
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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> source("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/Correlate_Genomic_Events.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-tTRUE", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BLCA-TP/8204552/transformed.cor.cli.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BLCA-TP/8282807/BLCA-TP.transferedmergedcluster.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ALL", "-oT=BLCA-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=BLCA-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BLCA-TP/8282807/BLCA-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BLCA-TP/8204552/transformed.cor.cli.txt"

nPatients in clinical file=253, in cluster file=130, common to both=130
[1]  23 130
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              26              104 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              26              104 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            64             66 
  TP53 MUTATED TP53 WILD-TYPE 
            64             66 
[1] "CDKN1A MUTATION ANALYSIS"
[1] 3
  CDKN1A MUTATED CDKN1A WILD-TYPE 
              18              112 
  CDKN1A MUTATED CDKN1A WILD-TYPE 
              18              112 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           17           113 
  RB1 MUTATED RB1 WILD-TYPE 
           17           113 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              32               98 
  ARID1A MUTATED ARID1A WILD-TYPE 
              32               98 
[1] "MLL2 MUTATION ANALYSIS"
[1] 3
  MLL2 MUTATED MLL2 WILD-TYPE 
            36             94 
  MLL2 MUTATED MLL2 WILD-TYPE 
            36             94 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             13             117 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             13             117 
[1] "KDM6A MUTATION ANALYSIS"
[1] 3
  KDM6A MUTATED KDM6A WILD-TYPE 
             31              99 
  KDM6A MUTATED KDM6A WILD-TYPE 
             31              99 
[1] "ELF3 MUTATION ANALYSIS"
[1] 3
  ELF3 MUTATED ELF3 WILD-TYPE 
            11            119 
  ELF3 MUTATED ELF3 WILD-TYPE 
            11            119 
[1] "FGFR3 MUTATION ANALYSIS"
[1] 3
  FGFR3 MUTATED FGFR3 WILD-TYPE 
             16             114 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
             16             114 
[1] "FOXQ1 MUTATION ANALYSIS"
[1] 3
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              7             123 
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              7             123 
[1] "STAG2 MUTATION ANALYSIS"
[1] 3
  STAG2 MUTATED STAG2 WILD-TYPE 
             14             116 
  STAG2 MUTATED STAG2 WILD-TYPE 
             14             116 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              11              119 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              11              119 
[1] "CDKN2A MUTATION ANALYSIS"
[1] 3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               7              123 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               7              123 
[1] "KLF5 MUTATION ANALYSIS"
[1] 3
  KLF5 MUTATED KLF5 WILD-TYPE 
            10            120 
  KLF5 MUTATED KLF5 WILD-TYPE 
            10            120 
[1] "ASXL2 MUTATION ANALYSIS"
[1] 3
  ASXL2 MUTATED ASXL2 WILD-TYPE 
              9             121 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
              9             121 
[1] "TSC1 MUTATION ANALYSIS"
[1] 3
  TSC1 MUTATED TSC1 WILD-TYPE 
            11            119 
  TSC1 MUTATED TSC1 WILD-TYPE 
            11            119 
[1] "ERCC2 MUTATION ANALYSIS"
[1] 3
  ERCC2 MUTATED ERCC2 WILD-TYPE 
             16             114 
  ERCC2 MUTATED ERCC2 WILD-TYPE 
             16             114 
[1] "TXNIP MUTATION ANALYSIS"
[1] 3
  TXNIP MUTATED TXNIP WILD-TYPE 
              9             121 
  TXNIP MUTATED TXNIP WILD-TYPE 
              9             121 
[1] "EP300 MUTATION ANALYSIS"
[1] 3
  EP300 MUTATED EP300 WILD-TYPE 
             21             109 
  EP300 MUTATED EP300 WILD-TYPE 
             21             109 
[1] "RXRA MUTATION ANALYSIS"
[1] 3
  RXRA MUTATED RXRA WILD-TYPE 
            12            118 
  RXRA MUTATED RXRA WILD-TYPE 
            12            118 
[1] "FOXA1 MUTATION ANALYSIS"
[1] 3
  FOXA1 MUTATED FOXA1 WILD-TYPE 
              7             123 
  FOXA1 MUTATED FOXA1 WILD-TYPE 
              7             123 
[1] "PHLDA3 MUTATION ANALYSIS"
[1] 3
  PHLDA3 MUTATED PHLDA3 WILD-TYPE 
               4              126 
  PHLDA3 MUTATED PHLDA3 WILD-TYPE 
               4              126 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 10 rows and 130 columns.

Variable 1:'CN_CNMF':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'RPPA_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'RPPA_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_MATURE_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 130 columns, 0 survival variables, and 10 non-survival variables.
CN_CNMF, nv=8, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=5, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = PIK3CA MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  PIK3CA MUTATED        1     10      3      2      2      4      1      3
  PIK3CA WILD-TYPE      8     31      9      5     20     13     13      2
D1V1, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED        9     12      5
  PIK3CA WILD-TYPE     42     41     21
D1V2, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              9               42
  CLUS_2             12               41
  CLUS_3              5               21
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PIK3CA MUTATED        5      6     11      0      2
  PIK3CA WILD-TYPE     31     22     22      5     15
D1V3, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PIK3CA MUTATED        9      2      4      9
  PIK3CA WILD-TYPE     33     16     13     33
D1V4, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              9               33
  CLUS_2              2               16
  CLUS_3              4               13
  CLUS_4              9               33
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED        8     10      8
  PIK3CA WILD-TYPE     46     28     29
D1V5, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              8               46
  CLUS_2             10               28
  CLUS_3              8               29
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED       11      9      6
  PIK3CA WILD-TYPE     43     22     38
D1V6, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             11               43
  CLUS_2              9               22
  CLUS_3              6               38
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED        5     13      8
  PIK3CA WILD-TYPE     28     43     33
D1V7, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              5               28
  CLUS_2             13               43
  CLUS_3              8               33
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED       19      4      3
  PIK3CA WILD-TYPE     70      5     29
D1V8, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             19               70
  CLUS_2              4                5
  CLUS_3              3               29
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED        3     10     13
  PIK3CA WILD-TYPE     23     39     42
D1V9, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              3               23
  CLUS_2             10               39
  CLUS_3             13               42
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED        6     17      3
  PIK3CA WILD-TYPE     25     57     22
D1V10, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              6               25
  CLUS_2             17               57
  CLUS_3              3               22

