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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/335929/PRAD-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/PRAD-TP/2667029/1.GDAC_mergedClustering.Finished/PRAD-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ONLYSIG", "-oT=PRAD-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=PRAD-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=178, in cluster file=83, common to both=83
[1] 13 83
[1] "NKX3-1 MUTATION ANALYSIS"
[1] 3
  NKX3-1 MUTATED NKX3-1 WILD-TYPE 
               5               78 
  NKX3-1 MUTATED NKX3-1 WILD-TYPE 
               5               78 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
             5             78 
  TP53 MUTATED TP53 WILD-TYPE 
             5             78 
[1] "FRG1 MUTATION ANALYSIS"
[1] 3
  FRG1 MUTATED FRG1 WILD-TYPE 
             4             79 
  FRG1 MUTATED FRG1 WILD-TYPE 
             4             79 
[1] "SPOP MUTATION ANALYSIS"
[1] 3
  SPOP MUTATED SPOP WILD-TYPE 
             4             79 
  SPOP MUTATED SPOP WILD-TYPE 
             4             79 
[1] "YBX1 MUTATION ANALYSIS"
[1] 3
  YBX1 MUTATED YBX1 WILD-TYPE 
             3             80 
  YBX1 MUTATED YBX1 WILD-TYPE 
             3             80 
[1] "CCNF MUTATION ANALYSIS"
[1] 3
  CCNF MUTATED CCNF WILD-TYPE 
             3             80 
  CCNF MUTATED CCNF WILD-TYPE 
             3             80 
[1] "CLSTN1 MUTATION ANALYSIS"
[1] 3
  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
               3               80 
  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
               3               80 
[1] "PRR21 MUTATION ANALYSIS"
[1] 3
  PRR21 MUTATED PRR21 WILD-TYPE 
              4              79 
  PRR21 MUTATED PRR21 WILD-TYPE 
              4              79 
[1] "AGT MUTATION ANALYSIS"
[1] 3
  AGT MUTATED AGT WILD-TYPE 
            3            80 
  AGT MUTATED AGT WILD-TYPE 
            3            80 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               3               80 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               3               80 
[1] "DUSP27 MUTATION ANALYSIS"
[1] 3
  DUSP27 MUTATED DUSP27 WILD-TYPE 
               3               80 
  DUSP27 MUTATED DUSP27 WILD-TYPE 
               3               80 
[1] "OR4D5 MUTATION ANALYSIS"
[1] 3
  OR4D5 MUTATED OR4D5 WILD-TYPE 
              3              80 
  OR4D5 MUTATED OR4D5 WILD-TYPE 
              3              80 
[1] "OR6N1 MUTATION ANALYSIS"
[1] 3
  OR6N1 MUTATED OR6N1 WILD-TYPE 
              3              80 
  OR6N1 MUTATED OR6N1 WILD-TYPE 
              3              80 
[1] "data2feature, selection=ALL"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "MRNASEQ_CNMF"         
[4] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 

Input Data has 6 rows and 83 columns.

Variable 1:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "MRNASEQ_CNMF"         
[4] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 83 columns, 0 survival variables, and 6 non-survival variables.
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, 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

Clustering(1) Variable = NKX3-1 MUTATION ANALYSIS
D1V1, multiclass
        clus
vv       NKX3-1 MUTATED NKX3-1 WILD-TYPE
  CLUS_1              1               10
  CLUS_2              3               42
  CLUS_3              0               26
D1V2, multiclass
        clus
vv       NKX3-1 MUTATED NKX3-1 WILD-TYPE
  CLUS_1              2               18
  CLUS_2              0               26
  CLUS_3              3               34
D1V3, multiclass
        clus
vv       NKX3-1 MUTATED NKX3-1 WILD-TYPE
  CLUS_1              2               20
  CLUS_2              0               22
  CLUS_3              2               26
D1V4, multiclass
        clus
vv       NKX3-1 MUTATED NKX3-1 WILD-TYPE
  CLUS_1              2               16
  CLUS_2              2               23
  CLUS_3              0               29
D1V5, multiclass
        clus
vv       NKX3-1 MUTATED NKX3-1 WILD-TYPE
  CLUS_1              4               35
  CLUS_2              0               35
  CLUS_3              1                7
D1V6, multiclass
        clus
vv       NKX3-1 MUTATED NKX3-1 WILD-TYPE
  CLUS_1              2               11
  CLUS_2              2               59
  CLUS_3              1                7

