
D23V10, multiclass
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  CLUS_1            4            119
  CLUS_2            5             36
  CLUS_3            1             12
  CLUS_4            3             60

Clustering(24) Variable = MAX MUTATION ANALYSIS
D24V1, multiclass
[1] "Remove cluster labels:" "MAX MUTATED"           
clus
  MAX MUTATED MAX WILD-TYPE 
            1            50 
   TCGA-A5-A0G3    TCGA-A5-A0G5    TCGA-A5-A0GA    TCGA-A5-A0GB    TCGA-A5-A0GE 
"MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" 
   TCGA-A5-A0GH    TCGA-A5-A0GM    TCGA-A5-A0GP    TCGA-A5-A0GU    TCGA-AP-A051 
"MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" 
   TCGA-AP-A052    TCGA-AP-A053    TCGA-AP-A054    TCGA-AP-A056    TCGA-AP-A05A 
"MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" 
   TCGA-AP-A05D    TCGA-AP-A05H    TCGA-AP-A05J    TCGA-AP-A05N    TCGA-AP-A05P 
"MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" 
   TCGA-AP-A0L8    TCGA-AP-A0L9    TCGA-AP-A0LD    TCGA-AP-A0LG    TCGA-AP-A0LH 
"MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" 
   TCGA-AP-A0LJ    TCGA-AP-A0LN    TCGA-AP-A0LT    TCGA-AP-A0LV    TCGA-AX-A05S 
"MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" 
   TCGA-AX-A05T    TCGA-AX-A05U    TCGA-AX-A05W    TCGA-AX-A05Y    TCGA-AX-A05Z 
"MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" 
   TCGA-AX-A060    TCGA-AX-A062    TCGA-AX-A064    TCGA-AX-A06B    TCGA-AX-A0IW 
"MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" 
   TCGA-AX-A0J1    TCGA-B5-A0JR    TCGA-B5-A0JZ    TCGA-B5-A0K0    TCGA-B5-A0K1 
"MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" 
   TCGA-B5-A0K4    TCGA-BG-A0LW    TCGA-BG-A0MI    TCGA-BK-A0C9    TCGA-BK-A0CC 
"MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" 
D24V2, multiclass
[1] "Remove cluster labels:" "MAX MUTATED"           
clus
  MAX MUTATED MAX WILD-TYPE 
            1            50 
   TCGA-A5-A0G3    TCGA-A5-A0G5    TCGA-A5-A0GA    TCGA-A5-A0GB    TCGA-A5-A0GE 
"MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" 
   TCGA-A5-A0GH    TCGA-A5-A0GM    TCGA-A5-A0GP    TCGA-A5-A0GU    TCGA-AP-A051 
"MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" 
   TCGA-AP-A052    TCGA-AP-A053    TCGA-AP-A054    TCGA-AP-A056    TCGA-AP-A05A 
"MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" 
   TCGA-AP-A05D    TCGA-AP-A05H    TCGA-AP-A05J    TCGA-AP-A05N    TCGA-AP-A05P 
"MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" 
   TCGA-AP-A0L8    TCGA-AP-A0L9    TCGA-AP-A0LD    TCGA-AP-A0LG    TCGA-AP-A0LH 
"MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" 
   TCGA-AP-A0LJ    TCGA-AP-A0LN    TCGA-AP-A0LT    TCGA-AP-A0LV    TCGA-AX-A05S 
"MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" 
   TCGA-AX-A05T    TCGA-AX-A05U    TCGA-AX-A05W    TCGA-AX-A05Y    TCGA-AX-A05Z 
"MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" 
   TCGA-AX-A060    TCGA-AX-A062    TCGA-AX-A064    TCGA-AX-A06B    TCGA-AX-A0IW 
"MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" 
   TCGA-AX-A0J1    TCGA-B5-A0JR    TCGA-B5-A0JZ    TCGA-B5-A0K0    TCGA-B5-A0K1 
"MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" 
   TCGA-B5-A0K4    TCGA-BG-A0LW    TCGA-BG-A0MI    TCGA-BK-A0C9    TCGA-BK-A0CC 
"MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" "MAX WILD-TYPE" 
D24V3, multiclass
D24V4, multiclass
        clus
vv       MAX MUTATED MAX WILD-TYPE
  CLUS_1           2            40
  CLUS_2           3            39
  CLUS_3           2            48
D24V5, multiclass
D24V6, binary
               cls
clus              0   1
  MAX MUTATED     5   4
  MAX WILD-TYPE 110  67
[1] "tbl2"
               cls
clus            [,1] [,2]
  MAX MUTATED      5    4
  MAX WILD-TYPE  110   67
        clus
vv       MAX MUTATED MAX WILD-TYPE
  CLUS_1           5           110
  CLUS_2           4            67
D24V7, multiclass
        clus
vv       MAX MUTATED MAX WILD-TYPE
  CLUS_1           4            75
  CLUS_2           2            78
  CLUS_3           5            77
D24V8, multiclass
        clus
vv       MAX MUTATED MAX WILD-TYPE
  CLUS_1           2            49
  CLUS_2           3            67
  CLUS_3           2            40
  CLUS_4           4            74
D24V9, multiclass
        clus
vv       MAX MUTATED MAX WILD-TYPE
  CLUS_1           3            68
  CLUS_2           4            87
  CLUS_3           4            74
D24V10, multiclass
        clus
vv       MAX MUTATED MAX WILD-TYPE
  CLUS_1           5           118
  CLUS_2           1            40
  CLUS_3           2            11
  CLUS_4           3            60

