
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/376909/READ-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/READ-TP/2909295/1.GDAC_mergedClustering.Finished/READ-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ONLYSIG", "-oT=READ-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=READ-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=166, in cluster file=69, common to both=69
[1] "Reduce the number of clustering variables from 17 to 16."
[1] 16 69
[1] "APC MUTATION ANALYSIS"
[1] 3
  APC MUTATED APC WILD-TYPE 
           57            12 
  APC MUTATED APC WILD-TYPE 
           57            12 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            38             31 
  KRAS MUTATED KRAS WILD-TYPE 
            38             31 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            45             24 
  TP53 MUTATED TP53 WILD-TYPE 
            45             24 
[1] "SMAD4 MUTATION ANALYSIS"
[1] 3
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              8              61 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              8              61 
[1] "KIAA1804 MUTATION ANALYSIS"
[1] 3
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 9                 60 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 9                 60 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              9              60 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              9              60 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
             5             64 
  NRAS MUTATED NRAS WILD-TYPE 
             5             64 
[1] "TCF7L2 MUTATION ANALYSIS"
[1] 3
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
               7               62 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
               7               62 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               7               62 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               7               62 
[1] "OPCML MUTATION ANALYSIS"
[1] 3
  OPCML MUTATED OPCML WILD-TYPE 
              6              63 
  OPCML MUTATED OPCML WILD-TYPE 
              6              63 
[1] "SMAD2 MUTATION ANALYSIS"
[1] 3
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              5              64 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              5              64 
[1] "SPATA8 MUTATION ANALYSIS"
[1] 3
  SPATA8 MUTATED SPATA8 WILD-TYPE 
               3               66 
  SPATA8 MUTATED SPATA8 WILD-TYPE 
               3               66 
[1] "ERBB2 MUTATION ANALYSIS"
[1] 3
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              4              65 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              4              65 
[1] "IL1RAPL2 MUTATION ANALYSIS"
[1] 3
  IL1RAPL2 MUTATED IL1RAPL2 WILD-TYPE 
                 5                 64 
  IL1RAPL2 MUTATED IL1RAPL2 WILD-TYPE 
                 5                 64 
[1] "FAM123B MUTATION ANALYSIS"
[1] 3
  FAM123B MUTATED FAM123B WILD-TYPE 
                6                63 
  FAM123B MUTATED FAM123B WILD-TYPE 
                6                63 
[1] "ZIM3 MUTATION ANALYSIS"
[1] 3
  ZIM3 MUTATED ZIM3 WILD-TYPE 
             5             64 
  ZIM3 MUTATED ZIM3 WILD-TYPE 
             5             64 
[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 69 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'CN_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 5:'RPPA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'RPPA_CHIERARCHICAL':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MRNASEQ_CNMF':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'MIRSEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "MRNA_CNMF"            "MRNA_CHIERARCHICAL"   "CN_CNMF"             
[4] "RPPA_CNMF"            "RPPA_CHIERARCHICAL"   "MIRSEQ_CNMF"         
[7] "MIRSEQ_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 69 columns, 0 survival variables, and 7 non-survival variables.
MRNA_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
CN_CNMF, nv=5, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = APC MUTATION ANALYSIS
D1V1, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          19             5
  CLUS_2          15             4
  CLUS_3          18             3
D1V2, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          15             2
  CLUS_2          18             5
  CLUS_3          19             5
D1V3, multiclass
D1V4, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          11             5
  CLUS_2          12             2
  CLUS_3          20             3
D1V5, multiclass
D1V6, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1           1             1
  CLUS_3           3             0
  CLUS_4           6             0
  CLUS_5          45             9
D1V7, binary
               cls
clus             0  1
  APC MUTATED    4 51
  APC WILD-TYPE  0 10
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED      4   51
  APC WILD-TYPE    0   10
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1           4             0
  CLUS_2          51            10