Clustering(2) Variable = TP53 MUTATION ANALYSIS
D2V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            0             11
  CLUS_2            0             45
  CLUS_3            5             21
D2V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2             18
  CLUS_2            0             26
  CLUS_3            3             34
D2V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1             21
  CLUS_2            0             22
  CLUS_3            3             25
D2V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1             17
  CLUS_2            3             22
  CLUS_3            0             29
D2V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            4             35
  CLUS_2            1             34
  CLUS_3            0              8
D2V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1             12
  CLUS_2            4             57
  CLUS_3            0              8

Clustering(3) Variable = FRG1 MUTATION ANALYSIS
D3V1, multiclass
        clus
vv       FRG1 MUTATED FRG1 WILD-TYPE
  CLUS_1            0             11
  CLUS_2            4             41
  CLUS_3            0             26
D3V2, multiclass
        clus
vv       FRG1 MUTATED FRG1 WILD-TYPE
  CLUS_1            0             20
  CLUS_2            3             23
  CLUS_3            1             36
D3V3, multiclass
        clus
vv       FRG1 MUTATED FRG1 WILD-TYPE
  CLUS_1            0             22
  CLUS_2            2             20
  CLUS_3            1             27
D3V4, multiclass
        clus
vv       FRG1 MUTATED FRG1 WILD-TYPE
  CLUS_1            0             18
  CLUS_2            1             24
  CLUS_3            2             27
D3V5, multiclass
        clus
vv       FRG1 MUTATED FRG1 WILD-TYPE
  CLUS_1            1             38
  CLUS_2            3             32
  CLUS_3            0              8
D3V6, multiclass
        clus
vv       FRG1 MUTATED FRG1 WILD-TYPE
  CLUS_1            0             13
  CLUS_2            4             57
  CLUS_3            0              8

Clustering(4) Variable = SPOP MUTATION ANALYSIS
D4V1, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            3              8
  CLUS_2            0             45
  CLUS_3            1             25
D4V2, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            3             17
  CLUS_2            0             26
  CLUS_3            1             36
D4V3, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            3             19
  CLUS_2            1             21
  CLUS_3            0             28
D4V4, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            2             16
  CLUS_2            0             25
  CLUS_3            2             27
D4V5, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            1             38
  CLUS_2            3             32
  CLUS_3            0              8
D4V6, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            0             13
  CLUS_2            4             57
  CLUS_3            0              8

Clustering(5) Variable = YBX1 MUTATION ANALYSIS
D5V1, multiclass
        clus
vv       YBX1 MUTATED YBX1 WILD-TYPE
  CLUS_1            0             11
  CLUS_2            1             44
  CLUS_3            2             24
D5V2, multiclass
        clus
vv       YBX1 MUTATED YBX1 WILD-TYPE
  CLUS_1            2             18
  CLUS_2            1             25
  CLUS_3            0             37
D5V3, multiclass
        clus
vv       YBX1 MUTATED YBX1 WILD-TYPE
  CLUS_1            2             20
  CLUS_2            1             21
  CLUS_3            0             28
D5V4, multiclass
        clus
vv       YBX1 MUTATED YBX1 WILD-TYPE
  CLUS_1            2             16
  CLUS_2            0             25
  CLUS_3            1             28
D5V5, multiclass
        clus
vv       YBX1 MUTATED YBX1 WILD-TYPE
  CLUS_1            2             37
  CLUS_2            1             34
  CLUS_3            0              8
D5V6, multiclass
        clus
vv       YBX1 MUTATED YBX1 WILD-TYPE
  CLUS_1            1             12
  CLUS_2            2             59
  CLUS_3            0              8