Clustering(25) Variable = ING1 MUTATION ANALYSIS
D25V1, multiclass
[1] "Remove cluster labels:" "ING1 MUTATED"          
clus
  ING1 MUTATED ING1 WILD-TYPE 
             1             50 
    TCGA-A5-A0G3     TCGA-A5-A0G5     TCGA-A5-A0GA     TCGA-A5-A0GB 
"ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" 
    TCGA-A5-A0GE     TCGA-A5-A0GH     TCGA-A5-A0GM     TCGA-A5-A0GP 
"ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" 
    TCGA-A5-A0GU     TCGA-AP-A051     TCGA-AP-A052     TCGA-AP-A053 
"ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" 
    TCGA-AP-A054     TCGA-AP-A05A     TCGA-AP-A05D     TCGA-AP-A05H 
"ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" 
    TCGA-AP-A05J     TCGA-AP-A05N     TCGA-AP-A05P     TCGA-AP-A0L8 
"ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" 
    TCGA-AP-A0L9     TCGA-AP-A0LD     TCGA-AP-A0LG     TCGA-AP-A0LH 
"ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" 
    TCGA-AP-A0LJ     TCGA-AP-A0LN     TCGA-AP-A0LT     TCGA-AP-A0LV 
"ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" 
    TCGA-AX-A05S     TCGA-AX-A05T     TCGA-AX-A05U     TCGA-AX-A05W 
"ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" 
    TCGA-AX-A05Y     TCGA-AX-A05Z     TCGA-AX-A060     TCGA-AX-A062 
"ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" 
    TCGA-AX-A063     TCGA-AX-A064     TCGA-AX-A06B     TCGA-AX-A0IW 
"ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" 
    TCGA-AX-A0J1     TCGA-B5-A0JR     TCGA-B5-A0JZ     TCGA-B5-A0K0 
"ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" 
    TCGA-B5-A0K1     TCGA-B5-A0K4     TCGA-BG-A0LW     TCGA-BG-A0MI 
"ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" 
    TCGA-BK-A0C9     TCGA-BK-A0CC 
"ING1 WILD-TYPE" "ING1 WILD-TYPE" 
D25V2, multiclass
[1] "Remove cluster labels:" "ING1 MUTATED"          
clus
  ING1 MUTATED ING1 WILD-TYPE 
             1             50 
    TCGA-A5-A0G3     TCGA-A5-A0G5     TCGA-A5-A0GA     TCGA-A5-A0GB 
"ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" 
    TCGA-A5-A0GE     TCGA-A5-A0GH     TCGA-A5-A0GM     TCGA-A5-A0GP 
"ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" 
    TCGA-A5-A0GU     TCGA-AP-A051     TCGA-AP-A052     TCGA-AP-A053 
"ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" 
    TCGA-AP-A054     TCGA-AP-A05A     TCGA-AP-A05D     TCGA-AP-A05H 
"ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" 
    TCGA-AP-A05J     TCGA-AP-A05N     TCGA-AP-A05P     TCGA-AP-A0L8 
"ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" 
    TCGA-AP-A0L9     TCGA-AP-A0LD     TCGA-AP-A0LG     TCGA-AP-A0LH 
"ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" 
    TCGA-AP-A0LJ     TCGA-AP-A0LN     TCGA-AP-A0LT     TCGA-AP-A0LV 
"ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" 
    TCGA-AX-A05S     TCGA-AX-A05T     TCGA-AX-A05U     TCGA-AX-A05W 
"ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" 
    TCGA-AX-A05Y     TCGA-AX-A05Z     TCGA-AX-A060     TCGA-AX-A062 
"ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" 
    TCGA-AX-A063     TCGA-AX-A064     TCGA-AX-A06B     TCGA-AX-A0IW 
"ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" 
    TCGA-AX-A0J1     TCGA-B5-A0JR     TCGA-B5-A0JZ     TCGA-B5-A0K0 
"ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" 
    TCGA-B5-A0K1     TCGA-B5-A0K4     TCGA-BG-A0LW     TCGA-BG-A0MI 
"ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" "ING1 WILD-TYPE" 
    TCGA-BK-A0C9     TCGA-BK-A0CC 
"ING1 WILD-TYPE" "ING1 WILD-TYPE" 
D25V3, multiclass
D25V4, multiclass
        clus
vv       ING1 MUTATED ING1 WILD-TYPE
  CLUS_1            3             39
  CLUS_2            1             41
  CLUS_3            4             46
D25V5, multiclass
D25V6, binary
                cls
clus               0   1
  ING1 MUTATED     5   8
  ING1 WILD-TYPE 110  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  ING1 MUTATED      5    8
  ING1 WILD-TYPE  110   63
        clus
vv       ING1 MUTATED ING1 WILD-TYPE
  CLUS_1            5            110
  CLUS_2            8             63
D25V7, multiclass
        clus
vv       ING1 MUTATED ING1 WILD-TYPE
  CLUS_1            5             74
  CLUS_2            5             75
  CLUS_3            3             79
D25V8, multiclass
        clus
vv       ING1 MUTATED ING1 WILD-TYPE
  CLUS_1            1             50
  CLUS_2            5             65
  CLUS_3            2             40
  CLUS_4            5             73
D25V9, multiclass
        clus
vv       ING1 MUTATED ING1 WILD-TYPE
  CLUS_1            3             68
  CLUS_2            6             85
  CLUS_3            3             75
D25V10, multiclass
        clus
vv       ING1 MUTATED ING1 WILD-TYPE
  CLUS_1            5            118
  CLUS_2            4             37
  CLUS_3            2             11
  CLUS_4            1             62

