[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTKICH-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KICH-TP/10668115/KICH-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KICH-TP/10685686/transformed.cor.cli.txt"

nPatients in clinical file=66, in cluster file=66, common to both=66
[1] "Reduce the number of clustering variables from 5 to 4."
[1]  4 66
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            22             44 
  TP53 MUTATED TP53 WILD-TYPE 
            22             44 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
             6             60 
  PTEN MUTATED PTEN WILD-TYPE 
             6             60 
[1] "PABPC1 MUTATION ANALYSIS"
[1] 3
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               7               59 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               7               59 
[1] "URGCP MUTATION ANALYSIS"
[1] 3
  URGCP MUTATED URGCP WILD-TYPE 
              3              63 
  URGCP MUTATED URGCP WILD-TYPE 
              3              63 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
[1] "CN_CNMF"                     "METHLYATION_CNMF"           
[3] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
[5] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[7] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 8 rows and 66 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=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_MATURE_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "CN_CNMF"                     "METHLYATION_CNMF"           
[3] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
[5] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[7] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 66 columns, 0 survival variables, and 8 non-survival variables.
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=7, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=7, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=7, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        2     14      6
  TP53 WILD-TYPE      3     33      8
D1V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2              3
  CLUS_2           14             33
  CLUS_3            6              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        3     16      3
  TP53 WILD-TYPE     15     19     10
D1V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            3             15
  CLUS_2           16             19
  CLUS_3            3             10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED        6      6      9      1
  TP53 WILD-TYPE     13     16      6      9
D1V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            6             13
  CLUS_2            6             16
  CLUS_3            9              6
  CLUS_4            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  TP53 MUTATED        5      6      1      0      7      3      0
  TP53 WILD-TYPE     14     10      6      6      3      1      4
D1V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            5             14
  CLUS_2            6             10
  CLUS_3            1              6
  CLUS_4            0              6
  CLUS_5            7              3
  CLUS_6            3              1
  CLUS_7            0              4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        5      9      8
  TP53 WILD-TYPE     15     15     14
D1V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            5             15
  CLUS_2            9             15
  CLUS_3            8             14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  TP53 MUTATED        7      5      3      1      1      3      2
  TP53 WILD-TYPE     11      6      9      5      4      2      7
D1V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            7             11
  CLUS_2            5              6
  CLUS_3            3              9
  CLUS_4            1              5
  CLUS_5            1              4
  CLUS_6            3              2
  CLUS_7            2              7
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TP53 MUTATED        5      5      4      3      5
  TP53 WILD-TYPE      5     11     12      7      9
D1V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            5              5
  CLUS_2            5             11
  CLUS_3            4             12
  CLUS_4            3              7
  CLUS_5            5              9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  TP53 MUTATED        7      3      4      0      2      5      1
  TP53 WILD-TYPE      7      5      9      5      7      4      7
D1V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            7              7
  CLUS_2            3              5
  CLUS_3            4              9
  CLUS_4            0              5
  CLUS_5            2              7
  CLUS_6            5              4
  CLUS_7            1              7
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = PTEN MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        2      3      1
  PTEN WILD-TYPE      3     44     13
D2V1, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            2              3
  CLUS_2            3             44
  CLUS_3            1             13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        3      3      0
  PTEN WILD-TYPE     15     32     13
D2V2, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            3             15
  CLUS_2            3             32
  CLUS_3            0             13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PTEN MUTATED        2      1      3      0
  PTEN WILD-TYPE     17     21     12     10
D2V3, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            2             17
  CLUS_2            1             21
  CLUS_3            3             12
  CLUS_4            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  PTEN MUTATED        2      1      0      0      3      0      0
  PTEN WILD-TYPE     17     15      7      6      7      4      4
D2V4, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            2             17
  CLUS_2            1             15
  CLUS_3            0              7
  CLUS_4            0              6
  CLUS_5            3              7
  CLUS_6            0              4
  CLUS_7            0              4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        1      4      1
  PTEN WILD-TYPE     19     20     21
D2V5, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             19
  CLUS_2            4             20
  CLUS_3            1             21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  PTEN MUTATED        5      0      0      0      0      1      0
  PTEN WILD-TYPE     13     11     12      6      5      4      9
D2V6, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            5             13
  CLUS_2            0             11
  CLUS_3            0             12
  CLUS_4            0              6
  CLUS_5            0              5
  CLUS_6            1              4
  CLUS_7            0              9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PTEN MUTATED        4      0      1      0      1
  PTEN WILD-TYPE      6     16     15     10     13
D2V7, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            4              6
  CLUS_2            0             16
  CLUS_3            1             15