Clustering(6) Variable = CCNF MUTATION ANALYSIS
D6V1, multiclass
        clus
vv       CCNF MUTATED CCNF WILD-TYPE
  CLUS_1            0             11
  CLUS_2            2             43
  CLUS_3            1             25
D6V2, multiclass
        clus
vv       CCNF MUTATED CCNF WILD-TYPE
  CLUS_1            0             20
  CLUS_2            1             25
  CLUS_3            2             35
D6V3, multiclass
        clus
vv       CCNF MUTATED CCNF WILD-TYPE
  CLUS_1            1             21
  CLUS_2            0             22
  CLUS_3            2             26
D6V4, multiclass
        clus
vv       CCNF MUTATED CCNF WILD-TYPE
  CLUS_1            1             17
  CLUS_2            1             24
  CLUS_3            1             28
D6V5, multiclass
        clus
vv       CCNF MUTATED CCNF WILD-TYPE
  CLUS_1            2             37
  CLUS_2            1             34
  CLUS_3            0              8
D6V6, multiclass
        clus
vv       CCNF MUTATED CCNF WILD-TYPE
  CLUS_1            0             13
  CLUS_2            3             58
  CLUS_3            0              8

Clustering(7) Variable = CLSTN1 MUTATION ANALYSIS
D7V1, multiclass
        clus
vv       CLSTN1 MUTATED CLSTN1 WILD-TYPE
  CLUS_1              0               11
  CLUS_2              2               43
  CLUS_3              1               25
D7V2, multiclass
        clus
vv       CLSTN1 MUTATED CLSTN1 WILD-TYPE
  CLUS_1              0               20
  CLUS_2              2               24
  CLUS_3              1               36
D7V3, multiclass
        clus
vv       CLSTN1 MUTATED CLSTN1 WILD-TYPE
  CLUS_1              0               22
  CLUS_2              2               20
  CLUS_3              1               27
D7V4, multiclass
        clus
vv       CLSTN1 MUTATED CLSTN1 WILD-TYPE
  CLUS_1              0               18
  CLUS_2              1               24
  CLUS_3              2               27
D7V5, multiclass
        clus
vv       CLSTN1 MUTATED CLSTN1 WILD-TYPE
  CLUS_1              1               38
  CLUS_2              2               33
  CLUS_3              0                8
D7V6, multiclass
        clus
vv       CLSTN1 MUTATED CLSTN1 WILD-TYPE
  CLUS_1              0               13
  CLUS_2              2               59
  CLUS_3              1                7

Clustering(8) Variable = PRR21 MUTATION ANALYSIS
D8V1, multiclass
        clus
vv       PRR21 MUTATED PRR21 WILD-TYPE
  CLUS_1             0              11
  CLUS_2             1              44
  CLUS_3             2              24
D8V2, multiclass
        clus
vv       PRR21 MUTATED PRR21 WILD-TYPE
  CLUS_1             1              19
  CLUS_2             0              26
  CLUS_3             3              34
D8V3, multiclass
        clus
vv       PRR21 MUTATED PRR21 WILD-TYPE
  CLUS_1             2              20
  CLUS_2             0              22
  CLUS_3             1              27
D8V4, multiclass
        clus
vv       PRR21 MUTATED PRR21 WILD-TYPE
  CLUS_1             2              16
  CLUS_2             1              24
  CLUS_3             0              29
D8V5, multiclass
        clus
vv       PRR21 MUTATED PRR21 WILD-TYPE
  CLUS_1             4              35
  CLUS_2             0              35
  CLUS_3             0               8
D8V6, multiclass
        clus
vv       PRR21 MUTATED PRR21 WILD-TYPE
  CLUS_1             0              13
  CLUS_2             4              57
  CLUS_3             0               8

Clustering(9) Variable = AGT MUTATION ANALYSIS
D9V1, multiclass
        clus
vv       AGT MUTATED AGT WILD-TYPE
  CLUS_1           0            11
  CLUS_2           1            44
  CLUS_3           2            24
D9V2, multiclass
        clus
vv       AGT MUTATED AGT WILD-TYPE
  CLUS_1           1            19
  CLUS_2           1            25
  CLUS_3           1            36
D9V3, multiclass
        clus
vv       AGT MUTATED AGT WILD-TYPE
  CLUS_1           1            21
  CLUS_2           1            21
  CLUS_3           1            27
D9V4, multiclass
        clus
vv       AGT MUTATED AGT WILD-TYPE
  CLUS_1           1            17
  CLUS_2           1            24
  CLUS_3           1            28
D9V5, multiclass
        clus
vv       AGT MUTATED AGT WILD-TYPE
  CLUS_1           2            37
  CLUS_2           1            34
  CLUS_3           0             8
D9V6, multiclass
        clus
vv       AGT MUTATED AGT WILD-TYPE
  CLUS_1           1            12
  CLUS_2           1            60
  CLUS_3           1             7