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            132 
    TCGA-A5-A0GQ     TCGA-A5-A0VO     TCGA-AJ-A23M     TCGA-AP-A059 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-AP-A0LF     TCGA-AP-A0LM     TCGA-AP-A1DQ     TCGA-AX-A06H 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-AX-A06L     TCGA-AX-A0IS     TCGA-AX-A0J0     TCGA-AX-A1C7 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-AX-A1C8     TCGA-AX-A1CP     TCGA-AX-A2H5     TCGA-AX-A2HF 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-B5-A0JT     TCGA-B5-A0K8     TCGA-B5-A11E     TCGA-B5-A11F 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-B5-A11G     TCGA-B5-A11H     TCGA-B5-A11I     TCGA-B5-A11J 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-B5-A11M     TCGA-B5-A11N     TCGA-B5-A11O     TCGA-B5-A11Q 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-B5-A11R     TCGA-B5-A11S     TCGA-B5-A11U     TCGA-B5-A11V 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-B5-A11W     TCGA-B5-A11X     TCGA-B5-A11Y     TCGA-B5-A11Z 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-B5-A121     TCGA-B5-A1MU     TCGA-B5-A1MY     TCGA-BG-A0VT 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BG-A0VV     TCGA-BG-A0VW     TCGA-BG-A0VX     TCGA-BG-A0VZ 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BG-A0W1     TCGA-BG-A0W2     TCGA-BG-A0YU     TCGA-BG-A0YV 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BG-A186     TCGA-BG-A187     TCGA-BG-A18A     TCGA-BG-A18B 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BG-A18C     TCGA-BG-A2AE     TCGA-BK-A0CA     TCGA-BK-A139 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BK-A13C     TCGA-BS-A0T9     TCGA-BS-A0U5     TCGA-BS-A0U9 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BS-A0UA     TCGA-BS-A0UL     TCGA-BS-A0V6     TCGA-BS-A0V7 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-BS-A0V8     TCGA-BS-A0WQ     TCGA-D1-A0ZN     TCGA-D1-A0ZO 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A0ZP     TCGA-D1-A0ZQ     TCGA-D1-A0ZR     TCGA-D1-A0ZS 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A0ZU     TCGA-D1-A0ZV     TCGA-D1-A0ZZ     TCGA-D1-A101 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A102     TCGA-D1-A103     TCGA-D1-A15V     TCGA-D1-A15W 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A15X     TCGA-D1-A15Z     TCGA-D1-A160     TCGA-D1-A161 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A163     TCGA-D1-A165     TCGA-D1-A167     TCGA-D1-A168 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A169     TCGA-D1-A16B     TCGA-D1-A16D     TCGA-D1-A16E 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A16F     TCGA-D1-A16G     TCGA-D1-A16I     TCGA-D1-A16J 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A16N     TCGA-D1-A16O     TCGA-D1-A16Q     TCGA-D1-A16R 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A16S     TCGA-D1-A16Y     TCGA-D1-A174     TCGA-D1-A176 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A177     TCGA-D1-A17A     TCGA-D1-A17B     TCGA-D1-A17C 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A17D     TCGA-D1-A17F     TCGA-D1-A17H     TCGA-D1-A17K 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A17L     TCGA-D1-A17M     TCGA-D1-A17N     TCGA-D1-A17R 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A17S     TCGA-D1-A17T     TCGA-D1-A17U     TCGA-D1-A1NU 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-D1-A1NX     TCGA-DI-A0WH     TCGA-DI-A1NN     TCGA-E6-A1LZ 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-EO-A1Y5     TCGA-EO-A1Y8     TCGA-EY-A1GS     TCGA-EY-A212 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
    TCGA-FI-A2D2     TCGA-FI-A2EW     TCGA-FI-A2EX     TCGA-FI-A2F8 
"ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" "ABI1 WILD-TYPE" 
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
        clus
vv       ABI1 MUTATED ABI1 WILD-TYPE
  CLUS_1            0             79
  CLUS_2            2             78
  CLUS_3            2             80
D26V8, multiclass
        clus
vv       ABI1 MUTATED ABI1 WILD-TYPE
  CLUS_1            0             51
  CLUS_2            2             68
  CLUS_3            1             41
  CLUS_4            1             77
D26V9, multiclass
        clus
vv       ABI1 MUTATED ABI1 WILD-TYPE
  CLUS_1            0             71
  CLUS_2            2             89
  CLUS_3            2             76
D26V10, multiclass
        clus
vv       ABI1 MUTATED ABI1 WILD-TYPE
  CLUS_1            3            120
  CLUS_2            1             40
  CLUS_3            0             13
  CLUS_4            0             63

Clustering(27) Variable = RPL14 MUTATION ANALYSIS
D27V1, multiclass
D27V2, multiclass
D27V3, multiclass
D27V4, multiclass
        clus
vv       RPL14 MUTATED RPL14 WILD-TYPE
  CLUS_1             2              40
  CLUS_2             1              41
  CLUS_3             3              47
D27V5, multiclass
D27V6, 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
D27V7, multiclass
        clus
vv       RPL14 MUTATED RPL14 WILD-TYPE
  CLUS_1             2              77
  CLUS_2             3              77
  CLUS_3             2              80
D27V8, multiclass
        clus
vv       RPL14 MUTATED RPL14 WILD-TYPE
  CLUS_1             1              50
  CLUS_2             3              67
  CLUS_3             2              40
  CLUS_4             1              77
D27V9, multiclass
        clus
vv       RPL14 MUTATED RPL14 WILD-TYPE
  CLUS_1             1              70
  CLUS_2             4              87
  CLUS_3             1              77
D27V10, multiclass
        clus
vv       RPL14 MUTATED RPL14 WILD-TYPE
  CLUS_1             4             119
  CLUS_2             1              40
  CLUS_3             0              13
  CLUS_4             1              62

Clustering(28) Variable = DNER MUTATION ANALYSIS
D28V1, multiclass
        clus
vv       DNER MUTATED DNER WILD-TYPE
  CLUS_1            3              8
  CLUS_2            2             17
  CLUS_3            0             13
  CLUS_4            0              8
D28V2, multiclass
        clus
vv       DNER MUTATED DNER WILD-TYPE
  CLUS_1            0             19
  CLUS_2            4              9
  CLUS_3            1             18
D28V3, multiclass
D28V4, multiclass
        clus
vv       DNER MUTATED DNER WILD-TYPE
  CLUS_1            3             39
  CLUS_2            1             41
  CLUS_3            4             46
D28V5, multiclass
D28V6, 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
D28V7, multiclass
        clus
vv       DNER MUTATED DNER WILD-TYPE
  CLUS_1            7             72
  CLUS_2            4             76
  CLUS_3            6             76
D28V8, multiclass
        clus
vv       DNER MUTATED DNER WILD-TYPE
  CLUS_1            0             51
  CLUS_2            4             66
  CLUS_3            7             35
  CLUS_4            6             72
D28V9, multiclass
        clus
vv       DNER MUTATED DNER WILD-TYPE
  CLUS_1            5             66
  CLUS_2            5             86
  CLUS_3            7             71
D28V10, multiclass
        clus
vv       DNER MUTATED DNER WILD-TYPE
  CLUS_1            6            117
  CLUS_2            3             38
  CLUS_3            3             10
  CLUS_4            5             58