Clustering(2) Variable = KRAS MUTATION ANALYSIS
D2V1, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           16              8
  CLUS_2            9             10
  CLUS_3           10             11
D2V2, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            7             10
  CLUS_2           16              7
  CLUS_3           12             12
D2V3, multiclass
D2V4, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            7              9
  CLUS_2            8              6
  CLUS_3           12             11
D2V5, multiclass
D2V6, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            1              1
  CLUS_3            2              1
  CLUS_4            1              5
  CLUS_5           30             24
D2V7, binary
                cls
clus              0  1
  KRAS MUTATED    0 34
  KRAS WILD-TYPE  4 27
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      0   34
  KRAS WILD-TYPE    4   27
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            0              4
  CLUS_2           34             27

Clustering(3) Variable = TP53 MUTATION ANALYSIS
D3V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            8             16
  CLUS_2           13              6
  CLUS_3           19              2
D3V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           15              2
  CLUS_2            8             15
  CLUS_3           17              7
D3V3, multiclass
D3V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           10              6
  CLUS_2           12              2
  CLUS_3           13             10
D3V5, multiclass
D3V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1              1
  CLUS_3            2              1
  CLUS_4            5              1
  CLUS_5           34             20
D3V7, binary
                cls
clus              0  1
  TP53 MUTATED    4 38
  TP53 WILD-TYPE  0 23
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      4   38
  TP53 WILD-TYPE    0   23
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            4              0
  CLUS_2           38             23

Clustering(4) Variable = SMAD4 MUTATION ANALYSIS
D4V1, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             5              19
  CLUS_2             0              19
  CLUS_3             2              19
D4V2, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             2              15
  CLUS_2             4              19
  CLUS_3             1              23
D4V3, multiclass
D4V4, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             0              16
  CLUS_2             3              11
  CLUS_3             4              19
D4V5, multiclass
D4V6, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             1               1
  CLUS_3             0               3
  CLUS_4             0               6
  CLUS_5             7              47
D4V7, binary
                 cls
clus               0  1
  SMAD4 MUTATED    0  8
  SMAD4 WILD-TYPE  4 53
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      0    8
  SMAD4 WILD-TYPE    4   53
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             0               4
  CLUS_2             8              53

Clustering(5) Variable = KIAA1804 MUTATION ANALYSIS
D5V1, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                3                 21
  CLUS_2                4                 15
  CLUS_3                1                 20
D5V2, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                1                 16
  CLUS_2                3                 20
  CLUS_3                4                 20
D5V3, multiclass
D5V4, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                2                 12
  CLUS_3                4                 19
D5V5, multiclass
D5V6, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                0                  2
  CLUS_3                0                  3
  CLUS_4                0                  6
  CLUS_5                9                 45
D5V7, binary
                    cls
clus                  0  1
  KIAA1804 MUTATED    0  9
  KIAA1804 WILD-TYPE  4 52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1804 MUTATED      0    9
  KIAA1804 WILD-TYPE    4   52
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                9                 52

Clustering(6) Variable = FBXW7 MUTATION ANALYSIS
D6V1, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             2              22
  CLUS_2             5              14
  CLUS_3             1              20
D6V2, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             1              16
  CLUS_2             1              22
  CLUS_3             6              18
D6V3, multiclass
D6V4, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             3              13
  CLUS_2             2              12
  CLUS_3             2              21
D6V5, multiclass
D6V6, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             0               2
  CLUS_3             0               3
  CLUS_4             0               6
  CLUS_5             9              45
D6V7, binary
                 cls
clus               0  1
  FBXW7 MUTATED    0  9
  FBXW7 WILD-TYPE  4 52
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      0    9
  FBXW7 WILD-TYPE    4   52
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             0               4
  CLUS_2             9              52