Clustering(10) Variable = CTNNB1 MUTATION ANALYSIS
D10V1, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              0               11
  CLUS_2              2               43
  CLUS_3              1               25
D10V2, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              1               19
  CLUS_2              0               26
  CLUS_3              2               35
D10V3, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              1               21
  CLUS_2              0               22
  CLUS_3              2               26
D10V4, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              1               17
  CLUS_2              2               23
  CLUS_3              0               29
D10V5, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              3               36
  CLUS_2              0               35
  CLUS_3              0                8
D10V6, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              0               13
  CLUS_2              2               59
  CLUS_3              1                7

Clustering(11) Variable = DUSP27 MUTATION ANALYSIS
D11V1, multiclass
        clus
vv       DUSP27 MUTATED DUSP27 WILD-TYPE
  CLUS_1              0               11
  CLUS_2              3               42
  CLUS_3              0               26
D11V2, multiclass
        clus
vv       DUSP27 MUTATED DUSP27 WILD-TYPE
  CLUS_1              0               20
  CLUS_2              2               24
  CLUS_3              1               36
D11V3, multiclass
[1] "Remove cluster labels:" "DUSP27 MUTATED"        
clus
  DUSP27 MUTATED DUSP27 WILD-TYPE 
               1               71 
      TCGA-CH-5737       TCGA-CH-5738       TCGA-CH-5739       TCGA-CH-5740 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-CH-5741       TCGA-CH-5744       TCGA-CH-5746       TCGA-CH-5748 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-CH-5750       TCGA-CH-5751       TCGA-CH-5752       TCGA-CH-5753 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-CH-5754       TCGA-CH-5762       TCGA-CH-5763       TCGA-CH-5764 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-CH-5765       TCGA-CH-5766       TCGA-CH-5767       TCGA-CH-5768 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-CH-5769       TCGA-CH-5771       TCGA-CH-5772       TCGA-CH-5788 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-CH-5789       TCGA-CH-5790       TCGA-CH-5791       TCGA-CH-5792 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-CH-5794       TCGA-EJ-5494       TCGA-EJ-5495       TCGA-EJ-5496 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-EJ-5497       TCGA-EJ-5498       TCGA-EJ-5499       TCGA-EJ-5501 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-EJ-5504       TCGA-EJ-5505       TCGA-EJ-5507       TCGA-EJ-5508 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-EJ-5509       TCGA-EJ-5510       TCGA-EJ-5511       TCGA-EJ-5512 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-EJ-5514       TCGA-EJ-5515       TCGA-EJ-5516       TCGA-EJ-5517 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-EJ-5518       TCGA-EJ-5519       TCGA-EJ-5521       TCGA-EJ-5522 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-EJ-5524       TCGA-EJ-5525       TCGA-EJ-5526       TCGA-EJ-5527 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-EJ-5530       TCGA-EJ-5531       TCGA-EJ-5532       TCGA-EJ-5542 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-G9-6332       TCGA-G9-6336       TCGA-G9-6348       TCGA-G9-6356 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-G9-6365       TCGA-G9-6371       TCGA-G9-6373       TCGA-G9-6378 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-G9-6384       TCGA-G9-6494       TCGA-G9-6496 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
D11V4, multiclass
[1] "Remove cluster labels:" "DUSP27 MUTATED"        
clus
  DUSP27 MUTATED DUSP27 WILD-TYPE 
               1               71 
      TCGA-CH-5737       TCGA-CH-5738       TCGA-CH-5739       TCGA-CH-5740 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-CH-5741       TCGA-CH-5744       TCGA-CH-5746       TCGA-CH-5748 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-CH-5750       TCGA-CH-5751       TCGA-CH-5752       TCGA-CH-5753 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-CH-5754       TCGA-CH-5762       TCGA-CH-5763       TCGA-CH-5764 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-CH-5765       TCGA-CH-5766       TCGA-CH-5767       TCGA-CH-5768 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-CH-5769       TCGA-CH-5771       TCGA-CH-5772       TCGA-CH-5788 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-CH-5789       TCGA-CH-5790       TCGA-CH-5791       TCGA-CH-5792 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-CH-5794       TCGA-EJ-5494       TCGA-EJ-5495       TCGA-EJ-5496 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-EJ-5497       TCGA-EJ-5498       TCGA-EJ-5499       TCGA-EJ-5501 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-EJ-5504       TCGA-EJ-5505       TCGA-EJ-5507       TCGA-EJ-5508 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-EJ-5509       TCGA-EJ-5510       TCGA-EJ-5511       TCGA-EJ-5512 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-EJ-5514       TCGA-EJ-5515       TCGA-EJ-5516       TCGA-EJ-5517 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-EJ-5518       TCGA-EJ-5519       TCGA-EJ-5521       TCGA-EJ-5522 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-EJ-5524       TCGA-EJ-5525       TCGA-EJ-5526       TCGA-EJ-5527 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-EJ-5530       TCGA-EJ-5531       TCGA-EJ-5532       TCGA-EJ-5542 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-G9-6332       TCGA-G9-6336       TCGA-G9-6348       TCGA-G9-6356 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-G9-6365       TCGA-G9-6371       TCGA-G9-6373       TCGA-G9-6378 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
      TCGA-G9-6384       TCGA-G9-6494       TCGA-G9-6496 
"DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" "DUSP27 WILD-TYPE" 
D11V5, multiclass
        clus
vv       DUSP27 MUTATED DUSP27 WILD-TYPE
  CLUS_1              1               38
  CLUS_2              2               33
  CLUS_3              0                8
D11V6, multiclass
        clus
vv       DUSP27 MUTATED DUSP27 WILD-TYPE
  CLUS_1              0               13
  CLUS_2              2               59
  CLUS_3              1                7

