[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/22539844/KICH-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KICH-TP/22507963/transformed.cor.cli.txt"

nPatients in clinical file=66, in cluster file=66, common to both=66
[1]  2 66
[1] "AMP PEAK 1(8Q23.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 1(8Q23.3) MUTATED AMP PEAK 1(8Q23.3) WILD-TYPE 
                          19                           47 
  AMP PEAK 1(8Q23.3) MUTATED AMP PEAK 1(8Q23.3) 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] "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 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:'RPPA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'RPPA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_MATURE_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=9,	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 10 non-survival variables.
[1] "* survival variables: "
NULL
[1] "* non-survival variables: "
 [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"
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=7, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=7, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=7, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=9, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK 1(8Q23.3) MUTATION ANALYSIS
                              vv
clus                           CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 1(8Q23.3) MUTATED       14      5      0
  AMP PEAK 1(8Q23.3) WILD-TYPE     24     21      2
D1V1, multiclass
        clus
vv       AMP PEAK 1(8Q23.3) MUTATED AMP PEAK 1(8Q23.3) WILD-TYPE
  CLUS_1                         14                           24
  CLUS_2                          5                           21
  CLUS_3                          0                            2
[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(8Q23.3) MUTATED        3      9      7
  AMP PEAK 1(8Q23.3) WILD-TYPE     16     20     11
D1V2, multiclass
        clus
vv       AMP PEAK 1(8Q23.3) MUTATED AMP PEAK 1(8Q23.3) WILD-TYPE
  CLUS_1                          3                           16
  CLUS_2                          9                           20
  CLUS_3                          7                           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(8Q23.3) MUTATED       10      6      3
  AMP PEAK 1(8Q23.3) WILD-TYPE     16     11     17
D1V3, multiclass
        clus
vv       AMP PEAK 1(8Q23.3) MUTATED AMP PEAK 1(8Q23.3) WILD-TYPE
  CLUS_1                         10                           16
  CLUS_2                          6                           11
  CLUS_3                          3                           17
[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(8Q23.3) MUTATED       12      2      5
  AMP PEAK 1(8Q23.3) WILD-TYPE     17     18      9
D1V4, multiclass
        clus
vv       AMP PEAK 1(8Q23.3) MUTATED AMP PEAK 1(8Q23.3) WILD-TYPE
  CLUS_1                         12                           17
  CLUS_2                          2                           18
  CLUS_3                          5                            9
[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
  AMP PEAK 1(8Q23.3) MUTATED        3      9      1      1      2      0      3
  AMP PEAK 1(8Q23.3) WILD-TYPE     14      6      4      5     12      4      2
D1V5, multiclass
        clus
vv       AMP PEAK 1(8Q23.3) MUTATED AMP PEAK 1(8Q23.3) WILD-TYPE
  CLUS_1                          3                           14
  CLUS_2                          9                            6
  CLUS_3                          1                            4
  CLUS_4                          1                            5
  CLUS_5                          2                           12
  CLUS_6                          0                            4
  CLUS_7                          3                            2
[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 CLUS_6 CLUS_7
  AMP PEAK 1(8Q23.3) MUTATED        3     10      3      1      2      0      0
  AMP PEAK 1(8Q23.3) WILD-TYPE     16      6      4      5      8      4      4
D1V6, multiclass
        clus
vv       AMP PEAK 1(8Q23.3) MUTATED AMP PEAK 1(8Q23.3) 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 CLUS_4
  AMP PEAK 1(8Q23.3) MUTATED        6      7      4      2
  AMP PEAK 1(8Q23.3) WILD-TYPE     12     19      6     10
D1V7, multiclass
        clus
vv       AMP PEAK 1(8Q23.3) MUTATED AMP PEAK 1(8Q23.3) WILD-TYPE
  CLUS_1                          6                           12
  CLUS_2                          7                           19
  CLUS_3                          4                            6
  CLUS_4                          2                           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
  AMP PEAK 1(8Q23.3) MUTATED        2      5      4      1      3      2      2
  AMP PEAK 1(8Q23.3) WILD-TYPE     16      6      8      5      2      3      7
D1V8, multiclass
        clus
vv       AMP PEAK 1(8Q23.3) MUTATED AMP PEAK 1(8Q23.3) 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"
                              vv
clus                           CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AMP PEAK 1(8Q23.3) MUTATED        1      7      3      6
  AMP PEAK 1(8Q23.3) WILD-TYPE      8      6     11      6
D1V9, multiclass
        clus
vv       AMP PEAK 1(8Q23.3) MUTATED AMP PEAK 1(8Q23.3) WILD-TYPE
  CLUS_1                          1                            8
  CLUS_2                          7                            6
  CLUS_3                          3                           11
  CLUS_4                          6                            6
[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
  AMP PEAK 1(8Q23.3) MUTATED        3      5      1      3      1      0      3
  AMP PEAK 1(8Q23.3) WILD-TYPE      2      1      4      5      4      4      3
                              vv
clus                           CLUS_8 CLUS_9