Clustering(2) Variable = TP53 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  TP53 MUTATED        4     12      8      5     12     12      7      3
  TP53 WILD-TYPE      5     29      4      2     10      5      7      2
D2V1, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       28     27      9
  TP53 WILD-TYPE     23     26     17
D2V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           28             23
  CLUS_2           27             26
  CLUS_3            9             17
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TP53 MUTATED       14     11     23      1      9
  TP53 WILD-TYPE     22     17     10      4      8
D2V3, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED       15      9     14     20
  TP53 WILD-TYPE     27      9      3     22
D2V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           15             27
  CLUS_2            9              9
  CLUS_3           14              3
  CLUS_4           20             22
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       21     23     20
  TP53 WILD-TYPE     33     15     17
D2V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           21             33
  CLUS_2           23             15
  CLUS_3           20             17
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       31     15     18
  TP53 WILD-TYPE     23     16     26
D2V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           31             23
  CLUS_2           15             16
  CLUS_3           18             26
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       13     30     21
  TP53 WILD-TYPE     20     26     20
D2V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           13             20
  CLUS_2           30             26
  CLUS_3           21             20
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       46      3     15
  TP53 WILD-TYPE     43      6     17
D2V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           46             43
  CLUS_2            3              6
  CLUS_3           15             17
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        9     25     30
  TP53 WILD-TYPE     17     24     25
D2V9, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            9             17
  CLUS_2           25             24
  CLUS_3           30             25
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       17     38      9
  TP53 WILD-TYPE     14     36     16
D2V10, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           17             14
  CLUS_2           38             36
  CLUS_3            9             16

Clustering(3) Variable = CDKN1A MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CDKN1A MUTATED        0      5      0      1      4      2      4      2
  CDKN1A WILD-TYPE      9     36     12      6     18     15     10      3
D3V1, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN1A MUTATED        9      7      2
  CDKN1A WILD-TYPE     42     46     24
D3V2, multiclass
        clus
vv       CDKN1A MUTATED CDKN1A WILD-TYPE
  CLUS_1              9               42
  CLUS_2              7               46
  CLUS_3              2               24
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CDKN1A MUTATED        6      4      5      1      1
  CDKN1A WILD-TYPE     30     24     28      4     16
D3V3, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CDKN1A MUTATED        7      2      4      4
  CDKN1A WILD-TYPE     35     16     13     38
D3V4, multiclass
        clus
vv       CDKN1A MUTATED CDKN1A WILD-TYPE
  CLUS_1              7               35
  CLUS_2              2               16
  CLUS_3              4               13
  CLUS_4              4               38
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN1A MUTATED        7      6      5
  CDKN1A WILD-TYPE     47     32     32
D3V5, multiclass
        clus
vv       CDKN1A MUTATED CDKN1A WILD-TYPE
  CLUS_1              7               47
  CLUS_2              6               32
  CLUS_3              5               32
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN1A MUTATED        8      3      7
  CDKN1A WILD-TYPE     46     28     37
D3V6, multiclass
        clus
vv       CDKN1A MUTATED CDKN1A WILD-TYPE
  CLUS_1              8               46
  CLUS_2              3               28
  CLUS_3              7               37
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN1A MUTATED        5      7      6
  CDKN1A WILD-TYPE     28     49     35
D3V7, multiclass
        clus
vv       CDKN1A MUTATED CDKN1A WILD-TYPE
  CLUS_1              5               28
  CLUS_2              7               49
  CLUS_3              6               35
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN1A MUTATED       12      1      5
  CDKN1A WILD-TYPE     77      8     27
D3V8, multiclass
        clus
vv       CDKN1A MUTATED CDKN1A WILD-TYPE
  CLUS_1             12               77
  CLUS_2              1                8
  CLUS_3              5               27
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN1A MUTATED        5      7      6
  CDKN1A WILD-TYPE     21     42     49
D3V9, multiclass
        clus
vv       CDKN1A MUTATED CDKN1A WILD-TYPE
  CLUS_1              5               21
  CLUS_2              7               42
  CLUS_3              6               49
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN1A MUTATED        3     10      5
  CDKN1A WILD-TYPE     28     64     20
D3V10, multiclass
        clus
vv       CDKN1A MUTATED CDKN1A WILD-TYPE
  CLUS_1              3               28
  CLUS_2             10               64
  CLUS_3              5               20

Clustering(4) Variable = RB1 MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  RB1 MUTATED        0      2      1      2      3      4      2      3
  RB1 WILD-TYPE      9     39     11      5     19     13     12      2
D4V1, multiclass
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        5     10      2
  RB1 WILD-TYPE     46     43     24
D4V2, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           5            46
  CLUS_2          10            43
  CLUS_3           2            24
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RB1 MUTATED        3      6      5      0      2
  RB1 WILD-TYPE     33     22     28      5     15
D4V3, multiclass
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RB1 MUTATED        2      2      4      8
  RB1 WILD-TYPE     40     16     13     34
D4V4, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           2            40
  CLUS_2           2            16
  CLUS_3           4            13
  CLUS_4           8            34
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        6      4      7
  RB1 WILD-TYPE     48     34     30
D4V5, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           6            48
  CLUS_2           4            34
  CLUS_3           7            30
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        9      3      5
  RB1 WILD-TYPE     45     28     39
D4V6, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           9            45
  CLUS_2           3            28
  CLUS_3           5            39
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        3      9      5
  RB1 WILD-TYPE     30     47     36
D4V7, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           3            30
  CLUS_2           9            47
  CLUS_3           5            36
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED       12      1      4
  RB1 WILD-TYPE     77      8     28
D4V8, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1          12            77
  CLUS_2           1             8
  CLUS_3           4            28
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        1      6     10
  RB1 WILD-TYPE     25     43     45
D4V9, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           1            25
  CLUS_2           6            43
  CLUS_3          10            45
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        4     12      1
  RB1 WILD-TYPE     27     62     24
D4V10, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           4            27
  CLUS_2          12            62
  CLUS_3           1            24

Clustering(5) Variable = ARID1A MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ARID1A MUTATED        2      9      3      1      7      6      4      0
  ARID1A WILD-TYPE      7     32      9      6     15     11     10      5
D5V1, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED       14     13      5
  ARID1A WILD-TYPE     37     40     21
D5V2, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1             14               37
  CLUS_2             13               40
  CLUS_3              5               21
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ARID1A MUTATED       11      8      6      2      3
  ARID1A WILD-TYPE     25     20     27      3     14
D5V3, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ARID1A MUTATED       10      2      3     15
  ARID1A WILD-TYPE     32     16     14     27
D5V4, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1             10               32
  CLUS_2              2               16
  CLUS_3              3               14
  CLUS_4             15               27
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED       14     11      7
  ARID1A WILD-TYPE     40     27     30
D5V5, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1             14               40
  CLUS_2             11               27
  CLUS_3              7               30
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED       13     10      9
  ARID1A WILD-TYPE     41     21     35
D5V6, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1             13               41
  CLUS_2             10               21
  CLUS_3              9               35
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED       10      8     14
  ARID1A WILD-TYPE     23     48     27
D5V7, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1             10               23
  CLUS_2              8               48
  CLUS_3             14               27
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED       18      2     12
  ARID1A WILD-TYPE     71      7     20
D5V8, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1             18               71
  CLUS_2              2                7
  CLUS_3             12               20
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        8      8     16
  ARID1A WILD-TYPE     18     41     39
D5V9, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              8               18
  CLUS_2              8               41
  CLUS_3             16               39
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        4     20      8
  ARID1A WILD-TYPE     27     54     17
D5V10, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              4               27
  CLUS_2             20               54
  CLUS_3              8               17

