[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/22569433/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 11 to 8."
[1]  8 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] "ZNF814 MUTATION ANALYSIS"
[1] 3
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               3               63 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               3               63 
[1] "CDC27 MUTATION ANALYSIS"
[1] 3
  CDC27 MUTATED CDC27 WILD-TYPE 
              6              60 
  CDC27 MUTATED CDC27 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] "AMAC1L3 MUTATION ANALYSIS"
[1] 3
  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE 
                5                61 
  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE 
                5                61 
[1] "GFM1 MUTATION ANALYSIS"
[1] 3
  GFM1 MUTATED GFM1 WILD-TYPE 
             3             63 
  GFM1 MUTATED GFM1 WILD-TYPE 
             3             63 
[1] "PABPC3 MUTATION ANALYSIS"
[1] 3
  PABPC3 MUTATED PABPC3 WILD-TYPE 
               7               59 
  PABPC3 MUTATED PABPC3 WILD-TYPE 
               7               59 
[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 = TP53 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       11     11      0
  TP53 WILD-TYPE     27     15      2
D1V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           11             27
  CLUS_2           11             15
  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
  TP53 MUTATED        4     14      4
  TP53 WILD-TYPE     15     15     14
D1V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            4             15
  CLUS_2           14             15
  CLUS_3            4             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
  TP53 MUTATED       12      6      4
  TP53 WILD-TYPE     14     11     16
D1V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           12             14
  CLUS_2            6             11
  CLUS_3            4             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
  TP53 MUTATED       14      3      5
  TP53 WILD-TYPE     15     17      9
D1V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           14             15
  CLUS_2            3             17
  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
  TP53 MUTATED        4      6      1      0      9      0      2
  TP53 WILD-TYPE     13      9      4      6      5      4      3
D1V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            4             13
  CLUS_2            6              9
  CLUS_3            1              4
  CLUS_4            0              6
  CLUS_5            9              5
  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 CLUS_7
  TP53 MUTATED        5      6      1      0      7      3      0
  TP53 WILD-TYPE     14     10      6      6      3      1      4
D1V6, 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 CLUS_4
  TP53 MUTATED        5      9      4      4
  TP53 WILD-TYPE     13     17      6      8
D1V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            5             13
  CLUS_2            9             17
  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 CLUS_7
  TP53 MUTATED        7      5      3      1      1      3      2
  TP53 WILD-TYPE     11      6      9      5      4      2      7
D1V8, 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
  TP53 MUTATED        3      4      7      4
  TP53 WILD-TYPE      6      9      7      8
D1V9, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            3              6
  CLUS_2            4              9
  CLUS_3            7              7
  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 CLUS_7 CLUS_8 CLUS_9
  TP53 MUTATED        1      3      3      2      2      1      3      3      0
  TP53 WILD-TYPE      4      3      2      6      3      3      3      2      4
D1V10, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1              4
  CLUS_2            3              3
  CLUS_3            3              2
  CLUS_4            2              6
  CLUS_5            2              3
  CLUS_6            1              3
  CLUS_7            3              3
  CLUS_8            3              2
  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 = PTEN MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        3      3      0
  PTEN WILD-TYPE     35     23      2
D2V1, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            3             35
  CLUS_2            3             23
  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
  PTEN MUTATED        3      3      0
  PTEN WILD-TYPE     16     26     18
D2V2, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            3             16
  CLUS_2            3             26
  CLUS_3            0             18
[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      2      0
  PTEN WILD-TYPE     23     15     20
D2V3, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            3             23
  CLUS_2            2             15
  CLUS_3            0             20
[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      1      1
  PTEN WILD-TYPE     26     19     13