Clustering(29) Variable = NRAS MUTATION ANALYSIS
D29V1, 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" 
D29V2, 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" 
D29V3, multiclass
D29V4, multiclass
[1] "Remove cluster labels:" "NRAS MUTATED"          
clus
  NRAS MUTATED NRAS WILD-TYPE 
             2            132 
    TCGA-A5-A0GQ     TCGA-A5-A0VO     TCGA-AJ-A23M     TCGA-AP-A059 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AP-A0LF     TCGA-AP-A0LM     TCGA-AP-A1DQ     TCGA-AX-A06H 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AX-A06L     TCGA-AX-A0IS     TCGA-AX-A1C7     TCGA-AX-A1C8 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AX-A1CP     TCGA-AX-A2H5     TCGA-AX-A2HF     TCGA-B5-A0JT 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-B5-A0K8     TCGA-B5-A11E     TCGA-B5-A11F     TCGA-B5-A11G 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-B5-A11H     TCGA-B5-A11I     TCGA-B5-A11J     TCGA-B5-A11M 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-B5-A11N     TCGA-B5-A11O     TCGA-B5-A11Q     TCGA-B5-A11R 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-B5-A11S     TCGA-B5-A11U     TCGA-B5-A11V     TCGA-B5-A11W 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-B5-A11X     TCGA-B5-A11Y     TCGA-B5-A11Z     TCGA-B5-A121 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-B5-A1MU     TCGA-B5-A1MY     TCGA-BG-A0VT     TCGA-BG-A0VV 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BG-A0VW     TCGA-BG-A0VX     TCGA-BG-A0VZ     TCGA-BG-A0W1 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BG-A0W2     TCGA-BG-A0YU     TCGA-BG-A0YV     TCGA-BG-A186 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BG-A187     TCGA-BG-A18A     TCGA-BG-A18B     TCGA-BG-A18C 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BG-A2AE     TCGA-BK-A0CA     TCGA-BK-A139     TCGA-BK-A13C 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BS-A0T9     TCGA-BS-A0U5     TCGA-BS-A0U9     TCGA-BS-A0UA 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BS-A0UL     TCGA-BS-A0V6     TCGA-BS-A0V7     TCGA-BS-A0V8 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-BS-A0WQ     TCGA-D1-A0ZN     TCGA-D1-A0ZO     TCGA-D1-A0ZP 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A0ZQ     TCGA-D1-A0ZR     TCGA-D1-A0ZS     TCGA-D1-A0ZU 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A0ZV     TCGA-D1-A0ZZ     TCGA-D1-A101     TCGA-D1-A102 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A103     TCGA-D1-A15V     TCGA-D1-A15W     TCGA-D1-A15X 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A15Z     TCGA-D1-A160     TCGA-D1-A161     TCGA-D1-A163 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A165     TCGA-D1-A167     TCGA-D1-A168     TCGA-D1-A169 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A16B     TCGA-D1-A16D     TCGA-D1-A16E     TCGA-D1-A16F 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A16G     TCGA-D1-A16I     TCGA-D1-A16J     TCGA-D1-A16N 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A16O     TCGA-D1-A16Q     TCGA-D1-A16R     TCGA-D1-A16S 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A16X     TCGA-D1-A16Y     TCGA-D1-A174     TCGA-D1-A176 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A177     TCGA-D1-A17A     TCGA-D1-A17B     TCGA-D1-A17C 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A17D     TCGA-D1-A17H     TCGA-D1-A17K     TCGA-D1-A17L 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A17M     TCGA-D1-A17N     TCGA-D1-A17Q     TCGA-D1-A17R 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A17S     TCGA-D1-A17T     TCGA-D1-A17U     TCGA-D1-A1NU 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-D1-A1NX     TCGA-DI-A0WH     TCGA-DI-A1NN     TCGA-E6-A1LZ 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-EO-A1Y5     TCGA-EO-A1Y8     TCGA-EY-A1GS     TCGA-EY-A212 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-FI-A2D2     TCGA-FI-A2EW     TCGA-FI-A2EX     TCGA-FI-A2F8 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
D29V5, multiclass
D29V6, 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
D29V7, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            3             76
  CLUS_2            2             78
  CLUS_3            4             78
D29V8, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            2             49
  CLUS_2            2             68
  CLUS_3            2             40
  CLUS_4            3             75
D29V9, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            3             68
  CLUS_2            2             89
  CLUS_3            4             74
D29V10, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            4            119
  CLUS_2            1             40
  CLUS_3            1             12
  CLUS_4            3             60

Clustering(30) Variable = HPD MUTATION ANALYSIS
D30V1, 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" 
D30V2, 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" 
D30V3, multiclass
D30V4, multiclass
        clus
vv       HPD MUTATED HPD WILD-TYPE
  CLUS_1           1            41
  CLUS_2           0            42
  CLUS_3           2            48
D30V5, multiclass
D30V6, 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
D30V7, multiclass
        clus
vv       HPD MUTATED HPD WILD-TYPE
  CLUS_1           1            78
  CLUS_2           1            79
  CLUS_3           4            78
D30V8, multiclass
        clus
vv       HPD MUTATED HPD WILD-TYPE
  CLUS_1           1            50
  CLUS_2           1            69
  CLUS_3           4            38
  CLUS_4           0            78
D30V9, multiclass
        clus
vv       HPD MUTATED HPD WILD-TYPE
  CLUS_1           1            70
  CLUS_2           2            89
  CLUS_3           4            74
D30V10, multiclass
        clus
vv       HPD MUTATED HPD WILD-TYPE
  CLUS_1           2           121
  CLUS_2           3            38
  CLUS_3           0            13
  CLUS_4           2            61

Clustering(31) Variable = RASA1 MUTATION ANALYSIS
D31V1, multiclass
        clus
vv       RASA1 MUTATED RASA1 WILD-TYPE
  CLUS_1             3               8
  CLUS_2             2              17
  CLUS_3             1              12
  CLUS_4             0               8
D31V2, multiclass
        clus
vv       RASA1 MUTATED RASA1 WILD-TYPE
  CLUS_1             1              18
  CLUS_2             4               9
  CLUS_3             1              18
D31V3, multiclass
D31V4, multiclass
        clus
vv       RASA1 MUTATED RASA1 WILD-TYPE
  CLUS_1             3              39
  CLUS_2             2              40
  CLUS_3             4              46
D31V5, multiclass
D31V6, binary
                 cls
clus                0   1
  RASA1 MUTATED    11   7
  RASA1 WILD-TYPE 104  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED     11    7
  RASA1 WILD-TYPE  104   64
        clus
vv       RASA1 MUTATED RASA1 WILD-TYPE
  CLUS_1            11             104
  CLUS_2             7              64
D31V7, multiclass
        clus
vv       RASA1 MUTATED RASA1 WILD-TYPE
  CLUS_1             6              73
  CLUS_2             6              74
  CLUS_3             9              73
D31V8, multiclass
        clus
vv       RASA1 MUTATED RASA1 WILD-TYPE
  CLUS_1             2              49
  CLUS_2             6              64
  CLUS_3             7              35
  CLUS_4             6              72
D31V9, multiclass
        clus
vv       RASA1 MUTATED RASA1 WILD-TYPE
  CLUS_1             5              66
  CLUS_2             7              84
  CLUS_3             9              69
D31V10, multiclass
        clus
vv       RASA1 MUTATED RASA1 WILD-TYPE
  CLUS_1             9             114
  CLUS_2             5              36
  CLUS_3             0              13
  CLUS_4             7              56