Clustering(7) Variable = NRAS MUTATION ANALYSIS
D7V1, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            2             22
  CLUS_2            2             17
  CLUS_3            1             20
D7V2, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            1             16
  CLUS_2            2             21
  CLUS_3            2             22
D7V3, multiclass
D7V4, multiclass
[1] "Remove cluster labels:" "NRAS MUTATED"          
clus
  NRAS MUTATED NRAS WILD-TYPE 
             1             52 
    TCGA-AF-2689     TCGA-AF-3400     TCGA-AG-3574     TCGA-AG-3578 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3609 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3612     TCGA-AG-3727     TCGA-AG-3878     TCGA-AG-3881 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3882     TCGA-AG-3893     TCGA-AG-3896     TCGA-AG-3898 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3901     TCGA-AG-3902     TCGA-AG-4001     TCGA-AG-4005 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-4015     TCGA-AG-A002 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-A008     TCGA-AG-A00C     TCGA-AG-A00H     TCGA-AG-A00Y 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-A011     TCGA-AG-A014     TCGA-AG-A015     TCGA-AG-A016 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-A01W     TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A026 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A036 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
D7V5, multiclass
[1] "Remove cluster labels:" "NRAS MUTATED"          
clus
  NRAS MUTATED NRAS WILD-TYPE 
             1             52 
    TCGA-AF-2689     TCGA-AF-3400     TCGA-AG-3574     TCGA-AG-3578 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3609 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3612     TCGA-AG-3727     TCGA-AG-3878     TCGA-AG-3881 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3882     TCGA-AG-3893     TCGA-AG-3896     TCGA-AG-3898 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3901     TCGA-AG-3902     TCGA-AG-4001     TCGA-AG-4005 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-4015     TCGA-AG-A002 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-A008     TCGA-AG-A00C     TCGA-AG-A00H     TCGA-AG-A00Y 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-A011     TCGA-AG-A014     TCGA-AG-A015     TCGA-AG-A016 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-A01W     TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A026 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A036 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
D7V6, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            1              1
  CLUS_3            0              3
  CLUS_4            1              5
  CLUS_5            3             51
D7V7, binary
                cls
clus              0  1
  NRAS MUTATED    0  5
  NRAS WILD-TYPE  4 56
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      0    5
  NRAS WILD-TYPE    4   56
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            0              4
  CLUS_2            5             56

Clustering(8) Variable = TCF7L2 MUTATION ANALYSIS
D8V1, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              2               22
  CLUS_2              2               17
  CLUS_3              3               18
D8V2, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              3               14
  CLUS_2              2               21
  CLUS_3              2               22
D8V3, multiclass
D8V4, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              2               14
  CLUS_2              2               12
  CLUS_3              0               23
D8V5, multiclass
D8V6, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              0                2
  CLUS_3              0                3
  CLUS_4              0                6
  CLUS_5              6               48
D8V7, binary
                  cls
clus                0  1
  TCF7L2 MUTATED    0  6
  TCF7L2 WILD-TYPE  4 55
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCF7L2 MUTATED      0    6
  TCF7L2 WILD-TYPE    4   55
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              0                4
  CLUS_2              6               55

Clustering(9) Variable = PIK3CA MUTATION ANALYSIS
D9V1, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              2               22
  CLUS_2              1               18
  CLUS_3              2               19
D9V2, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              2               15
  CLUS_2              2               21
  CLUS_3              1               23
D9V3, multiclass
D9V4, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              1               15
  CLUS_2              3               11
  CLUS_3              2               21
D9V5, multiclass
D9V6, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              1                1
  CLUS_3              0                3
  CLUS_4              0                6
  CLUS_5              5               49
D9V7, binary
                  cls
clus                0  1
  PIK3CA MUTATED    1  5
  PIK3CA WILD-TYPE  3 56
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      1    5
  PIK3CA WILD-TYPE    3   56
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              1                3
  CLUS_2              5               56