D2V4, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            3             26
  CLUS_2            1             19
  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 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  PTEN MUTATED        2      0      0      0      3      0      1
  PTEN WILD-TYPE     15     15      5      6     11      4      4
D2V5, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            2             15
  CLUS_2            0             15
  CLUS_3            0              5
  CLUS_4            0              6
  CLUS_5            3             11
  CLUS_6            0              4
  CLUS_7            1              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 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
D2V6, 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 CLUS_4
  PTEN MUTATED        1      4      1      0
  PTEN WILD-TYPE     17     22      9     12
D2V7, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             17
  CLUS_2            4             22
  CLUS_3            1              9
  CLUS_4            0             12
[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        5      0      0      0      0      1      0
  PTEN WILD-TYPE     13     11     12      6      5      4      9
D2V8, 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
  PTEN MUTATED        4      0      1      0
  PTEN WILD-TYPE      5     13     13     12
D2V9, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            4              5
  CLUS_2            0             13
  CLUS_3            1             13
  CLUS_4            0             12
[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 CLUS_8 CLUS_9
  PTEN MUTATED        3      0      1      0      0      0      0      1      0
  PTEN WILD-TYPE      2      6      4      8      5      4      6      4      4
D2V10, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            3              2
  CLUS_2            0              6
  CLUS_3            1              4
  CLUS_4            0              8
  CLUS_5            0              5
  CLUS_6            0              4
  CLUS_7            0              6
  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(3) Variable = ZNF814 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF814 MUTATED        1      2      0
  ZNF814 WILD-TYPE     37     24      2
D3V1, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              1               37
  CLUS_2              2               24
  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
  ZNF814 MUTATED        1      0      2
  ZNF814 WILD-TYPE     18     29     16
D3V2, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              1               18
  CLUS_2              0               29
  CLUS_3              2               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
  ZNF814 MUTATED        1      1      1
  ZNF814 WILD-TYPE     25     16     19
D3V3, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              1               25
  CLUS_2              1               16
  CLUS_3              1               19
[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
  ZNF814 MUTATED        1      1      1
  ZNF814 WILD-TYPE     28     19     13
D3V4, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              1               28
  CLUS_2              1               19
  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 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  ZNF814 MUTATED        0      1      0      2      0      0      0
  ZNF814 WILD-TYPE     17     14      5      4     14      4      5
D3V5, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              0               17
  CLUS_2              1               14
  CLUS_3              0                5
  CLUS_4              2                4
  CLUS_5              0               14
  CLUS_6              0                4
  CLUS_7              0                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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  ZNF814 MUTATED        0      1      0      2      0      0      0
  ZNF814 WILD-TYPE     19     15      7      4     10      4      4
D3V6, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              0               19
  CLUS_2              1               15
  CLUS_3              0                7
  CLUS_4              2                4
  CLUS_5              0               10
  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
  ZNF814 MUTATED        2      0      0      1
  ZNF814 WILD-TYPE     16     26     10     11
D3V7, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              2               16
  CLUS_2              0               26
  CLUS_3              0               10
  CLUS_4              1               11
[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
  ZNF814 MUTATED        0      0      1      0      1      0      1
  ZNF814 WILD-TYPE     18     11     11      6      4      5      8
D3V8, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              0               18
  CLUS_2              0               11
  CLUS_3              1               11