Clustering(6) Variable = MLL2 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  MLL2 MUTATED        1     12      2      1      8      7      1      2
  MLL2 WILD-TYPE      8     29     10      6     14     10     13      3
D6V1, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLL2 MUTATED       13     17      6
  MLL2 WILD-TYPE     38     36     20
D6V2, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1           13             38
  CLUS_2           17             36
  CLUS_3            6             20
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MLL2 MUTATED        9      5     12      1      7
  MLL2 WILD-TYPE     27     23     21      4     10
D6V3, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MLL2 MUTATED       12      8      6      8
  MLL2 WILD-TYPE     30     10     11     34
D6V4, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1           12             30
  CLUS_2            8             10
  CLUS_3            6             11
  CLUS_4            8             34
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLL2 MUTATED       12      9     14
  MLL2 WILD-TYPE     42     29     23
D6V5, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1           12             42
  CLUS_2            9             29
  CLUS_3           14             23
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLL2 MUTATED       17      8     10
  MLL2 WILD-TYPE     37     23     34
D6V6, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1           17             37
  CLUS_2            8             23
  CLUS_3           10             34
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLL2 MUTATED        9     18      9
  MLL2 WILD-TYPE     24     38     32
D6V7, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            9             24
  CLUS_2           18             38
  CLUS_3            9             32
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLL2 MUTATED       25      3      8
  MLL2 WILD-TYPE     64      6     24
D6V8, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1           25             64
  CLUS_2            3              6
  CLUS_3            8             24
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLL2 MUTATED        5     16     15
  MLL2 WILD-TYPE     21     33     40
D6V9, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            5             21
  CLUS_2           16             33
  CLUS_3           15             40
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLL2 MUTATED        7     23      6
  MLL2 WILD-TYPE     24     51     19
D6V10, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            7             24
  CLUS_2           23             51
  CLUS_3            6             19

Clustering(7) Variable = FBXW7 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  FBXW7 MUTATED        1      5      2      0      2      1      1      0
  FBXW7 WILD-TYPE      8     36     10      7     20     16     13      5
D7V1, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FBXW7 MUTATED        2     10      1
  FBXW7 WILD-TYPE     49     43     25
D7V2, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             2              49
  CLUS_2            10              43
  CLUS_3             1              25
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FBXW7 MUTATED        1      3      5      1      1
  FBXW7 WILD-TYPE     35     25     28      4     16
D7V3, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FBXW7 MUTATED        2      1      3      5
  FBXW7 WILD-TYPE     40     17     14     37
D7V4, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             2              40
  CLUS_2             1              17
  CLUS_3             3              14
  CLUS_4             5              37
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FBXW7 MUTATED        2      5      6
  FBXW7 WILD-TYPE     52     33     31
D7V5, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             2              52
  CLUS_2             5              33
  CLUS_3             6              31
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FBXW7 MUTATED        9      2      2
  FBXW7 WILD-TYPE     45     29     42
D7V6, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             9              45
  CLUS_2             2              29
  CLUS_3             2              42
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FBXW7 MUTATED        6      4      3
  FBXW7 WILD-TYPE     27     52     38
D7V7, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             6              27
  CLUS_2             4              52
  CLUS_3             3              38
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FBXW7 MUTATED        7      0      6
  FBXW7 WILD-TYPE     82      9     26
D7V8, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             7              82
  CLUS_2             0               9
  CLUS_3             6              26
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FBXW7 MUTATED        6      1      6
  FBXW7 WILD-TYPE     20     48     49
D7V9, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             6              20
  CLUS_2             1              48
  CLUS_3             6              49
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FBXW7 MUTATED        1      7      5
  FBXW7 WILD-TYPE     30     67     20
D7V10, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             1              30
  CLUS_2             7              67
  CLUS_3             5              20

Clustering(8) Variable = KDM6A MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  KDM6A MUTATED        3      7      5      3      4      4      5      0
  KDM6A WILD-TYPE      6     34      7      4     18     13      9      5
D8V1, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KDM6A MUTATED       13     12      6
  KDM6A WILD-TYPE     38     41     20
D8V2, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1            13              38
  CLUS_2            12              41
  CLUS_3             6              20
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KDM6A MUTATED        9      4     10      2      2
  KDM6A WILD-TYPE     27     24     23      3     15
D8V3, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KDM6A MUTATED        8      2      7     10
  KDM6A WILD-TYPE     34     16     10     32
D8V4, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1             8              34
  CLUS_2             2              16
  CLUS_3             7              10
  CLUS_4            10              32
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KDM6A MUTATED       13      7     11
  KDM6A WILD-TYPE     41     31     26
D8V5, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1            13              41
  CLUS_2             7              31
  CLUS_3            11              26
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KDM6A MUTATED       12      8     11
  KDM6A WILD-TYPE     42     23     33
D8V6, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1            12              42
  CLUS_2             8              23
  CLUS_3            11              33
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KDM6A MUTATED        4     17     10
  KDM6A WILD-TYPE     29     39     31
D8V7, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1             4              29
  CLUS_2            17              39
  CLUS_3            10              31
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KDM6A MUTATED       24      0      7
  KDM6A WILD-TYPE     65      9     25
D8V8, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1            24              65
  CLUS_2             0               9
  CLUS_3             7              25
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KDM6A MUTATED        5     13     13
  KDM6A WILD-TYPE     21     36     42
D8V9, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1             5              21
  CLUS_2            13              36
  CLUS_3            13              42
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KDM6A MUTATED       10     18      3
  KDM6A WILD-TYPE     21     56     22
D8V10, multiclass
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  CLUS_1            10              21
  CLUS_2            18              56
  CLUS_3             3              22

Clustering(9) Variable = ELF3 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ELF3 MUTATED        1      4      2      1      1      1      0      1
  ELF3 WILD-TYPE      8     37     10      6     21     16     14      4
D9V1, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ELF3 MUTATED        5      1      5
  ELF3 WILD-TYPE     46     52     21
D9V2, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            5             46
  CLUS_2            1             52
  CLUS_3            5             21
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ELF3 MUTATED        4      3      3      0      0
  ELF3 WILD-TYPE     32     25     30      5     17
D9V3, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ELF3 MUTATED        4      0      2      4
  ELF3 WILD-TYPE     38     18     15     38
D9V4, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            4             38
  CLUS_2            0             18
  CLUS_3            2             15
  CLUS_4            4             38
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ELF3 MUTATED        6      3      2
  ELF3 WILD-TYPE     48     35     35
D9V5, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            6             48
  CLUS_2            3             35
  CLUS_3            2             35
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ELF3 MUTATED        2      5      4
  ELF3 WILD-TYPE     52     26     40
D9V6, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            2             52
  CLUS_2            5             26
  CLUS_3            4             40
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ELF3 MUTATED        3      3      5
  ELF3 WILD-TYPE     30     53     36
D9V7, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            3             30
  CLUS_2            3             53
  CLUS_3            5             36
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ELF3 MUTATED        7      1      3
  ELF3 WILD-TYPE     82      8     29
D9V8, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            7             82
  CLUS_2            1              8
  CLUS_3            3             29
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ELF3 MUTATED        2      3      6
  ELF3 WILD-TYPE     24     46     49
D9V9, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            2             24
  CLUS_2            3             46
  CLUS_3            6             49
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ELF3 MUTATED        1      7      3
  ELF3 WILD-TYPE     30     67     22
D9V10, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            1             30
  CLUS_2            7             67
  CLUS_3            3             22