Clustering(10) Variable = OPCML MUTATION ANALYSIS
D10V1, multiclass
        clus
vv       OPCML MUTATED OPCML WILD-TYPE
  CLUS_1             4              20
  CLUS_2             0              19
  CLUS_3             2              19
D10V2, multiclass
        clus
vv       OPCML MUTATED OPCML WILD-TYPE
  CLUS_1             2              15
  CLUS_2             4              19
  CLUS_3             0              24
D10V3, multiclass
D10V4, multiclass
        clus
vv       OPCML MUTATED OPCML WILD-TYPE
  CLUS_1             1              15
  CLUS_2             2              12
  CLUS_3             1              22
D10V5, multiclass
D10V6, multiclass
        clus
vv       OPCML MUTATED OPCML WILD-TYPE
  CLUS_1             0               2
  CLUS_3             0               3
  CLUS_4             0               6
  CLUS_5             5              49
D10V7, binary
                 cls
clus               0  1
  OPCML MUTATED    0  5
  OPCML WILD-TYPE  4 56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPCML MUTATED      0    5
  OPCML WILD-TYPE    4   56
        clus
vv       OPCML MUTATED OPCML WILD-TYPE
  CLUS_1             0               4
  CLUS_2             5              56

Clustering(11) Variable = SMAD2 MUTATION ANALYSIS
D11V1, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             2              22
  CLUS_2             1              18
  CLUS_3             1              20
D11V2, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             1              16
  CLUS_2             1              22
  CLUS_3             2              22
D11V3, multiclass
D11V4, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             0              16
  CLUS_2             1              13
  CLUS_3             2              21
D11V5, multiclass
D11V6, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             0               2
  CLUS_3             0               3
  CLUS_4             0               6
  CLUS_5             5              49
D11V7, binary
                 cls
clus               0  1
  SMAD2 MUTATED    0  5
  SMAD2 WILD-TYPE  4 56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      0    5
  SMAD2 WILD-TYPE    4   56
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             0               4
  CLUS_2             5              56