  CLUS_4              0                6
  CLUS_5              1                4
  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
  ZNF814 MUTATED        0      0      0      2
  ZNF814 WILD-TYPE      9     13     14     10
D3V9, multiclass
[1] "Remove cluster labels:" "ZNF814 MUTATED"        
clus
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               2               46 
      TCGA-KL-8323       TCGA-KL-8324       TCGA-KL-8327       TCGA-KL-8328 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KL-8331       TCGA-KL-8332       TCGA-KL-8334       TCGA-KL-8335 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KL-8336       TCGA-KL-8338       TCGA-KL-8339       TCGA-KL-8340 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KL-8341       TCGA-KL-8342       TCGA-KL-8343       TCGA-KL-8345 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KM-8438       TCGA-KM-8439       TCGA-KM-8441       TCGA-KM-8442 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KM-8639       TCGA-KN-8418       TCGA-KN-8419       TCGA-KN-8422 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KN-8423       TCGA-KN-8424       TCGA-KN-8426       TCGA-KN-8427 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KN-8428       TCGA-KN-8429       TCGA-KN-8430       TCGA-KN-8431 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KN-8432       TCGA-KN-8433       TCGA-KN-8434       TCGA-KN-8436 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KN-8437       TCGA-KO-8404       TCGA-KO-8405       TCGA-KO-8408 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KO-8409       TCGA-KO-8410       TCGA-KO-8413       TCGA-KO-8415 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KO-8416       TCGA-KO-8417 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ZNF814 MUTATED        0      0      0      0      0      0      1      1
  ZNF814 WILD-TYPE      5      6      5      8      5      4      5      4
                  vv
clus               CLUS_9
  ZNF814 MUTATED        0
  ZNF814 WILD-TYPE      4
D3V10, multiclass
[1] "Remove cluster labels:" "ZNF814 MUTATED"        
clus
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               2               46 
      TCGA-KL-8323       TCGA-KL-8324       TCGA-KL-8327       TCGA-KL-8328 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KL-8331       TCGA-KL-8332       TCGA-KL-8334       TCGA-KL-8335 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KL-8336       TCGA-KL-8338       TCGA-KL-8339       TCGA-KL-8340 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KL-8341       TCGA-KL-8342       TCGA-KL-8343       TCGA-KL-8345 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KM-8438       TCGA-KM-8439       TCGA-KM-8441       TCGA-KM-8442 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KM-8639       TCGA-KN-8418       TCGA-KN-8419       TCGA-KN-8422 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KN-8423       TCGA-KN-8424       TCGA-KN-8426       TCGA-KN-8427 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KN-8428       TCGA-KN-8429       TCGA-KN-8430       TCGA-KN-8431 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KN-8432       TCGA-KN-8433       TCGA-KN-8434       TCGA-KN-8436 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KN-8437       TCGA-KO-8404       TCGA-KO-8405       TCGA-KO-8408 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KO-8409       TCGA-KO-8410       TCGA-KO-8413       TCGA-KO-8415 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KO-8416       TCGA-KO-8417 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 

Clustering(4) Variable = CDC27 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CDC27 MUTATED        4      2      0
  CDC27 WILD-TYPE     34     24      2
D4V1, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             4              34
  CLUS_2             2              24
  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
  CDC27 MUTATED        2      3      1
  CDC27 WILD-TYPE     17     26     17
D4V2, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             2              17
  CLUS_2             3              26
  CLUS_3             1              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
  CDC27 MUTATED        4      1      1
  CDC27 WILD-TYPE     22     16     19
D4V3, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             4              22
  CLUS_2             1              16
  CLUS_3             1              19
[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
  CDC27 MUTATED        4      1      1
  CDC27 WILD-TYPE     25     19     13
D4V4, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             4              25
  CLUS_2             1              19
  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 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  CDC27 MUTATED        1      4      0      0      0      0      1
  CDC27 WILD-TYPE     16     11      5      6     14      4      4
D4V5, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             1              16
  CLUS_2             4              11
  CLUS_3             0               5
  CLUS_4             0               6