Clustering(32) Variable = ZNF267 MUTATION ANALYSIS
D32V1, multiclass
        clus
vv       ZNF267 MUTATED ZNF267 WILD-TYPE
  CLUS_1              1               10
  CLUS_2              4               15
  CLUS_3              0               13
  CLUS_4              1                7
D32V2, multiclass
        clus
vv       ZNF267 MUTATED ZNF267 WILD-TYPE
  CLUS_1              1               18
  CLUS_2              2               11
  CLUS_3              3               16
D32V3, multiclass
D32V4, multiclass
        clus
vv       ZNF267 MUTATED ZNF267 WILD-TYPE
  CLUS_1              2               40
  CLUS_2              2               40
  CLUS_3              2               48
D32V5, multiclass
D32V6, binary
                  cls
clus                 0   1
  ZNF267 MUTATED     6   7
  ZNF267 WILD-TYPE 109  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF267 MUTATED      6    7
  ZNF267 WILD-TYPE  109   64
        clus
vv       ZNF267 MUTATED ZNF267 WILD-TYPE
  CLUS_1              6              109
  CLUS_2              7               64
D32V7, multiclass
        clus
vv       ZNF267 MUTATED ZNF267 WILD-TYPE
  CLUS_1              7               72
  CLUS_2              3               77
  CLUS_3              6               76
D32V8, multiclass
        clus
vv       ZNF267 MUTATED ZNF267 WILD-TYPE
  CLUS_1              2               49
  CLUS_2              3               67
  CLUS_3              3               39
  CLUS_4              8               70
D32V9, multiclass
        clus
vv       ZNF267 MUTATED ZNF267 WILD-TYPE
  CLUS_1              4               67
  CLUS_2              4               87
  CLUS_3              6               72
D32V10, multiclass
        clus
vv       ZNF267 MUTATED ZNF267 WILD-TYPE
  CLUS_1              5              118
  CLUS_2              5               36
  CLUS_3              1               12
  CLUS_4              3               60

Clustering(33) Variable = SGK1 MUTATION ANALYSIS
D33V1, multiclass
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  CLUS_1            2              9
  CLUS_2            1             18
  CLUS_3            0             13
  CLUS_4            0              8
D33V2, multiclass
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  CLUS_1            0             19
  CLUS_2            3             10
  CLUS_3            0             19
D33V3, multiclass
D33V4, multiclass
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  CLUS_1            1             41
  CLUS_2            1             41
  CLUS_3            3             47
D33V5, multiclass
D33V6, 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
D33V7, multiclass
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  CLUS_1            4             75
  CLUS_2            6             74
  CLUS_3            5             77
D33V8, multiclass
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  CLUS_1            3             48
  CLUS_2            4             66
  CLUS_3            4             38
  CLUS_4            4             74
D33V9, multiclass
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  CLUS_1            2             69
  CLUS_2            5             86
  CLUS_3            7             71
D33V10, multiclass
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  CLUS_1            7            116
  CLUS_2            2             39
  CLUS_3            2             11
  CLUS_4            3             60

Clustering(34) Variable = ARID5B MUTATION ANALYSIS
D34V1, multiclass
        clus
vv       ARID5B MUTATED ARID5B WILD-TYPE
  CLUS_1              3                8
  CLUS_2              3               16
  CLUS_3              3               10
  CLUS_4              1                7
D34V2, multiclass
        clus
vv       ARID5B MUTATED ARID5B WILD-TYPE
  CLUS_1              2               17
  CLUS_2              5                8
  CLUS_3              3               16
D34V3, multiclass
D34V4, multiclass
        clus
vv       ARID5B MUTATED ARID5B WILD-TYPE
  CLUS_1              1               41
  CLUS_2              1               41
  CLUS_3              6               44
D34V5, multiclass
D34V6, 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
D34V7, multiclass
        clus
vv       ARID5B MUTATED ARID5B WILD-TYPE
  CLUS_1              6               73
  CLUS_2             11               69
  CLUS_3             12               70
D34V8, multiclass
        clus
vv       ARID5B MUTATED ARID5B WILD-TYPE
  CLUS_1              3               48
  CLUS_2             11               59
  CLUS_3              9               33
  CLUS_4              6               72
D34V9, multiclass
        clus
vv       ARID5B MUTATED ARID5B WILD-TYPE
  CLUS_1              5               66
  CLUS_2             13               78
  CLUS_3              9               69
D34V10, multiclass
        clus
vv       ARID5B MUTATED ARID5B WILD-TYPE
  CLUS_1             16              107
  CLUS_2              6               35
  CLUS_3              2               11
  CLUS_4              3               60

Clustering(35) Variable = CYLC1 MUTATION ANALYSIS
D35V1, multiclass
        clus
vv       CYLC1 MUTATED CYLC1 WILD-TYPE
  CLUS_1             3               8
  CLUS_2             2              17
  CLUS_3             0              13
  CLUS_4             0               8
D35V2, multiclass
        clus
vv       CYLC1 MUTATED CYLC1 WILD-TYPE
  CLUS_1             0              19
  CLUS_2             4               9
  CLUS_3             1              18
D35V3, multiclass
D35V4, multiclass
        clus
vv       CYLC1 MUTATED CYLC1 WILD-TYPE
  CLUS_1             2              40
  CLUS_2             3              39
  CLUS_3             4              46
D35V5, multiclass
D35V6, binary
                 cls
clus                0   1
  CYLC1 MUTATED     7   8
  CYLC1 WILD-TYPE 108  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYLC1 MUTATED      7    8
  CYLC1 WILD-TYPE  108   63
        clus
vv       CYLC1 MUTATED CYLC1 WILD-TYPE
  CLUS_1             7             108
  CLUS_2             8              63
D35V7, multiclass
        clus
vv       CYLC1 MUTATED CYLC1 WILD-TYPE
  CLUS_1             6              73
  CLUS_2             4              76
  CLUS_3             8              74
D35V8, multiclass
        clus
vv       CYLC1 MUTATED CYLC1 WILD-TYPE
  CLUS_1             1              50
  CLUS_2             4              66
  CLUS_3             4              38
  CLUS_4             9              69
D35V9, multiclass
        clus
vv       CYLC1 MUTATED CYLC1 WILD-TYPE
  CLUS_1             5              66
  CLUS_2             4              87
  CLUS_3             8              70
D35V10, multiclass
        clus
vv       CYLC1 MUTATED CYLC1 WILD-TYPE
  CLUS_1             6             117
  CLUS_2             5              36
  CLUS_3             2              11
  CLUS_4             4              59