Clustering(10) Variable = FGFR3 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  FGFR3 MUTATED        1      7      3      1      3      1      0      0
  FGFR3 WILD-TYPE      8     34      9      6     19     16     14      5
D10V1, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FGFR3 MUTATED        8      3      5
  FGFR3 WILD-TYPE     43     50     21
D10V2, multiclass
        clus
vv       FGFR3 MUTATED FGFR3 WILD-TYPE
  CLUS_1             8              43
  CLUS_2             3              50
  CLUS_3             5              21
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FGFR3 MUTATED        9      2      4      0      0
  FGFR3 WILD-TYPE     27     26     29      5     17
D10V3, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FGFR3 MUTATED       10      2      2      1
  FGFR3 WILD-TYPE     32     16     15     41
D10V4, multiclass
        clus
vv       FGFR3 MUTATED FGFR3 WILD-TYPE
  CLUS_1            10              32
  CLUS_2             2              16
  CLUS_3             2              15
  CLUS_4             1              41
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FGFR3 MUTATED       11      2      3
  FGFR3 WILD-TYPE     43     36     34
D10V5, multiclass
        clus
vv       FGFR3 MUTATED FGFR3 WILD-TYPE
  CLUS_1            11              43
  CLUS_2             2              36
  CLUS_3             3              34
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FGFR3 MUTATED        3      2     11
  FGFR3 WILD-TYPE     51     29     33
D10V6, multiclass
        clus
vv       FGFR3 MUTATED FGFR3 WILD-TYPE
  CLUS_1             3              51
  CLUS_2             2              29
  CLUS_3            11              33
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FGFR3 MUTATED        3     10      3
  FGFR3 WILD-TYPE     30     46     38
D10V7, multiclass
        clus
vv       FGFR3 MUTATED FGFR3 WILD-TYPE
  CLUS_1             3              30
  CLUS_2            10              46
  CLUS_3             3              38
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FGFR3 MUTATED       13      0      3
  FGFR3 WILD-TYPE     76      9     29
D10V8, multiclass
        clus
vv       FGFR3 MUTATED FGFR3 WILD-TYPE
  CLUS_1            13              76
  CLUS_2             0               9
  CLUS_3             3              29
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FGFR3 MUTATED        3     11      2
  FGFR3 WILD-TYPE     23     38     53
D10V9, multiclass
        clus
vv       FGFR3 MUTATED FGFR3 WILD-TYPE
  CLUS_1             3              23
  CLUS_2            11              38
  CLUS_3             2              53
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FGFR3 MUTATED        8      5      3
  FGFR3 WILD-TYPE     23     69     22
D10V10, multiclass
        clus
vv       FGFR3 MUTATED FGFR3 WILD-TYPE
  CLUS_1             8              23
  CLUS_2             5              69
  CLUS_3             3              22

Clustering(11) Variable = FOXQ1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  FOXQ1 MUTATED        0      2      0      1      1      2      0      1
  FOXQ1 WILD-TYPE      9     39     12      6     21     15     14      4
D11V1, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FOXQ1 MUTATED        1      4      2
  FOXQ1 WILD-TYPE     50     49     24
D11V2, multiclass
        clus
vv       FOXQ1 MUTATED FOXQ1 WILD-TYPE
  CLUS_1             1              50
  CLUS_2             4              49
  CLUS_3             2              24
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FOXQ1 MUTATED        2      0      2      0      2
  FOXQ1 WILD-TYPE     34     28     31      5     15
D11V3, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FOXQ1 MUTATED        3      2      0      1
  FOXQ1 WILD-TYPE     39     16     17     41
D11V4, multiclass
        clus
vv       FOXQ1 MUTATED FOXQ1 WILD-TYPE
  CLUS_1             3              39
  CLUS_2             2              16
  CLUS_3             0              17
  CLUS_4             1              41
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FOXQ1 MUTATED        4      1      2
  FOXQ1 WILD-TYPE     50     37     35
D11V5, multiclass
        clus
vv       FOXQ1 MUTATED FOXQ1 WILD-TYPE
  CLUS_1             4              50
  CLUS_2             1              37
  CLUS_3             2              35
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FOXQ1 MUTATED        3      1      3
  FOXQ1 WILD-TYPE     51     30     41
D11V6, multiclass
        clus
vv       FOXQ1 MUTATED FOXQ1 WILD-TYPE
  CLUS_1             3              51
  CLUS_2             1              30
  CLUS_3             3              41
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FOXQ1 MUTATED        0      5      2
  FOXQ1 WILD-TYPE     33     51     39
D11V7, multiclass
        clus
vv       FOXQ1 MUTATED FOXQ1 WILD-TYPE
  CLUS_1             0              33
  CLUS_2             5              51
  CLUS_3             2              39
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FOXQ1 MUTATED        6      0      1
  FOXQ1 WILD-TYPE     83      9     31
D11V8, multiclass
        clus
vv       FOXQ1 MUTATED FOXQ1 WILD-TYPE
  CLUS_1             6              83
  CLUS_2             0               9
  CLUS_3             1              31
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FOXQ1 MUTATED        0      4      3
  FOXQ1 WILD-TYPE     26     45     52
D11V9, multiclass
        clus
vv       FOXQ1 MUTATED FOXQ1 WILD-TYPE
  CLUS_1             0              26
  CLUS_2             4              45
  CLUS_3             3              52
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FOXQ1 MUTATED        2      5      0
  FOXQ1 WILD-TYPE     29     69     25
D11V10, multiclass
        clus
vv       FOXQ1 MUTATED FOXQ1 WILD-TYPE
  CLUS_1             2              29
  CLUS_2             5              69
  CLUS_3             0              25

Clustering(12) Variable = STAG2 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  STAG2 MUTATED        1      6      3      0      1      0      2      1
  STAG2 WILD-TYPE      8     35      9      7     21     17     12      4
D12V1, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  STAG2 MUTATED        6      3      5
  STAG2 WILD-TYPE     45     50     21
D12V2, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             6              45
  CLUS_2             3              50
  CLUS_3             5              21
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  STAG2 MUTATED        7      3      3      0      0
  STAG2 WILD-TYPE     29     25     30      5     17
D12V3, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  STAG2 MUTATED        7      2      1      3
  STAG2 WILD-TYPE     35     16     16     39
D12V4, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             7              35
  CLUS_2             2              16
  CLUS_3             1              16
  CLUS_4             3              39
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  STAG2 MUTATED        8      4      2
  STAG2 WILD-TYPE     46     34     35
D12V5, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             8              46
  CLUS_2             4              34
  CLUS_3             2              35
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  STAG2 MUTATED        3      3      8
  STAG2 WILD-TYPE     51     28     36
D12V6, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             3              51
  CLUS_2             3              28
  CLUS_3             8              36
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  STAG2 MUTATED        2      9      3
  STAG2 WILD-TYPE     31     47     38
D12V7, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             2              31
  CLUS_2             9              47
  CLUS_3             3              38
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  STAG2 MUTATED       11      1      2
  STAG2 WILD-TYPE     78      8     30
D12V8, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1            11              78
  CLUS_2             1               8
  CLUS_3             2              30
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  STAG2 MUTATED        2      9      3
  STAG2 WILD-TYPE     24     40     52
D12V9, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             2              24
  CLUS_2             9              40
  CLUS_3             3              52
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  STAG2 MUTATED        8      4      2
  STAG2 WILD-TYPE     23     70     23
D12V10, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             8              23
  CLUS_2             4              70
  CLUS_3             2              23