  CLUS_5             0              14
  CLUS_6             0               4
  CLUS_7             1               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 CLUS_5 CLUS_6 CLUS_7
  CDC27 MUTATED        1      4      1      0      0      0      0
  CDC27 WILD-TYPE     18     12      6      6     10      4      4
D4V6, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             1              18
  CLUS_2             4              12
  CLUS_3             1               6
  CLUS_4             0               6
  CLUS_5             0              10
  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
  CDC27 MUTATED        2      2      0      2
  CDC27 WILD-TYPE     16     24     10     10
D4V7, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             2              16
  CLUS_2             2              24
  CLUS_3             0              10
  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
  CDC27 MUTATED        1      1      2      0      0      1      1
  CDC27 WILD-TYPE     17     10     10      6      5      4      8
D4V8, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             1              17
  CLUS_2             1              10
  CLUS_3             2              10
  CLUS_4             0               6
  CLUS_5             0               5
  CLUS_6             1               4
  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
  CDC27 MUTATED        0      2      1      1
  CDC27 WILD-TYPE      9     11     13     11
D4V9, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             2              11
  CLUS_3             1              13
  CLUS_4             1              11
[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 CLUS_8
  CDC27 MUTATED        0      2      0      1      0      0      1      0
  CDC27 WILD-TYPE      5      4      5      7      5      4      5      5
                 vv
clus              CLUS_9
  CDC27 MUTATED        0
  CDC27 WILD-TYPE      4
D4V10, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             0               5
  CLUS_2             2               4
  CLUS_3             0               5
  CLUS_4             1               7
  CLUS_5             0               5
  CLUS_6             0               4
  CLUS_7             1               5
  CLUS_8             0               5
  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(5) Variable = PABPC1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PABPC1 MUTATED        4      3      0
  PABPC1 WILD-TYPE     34     23      2
D5V1, multiclass
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  CLUS_1              4               34
  CLUS_2              3               23
  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
  PABPC1 MUTATED        2      2      3
  PABPC1 WILD-TYPE     17     27     15
D5V2, multiclass
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  CLUS_1              2               17
  CLUS_2              2               27
  CLUS_3              3               15
[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        4      2      1
  PABPC1 WILD-TYPE     22     15     19
D5V3, multiclass
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  CLUS_1              4               22
  CLUS_2              2               15
  CLUS_3              1               19
[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        4      1      2
  PABPC1 WILD-TYPE     25     19     12
D5V4, multiclass
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  CLUS_1              4               25
  CLUS_2              1               19
  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 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  PABPC1 MUTATED        2      1      0      1      1      0      2
  PABPC1 WILD-TYPE     15     14      5      5     13      4      3
D5V5, multiclass
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  CLUS_1              2               15
  CLUS_2              1               14
  CLUS_3              0                5
  CLUS_4              1                5
  CLUS_5              1               13
  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 CLUS_7
  PABPC1 MUTATED        2      1      2      1      1      0      0
  PABPC1 WILD-TYPE     17     15      5      5      9      4      4
D5V6, 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 CLUS_4
  PABPC1 MUTATED        2      4      0      1
  PABPC1 WILD-TYPE     16     22     10     11
D5V7, multiclass
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  CLUS_1              2               16
  CLUS_2              4               22
  CLUS_3              0               10
  CLUS_4              1               11
[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      0      1      0      0      3
  PABPC1 WILD-TYPE     16     10     12      5      5      5      6
D5V8, 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
  PABPC1 MUTATED        0      1      1      2
  PABPC1 WILD-TYPE      9     12     13     10
D5V9, multiclass
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  CLUS_1              0                9
  CLUS_2              1               12