Clustering(12) Variable = SPATA8 MUTATION ANALYSIS
D12V1, multiclass
[1] "Remove cluster labels:" "SPATA8 MUTATED"        
clus
  SPATA8 MUTATED SPATA8 WILD-TYPE 
               2               62 
      TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692       TCGA-AF-3400 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AF-3913       TCGA-AG-3574       TCGA-AG-3575       TCGA-AG-3578 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3580       TCGA-AG-3581       TCGA-AG-3582       TCGA-AG-3583 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3584       TCGA-AG-3586       TCGA-AG-3587       TCGA-AG-3593 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3594       TCGA-AG-3598       TCGA-AG-3599       TCGA-AG-3600 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3601       TCGA-AG-3602       TCGA-AG-3605       TCGA-AG-3608 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3609       TCGA-AG-3611       TCGA-AG-3612       TCGA-AG-3726 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3727       TCGA-AG-3878       TCGA-AG-3881       TCGA-AG-3882 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3883       TCGA-AG-3887       TCGA-AG-3890       TCGA-AG-3892 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3893       TCGA-AG-3894       TCGA-AG-3896       TCGA-AG-3898 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3901       TCGA-AG-3902       TCGA-AG-3999       TCGA-AG-4005 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-4007       TCGA-AG-4008       TCGA-AG-4015       TCGA-AG-A002 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A008       TCGA-AG-A00C       TCGA-AG-A00H       TCGA-AG-A00Y 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A011       TCGA-AG-A014       TCGA-AG-A015       TCGA-AG-A016 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A01L       TCGA-AG-A025       TCGA-AG-A026       TCGA-AG-A02G 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A02X       TCGA-AG-A032 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
D12V2, multiclass
[1] "Remove cluster labels:" "SPATA8 MUTATED"        
clus
  SPATA8 MUTATED SPATA8 WILD-TYPE 
               2               62 
      TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692       TCGA-AF-3400 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AF-3913       TCGA-AG-3574       TCGA-AG-3575       TCGA-AG-3578 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3580       TCGA-AG-3581       TCGA-AG-3582       TCGA-AG-3583 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3584       TCGA-AG-3586       TCGA-AG-3587       TCGA-AG-3593 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3594       TCGA-AG-3598       TCGA-AG-3599       TCGA-AG-3600 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3601       TCGA-AG-3602       TCGA-AG-3605       TCGA-AG-3608 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3609       TCGA-AG-3611       TCGA-AG-3612       TCGA-AG-3726 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3727       TCGA-AG-3878       TCGA-AG-3881       TCGA-AG-3882 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3883       TCGA-AG-3887       TCGA-AG-3890       TCGA-AG-3892 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3893       TCGA-AG-3894       TCGA-AG-3896       TCGA-AG-3898 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3901       TCGA-AG-3902       TCGA-AG-3999       TCGA-AG-4005 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-4007       TCGA-AG-4008       TCGA-AG-4015       TCGA-AG-A002 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A008       TCGA-AG-A00C       TCGA-AG-A00H       TCGA-AG-A00Y 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A011       TCGA-AG-A014       TCGA-AG-A015       TCGA-AG-A016 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A01L       TCGA-AG-A025       TCGA-AG-A026       TCGA-AG-A02G 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A02X       TCGA-AG-A032 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
D12V3, multiclass
D12V4, multiclass
[1] "Remove cluster labels:" "SPATA8 MUTATED"        
clus
  SPATA8 MUTATED SPATA8 WILD-TYPE 
               2               51 
      TCGA-AF-2689       TCGA-AF-3400       TCGA-AF-3913       TCGA-AG-3574 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3578       TCGA-AG-3580       TCGA-AG-3581       TCGA-AG-3582 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3583       TCGA-AG-3584       TCGA-AG-3586       TCGA-AG-3587 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3593       TCGA-AG-3594       TCGA-AG-3598       TCGA-AG-3599 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3600       TCGA-AG-3601       TCGA-AG-3602       TCGA-AG-3605 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3609       TCGA-AG-3612       TCGA-AG-3727       TCGA-AG-3878 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3881       TCGA-AG-3882       TCGA-AG-3893       TCGA-AG-3896 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3898       TCGA-AG-3901       TCGA-AG-3902       TCGA-AG-4005 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-4007       TCGA-AG-4008       TCGA-AG-4015       TCGA-AG-A002 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A008       TCGA-AG-A00C       TCGA-AG-A00H       TCGA-AG-A00Y 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A011       TCGA-AG-A014       TCGA-AG-A015       TCGA-AG-A016 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A01Y       TCGA-AG-A020       TCGA-AG-A026       TCGA-AG-A02G 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A02N       TCGA-AG-A02X       TCGA-AG-A036 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
D12V5, multiclass
[1] "Remove cluster labels:" "SPATA8 MUTATED"        
clus
  SPATA8 MUTATED SPATA8 WILD-TYPE 
               2               51 
      TCGA-AF-2689       TCGA-AF-3400       TCGA-AF-3913       TCGA-AG-3574 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3578       TCGA-AG-3580       TCGA-AG-3581       TCGA-AG-3582 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3583       TCGA-AG-3584       TCGA-AG-3586       TCGA-AG-3587 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3593       TCGA-AG-3594       TCGA-AG-3598       TCGA-AG-3599 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3600       TCGA-AG-3601       TCGA-AG-3602       TCGA-AG-3605 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3609       TCGA-AG-3612       TCGA-AG-3727       TCGA-AG-3878 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3881       TCGA-AG-3882       TCGA-AG-3893       TCGA-AG-3896 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3898       TCGA-AG-3901       TCGA-AG-3902       TCGA-AG-4005 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-4007       TCGA-AG-4008       TCGA-AG-4015       TCGA-AG-A002 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A008       TCGA-AG-A00C       TCGA-AG-A00H       TCGA-AG-A00Y 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A011       TCGA-AG-A014       TCGA-AG-A015       TCGA-AG-A016 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A01Y       TCGA-AG-A020       TCGA-AG-A026       TCGA-AG-A02G 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A02N       TCGA-AG-A02X       TCGA-AG-A036 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
D12V6, multiclass
        clus
vv       SPATA8 MUTATED SPATA8 WILD-TYPE
  CLUS_1              0                2
  CLUS_3              0                3
  CLUS_4              1                5
  CLUS_5              2               52
D12V7, binary
                  cls
clus                0  1
  SPATA8 MUTATED    1  2
  SPATA8 WILD-TYPE  3 59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPATA8 MUTATED      1    2
  SPATA8 WILD-TYPE    3   59
        clus
vv       SPATA8 MUTATED SPATA8 WILD-TYPE
  CLUS_1              1                3
  CLUS_2              2               59