  AMP PEAK 1(8Q23.3) MUTATED        1      0
  AMP PEAK 1(8Q23.3) WILD-TYPE      4      4
D1V10, multiclass
        clus
vv       AMP PEAK 1(8Q23.3) MUTATED AMP PEAK 1(8Q23.3) WILD-TYPE
  CLUS_1                          3                            2
  CLUS_2                          5                            1
  CLUS_3                          1                            4
  CLUS_4                          3                            5
  CLUS_5                          1                            4
  CLUS_6                          0                            4
  CLUS_7                          3                            3
  CLUS_8                          1                            4
  CLUS_9                          0                            4
[1] 9 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       11     12      0
  AMP PEAK 2(15Q22.31) WILD-TYPE     27     14      2
D2V1, multiclass
        clus
vv       AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  CLUS_1                           11                             27
  CLUS_2                           12                             14
  CLUS_3                            0                              2
[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     12      5
  AMP PEAK 2(15Q22.31) WILD-TYPE     13     17     13
D2V2, multiclass
        clus
vv       AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  CLUS_1                            6                             13
  CLUS_2                           12                             17
  CLUS_3                            5                             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
  AMP PEAK 2(15Q22.31) MUTATED       13      4      6
  AMP PEAK 2(15Q22.31) WILD-TYPE     13     13     14
D2V3, multiclass
        clus
vv       AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  CLUS_1                           13                             13
  CLUS_2                            4                             13
  CLUS_3                            6                             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
  AMP PEAK 2(15Q22.31) MUTATED       13      5      5
  AMP PEAK 2(15Q22.31) WILD-TYPE     16     15      9
D2V4, multiclass
        clus
vv       AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  CLUS_1                           13                             16
  CLUS_2                            5                             15
  CLUS_3                            5                              9
[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        5      9      1      1      5      0
  AMP PEAK 2(15Q22.31) WILD-TYPE     12      6      4      5      9      4
                                vv
clus                             CLUS_7
  AMP PEAK 2(15Q22.31) MUTATED        2
  AMP PEAK 2(15Q22.31) WILD-TYPE      3
D2V5, multiclass
        clus
vv       AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  CLUS_1                            5                             12
  CLUS_2                            9                              6
  CLUS_3                            1                              4
  CLUS_4                            1                              5
  CLUS_5                            5                              9
  CLUS_6                            0                              4
  CLUS_7                            2                              3
[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 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
D2V6, 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 CLUS_4
  AMP PEAK 2(15Q22.31) MUTATED        5     10      4      4
  AMP PEAK 2(15Q22.31) WILD-TYPE     13     16      6      8
D2V7, multiclass
        clus
vv       AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  CLUS_1                            5                             13
  CLUS_2                           10                             16
  CLUS_3                            4                              6
  CLUS_4                            4                              8
[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        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
D2V8, 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"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AMP PEAK 2(15Q22.31) MUTATED        2      7      4      5
  AMP PEAK 2(15Q22.31) WILD-TYPE      7      6     10      7
D2V9, multiclass
        clus
vv       AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  CLUS_1                            2                              7
  CLUS_2                            7                              6
  CLUS_3                            4                             10
  CLUS_4                            5                              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
  AMP PEAK 2(15Q22.31) MUTATED        3      4      3      3      1      0
  AMP PEAK 2(15Q22.31) WILD-TYPE      2      2      2      5      4      4
                                vv
clus                             CLUS_7 CLUS_8 CLUS_9
  AMP PEAK 2(15Q22.31) MUTATED        2      2      0
  AMP PEAK 2(15Q22.31) WILD-TYPE      4      3      4
D2V10, multiclass
        clus
vv       AMP PEAK 2(15Q22.31) MUTATED AMP PEAK 2(15Q22.31) WILD-TYPE
  CLUS_1                            3                              2
  CLUS_2                            4                              2
  CLUS_3                            3                              2
  CLUS_4                            3                              5
  CLUS_5                            1                              4
  CLUS_6                            0                              4
  CLUS_7                            2                              4
  CLUS_8                            2                              3
  CLUS_9                            0                              4
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