  CLUS_3              1               13
  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 CLUS_8
  PABPC1 MUTATED        0      0      1      0      0      0      2      1
  PABPC1 WILD-TYPE      5      6      4      8      5      4      4      4
                  vv
clus               CLUS_9
  PABPC1 MUTATED        0
  PABPC1 WILD-TYPE      4
D5V10, multiclass
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  CLUS_1              0                5
  CLUS_2              0                6
  CLUS_3              1                4
  CLUS_4              0                8
  CLUS_5              0                5
  CLUS_6              0                4
  CLUS_7              2                4
  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(6) Variable = AMAC1L3 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  AMAC1L3 MUTATED        3      2      0
  AMAC1L3 WILD-TYPE     35     24      2
D6V1, multiclass
        clus
vv       AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  CLUS_1               3                35
  CLUS_2               2                24
  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
  AMAC1L3 MUTATED        0      4      1
  AMAC1L3 WILD-TYPE     19     25     17
D6V2, multiclass
        clus
vv       AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  CLUS_1               0                19
  CLUS_2               4                25
  CLUS_3               1                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
  AMAC1L3 MUTATED        2      0      2
  AMAC1L3 WILD-TYPE     24     17     18
D6V3, multiclass
        clus
vv       AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  CLUS_1               2                24
  CLUS_2               0                17
  CLUS_3               2                18
[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
  AMAC1L3 MUTATED        2      2      0
  AMAC1L3 WILD-TYPE     27     18     14
D6V4, multiclass
        clus
vv       AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  CLUS_1               2                27
  CLUS_2               2                18
  CLUS_3               0                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
  AMAC1L3 MUTATED        0      1      0      1      3      0      0
  AMAC1L3 WILD-TYPE     17     14      5      5     11      4      5
D6V5, multiclass
        clus
vv       AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  CLUS_1               0                17
  CLUS_2               1                14
  CLUS_3               0                 5
  CLUS_4               1                 5
  CLUS_5               3                11
  CLUS_6               0                 4
  CLUS_7               0                 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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  AMAC1L3 MUTATED        0      1      0      1      1      2      0
  AMAC1L3 WILD-TYPE     19     15      7      5      9      2      4
D6V6, multiclass
        clus
vv       AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  CLUS_1               0                19
  CLUS_2               1                15
  CLUS_3               0                 7
  CLUS_4               1                 5
  CLUS_5               1                 9
  CLUS_6               2                 2
  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
  AMAC1L3 MUTATED        2      1      0      2
  AMAC1L3 WILD-TYPE     16     25     10     10
D6V7, multiclass
        clus
vv       AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  CLUS_1               2                16
  CLUS_2               1                25
  CLUS_3               0                10
  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
  AMAC1L3 MUTATED        0      2      1      2      0      0      0
  AMAC1L3 WILD-TYPE     18      9     11      4      5      5      9
D6V8, multiclass
        clus
vv       AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  CLUS_1               0                18
  CLUS_2               2                 9
  CLUS_3               1                11
  CLUS_4               2                 4
  CLUS_5               0                 5
  CLUS_6               0                 5
  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
  AMAC1L3 MUTATED        0      1      1      1
  AMAC1L3 WILD-TYPE      9     12     13     11
D6V9, multiclass
        clus
vv       AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               1                12
  CLUS_3               1                13
  CLUS_4               1                11
[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 CLUS_8
  AMAC1L3 MUTATED        0      0      1      0      0      0      1      1
  AMAC1L3 WILD-TYPE      5      6      4      8      5      4      5      4
                   vv
clus                CLUS_9
  AMAC1L3 MUTATED        0
  AMAC1L3 WILD-TYPE      4
D6V10, multiclass
        clus
vv       AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  CLUS_1               0                 5
  CLUS_2               0                 6
  CLUS_3               1                 4
  CLUS_4               0                 8