Clustering(13) Variable = ERBB2 MUTATION ANALYSIS
D13V1, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             2              22
  CLUS_2             0              19
  CLUS_3             2              19
D13V2, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             1              16
  CLUS_2             1              22
  CLUS_3             2              22
D13V3, multiclass
D13V4, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             2              12
  CLUS_3             1              22
D13V5, multiclass
D13V6, multiclass
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             0               2
  CLUS_3             0               3
  CLUS_4             0               6
  CLUS_5             4              50
D13V7, binary
                 cls
clus               0  1
  ERBB2 MUTATED    0  4
  ERBB2 WILD-TYPE  4 57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      0    4
  ERBB2 WILD-TYPE    4   57
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  CLUS_1             0               4
  CLUS_2             4              57

Clustering(14) Variable = IL1RAPL2 MUTATION ANALYSIS
D14V1, multiclass
        clus
vv       IL1RAPL2 MUTATED IL1RAPL2 WILD-TYPE
  CLUS_1                3                 21
  CLUS_2                1                 18
  CLUS_3                1                 20
D14V2, multiclass
        clus
vv       IL1RAPL2 MUTATED IL1RAPL2 WILD-TYPE
  CLUS_1                1                 16
  CLUS_2                3                 20
  CLUS_3                1                 23
D14V3, multiclass
D14V4, multiclass
[1] "Remove cluster labels:" "IL1RAPL2 MUTATED"      
clus
  IL1RAPL2 MUTATED IL1RAPL2 WILD-TYPE 
                 2                 51 
        TCGA-AF-2689         TCGA-AF-3400         TCGA-AF-3913 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-3574         TCGA-AG-3578         TCGA-AG-3580 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-3584         TCGA-AG-3586         TCGA-AG-3587 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-3593         TCGA-AG-3594         TCGA-AG-3598 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-3599         TCGA-AG-3600         TCGA-AG-3601 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-3602         TCGA-AG-3605         TCGA-AG-3609 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-3612         TCGA-AG-3727         TCGA-AG-3878 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-3881         TCGA-AG-3882         TCGA-AG-3893 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-3896         TCGA-AG-3898         TCGA-AG-3902 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-4001         TCGA-AG-4005         TCGA-AG-4007 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4015         TCGA-AG-A008 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-A00C         TCGA-AG-A00H         TCGA-AG-A00Y 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-A011         TCGA-AG-A014         TCGA-AG-A015 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-A016         TCGA-AG-A01W         TCGA-AG-A01Y 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-A020         TCGA-AG-A026         TCGA-AG-A02G 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A036 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
D14V5, multiclass
[1] "Remove cluster labels:" "IL1RAPL2 MUTATED"      
clus
  IL1RAPL2 MUTATED IL1RAPL2 WILD-TYPE 
                 2                 51 
        TCGA-AF-2689         TCGA-AF-3400         TCGA-AF-3913 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-3574         TCGA-AG-3578         TCGA-AG-3580 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-3584         TCGA-AG-3586         TCGA-AG-3587 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-3593         TCGA-AG-3594         TCGA-AG-3598 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-3599         TCGA-AG-3600         TCGA-AG-3601 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-3602         TCGA-AG-3605         TCGA-AG-3609 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-3612         TCGA-AG-3727         TCGA-AG-3878 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-3881         TCGA-AG-3882         TCGA-AG-3893 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-3896         TCGA-AG-3898         TCGA-AG-3902 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-4001         TCGA-AG-4005         TCGA-AG-4007 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4015         TCGA-AG-A008 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-A00C         TCGA-AG-A00H         TCGA-AG-A00Y 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-A011         TCGA-AG-A014         TCGA-AG-A015 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-A016         TCGA-AG-A01W         TCGA-AG-A01Y 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-A020         TCGA-AG-A026         TCGA-AG-A02G 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A036 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
D14V6, multiclass
        clus
vv       IL1RAPL2 MUTATED IL1RAPL2 WILD-TYPE
  CLUS_1                1                  1
  CLUS_3                0                  3
  CLUS_4                0                  6
  CLUS_5                4                 50
D14V7, binary
                    cls
clus                  0  1
  IL1RAPL2 MUTATED    0  5
  IL1RAPL2 WILD-TYPE  4 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  IL1RAPL2 MUTATED      0    5
  IL1RAPL2 WILD-TYPE    4   56
        clus
vv       IL1RAPL2 MUTATED IL1RAPL2 WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                5                 56