Clustering(13) Variable = NFE2L2 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  NFE2L2 MUTATED        0      7      1      0      3      0      0      0
  NFE2L2 WILD-TYPE      9     34     11      7     19     17     14      5
D13V1, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NFE2L2 MUTATED        5      6      0
  NFE2L2 WILD-TYPE     46     47     26
D13V2, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              5               46
  CLUS_2              6               47
  CLUS_3              0               26
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NFE2L2 MUTATED        1      4      3      1      2
  NFE2L2 WILD-TYPE     35     24     30      4     15
D13V3, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NFE2L2 MUTATED        3      1      3      4
  NFE2L2 WILD-TYPE     39     17     14     38
D13V4, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              3               39
  CLUS_2              1               17
  CLUS_3              3               14
  CLUS_4              4               38
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NFE2L2 MUTATED        1      4      5
  NFE2L2 WILD-TYPE     53     34     32
D13V5, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              1               53
  CLUS_2              4               34
  CLUS_3              5               32
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NFE2L2 MUTATED        6      3      1
  NFE2L2 WILD-TYPE     48     28     43
D13V6, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              6               48
  CLUS_2              3               28
  CLUS_3              1               43
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NFE2L2 MUTATED        3      4      4
  NFE2L2 WILD-TYPE     30     52     37
D13V7, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              3               30
  CLUS_2              4               52
  CLUS_3              4               37
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NFE2L2 MUTATED        7      2      2
  NFE2L2 WILD-TYPE     82      7     30
D13V8, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              7               82
  CLUS_2              2                7
  CLUS_3              2               30
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NFE2L2 MUTATED        2      4      5
  NFE2L2 WILD-TYPE     24     45     50
D13V9, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              2               24
  CLUS_2              4               45
  CLUS_3              5               50
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NFE2L2 MUTATED        2      8      1
  NFE2L2 WILD-TYPE     29     66     24
D13V10, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              2               29
  CLUS_2              8               66
  CLUS_3              1               24

Clustering(14) Variable = CDKN2A MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CDKN2A MUTATED        0      1      2      1      1      2      0      0
  CDKN2A WILD-TYPE      9     40     10      6     21     15     14      5
D14V1, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN2A MUTATED        3      4      0
  CDKN2A WILD-TYPE     48     49     26
D14V2, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              3               48
  CLUS_2              4               49
  CLUS_3              0               26
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CDKN2A MUTATED        2      0      4      0      1
  CDKN2A WILD-TYPE     34     28     29      5     16
D14V3, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CDKN2A MUTATED        4      2      1      0
  CDKN2A WILD-TYPE     38     16     16     42
D14V4, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              4               38
  CLUS_2              2               16
  CLUS_3              1               16
  CLUS_4              0               42
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN2A MUTATED        3      2      2
  CDKN2A WILD-TYPE     51     36     35
D14V5, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              3               51
  CLUS_2              2               36
  CLUS_3              2               35
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN2A MUTATED        3      1      3
  CDKN2A WILD-TYPE     51     30     41
D14V6, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              3               51
  CLUS_2              1               30
  CLUS_3              3               41
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN2A MUTATED        1      5      1
  CDKN2A WILD-TYPE     32     51     40
D14V7, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              1               32
  CLUS_2              5               51
  CLUS_3              1               40
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN2A MUTATED        6      0      1
  CDKN2A WILD-TYPE     83      9     31
D14V8, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              6               83
  CLUS_2              0                9
  CLUS_3              1               31
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN2A MUTATED        0      4      3
  CDKN2A WILD-TYPE     26     45     52
D14V9, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              0               26
  CLUS_2              4               45
  CLUS_3              3               52
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN2A MUTATED        2      4      1
  CDKN2A WILD-TYPE     29     70     24
D14V10, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              2               29
  CLUS_2              4               70
  CLUS_3              1               24

Clustering(15) Variable = KLF5 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  KLF5 MUTATED        0      4      2      1      2      0      1      0
  KLF5 WILD-TYPE      9     37     10      6     20     17     13      5
D15V1, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KLF5 MUTATED        5      4      1
  KLF5 WILD-TYPE     46     49     25
D15V2, multiclass
        clus
vv       KLF5 MUTATED KLF5 WILD-TYPE
  CLUS_1            5             46
  CLUS_2            4             49
  CLUS_3            1             25
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KLF5 MUTATED        4      1      4      1      0
  KLF5 WILD-TYPE     32     27     29      4     17
D15V3, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KLF5 MUTATED        6      0      1      3
  KLF5 WILD-TYPE     36     18     16     39
D15V4, multiclass
        clus
vv       KLF5 MUTATED KLF5 WILD-TYPE
  CLUS_1            6             36
  CLUS_2            0             18
  CLUS_3            1             16
  CLUS_4            3             39
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KLF5 MUTATED        5      3      2
  KLF5 WILD-TYPE     49     35     35
D15V5, multiclass
        clus
vv       KLF5 MUTATED KLF5 WILD-TYPE
  CLUS_1            5             49
  CLUS_2            3             35
  CLUS_3            2             35
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KLF5 MUTATED        5      0      5
  KLF5 WILD-TYPE     49     31     39
D15V6, multiclass
        clus
vv       KLF5 MUTATED KLF5 WILD-TYPE
  CLUS_1            5             49
  CLUS_2            0             31
  CLUS_3            5             39
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KLF5 MUTATED        3      5      2
  KLF5 WILD-TYPE     30     51     39
D15V7, multiclass
        clus
vv       KLF5 MUTATED KLF5 WILD-TYPE
  CLUS_1            3             30
  CLUS_2            5             51
  CLUS_3            2             39
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KLF5 MUTATED        7      0      3
  KLF5 WILD-TYPE     82      9     29
D15V8, multiclass
        clus
vv       KLF5 MUTATED KLF5 WILD-TYPE
  CLUS_1            7             82
  CLUS_2            0              9
  CLUS_3            3             29
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KLF5 MUTATED        3      5      2
  KLF5 WILD-TYPE     23     44     53
D15V9, multiclass
        clus
vv       KLF5 MUTATED KLF5 WILD-TYPE
  CLUS_1            3             23
  CLUS_2            5             44
  CLUS_3            2             53
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KLF5 MUTATED        5      2      3
  KLF5 WILD-TYPE     26     72     22
D15V10, multiclass
        clus
vv       KLF5 MUTATED KLF5 WILD-TYPE
  CLUS_1            5             26
  CLUS_2            2             72
  CLUS_3            3             22