  CLUS_5               0                 5
  CLUS_6               0                 4
  CLUS_7               1                 5
  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(7) Variable = GFM1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GFM1 MUTATED        2      1      0
  GFM1 WILD-TYPE     36     25      2
D7V1, multiclass
        clus
vv       GFM1 MUTATED GFM1 WILD-TYPE
  CLUS_1            2             36
  CLUS_2            1             25
  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
  GFM1 MUTATED        1      2      0
  GFM1 WILD-TYPE     18     27     18
D7V2, multiclass
        clus
vv       GFM1 MUTATED GFM1 WILD-TYPE
  CLUS_1            1             18
  CLUS_2            2             27
  CLUS_3            0             18
[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
  GFM1 MUTATED        2      1      0
  GFM1 WILD-TYPE     24     16     20
D7V3, multiclass
        clus
vv       GFM1 MUTATED GFM1 WILD-TYPE
  CLUS_1            2             24
  CLUS_2            1             16
  CLUS_3            0             20
[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
  GFM1 MUTATED        2      0      1
  GFM1 WILD-TYPE     27     20     13
D7V4, multiclass
        clus
vv       GFM1 MUTATED GFM1 WILD-TYPE
  CLUS_1            2             27
  CLUS_2            0             20
  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 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  GFM1 MUTATED        1      1      0      0      1      0      0
  GFM1 WILD-TYPE     16     14      5      6     13      4      5
D7V5, multiclass
        clus
vv       GFM1 MUTATED GFM1 WILD-TYPE
  CLUS_1            1             16
  CLUS_2            1             14
  CLUS_3            0              5
  CLUS_4            0              6
  CLUS_5            1             13
  CLUS_6            0              4
  CLUS_7            0              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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  GFM1 MUTATED        1      1      0      0      1      0      0
  GFM1 WILD-TYPE     18     15      7      6      9      4      4
D7V6, multiclass
        clus
vv       GFM1 MUTATED GFM1 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 CLUS_4
  GFM1 MUTATED        0      2      1      0
  GFM1 WILD-TYPE     18     24      9     12
D7V7, multiclass
        clus
vv       GFM1 MUTATED GFM1 WILD-TYPE
  CLUS_1            0             18
  CLUS_2            2             24
  CLUS_3            1              9
  CLUS_4            0             12
[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
  GFM1 MUTATED        1      1      0      0      0      1      0
  GFM1 WILD-TYPE     17     10     12      6      5      4      9
D7V8, multiclass
        clus
vv       GFM1 MUTATED GFM1 WILD-TYPE
  CLUS_1            1             17
  CLUS_2            1             10
  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
  GFM1 MUTATED        0      1      1      0
  GFM1 WILD-TYPE      9     12     13     12
D7V9, multiclass
[1] "Remove cluster labels:" "GFM1 MUTATED"          
clus
  GFM1 MUTATED GFM1 WILD-TYPE 
             2             46 
    TCGA-KL-8323     TCGA-KL-8324     TCGA-KL-8327     TCGA-KL-8328 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KL-8331     TCGA-KL-8332     TCGA-KL-8333     TCGA-KL-8334 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KL-8335     TCGA-KL-8336     TCGA-KL-8338     TCGA-KL-8339 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KL-8340     TCGA-KL-8341     TCGA-KL-8342     TCGA-KL-8343 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KL-8344     TCGA-KL-8345     TCGA-KM-8438     TCGA-KM-8439 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KM-8441     TCGA-KM-8442     TCGA-KM-8639     TCGA-KN-8418 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KN-8419     TCGA-KN-8422     TCGA-KN-8423     TCGA-KN-8424 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KN-8427     TCGA-KN-8428     TCGA-KN-8429     TCGA-KN-8430 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KN-8431     TCGA-KN-8432     TCGA-KN-8433     TCGA-KN-8434 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KN-8436     TCGA-KN-8437     TCGA-KO-8404     TCGA-KO-8405 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KO-8409     TCGA-KO-8410     TCGA-KO-8413     TCGA-KO-8415 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KO-8416     TCGA-KO-8417 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
  GFM1 MUTATED        1      0      0      0      0      0      0      1      0
  GFM1 WILD-TYPE      4      6      5      8      5      4      6      4      4
D7V10, multiclass
[1] "Remove cluster labels:" "GFM1 MUTATED"          
clus
  GFM1 MUTATED GFM1 WILD-TYPE 
             2             46 