Clustering(36) Variable = DYRK1A MUTATION ANALYSIS
D36V1, multiclass
        clus
vv       DYRK1A MUTATED DYRK1A WILD-TYPE
  CLUS_1              1               10
  CLUS_2              2               17
  CLUS_3              0               13
  CLUS_4              0                8
D36V2, multiclass
        clus
vv       DYRK1A MUTATED DYRK1A WILD-TYPE
  CLUS_1              0               19
  CLUS_2              1               12
  CLUS_3              2               17
D36V3, multiclass
D36V4, multiclass
        clus
vv       DYRK1A MUTATED DYRK1A WILD-TYPE
  CLUS_1              3               39
  CLUS_2              0               42
  CLUS_3              3               47
D36V5, multiclass
D36V6, binary
                  cls
clus                 0   1
  DYRK1A MUTATED     4   5
  DYRK1A WILD-TYPE 111  66
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DYRK1A MUTATED      4    5
  DYRK1A WILD-TYPE  111   66
        clus
vv       DYRK1A MUTATED DYRK1A WILD-TYPE
  CLUS_1              4              111
  CLUS_2              5               66
D36V7, multiclass
        clus
vv       DYRK1A MUTATED DYRK1A WILD-TYPE
  CLUS_1              5               74
  CLUS_2              3               77
  CLUS_3              4               78
D36V8, multiclass
        clus
vv       DYRK1A MUTATED DYRK1A WILD-TYPE
  CLUS_1              0               51
  CLUS_2              2               68
  CLUS_3              6               36
  CLUS_4              4               74
D36V9, multiclass
        clus
vv       DYRK1A MUTATED DYRK1A WILD-TYPE
  CLUS_1              5               66
  CLUS_2              3               88
  CLUS_3              4               74
D36V10, multiclass
        clus
vv       DYRK1A MUTATED DYRK1A WILD-TYPE
  CLUS_1              3              120
  CLUS_2              2               39
  CLUS_3              1               12
  CLUS_4              6               57

Clustering(37) Variable = METTL14 MUTATION ANALYSIS
D37V1, multiclass
        clus
vv       METTL14 MUTATED METTL14 WILD-TYPE
  CLUS_1               2                 9
  CLUS_2               1                18
  CLUS_3               0                13
  CLUS_4               0                 8
D37V2, multiclass
        clus
vv       METTL14 MUTATED METTL14 WILD-TYPE
  CLUS_1               0                19
  CLUS_2               2                11
  CLUS_3               1                18
D37V3, multiclass
D37V4, multiclass
        clus
vv       METTL14 MUTATED METTL14 WILD-TYPE
  CLUS_1               1                41
  CLUS_2               3                39
  CLUS_3               2                48
D37V5, multiclass
D37V6, binary
                   cls
clus                  0   1
  METTL14 MUTATED     5   5
  METTL14 WILD-TYPE 110  66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  METTL14 MUTATED      5    5
  METTL14 WILD-TYPE  110   66
        clus
vv       METTL14 MUTATED METTL14 WILD-TYPE
  CLUS_1               5               110
  CLUS_2               5                66
D37V7, multiclass
        clus
vv       METTL14 MUTATED METTL14 WILD-TYPE
  CLUS_1               2                77
  CLUS_2               2                78
  CLUS_3               6                76
D37V8, multiclass
        clus
vv       METTL14 MUTATED METTL14 WILD-TYPE
  CLUS_1               0                51
  CLUS_2               2                68
  CLUS_3               6                36
  CLUS_4               2                76
D37V9, multiclass
        clus
vv       METTL14 MUTATED METTL14 WILD-TYPE
  CLUS_1               0                71
  CLUS_2               3                88
  CLUS_3               7                71
D37V10, multiclass
        clus
vv       METTL14 MUTATED METTL14 WILD-TYPE
  CLUS_1               4               119
  CLUS_2               3                38
  CLUS_3               1                12
  CLUS_4               2                61