Clustering(16) Variable = ASXL2 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ASXL2 MUTATED        0      2      1      2      2      2      0      0
  ASXL2 WILD-TYPE      9     39     11      5     20     15     14      5
D16V1, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ASXL2 MUTATED        5      2      2
  ASXL2 WILD-TYPE     46     51     24
D16V2, multiclass
        clus
vv       ASXL2 MUTATED ASXL2 WILD-TYPE
  CLUS_1             5              46
  CLUS_2             2              51
  CLUS_3             2              24
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ASXL2 MUTATED        4      1      3      1      0
  ASXL2 WILD-TYPE     32     27     30      4     17
D16V3, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ASXL2 MUTATED        4      0      3      2
  ASXL2 WILD-TYPE     38     18     14     40
D16V4, multiclass
        clus
vv       ASXL2 MUTATED ASXL2 WILD-TYPE
  CLUS_1             4              38
  CLUS_2             0              18
  CLUS_3             3              14
  CLUS_4             2              40
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ASXL2 MUTATED        3      2      4
  ASXL2 WILD-TYPE     51     36     33
D16V5, multiclass
        clus
vv       ASXL2 MUTATED ASXL2 WILD-TYPE
  CLUS_1             3              51
  CLUS_2             2              36
  CLUS_3             4              33
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ASXL2 MUTATED        3      4      2
  ASXL2 WILD-TYPE     51     27     42
D16V6, multiclass
        clus
vv       ASXL2 MUTATED ASXL2 WILD-TYPE
  CLUS_1             3              51
  CLUS_2             4              27
  CLUS_3             2              42
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ASXL2 MUTATED        3      3      3
  ASXL2 WILD-TYPE     30     53     38
D16V7, multiclass
        clus
vv       ASXL2 MUTATED ASXL2 WILD-TYPE
  CLUS_1             3              30
  CLUS_2             3              53
  CLUS_3             3              38
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ASXL2 MUTATED        6      0      3
  ASXL2 WILD-TYPE     83      9     29
D16V8, multiclass
        clus
vv       ASXL2 MUTATED ASXL2 WILD-TYPE
  CLUS_1             6              83
  CLUS_2             0               9
  CLUS_3             3              29
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ASXL2 MUTATED        4      3      2
  ASXL2 WILD-TYPE     22     46     53
D16V9, multiclass
        clus
vv       ASXL2 MUTATED ASXL2 WILD-TYPE
  CLUS_1             4              22
  CLUS_2             3              46
  CLUS_3             2              53
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ASXL2 MUTATED        2      4      3
  ASXL2 WILD-TYPE     29     70     22
D16V10, multiclass
        clus
vv       ASXL2 MUTATED ASXL2 WILD-TYPE
  CLUS_1             2              29
  CLUS_2             4              70
  CLUS_3             3              22

Clustering(17) Variable = TSC1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  TSC1 MUTATED        0      5      0      1      3      0      2      0
  TSC1 WILD-TYPE      9     36     12      6     19     17     12      5
D17V1, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TSC1 MUTATED        6      3      2
  TSC1 WILD-TYPE     45     50     24
D17V2, multiclass
        clus
vv       TSC1 MUTATED TSC1 WILD-TYPE
  CLUS_1            6             45
  CLUS_2            3             50
  CLUS_3            2             24
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TSC1 MUTATED        6      1      2      0      2
  TSC1 WILD-TYPE     30     27     31      5     15
D17V3, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TSC1 MUTATED        7      2      0      2
  TSC1 WILD-TYPE     35     16     17     40
D17V4, multiclass
        clus
vv       TSC1 MUTATED TSC1 WILD-TYPE
  CLUS_1            7             35
  CLUS_2            2             16
  CLUS_3            0             17
  CLUS_4            2             40
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TSC1 MUTATED        6      4      1
  TSC1 WILD-TYPE     48     34     36
D17V5, multiclass
        clus
vv       TSC1 MUTATED TSC1 WILD-TYPE
  CLUS_1            6             48
  CLUS_2            4             34
  CLUS_3            1             36
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TSC1 MUTATED        1      6      4
  TSC1 WILD-TYPE     53     25     40
D17V6, multiclass
        clus
vv       TSC1 MUTATED TSC1 WILD-TYPE
  CLUS_1            1             53
  CLUS_2            6             25
  CLUS_3            4             40
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TSC1 MUTATED        4      3      4
  TSC1 WILD-TYPE     29     53     37
D17V7, multiclass
        clus
vv       TSC1 MUTATED TSC1 WILD-TYPE
  CLUS_1            4             29
  CLUS_2            3             53
  CLUS_3            4             37
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TSC1 MUTATED        7      1      3
  TSC1 WILD-TYPE     82      8     29
D17V8, multiclass
        clus
vv       TSC1 MUTATED TSC1 WILD-TYPE
  CLUS_1            7             82
  CLUS_2            1              8
  CLUS_3            3             29
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TSC1 MUTATED        3      3      5
  TSC1 WILD-TYPE     23     46     50
D17V9, multiclass
        clus
vv       TSC1 MUTATED TSC1 WILD-TYPE
  CLUS_1            3             23
  CLUS_2            3             46
  CLUS_3            5             50
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TSC1 MUTATED        0      8      3
  TSC1 WILD-TYPE     31     66     22
D17V10, multiclass
        clus
vv       TSC1 MUTATED TSC1 WILD-TYPE
  CLUS_1            0             31
  CLUS_2            8             66
  CLUS_3            3             22