Clustering(12) Variable = OR4D5 MUTATION ANALYSIS
D12V1, multiclass
        clus
vv       OR4D5 MUTATED OR4D5 WILD-TYPE
  CLUS_1             1              10
  CLUS_2             2              43
  CLUS_3             0              26
D12V2, multiclass
        clus
vv       OR4D5 MUTATED OR4D5 WILD-TYPE
  CLUS_1             1              19
  CLUS_2             1              25
  CLUS_3             1              36
D12V3, multiclass
[1] "Remove cluster labels:" "OR4D5 MUTATED"         
clus
  OR4D5 MUTATED OR4D5 WILD-TYPE 
              1              71 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5744      TCGA-CH-5746      TCGA-CH-5748 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-CH-5750      TCGA-CH-5751      TCGA-CH-5752      TCGA-CH-5753 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-CH-5754      TCGA-CH-5762      TCGA-CH-5763      TCGA-CH-5764 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-CH-5765      TCGA-CH-5766      TCGA-CH-5767      TCGA-CH-5768 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-CH-5769      TCGA-CH-5771      TCGA-CH-5772      TCGA-CH-5788 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-CH-5789      TCGA-CH-5790      TCGA-CH-5791      TCGA-CH-5792 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-CH-5794      TCGA-EJ-5494      TCGA-EJ-5495      TCGA-EJ-5496 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-EJ-5497      TCGA-EJ-5498      TCGA-EJ-5499      TCGA-EJ-5501 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-EJ-5504      TCGA-EJ-5507      TCGA-EJ-5508      TCGA-EJ-5509 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-EJ-5510      TCGA-EJ-5511      TCGA-EJ-5512      TCGA-EJ-5514 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-EJ-5515      TCGA-EJ-5516      TCGA-EJ-5517      TCGA-EJ-5518 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-EJ-5519      TCGA-EJ-5521      TCGA-EJ-5522      TCGA-EJ-5524 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-EJ-5525      TCGA-EJ-5526      TCGA-EJ-5527      TCGA-EJ-5530 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-EJ-5531      TCGA-EJ-5532      TCGA-EJ-5542      TCGA-G9-6332 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-G9-6336      TCGA-G9-6348      TCGA-G9-6356      TCGA-G9-6364 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-G9-6365      TCGA-G9-6371      TCGA-G9-6373      TCGA-G9-6378 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-G9-6384      TCGA-G9-6494      TCGA-G9-6496 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
D12V4, multiclass
[1] "Remove cluster labels:" "OR4D5 MUTATED"         
clus
  OR4D5 MUTATED OR4D5 WILD-TYPE 
              1              71 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5744      TCGA-CH-5746      TCGA-CH-5748 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-CH-5750      TCGA-CH-5751      TCGA-CH-5752      TCGA-CH-5753 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-CH-5754      TCGA-CH-5762      TCGA-CH-5763      TCGA-CH-5764 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-CH-5765      TCGA-CH-5766      TCGA-CH-5767      TCGA-CH-5768 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-CH-5769      TCGA-CH-5771      TCGA-CH-5772      TCGA-CH-5788 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-CH-5789      TCGA-CH-5790      TCGA-CH-5791      TCGA-CH-5792 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-CH-5794      TCGA-EJ-5494      TCGA-EJ-5495      TCGA-EJ-5496 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-EJ-5497      TCGA-EJ-5498      TCGA-EJ-5499      TCGA-EJ-5501 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-EJ-5504      TCGA-EJ-5507      TCGA-EJ-5508      TCGA-EJ-5509 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-EJ-5510      TCGA-EJ-5511      TCGA-EJ-5512      TCGA-EJ-5514 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-EJ-5515      TCGA-EJ-5516      TCGA-EJ-5517      TCGA-EJ-5518 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-EJ-5519      TCGA-EJ-5521      TCGA-EJ-5522      TCGA-EJ-5524 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-EJ-5525      TCGA-EJ-5526      TCGA-EJ-5527      TCGA-EJ-5530 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-EJ-5531      TCGA-EJ-5532      TCGA-EJ-5542      TCGA-G9-6332 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-G9-6336      TCGA-G9-6348      TCGA-G9-6356      TCGA-G9-6364 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-G9-6365      TCGA-G9-6371      TCGA-G9-6373      TCGA-G9-6378 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
     TCGA-G9-6384      TCGA-G9-6494      TCGA-G9-6496 
"OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" "OR4D5 WILD-TYPE" 
D12V5, multiclass
        clus
vv       OR4D5 MUTATED OR4D5 WILD-TYPE
  CLUS_1             1              38
  CLUS_2             2              33
  CLUS_3             0               8
D12V6, multiclass
        clus
vv       OR4D5 MUTATED OR4D5 WILD-TYPE
  CLUS_1             0              13
  CLUS_2             3              58
  CLUS_3             0               8