  CLUS_4            0             10
  CLUS_5            1             13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  PTEN MUTATED        4      0      0      0      1      1      0
  PTEN WILD-TYPE     10      8     13      5      8      8      8
D2V8, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            4             10
  CLUS_2            0              8
  CLUS_3            0             13
  CLUS_4            0              5
  CLUS_5            1              8
  CLUS_6            1              8
  CLUS_7            0              8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = PABPC1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PABPC1 MUTATED        1      4      2
  PABPC1 WILD-TYPE      4     43     12
D3V1, multiclass
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  CLUS_1              1                4
  CLUS_2              4               43
  CLUS_3              2               12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PABPC1 MUTATED        2      2      3
  PABPC1 WILD-TYPE     16     33     10
D3V2, multiclass
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  CLUS_1              2               16
  CLUS_2              2               33
  CLUS_3              3               10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PABPC1 MUTATED        2      1      1      3
  PABPC1 WILD-TYPE     17     21     14      7
D3V3, multiclass
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  CLUS_1              2               17
  CLUS_2              1               21
  CLUS_3              1               14
  CLUS_4              3                7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  PABPC1 MUTATED        2      1      2      1      1      0      0
  PABPC1 WILD-TYPE     17     15      5      5      9      4      4
D3V4, multiclass
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  CLUS_1              2               17
  CLUS_2              1               15
  CLUS_3              2                5
  CLUS_4              1                5
  CLUS_5              1                9
  CLUS_6              0                4
  CLUS_7              0                4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PABPC1 MUTATED        3      3      1
  PABPC1 WILD-TYPE     17     21     21
D3V5, multiclass
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  CLUS_1              3               17
  CLUS_2              3               21
  CLUS_3              1               21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  PABPC1 MUTATED        2      1      0      1      0      0      3
  PABPC1 WILD-TYPE     16     10     12      5      5      5      6
D3V6, multiclass
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  CLUS_1              2               16
  CLUS_2              1               10
  CLUS_3              0               12
  CLUS_4              1                5
  CLUS_5              0                5
  CLUS_6              0                5
  CLUS_7              3                6
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PABPC1 MUTATED        1      3      1      0      2
  PABPC1 WILD-TYPE      9     13     15     10     12
D3V7, multiclass
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  CLUS_1              1                9
  CLUS_2              3               13
  CLUS_3              1               15
  CLUS_4              0               10
  CLUS_5              2               12
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  PABPC1 MUTATED        1      0      0      1      2      0      3
  PABPC1 WILD-TYPE     13      8     13      4      7      9      5
D3V8, multiclass
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  CLUS_1              1               13
  CLUS_2              0                8
  CLUS_3              0               13
  CLUS_4              1                4
  CLUS_5              2                7
  CLUS_6              0                9
  CLUS_7              3                5
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = URGCP MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  URGCP MUTATED        0      2      1
  URGCP WILD-TYPE      5     45     13
D4V1, multiclass
        clus
vv       URGCP MUTATED URGCP WILD-TYPE
  CLUS_1             0               5
  CLUS_2             2              45
  CLUS_3             1              13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  URGCP MUTATED        1      2      0
  URGCP WILD-TYPE     17     33     13
D4V2, multiclass
        clus
vv       URGCP MUTATED URGCP WILD-TYPE
  CLUS_1             1              17
  CLUS_2             2              33
  CLUS_3             0              13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  URGCP MUTATED        1      1      1      0
  URGCP WILD-TYPE     18     21     14     10
D4V3, multiclass
        clus
vv       URGCP MUTATED URGCP WILD-TYPE
  CLUS_1             1              18
  CLUS_2             1              21
  CLUS_3             1              14
  CLUS_4             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  URGCP MUTATED        1      1      0      0      1      0      0
  URGCP WILD-TYPE     18     15      7      6      9      4      4
D4V4, multiclass
        clus
vv       URGCP MUTATED URGCP WILD-TYPE
  CLUS_1             1              18
  CLUS_2             1              15
  CLUS_3             0               7
  CLUS_4             0               6
  CLUS_5             1               9
  CLUS_6             0               4
  CLUS_7             0               4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  URGCP MUTATED        2      0      1
  URGCP WILD-TYPE     18     24     21
D4V5, multiclass
        clus
vv       URGCP MUTATED URGCP WILD-TYPE
  CLUS_1             2              18
  CLUS_2             0              24
  CLUS_3             1              21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  URGCP MUTATED        1      0      0      1      0      0      1
  URGCP WILD-TYPE     17     11     12      5      5      5      8
D4V6, multiclass
        clus
vv       URGCP MUTATED URGCP WILD-TYPE
  CLUS_1             1              17
  CLUS_2             0              11
  CLUS_3             0              12
  CLUS_4             1               5
  CLUS_5             0               5
  CLUS_6             0               5
  CLUS_7             1               8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  URGCP MUTATED        1      1      0      0      1
  URGCP WILD-TYPE      9     15     16     10     13
D4V7, multiclass
        clus
vv       URGCP MUTATED URGCP WILD-TYPE
  CLUS_1             1               9
  CLUS_2             1              15
  CLUS_3             0              16
  CLUS_4             0              10
  CLUS_5             1              13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  URGCP MUTATED        1      0      0      1      0      1      0
  URGCP WILD-TYPE     13      8     13      4      9      8      8
D4V8, multiclass
        clus
vv       URGCP MUTATED URGCP WILD-TYPE
  CLUS_1             1              13
  CLUS_2             0               8
  CLUS_3             0              13
  CLUS_4             1               4
  CLUS_5             0               9
  CLUS_6             1               8
  CLUS_7             0               8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