    TCGA-KL-8323     TCGA-KL-8324     TCGA-KL-8327     TCGA-KL-8328 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KL-8331     TCGA-KL-8332     TCGA-KL-8333     TCGA-KL-8334 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KL-8335     TCGA-KL-8336     TCGA-KL-8338     TCGA-KL-8339 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KL-8340     TCGA-KL-8341     TCGA-KL-8342     TCGA-KL-8343 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KL-8344     TCGA-KL-8345     TCGA-KM-8438     TCGA-KM-8439 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KM-8441     TCGA-KM-8442     TCGA-KM-8639     TCGA-KN-8418 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KN-8419     TCGA-KN-8422     TCGA-KN-8423     TCGA-KN-8424 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KN-8427     TCGA-KN-8428     TCGA-KN-8429     TCGA-KN-8430 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KN-8431     TCGA-KN-8432     TCGA-KN-8433     TCGA-KN-8434 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KN-8436     TCGA-KN-8437     TCGA-KO-8404     TCGA-KO-8405 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KO-8409     TCGA-KO-8410     TCGA-KO-8413     TCGA-KO-8415 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KO-8416     TCGA-KO-8417 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 

Clustering(8) Variable = PABPC3 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PABPC3 MUTATED        4      3      0
  PABPC3 WILD-TYPE     34     23      2
D8V1, multiclass
        clus
vv       PABPC3 MUTATED PABPC3 WILD-TYPE
  CLUS_1              4               34
  CLUS_2              3               23
  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
  PABPC3 MUTATED        3      2      2
  PABPC3 WILD-TYPE     16     27     16
D8V2, multiclass
        clus
vv       PABPC3 MUTATED PABPC3 WILD-TYPE
  CLUS_1              3               16
  CLUS_2              2               27
  CLUS_3              2               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
  PABPC3 MUTATED        3      1      3
  PABPC3 WILD-TYPE     23     16     17
D8V3, multiclass
        clus
vv       PABPC3 MUTATED PABPC3 WILD-TYPE
  CLUS_1              3               23
  CLUS_2              1               16
  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
  PABPC3 MUTATED        3      4      0
  PABPC3 WILD-TYPE     26     16     14
D8V4, multiclass
        clus
vv       PABPC3 MUTATED PABPC3 WILD-TYPE
  CLUS_1              3               26
  CLUS_2              4               16
  CLUS_3              0               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
  PABPC3 MUTATED        3      2      0      0      1      0      1
  PABPC3 WILD-TYPE     14     13      5      6     13      4      4
D8V5, multiclass
        clus
vv       PABPC3 MUTATED PABPC3 WILD-TYPE
  CLUS_1              3               14
  CLUS_2              2               13
  CLUS_3              0                5
  CLUS_4              0                6
  CLUS_5              1               13
  CLUS_6              0                4
  CLUS_7              1                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 CLUS_5 CLUS_6 CLUS_7
  PABPC3 MUTATED        3      2      1      0      0      1      0
  PABPC3 WILD-TYPE     16     14      6      6     10      3      4
D8V6, multiclass
        clus
vv       PABPC3 MUTATED PABPC3 WILD-TYPE
  CLUS_1              3               16
  CLUS_2              2               14
  CLUS_3              1                6
  CLUS_4              0                6
  CLUS_5              0               10
  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
  PABPC3 MUTATED        2      3      1      1
  PABPC3 WILD-TYPE     16     23      9     11
D8V7, multiclass
        clus
vv       PABPC3 MUTATED PABPC3 WILD-TYPE
  CLUS_1              2               16
  CLUS_2              3               23
  CLUS_3              1                9
  CLUS_4              1               11
[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
  PABPC3 MUTATED        3      1      0      0      2      0      1
  PABPC3 WILD-TYPE     15     10     12      6      3      5      8
D8V8, multiclass
        clus
vv       PABPC3 MUTATED PABPC3 WILD-TYPE
  CLUS_1              3               15
  CLUS_2              1               10
  CLUS_3              0               12
  CLUS_4              0                6
  CLUS_5              2                3
  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
  PABPC3 MUTATED        1      1      1      3
  PABPC3 WILD-TYPE      8     12     13      9
D8V9, multiclass
        clus
vv       PABPC3 MUTATED PABPC3 WILD-TYPE
  CLUS_1              1                8
  CLUS_2              1               12
  CLUS_3              1               13
  CLUS_4              3                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 CLUS_8
  PABPC3 MUTATED        0      0      2      1      0      1      1      1
  PABPC3 WILD-TYPE      5      6      3      7      5      3      5      4
                  vv
clus               CLUS_9
  PABPC3 MUTATED        0
  PABPC3 WILD-TYPE      4
D8V10, multiclass
        clus
vv       PABPC3 MUTATED PABPC3 WILD-TYPE
  CLUS_1              0                5
  CLUS_2              0                6
  CLUS_3              2                3
  CLUS_4              1                7
  CLUS_5              0                5
  CLUS_6              1                3
  CLUS_7              1                5
  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"