Clustering(38) Variable = TPTE MUTATION ANALYSIS
D38V1, multiclass
[1] "Remove cluster labels:" "TPTE MUTATED"          
clus
  TPTE MUTATED TPTE WILD-TYPE 
             2             49 
    TCGA-A5-A0G3     TCGA-A5-A0G5     TCGA-A5-A0GA     TCGA-A5-A0GB 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-A5-A0GE     TCGA-A5-A0GH     TCGA-A5-A0GM     TCGA-A5-A0GP 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-A5-A0GU     TCGA-AP-A052     TCGA-AP-A053     TCGA-AP-A054 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-AP-A05A     TCGA-AP-A05D     TCGA-AP-A05H     TCGA-AP-A05J 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-AP-A05N     TCGA-AP-A05P     TCGA-AP-A0L8     TCGA-AP-A0L9 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-AP-A0LD     TCGA-AP-A0LG     TCGA-AP-A0LH     TCGA-AP-A0LJ 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-AP-A0LN     TCGA-AP-A0LT     TCGA-AP-A0LV     TCGA-AX-A05S 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-AX-A05T     TCGA-AX-A05U     TCGA-AX-A05W     TCGA-AX-A05Y 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-AX-A05Z     TCGA-AX-A060     TCGA-AX-A062     TCGA-AX-A063 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-AX-A064     TCGA-AX-A06B     TCGA-AX-A0IW     TCGA-AX-A0J1 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-B5-A0JR     TCGA-B5-A0JZ     TCGA-B5-A0K0     TCGA-B5-A0K1 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-B5-A0K4     TCGA-BG-A0LW     TCGA-BG-A0MI     TCGA-BK-A0C9 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-BK-A0CC 
"TPTE WILD-TYPE" 
D38V2, multiclass
[1] "Remove cluster labels:" "TPTE MUTATED"          
clus
  TPTE MUTATED TPTE WILD-TYPE 
             2             49 
    TCGA-A5-A0G3     TCGA-A5-A0G5     TCGA-A5-A0GA     TCGA-A5-A0GB 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-A5-A0GE     TCGA-A5-A0GH     TCGA-A5-A0GM     TCGA-A5-A0GP 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-A5-A0GU     TCGA-AP-A052     TCGA-AP-A053     TCGA-AP-A054 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-AP-A05A     TCGA-AP-A05D     TCGA-AP-A05H     TCGA-AP-A05J 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-AP-A05N     TCGA-AP-A05P     TCGA-AP-A0L8     TCGA-AP-A0L9 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-AP-A0LD     TCGA-AP-A0LG     TCGA-AP-A0LH     TCGA-AP-A0LJ 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-AP-A0LN     TCGA-AP-A0LT     TCGA-AP-A0LV     TCGA-AX-A05S 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-AX-A05T     TCGA-AX-A05U     TCGA-AX-A05W     TCGA-AX-A05Y 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-AX-A05Z     TCGA-AX-A060     TCGA-AX-A062     TCGA-AX-A063 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-AX-A064     TCGA-AX-A06B     TCGA-AX-A0IW     TCGA-AX-A0J1 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-B5-A0JR     TCGA-B5-A0JZ     TCGA-B5-A0K0     TCGA-B5-A0K1 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-B5-A0K4     TCGA-BG-A0LW     TCGA-BG-A0MI     TCGA-BK-A0C9 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-BK-A0CC 
"TPTE WILD-TYPE" 
D38V3, multiclass
D38V4, multiclass
        clus
vv       TPTE MUTATED TPTE WILD-TYPE
  CLUS_1            1             41
  CLUS_2            3             39
  CLUS_3            4             46
D38V5, multiclass
D38V6, binary
                cls
clus               0   1
  TPTE MUTATED     7   5
  TPTE WILD-TYPE 108  66
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPTE MUTATED      7    5
  TPTE WILD-TYPE  108   66
        clus
vv       TPTE MUTATED TPTE WILD-TYPE
  CLUS_1            7            108
  CLUS_2            5             66
D38V7, multiclass
        clus
vv       TPTE MUTATED TPTE WILD-TYPE
  CLUS_1            5             74
  CLUS_2            5             75
  CLUS_3            5             77
D38V8, multiclass
        clus
vv       TPTE MUTATED TPTE WILD-TYPE
  CLUS_1            1             50
  CLUS_2            5             65
  CLUS_3            1             41
  CLUS_4            8             70
D38V9, multiclass
        clus
vv       TPTE MUTATED TPTE WILD-TYPE
  CLUS_1            4             67
  CLUS_2            5             86
  CLUS_3            5             73
D38V10, multiclass
        clus
vv       TPTE MUTATED TPTE WILD-TYPE
  CLUS_1            6            117
  CLUS_2            2             39
  CLUS_3            2             11
  CLUS_4            4             59

Clustering(39) Variable = UPF3B MUTATION ANALYSIS
D39V1, multiclass
        clus
vv       UPF3B MUTATED UPF3B WILD-TYPE
  CLUS_1             1              10
  CLUS_2             3              16
  CLUS_3             0              13
  CLUS_4             0               8
D39V2, multiclass
        clus
vv       UPF3B MUTATED UPF3B WILD-TYPE
  CLUS_1             0              19
  CLUS_2             2              11
  CLUS_3             2              17
D39V3, multiclass
D39V4, multiclass
        clus
vv       UPF3B MUTATED UPF3B WILD-TYPE
  CLUS_1             1              41
  CLUS_2             4              38
  CLUS_3             4              46
D39V5, multiclass
D39V6, binary
                 cls
clus                0   1
  UPF3B MUTATED     7   8
  UPF3B WILD-TYPE 108  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UPF3B MUTATED      7    8
  UPF3B WILD-TYPE  108   63
        clus
vv       UPF3B MUTATED UPF3B WILD-TYPE
  CLUS_1             7             108
  CLUS_2             8              63
D39V7, multiclass
        clus
vv       UPF3B MUTATED UPF3B WILD-TYPE
  CLUS_1             5              74
  CLUS_2             6              74
  CLUS_3             5              77
D39V8, multiclass
        clus
vv       UPF3B MUTATED UPF3B WILD-TYPE
  CLUS_1             1              50
  CLUS_2             6              64
  CLUS_3             3              39
  CLUS_4             6              72
D39V9, multiclass
        clus
vv       UPF3B MUTATED UPF3B WILD-TYPE
  CLUS_1             3              68
  CLUS_2             6              85
  CLUS_3             6              72
D39V10, multiclass
        clus
vv       UPF3B MUTATED UPF3B WILD-TYPE
  CLUS_1             7             116
  CLUS_2             2              39
  CLUS_3             1              12
  CLUS_4             5              58

Clustering(40) Variable = UBE2QL1 MUTATION ANALYSIS
D40V1, multiclass
D40V2, multiclass
D40V3, multiclass
D40V4, multiclass
        clus
vv       UBE2QL1 MUTATED UBE2QL1 WILD-TYPE
  CLUS_1               2                40
  CLUS_2               2                40
  CLUS_3               1                49
D40V5, multiclass
D40V6, binary
                   cls
clus                  0   1
  UBE2QL1 MUTATED     0   4
  UBE2QL1 WILD-TYPE 115  67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UBE2QL1 MUTATED      0    4
  UBE2QL1 WILD-TYPE  115   67
        clus
vv       UBE2QL1 MUTATED UBE2QL1 WILD-TYPE
  CLUS_1               0               115
  CLUS_2               4                67
D40V7, multiclass
        clus
vv       UBE2QL1 MUTATED UBE2QL1 WILD-TYPE
  CLUS_1               2                77
  CLUS_2               3                77
  CLUS_3               0                82
D40V8, multiclass
        clus
vv       UBE2QL1 MUTATED UBE2QL1 WILD-TYPE
  CLUS_1               0                51
  CLUS_2               3                67
  CLUS_3               2                40
  CLUS_4               0                78
D40V9, multiclass
        clus
vv       UBE2QL1 MUTATED UBE2QL1 WILD-TYPE
  CLUS_1               1                70
  CLUS_2               3                88
  CLUS_3               1                77
D40V10, multiclass
        clus
vv       UBE2QL1 MUTATED UBE2QL1 WILD-TYPE
  CLUS_1               3               120
  CLUS_2               1                40
  CLUS_3               0                13
  CLUS_4               1                62

