[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/15095894/KICH-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KICH-TP/15084590/transformed.cor.cli.txt"

nPatients in clinical file=66, in cluster file=66, common to both=66
[1]  2 66
[1] "AMP PEAK 1(8Q11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE 
                           19                            47 
  AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE 
                           19                            47 
[1] "AMP PEAK 2(15Q22.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE 
                            23                             43 
  AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE 
                            23                             43 
[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=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
NULL
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 66 columns, 0 survival variables, and 8 non-survival variables.
[1] "* survival variables: "
NULL
[1] "* non-survival variables: "
[1] "CN_CNMF"                     "METHLYATION_CNMF"           
[3] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
[5] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[7] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
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=2, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=8, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK 1(8Q11.23) MUTATION ANALYSIS
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 1(8Q11.23) MUTATED        0     16      3
  AMP PEAK 1(8Q11.23) WILD-TYPE      5     31     11
D1V1, multiclass
        clus
vv       AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE
  CLUS_1                           0                             5
  CLUS_2                          16                            31
  CLUS_3                           3                            11
[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
  AMP PEAK 1(8Q11.23) MUTATED        4     10      5
  AMP PEAK 1(8Q11.23) WILD-TYPE     14     25      8
D1V2, multiclass
        clus
vv       AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE
  CLUS_1                           4                            14
  CLUS_2                          10                            25
  CLUS_3                           5                             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 CLUS_4
  AMP PEAK 1(8Q11.23) MUTATED        3     13      2      1
  AMP PEAK 1(8Q11.23) WILD-TYPE     16      9     13      9
D1V3, multiclass
        clus
vv       AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE
  CLUS_1                           3                            16
  CLUS_2                          13                             9
  CLUS_3                           2                            13
  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
  AMP PEAK 1(8Q11.23) MUTATED        3     10      3      1      2      0
  AMP PEAK 1(8Q11.23) WILD-TYPE     16      6      4      5      8      4
                               vv
clus                            CLUS_7
  AMP PEAK 1(8Q11.23) MUTATED        0
  AMP PEAK 1(8Q11.23) WILD-TYPE      4
D1V4, multiclass
        clus
vv       AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE
  CLUS_1                           3                            16
  CLUS_2                          10                             6
  CLUS_3                           3                             4
  CLUS_4                           1                             5
  CLUS_5                           2                             8
  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
  AMP PEAK 1(8Q11.23) MUTATED        6      7      6
  AMP PEAK 1(8Q11.23) WILD-TYPE     14     17     16
D1V5, multiclass
        clus
vv       AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE
  CLUS_1                           6                            14
  CLUS_2                           7                            17
  CLUS_3                           6                            16
[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
  AMP PEAK 1(8Q11.23) MUTATED        2      5      4      1      3      2
  AMP PEAK 1(8Q11.23) WILD-TYPE     16      6      8      5      2      3
                               vv
clus                            CLUS_7
  AMP PEAK 1(8Q11.23) MUTATED        2
  AMP PEAK 1(8Q11.23) WILD-TYPE      7
D1V6, multiclass
        clus
vv       AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE
  CLUS_1                           2                            16
  CLUS_2                           5                             6
  CLUS_3                           4                             8
  CLUS_4                           1                             5
  CLUS_5                           3                             2
  CLUS_6                           2                             3
  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"
D1V7, binary
                               cls
clus                             0  1
  AMP PEAK 1(8Q11.23) MUTATED    5 12
  AMP PEAK 1(8Q11.23) WILD-TYPE 14 17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 1(8Q11.23) MUTATED      5   12
  AMP PEAK 1(8Q11.23) WILD-TYPE   14   17
        clus
vv       AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE
  CLUS_1                           5                            14
  CLUS_2                          12                            17
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  AMP PEAK 1(8Q11.23) MUTATED        4      5      1      3      0      3
  AMP PEAK 1(8Q11.23) WILD-TYPE      6      1      4      5      4      3
                               vv
clus                            CLUS_7 CLUS_8
  AMP PEAK 1(8Q11.23) MUTATED        1      0