Clustering(13) Variable = OR6N1 MUTATION ANALYSIS
D13V1, multiclass
        clus
vv       OR6N1 MUTATED OR6N1 WILD-TYPE
  CLUS_1             1              10
  CLUS_2             1              44
  CLUS_3             1              25
D13V2, multiclass
        clus
vv       OR6N1 MUTATED OR6N1 WILD-TYPE
  CLUS_1             1              19
  CLUS_2             1              25
  CLUS_3             1              36
D13V3, multiclass
        clus
vv       OR6N1 MUTATED OR6N1 WILD-TYPE
  CLUS_1             1              21
  CLUS_2             1              21
  CLUS_3             1              27
D13V4, multiclass
        clus
vv       OR6N1 MUTATED OR6N1 WILD-TYPE
  CLUS_1             1              17
  CLUS_2             0              25
  CLUS_3             2              27
D13V5, multiclass
        clus
vv       OR6N1 MUTATED OR6N1 WILD-TYPE
  CLUS_1             0              39
  CLUS_2             2              33
  CLUS_3             1               7
D13V6, multiclass
        clus
vv       OR6N1 MUTATED OR6N1 WILD-TYPE
  CLUS_1             1              12
  CLUS_2             2              59
  CLUS_3             0               8
                     V1                      V2                      V3 
              "CN_CNMF"      "METHLYATION_CNMF"          "MRNASEQ_CNMF" 
                     V4                      V5                      V6 
"MRNASEQ_CHIERARCHICAL"           "MIRSEQ_CNMF"  "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