Clustering(41) Variable = ZNF286A MUTATION ANALYSIS
D41V1, multiclass
[1] "Remove cluster labels:" "ZNF286A MUTATED"       
clus
  ZNF286A MUTATED ZNF286A WILD-TYPE 
                2                49 
       TCGA-A5-A0G3        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" 
       TCGA-AP-A0L8        TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG 
"ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT 
"ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A060        TCGA-AX-A062 
"ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A0IW 
"ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" 
       TCGA-B5-A0JR        TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1 
"ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" 
       TCGA-B5-A0K4        TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9 
"ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" 
       TCGA-BK-A0CC 
"ZNF286A WILD-TYPE" 
D41V2, multiclass
[1] "Remove cluster labels:" "ZNF286A MUTATED"       
clus
  ZNF286A MUTATED ZNF286A WILD-TYPE 
                2                49 
       TCGA-A5-A0G3        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" 
       TCGA-AP-A0L8        TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG 
"ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT 
"ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A060        TCGA-AX-A062 
"ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A0IW 
"ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" 
       TCGA-B5-A0JR        TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1 
"ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" 
       TCGA-B5-A0K4        TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9 
"ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" "ZNF286A WILD-TYPE" 
       TCGA-BK-A0CC 
"ZNF286A WILD-TYPE" 
D41V3, multiclass
D41V4, multiclass
        clus
vv       ZNF286A MUTATED ZNF286A WILD-TYPE
  CLUS_1               2                40
  CLUS_2               0                42
  CLUS_3               3                47
D41V5, multiclass
D41V6, binary
                   cls
clus                  0   1
  ZNF286A MUTATED     8   2
  ZNF286A WILD-TYPE 107  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF286A MUTATED      8    2
  ZNF286A WILD-TYPE  107   69
        clus
vv       ZNF286A MUTATED ZNF286A WILD-TYPE
  CLUS_1               8               107
  CLUS_2               2                69
D41V7, multiclass
        clus
vv       ZNF286A MUTATED ZNF286A WILD-TYPE
  CLUS_1               3                76
  CLUS_2               4                76
  CLUS_3               5                77
D41V8, multiclass
        clus
vv       ZNF286A MUTATED ZNF286A WILD-TYPE
  CLUS_1               0                51
  CLUS_2               4                66
  CLUS_3               4                38
  CLUS_4               4                74
D41V9, multiclass
        clus
vv       ZNF286A MUTATED ZNF286A WILD-TYPE
  CLUS_1               3                68
  CLUS_2               5                86
  CLUS_3               4                74
D41V10, multiclass
        clus
vv       ZNF286A MUTATED ZNF286A WILD-TYPE
  CLUS_1               6               117
  CLUS_2               2                39
  CLUS_3               1                12
  CLUS_4               3                60

Clustering(42) Variable = ZNF263 MUTATION ANALYSIS
D42V1, multiclass
        clus
vv       ZNF263 MUTATED ZNF263 WILD-TYPE
  CLUS_1              3                8
  CLUS_2              0               19
  CLUS_3              0               13
  CLUS_4              0                8
D42V2, multiclass
        clus
vv       ZNF263 MUTATED ZNF263 WILD-TYPE
  CLUS_1              0               19
  CLUS_2              3               10
  CLUS_3              0               19
D42V3, multiclass
D42V4, multiclass
        clus
vv       ZNF263 MUTATED ZNF263 WILD-TYPE
  CLUS_1              1               41
  CLUS_2              0               42
  CLUS_3              3               47
D42V5, multiclass
D42V6, 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
D42V7, multiclass
        clus
vv       ZNF263 MUTATED ZNF263 WILD-TYPE
  CLUS_1              1               78
  CLUS_2              2               78
  CLUS_3              5               77
D42V8, multiclass
        clus
vv       ZNF263 MUTATED ZNF263 WILD-TYPE
  CLUS_1              0               51
  CLUS_2              2               68
  CLUS_3              4               38
  CLUS_4              2               76
D42V9, multiclass
        clus
vv       ZNF263 MUTATED ZNF263 WILD-TYPE
  CLUS_1              0               71
  CLUS_2              4               87
  CLUS_3              4               74
D42V10, multiclass
        clus
vv       ZNF263 MUTATED ZNF263 WILD-TYPE
  CLUS_1              4              119
  CLUS_2              4               37
  CLUS_3              0               13
  CLUS_4              0               63

Clustering(43) Variable = TAB3 MUTATION ANALYSIS
D43V1, multiclass
        clus
vv       TAB3 MUTATED TAB3 WILD-TYPE
  CLUS_1            3              8
  CLUS_2            1             18
  CLUS_3            0             13
  CLUS_4            0              8
D43V2, multiclass
        clus
vv       TAB3 MUTATED TAB3 WILD-TYPE
  CLUS_1            0             19
  CLUS_2            3             10
  CLUS_3            1             18
D43V3, multiclass
D43V4, multiclass
        clus
vv       TAB3 MUTATED TAB3 WILD-TYPE
  CLUS_1            2             40
  CLUS_2            4             38
  CLUS_3            5             45
D43V5, multiclass
D43V6, binary
                cls
clus               0   1
  TAB3 MUTATED     8   4
  TAB3 WILD-TYPE 107  67
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAB3 MUTATED      8    4
  TAB3 WILD-TYPE  107   67
        clus
vv       TAB3 MUTATED TAB3 WILD-TYPE
  CLUS_1            8            107
  CLUS_2            4             67
D43V7, multiclass
        clus
vv       TAB3 MUTATED TAB3 WILD-TYPE
  CLUS_1            3             76
  CLUS_2            5             75
  CLUS_3           10             72
D43V8, multiclass
        clus
vv       TAB3 MUTATED TAB3 WILD-TYPE
  CLUS_1            1             50
  CLUS_2            5             65
  CLUS_3            8             34
  CLUS_4            4             74
D43V9, multiclass
        clus
vv       TAB3 MUTATED TAB3 WILD-TYPE
  CLUS_1            3             68
  CLUS_2            8             83
  CLUS_3            7             71
D43V10, multiclass
        clus
vv       TAB3 MUTATED TAB3 WILD-TYPE
  CLUS_1            8            115
  CLUS_2            5             36
  CLUS_3            1             12
  CLUS_4            4             59
                     V1                      V2                      V3 
            "MRNA_CNMF"    "MRNA_CHIERARCHICAL"               "CN_CNMF" 
                     V4                      V5                      V6 
     "METHLYATION_CNMF"             "RPPA_CNMF"    "RPPA_CHIERARCHICAL" 
                     V7                      V8                      V9 
         "MRNASEQ_CNMF" "MRNASEQ_CHIERARCHICAL"           "MIRSEQ_CNMF" 
                    V10 
 "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