  AMP PEAK 1(8Q11.23) WILD-TYPE      4      4
D1V8, multiclass
        clus
vv       AMP PEAK 1(8Q11.23) MUTATED AMP PEAK 1(8Q11.23) WILD-TYPE
  CLUS_1                           4                             6
  CLUS_2                           5                             1
  CLUS_3                           1                             4
  CLUS_4                           3                             5
  CLUS_5                           0                             4
  CLUS_6                           3                             3
  CLUS_7                           1                             4
  CLUS_8                           0                             4
[1] 8 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 = AMP PEAK 2(15Q22.31) MUTATION ANALYSIS
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 2(15Q22.31) MUTATED        0     15      8
  AMP PEAK 2(15Q22.31) WILD-TYPE      5     32      6
D2V1, multiclass
        clus
vv       AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  CLUS_1                            0                              5
  CLUS_2                           15                             32
  CLUS_3                            8                              6
[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
  AMP PEAK 2(15Q22.31) MUTATED        6     14      3
  AMP PEAK 2(15Q22.31) WILD-TYPE     12     21     10
D2V2, multiclass
        clus
vv       AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  CLUS_1                            6                             12
  CLUS_2                           14                             21
  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
  AMP PEAK 2(15Q22.31) MUTATED        5     13      5      0
  AMP PEAK 2(15Q22.31) WILD-TYPE     14      9     10     10
D2V3, multiclass
        clus
vv       AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  CLUS_1                            5                             14
  CLUS_2                           13                              9
  CLUS_3                            5                             10
  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
  AMP PEAK 2(15Q22.31) MUTATED        5     10      2      1      4      1
  AMP PEAK 2(15Q22.31) WILD-TYPE     14      6      5      5      6      3
                                vv
clus                             CLUS_7
  AMP PEAK 2(15Q22.31) MUTATED        0
  AMP PEAK 2(15Q22.31) WILD-TYPE      4
D2V4, multiclass
        clus
vv       AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  CLUS_1                            5                             14
  CLUS_2                           10                              6
  CLUS_3                            2                              5
  CLUS_4                            1                              5
  CLUS_5                            4                              6
  CLUS_6                            1                              3
  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
  AMP PEAK 2(15Q22.31) MUTATED        5     10      8
  AMP PEAK 2(15Q22.31) WILD-TYPE     15     14     14
D2V5, multiclass
        clus
vv       AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  CLUS_1                            5                             15
  CLUS_2                           10                             14
  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
  AMP PEAK 2(15Q22.31) MUTATED        4      5      5      2      3      3
  AMP PEAK 2(15Q22.31) WILD-TYPE     14      6      7      4      2      2
                                vv
clus                             CLUS_7
  AMP PEAK 2(15Q22.31) MUTATED        1
  AMP PEAK 2(15Q22.31) WILD-TYPE      8
D2V6, multiclass
        clus
vv       AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  CLUS_1                            4                             14
  CLUS_2                            5                              6
  CLUS_3                            5                              7
  CLUS_4                            2                              4
  CLUS_5                            3                              2
  CLUS_6                            3                              2
  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"
D2V7, binary
                                cls
clus                              0  1
  AMP PEAK 2(15Q22.31) MUTATED    6 12
  AMP PEAK 2(15Q22.31) WILD-TYPE 13 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 2(15Q22.31) MUTATED      6   12
  AMP PEAK 2(15Q22.31) WILD-TYPE   13   17
        clus
vv       AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  CLUS_1                            6                             13
  CLUS_2                           12                             17
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  AMP PEAK 2(15Q22.31) MUTATED        4      4      3      3      0      2
  AMP PEAK 2(15Q22.31) WILD-TYPE      6      2      2      5      4      4
                                vv
clus                             CLUS_7 CLUS_8
  AMP PEAK 2(15Q22.31) MUTATED        2      0
  AMP PEAK 2(15Q22.31) WILD-TYPE      3      4
D2V8, multiclass
        clus
vv       AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  CLUS_1                            4                              6
  CLUS_2                            4                              2
  CLUS_3                            3                              2
  CLUS_4                            3                              5
  CLUS_5                            0                              4
  CLUS_6                            2                              4
  CLUS_7                            2                              3
  CLUS_8                            0                              4
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