Clustering(15) Variable = FAM123B MUTATION ANALYSIS
D15V1, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               2                22
  CLUS_2               1                18
  CLUS_3               2                19
D15V2, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               2                15
  CLUS_2               2                21
  CLUS_3               1                23
D15V3, multiclass
D15V4, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               0                16
  CLUS_2               1                13
  CLUS_3               4                19
D15V5, multiclass
D15V6, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               0                 2
  CLUS_3               0                 3
  CLUS_4               0                 6
  CLUS_5               6                48
D15V7, binary
                   cls
clus                 0  1
  FAM123B MUTATED    0  6
  FAM123B WILD-TYPE  4 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123B MUTATED      0    6
  FAM123B WILD-TYPE    4   55
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               6                55

Clustering(16) Variable = ZIM3 MUTATION ANALYSIS
D16V1, multiclass
        clus
vv       ZIM3 MUTATED ZIM3 WILD-TYPE
  CLUS_1            1             23
  CLUS_2            1             18
  CLUS_3            2             19
D16V2, multiclass
        clus
vv       ZIM3 MUTATED ZIM3 WILD-TYPE
  CLUS_1            2             15
  CLUS_2            1             22
  CLUS_3            1             23
D16V3, multiclass
D16V4, multiclass
        clus
vv       ZIM3 MUTATED ZIM3 WILD-TYPE
  CLUS_1            0             16
  CLUS_2            1             13
  CLUS_3            3             20
D16V5, multiclass
D16V6, multiclass
        clus
vv       ZIM3 MUTATED ZIM3 WILD-TYPE
  CLUS_1            0              2
  CLUS_3            1              2
  CLUS_4            0              6
  CLUS_5            4             50
D16V7, binary
                cls
clus              0  1
  ZIM3 MUTATED    1  4
  ZIM3 WILD-TYPE  3 57
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZIM3 MUTATED      1    4
  ZIM3 WILD-TYPE    3   57
        clus
vv       ZIM3 MUTATED ZIM3 WILD-TYPE
  CLUS_1            1              3
  CLUS_2            4             57
                    V1                     V2                     V3 
           "MRNA_CNMF"   "MRNA_CHIERARCHICAL"              "CN_CNMF" 
                    V4                     V5                     V6 
           "RPPA_CNMF"   "RPPA_CHIERARCHICAL"          "MIRSEQ_CNMF" 
                    V7 
"MIRSEQ_CHIERARCHICAL" 
> q(save="no")