Clustering(18) Variable = ERCC2 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ERCC2 MUTATED        1      4      2      1      2      3      3      0
  ERCC2 WILD-TYPE      8     37     10      6     20     14     11      5
D18V1, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ERCC2 MUTATED        8      6      2
  ERCC2 WILD-TYPE     43     47     24
D18V2, multiclass
        clus
vv       ERCC2 MUTATED ERCC2 WILD-TYPE
  CLUS_1             8              43
  CLUS_2             6              47
  CLUS_3             2              24
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ERCC2 MUTATED        3      0      6      1      1
  ERCC2 WILD-TYPE     33     28     27      4     16
D18V3, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ERCC2 MUTATED        3      1      5      2
  ERCC2 WILD-TYPE     39     17     12     40
D18V4, multiclass
        clus
vv       ERCC2 MUTATED ERCC2 WILD-TYPE
  CLUS_1             3              39
  CLUS_2             1              17
  CLUS_3             5              12
  CLUS_4             2              40
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ERCC2 MUTATED        4      4      8
  ERCC2 WILD-TYPE     50     34     29
D18V5, multiclass
        clus
vv       ERCC2 MUTATED ERCC2 WILD-TYPE
  CLUS_1             4              50
  CLUS_2             4              34
  CLUS_3             8              29
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ERCC2 MUTATED       10      3      3
  ERCC2 WILD-TYPE     44     28     41
D18V6, multiclass
        clus
vv       ERCC2 MUTATED ERCC2 WILD-TYPE
  CLUS_1            10              44
  CLUS_2             3              28
  CLUS_3             3              41
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ERCC2 MUTATED        6      8      2
  ERCC2 WILD-TYPE     27     48     39
D18V7, multiclass
        clus
vv       ERCC2 MUTATED ERCC2 WILD-TYPE
  CLUS_1             6              27
  CLUS_2             8              48
  CLUS_3             2              39
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ERCC2 MUTATED        9      1      6
  ERCC2 WILD-TYPE     80      8     26
D18V8, multiclass
        clus
vv       ERCC2 MUTATED ERCC2 WILD-TYPE
  CLUS_1             9              80
  CLUS_2             1               8
  CLUS_3             6              26
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ERCC2 MUTATED        4      6      6
  ERCC2 WILD-TYPE     22     43     49
D18V9, multiclass
        clus
vv       ERCC2 MUTATED ERCC2 WILD-TYPE
  CLUS_1             4              22
  CLUS_2             6              43
  CLUS_3             6              49
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ERCC2 MUTATED        4      9      3
  ERCC2 WILD-TYPE     27     65     22
D18V10, multiclass
        clus
vv       ERCC2 MUTATED ERCC2 WILD-TYPE
  CLUS_1             4              27
  CLUS_2             9              65
  CLUS_3             3              22

Clustering(19) Variable = TXNIP MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  TXNIP MUTATED        1      4      1      1      0      0      1      0
  TXNIP WILD-TYPE      8     37     11      6     22     17     13      5
D19V1, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TXNIP MUTATED        4      3      2
  TXNIP WILD-TYPE     47     50     24
D19V2, multiclass
        clus
vv       TXNIP MUTATED TXNIP WILD-TYPE
  CLUS_1             4              47
  CLUS_2             3              50
  CLUS_3             2              24
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TXNIP MUTATED        2      2      4      0      1
  TXNIP WILD-TYPE     34     26     29      5     16
D19V3, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TXNIP MUTATED        3      1      3      2
  TXNIP WILD-TYPE     39     17     14     40
D19V4, multiclass
        clus
vv       TXNIP MUTATED TXNIP WILD-TYPE
  CLUS_1             3              39
  CLUS_2             1              17
  CLUS_3             3              14
  CLUS_4             2              40
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TXNIP MUTATED        5      3      1
  TXNIP WILD-TYPE     49     35     36
D19V5, multiclass
        clus
vv       TXNIP MUTATED TXNIP WILD-TYPE
  CLUS_1             5              49
  CLUS_2             3              35
  CLUS_3             1              36
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TXNIP MUTATED        2      3      4
  TXNIP WILD-TYPE     52     28     40
D19V6, multiclass
        clus
vv       TXNIP MUTATED TXNIP WILD-TYPE
  CLUS_1             2              52
  CLUS_2             3              28
  CLUS_3             4              40
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TXNIP MUTATED        2      4      3
  TXNIP WILD-TYPE     31     52     38
D19V7, multiclass
        clus
vv       TXNIP MUTATED TXNIP WILD-TYPE
  CLUS_1             2              31
  CLUS_2             4              52
  CLUS_3             3              38
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TXNIP MUTATED        4      2      3
  TXNIP WILD-TYPE     85      7     29
D19V8, multiclass
        clus
vv       TXNIP MUTATED TXNIP WILD-TYPE
  CLUS_1             4              85
  CLUS_2             2               7
  CLUS_3             3              29
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TXNIP MUTATED        3      2      4
  TXNIP WILD-TYPE     23     47     51
D19V9, multiclass
        clus
vv       TXNIP MUTATED TXNIP WILD-TYPE
  CLUS_1             3              23
  CLUS_2             2              47
  CLUS_3             4              51
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TXNIP MUTATED        2      5      2
  TXNIP WILD-TYPE     29     69     23
D19V10, multiclass
        clus
vv       TXNIP MUTATED TXNIP WILD-TYPE
  CLUS_1             2              29
  CLUS_2             5              69
  CLUS_3             2              23

Clustering(20) Variable = EP300 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  EP300 MUTATED        1      8      2      2      1      3      2      2
  EP300 WILD-TYPE      8     33     10      5     21     14     12      3
D20V1, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EP300 MUTATED        9     10      2
  EP300 WILD-TYPE     42     43     24
D20V2, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             9              42
  CLUS_2            10              43
  CLUS_3             2              24
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  EP300 MUTATED        4      3      4      2      3
  EP300 WILD-TYPE     32     25     29      3     14
D20V3, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EP300 MUTATED        6      4      2      4
  EP300 WILD-TYPE     36     14     15     38
D20V4, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             6              36
  CLUS_2             4              14
  CLUS_3             2              15
  CLUS_4             4              38
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EP300 MUTATED        7      6      8
  EP300 WILD-TYPE     47     32     29
D20V5, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             7              47
  CLUS_2             6              32
  CLUS_3             8              29
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EP300 MUTATED       10      4      7
  EP300 WILD-TYPE     44     27     37
D20V6, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1            10              44
  CLUS_2             4              27
  CLUS_3             7              37
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EP300 MUTATED        5     12      4
  EP300 WILD-TYPE     28     44     37
D20V7, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             5              28
  CLUS_2            12              44
  CLUS_3             4              37
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EP300 MUTATED       13      2      6
  EP300 WILD-TYPE     76      7     26
D20V8, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1            13              76
  CLUS_2             2               7
  CLUS_3             6              26
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EP300 MUTATED        3     11      7
  EP300 WILD-TYPE     23     38     48
D20V9, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             3              23
  CLUS_2            11              38
  CLUS_3             7              48
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EP300 MUTATED        7     12      2
  EP300 WILD-TYPE     24     62     23
D20V10, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             7              24
  CLUS_2            12              62
  CLUS_3             2              23

