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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/376875/PRAD-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/PRAD-TP/2907382/1.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=188, 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                9
  CLUS_2              3               41
  CLUS_3              0               28
D1V2, multiclass
        clus
vv       NKX3-1 MUTATED NKX3-1 WILD-TYPE
  CLUS_1              2               18
  CLUS_2              3               36
  CLUS_3              0               24
D1V3, multiclass
        clus
vv       NKX3-1 MUTATED NKX3-1 WILD-TYPE
  CLUS_1              2               19
  CLUS_2              1               28
  CLUS_3              2               30
D1V4, multiclass
        clus
vv       NKX3-1 MUTATED NKX3-1 WILD-TYPE
  CLUS_1              2               14
  CLUS_2              2               38
  CLUS_3              1               25
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             10
  CLUS_2            0             44
  CLUS_3            5             23
D2V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2             18
  CLUS_2            3             36
  CLUS_3            0             24
D2V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2             19
  CLUS_2            0             29
  CLUS_3            3             29
D2V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            0             16
  CLUS_2            5             35
  CLUS_3            0             26
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             10
  CLUS_2            4             40
  CLUS_3            0             28
D3V2, multiclass
        clus
vv       FRG1 MUTATED FRG1 WILD-TYPE
  CLUS_1            0             20
  CLUS_2            2             37
  CLUS_3            2             22
D3V3, multiclass
        clus
vv       FRG1 MUTATED FRG1 WILD-TYPE
  CLUS_1            0             21
  CLUS_2            3             26
  CLUS_3            1             31
D3V4, multiclass
        clus
vv       FRG1 MUTATED FRG1 WILD-TYPE
  CLUS_1            0             16
  CLUS_2            2             38
  CLUS_3            2             24
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            2              8
  CLUS_2            0             44
  CLUS_3            2             26
D4V2, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            3             17
  CLUS_2            1             38
  CLUS_3            0             24
D4V3, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            3             18
  CLUS_2            1             28
  CLUS_3            0             32
D4V4, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            3             13
  CLUS_2            0             40
  CLUS_3            1             25
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             10
  CLUS_2            1             43
  CLUS_3            2             26
D5V2, multiclass
        clus
vv       YBX1 MUTATED YBX1 WILD-TYPE
  CLUS_1            2             18
  CLUS_2            1             38
  CLUS_3            0             24
D5V3, multiclass
        clus
vv       YBX1 MUTATED YBX1 WILD-TYPE
  CLUS_1            1             20
  CLUS_2            1             28
  CLUS_3            1             31
D5V4, multiclass
        clus
vv       YBX1 MUTATED YBX1 WILD-TYPE
  CLUS_1            0             16
  CLUS_2            3             37
  CLUS_3            0             26
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             10
  CLUS_2            2             42
  CLUS_3            1             27
D6V2, multiclass
        clus
vv       CCNF MUTATED CCNF WILD-TYPE
  CLUS_1            0             20
  CLUS_2            2             37
  CLUS_3            1             23
D6V3, multiclass
        clus
vv       CCNF MUTATED CCNF WILD-TYPE
  CLUS_1            1             20
  CLUS_2            0             29
  CLUS_3            2             30
D6V4, multiclass
        clus
vv       CCNF MUTATED CCNF WILD-TYPE
  CLUS_1            1             15
  CLUS_2            2             38
  CLUS_3            0             26
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               10
  CLUS_2              2               42
  CLUS_3              1               27
D7V2, multiclass
        clus
vv       CLSTN1 MUTATED CLSTN1 WILD-TYPE
  CLUS_1              0               20
  CLUS_2              1               38
  CLUS_3              2               22
D7V3, multiclass
        clus
vv       CLSTN1 MUTATED CLSTN1 WILD-TYPE
  CLUS_1              0               21
  CLUS_2              2               27
  CLUS_3              1               31
D7V4, multiclass
        clus
vv       CLSTN1 MUTATED CLSTN1 WILD-TYPE
  CLUS_1              0               16
  CLUS_2              2               38
  CLUS_3              1               25
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              10
  CLUS_2             1              43
  CLUS_3             2              26
D8V2, multiclass
        clus
vv       PRR21 MUTATED PRR21 WILD-TYPE
  CLUS_1             1              19
  CLUS_2             3              36
  CLUS_3             0              24
D8V3, multiclass
        clus
vv       PRR21 MUTATED PRR21 WILD-TYPE
  CLUS_1             1              20
  CLUS_2             1              28
  CLUS_3             2              30
D8V4, multiclass
        clus
vv       PRR21 MUTATED PRR21 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             2              38
  CLUS_3             1              25
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            10
  CLUS_2           1            43
  CLUS_3           2            26
D9V2, multiclass
        clus
vv       AGT MUTATED AGT WILD-TYPE
  CLUS_1           1            19
  CLUS_2           1            38
  CLUS_3           1            23
D9V3, multiclass
        clus
vv       AGT MUTATED AGT WILD-TYPE
  CLUS_1           1            20
  CLUS_2           1            28
  CLUS_3           1            31
D9V4, multiclass
        clus
vv       AGT MUTATED AGT WILD-TYPE
  CLUS_1           1            15
  CLUS_2           1            39
  CLUS_3           1            25
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               10
  CLUS_2              2               42
  CLUS_3              1               27
D10V2, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              1               19
  CLUS_2              2               37
  CLUS_3              0               24
D10V3, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              1               20
  CLUS_2              0               29
  CLUS_3              2               30
D10V4, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              1               15
  CLUS_2              2               38
  CLUS_3              0               26
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               10
  CLUS_2              3               41
  CLUS_3              0               28
D11V2, multiclass
        clus
vv       DUSP27 MUTATED DUSP27 WILD-TYPE
  CLUS_1              0               20
  CLUS_2              1               38
  CLUS_3              2               22
D11V3, multiclass
        clus
vv       DUSP27 MUTATED DUSP27 WILD-TYPE
  CLUS_1              0               21
  CLUS_2              2               27
  CLUS_3              1               31
D11V4, multiclass
        clus
vv       DUSP27 MUTATED DUSP27 WILD-TYPE
  CLUS_1              0               16
  CLUS_2              1               39
  CLUS_3              2               24
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               9
  CLUS_2             2              42
  CLUS_3             0              28
D12V2, multiclass
        clus
vv       OR4D5 MUTATED OR4D5 WILD-TYPE
  CLUS_1             1              19
  CLUS_2             1              38
  CLUS_3             1              23
D12V3, multiclass
        clus
vv       OR4D5 MUTATED OR4D5 WILD-TYPE
  CLUS_1             1              20
  CLUS_2             1              28
  CLUS_3             1              31
D12V4, multiclass
        clus
vv       OR4D5 MUTATED OR4D5 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             1              39
  CLUS_3             1              25
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               9
  CLUS_2             1              43
  CLUS_3             1              27
D13V2, multiclass
        clus
vv       OR6N1 MUTATED OR6N1 WILD-TYPE
  CLUS_1             1              19
  CLUS_2             1              38
  CLUS_3             1              23
D13V3, multiclass
        clus
vv       OR6N1 MUTATED OR6N1 WILD-TYPE
  CLUS_1             1              20
  CLUS_2             1              28
  CLUS_3             1              31
D13V4, multiclass
        clus
vv       OR6N1 MUTATED OR6N1 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             1              39
  CLUS_3             1              25
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")