Clustering(21) Variable = RXRA MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  RXRA MUTATED        1      2      1      1      2      3      2      0
  RXRA WILD-TYPE      8     39     11      6     20     14     12      5
D21V1, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RXRA MUTATED        8      4      0
  RXRA WILD-TYPE     43     49     26
D21V2, multiclass
        clus
vv       RXRA MUTATED RXRA WILD-TYPE
  CLUS_1            8             43
  CLUS_2            4             49
  CLUS_3            0             26
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RXRA MUTATED        7      1      2      1      1
  RXRA WILD-TYPE     29     27     31      4     16
D21V3, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RXRA MUTATED        4      2      2      4
  RXRA WILD-TYPE     38     16     15     38
D21V4, multiclass
        clus
vv       RXRA MUTATED RXRA WILD-TYPE
  CLUS_1            4             38
  CLUS_2            2             16
  CLUS_3            2             15
  CLUS_4            4             38
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RXRA MUTATED        6      4      2
  RXRA WILD-TYPE     48     34     35
D21V5, multiclass
        clus
vv       RXRA MUTATED RXRA WILD-TYPE
  CLUS_1            6             48
  CLUS_2            4             34
  CLUS_3            2             35
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RXRA MUTATED        2      5      5
  RXRA WILD-TYPE     52     26     39
D21V6, multiclass
        clus
vv       RXRA MUTATED RXRA WILD-TYPE
  CLUS_1            2             52
  CLUS_2            5             26
  CLUS_3            5             39
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RXRA MUTATED        5      4      3
  RXRA WILD-TYPE     28     52     38
D21V7, multiclass
        clus
vv       RXRA MUTATED RXRA WILD-TYPE
  CLUS_1            5             28
  CLUS_2            4             52
  CLUS_3            3             38
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RXRA MUTATED        6      1      5
  RXRA WILD-TYPE     83      8     27
D21V8, multiclass
        clus
vv       RXRA MUTATED RXRA WILD-TYPE
  CLUS_1            6             83
  CLUS_2            1              8
  CLUS_3            5             27
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RXRA MUTATED        3      4      5
  RXRA WILD-TYPE     23     45     50
D21V9, multiclass
        clus
vv       RXRA MUTATED RXRA WILD-TYPE
  CLUS_1            3             23
  CLUS_2            4             45
  CLUS_3            5             50
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RXRA MUTATED        2      6      4
  RXRA WILD-TYPE     29     68     21
D21V10, multiclass
        clus
vv       RXRA MUTATED RXRA WILD-TYPE
  CLUS_1            2             29
  CLUS_2            6             68
  CLUS_3            4             21

Clustering(22) Variable = FOXA1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  FOXA1 MUTATED        1      1      1      0      0      1      2      1
  FOXA1 WILD-TYPE      8     40     11      7     22     16     12      4
D22V1, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FOXA1 MUTATED        4      2      1
  FOXA1 WILD-TYPE     47     51     25
D22V2, multiclass
        clus
vv       FOXA1 MUTATED FOXA1 WILD-TYPE
  CLUS_1             4              47
  CLUS_2             2              51
  CLUS_3             1              25
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FOXA1 MUTATED        2      2      1      1      1
  FOXA1 WILD-TYPE     34     26     32      4     16
D22V3, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FOXA1 MUTATED        3      0      1      3
  FOXA1 WILD-TYPE     39     18     16     39
D22V4, multiclass
        clus
vv       FOXA1 MUTATED FOXA1 WILD-TYPE
  CLUS_1             3              39
  CLUS_2             0              18
  CLUS_3             1              16
  CLUS_4             3              39
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FOXA1 MUTATED        2      4      1
  FOXA1 WILD-TYPE     52     34     36
D22V5, multiclass
        clus
vv       FOXA1 MUTATED FOXA1 WILD-TYPE
  CLUS_1             2              52
  CLUS_2             4              34
  CLUS_3             1              36
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FOXA1 MUTATED        2      3      2
  FOXA1 WILD-TYPE     52     28     42
D22V6, multiclass
        clus
vv       FOXA1 MUTATED FOXA1 WILD-TYPE
  CLUS_1             2              52
  CLUS_2             3              28
  CLUS_3             2              42
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FOXA1 MUTATED        2      2      3
  FOXA1 WILD-TYPE     31     54     38
D22V7, multiclass
        clus
vv       FOXA1 MUTATED FOXA1 WILD-TYPE
  CLUS_1             2              31
  CLUS_2             2              54
  CLUS_3             3              38
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FOXA1 MUTATED        5      0      2
  FOXA1 WILD-TYPE     84      9     30
D22V8, multiclass
        clus
vv       FOXA1 MUTATED FOXA1 WILD-TYPE
  CLUS_1             5              84
  CLUS_2             0               9
  CLUS_3             2              30
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FOXA1 MUTATED        2      3      2
  FOXA1 WILD-TYPE     24     46     53
D22V9, multiclass
        clus
vv       FOXA1 MUTATED FOXA1 WILD-TYPE
  CLUS_1             2              24
  CLUS_2             3              46
  CLUS_3             2              53
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FOXA1 MUTATED        2      3      2
  FOXA1 WILD-TYPE     29     71     23
D22V10, multiclass
        clus
vv       FOXA1 MUTATED FOXA1 WILD-TYPE
  CLUS_1             2              29
  CLUS_2             3              71
  CLUS_3             2              23

Clustering(23) Variable = PHLDA3 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  PHLDA3 MUTATED        0      1      0      0      1      1      0      1
  PHLDA3 WILD-TYPE      9     40     12      7     21     16     14      4
D23V1, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PHLDA3 MUTATED        1      3      0
  PHLDA3 WILD-TYPE     50     50     26
D23V2, multiclass
        clus
vv       PHLDA3 MUTATED PHLDA3 WILD-TYPE
  CLUS_1              1               50
  CLUS_2              3               50
  CLUS_3              0               26
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PHLDA3 MUTATED        0      1      2      0      0
  PHLDA3 WILD-TYPE     36     27     31      5     17
D23V3, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PHLDA3 MUTATED        0      1      0      2
  PHLDA3 WILD-TYPE     42     17     17     40
D23V4, multiclass
        clus
vv       PHLDA3 MUTATED PHLDA3 WILD-TYPE
  CLUS_1              0               42
  CLUS_2              1               17
  CLUS_3              0               17
  CLUS_4              2               40
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PHLDA3 MUTATED        0      2      2
  PHLDA3 WILD-TYPE     54     36     35
D23V5, multiclass
        clus
vv       PHLDA3 MUTATED PHLDA3 WILD-TYPE
  CLUS_1              0               54
  CLUS_2              2               36
  CLUS_3              2               35
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PHLDA3 MUTATED        3      1      0
  PHLDA3 WILD-TYPE     51     30     44
D23V6, multiclass
        clus
vv       PHLDA3 MUTATED PHLDA3 WILD-TYPE
  CLUS_1              3               51
  CLUS_2              1               30
  CLUS_3              0               44
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PHLDA3 MUTATED        0      2      2
  PHLDA3 WILD-TYPE     33     54     39
D23V7, multiclass
        clus
vv       PHLDA3 MUTATED PHLDA3 WILD-TYPE
  CLUS_1              0               33
  CLUS_2              2               54
  CLUS_3              2               39
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PHLDA3 MUTATED        3      0      1
  PHLDA3 WILD-TYPE     86      9     31
D23V8, multiclass
        clus
vv       PHLDA3 MUTATED PHLDA3 WILD-TYPE
  CLUS_1              3               86
  CLUS_2              0                9
  CLUS_3              1               31
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PHLDA3 MUTATED        0      2      2
  PHLDA3 WILD-TYPE     26     47     53
D23V9, multiclass
        clus
vv       PHLDA3 MUTATED PHLDA3 WILD-TYPE
  CLUS_1              0               26
  CLUS_2              2               47
  CLUS_3              2               53
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PHLDA3 MUTATED        0      4      0
  PHLDA3 WILD-TYPE     31     70     25
D23V10, multiclass
        clus
vv       PHLDA3 MUTATED PHLDA3 WILD-TYPE
  CLUS_1              0               31
  CLUS_2              4               70
  CLUS_3              0               25
> q(save="no")
