[1] "ofn"        "-oTTHYM-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/THYM-TP/15111344/THYM-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/THYM-TP/15104465/transformed.cor.cli.txt"

nPatients in clinical file=124, in cluster file=123, common to both=123
[1]  12 123
[1] "DEL PEAK  1(2Q37.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(2Q37.1) MUTATED DEL PEAK  1(2Q37.1) WILD-TYPE 
                            5                           118 
  DEL PEAK  1(2Q37.1) MUTATED DEL PEAK  1(2Q37.1) WILD-TYPE 
                            5                           118 
[1] "DEL PEAK  2(3P22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(3P22.2) MUTATED DEL PEAK  2(3P22.2) WILD-TYPE 
                           14                           109 
  DEL PEAK  2(3P22.2) MUTATED DEL PEAK  2(3P22.2) WILD-TYPE 
                           14                           109 
[1] "DEL PEAK  3(6P25.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(6P25.2) MUTATED DEL PEAK  3(6P25.2) WILD-TYPE 
                           26                            97 
  DEL PEAK  3(6P25.2) MUTATED DEL PEAK  3(6P25.2) WILD-TYPE 
                           26                            97 
[1] "DEL PEAK  4(6Q21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE 
                         20                         103 
  DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE 
                         20                         103 
[1] "DEL PEAK  5(7Q36.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(7Q36.3) MUTATED DEL PEAK  5(7Q36.3) WILD-TYPE 
                            3                           120 
  DEL PEAK  5(7Q36.3) MUTATED DEL PEAK  5(7Q36.3) WILD-TYPE 
                            3                           120 
[1] "DEL PEAK  6(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE 
                           11                           112 
  DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE 
                           11                           112 
[1] "DEL PEAK  7(9Q22.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(9Q22.33) MUTATED DEL PEAK  7(9Q22.33) WILD-TYPE 
                             3                            120 
  DEL PEAK  7(9Q22.33) MUTATED DEL PEAK  7(9Q22.33) WILD-TYPE 
                             3                            120 
[1] "DEL PEAK  8(10Q26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(10Q26.3) MUTATED DEL PEAK  8(10Q26.3) WILD-TYPE 
                             6                            117 
  DEL PEAK  8(10Q26.3) MUTATED DEL PEAK  8(10Q26.3) WILD-TYPE 
                             6                            117 
[1] "DEL PEAK  9(11Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(11Q22.1) MUTATED DEL PEAK  9(11Q22.1) WILD-TYPE 
                             7                            116 
  DEL PEAK  9(11Q22.1) MUTATED DEL PEAK  9(11Q22.1) WILD-TYPE 
                             7                            116 
[1] "DEL PEAK 10(19P13.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(19P13.11) MUTATED DEL PEAK 10(19P13.11) WILD-TYPE 
                              5                             118 
  DEL PEAK 10(19P13.11) MUTATED DEL PEAK 10(19P13.11) WILD-TYPE 
                              5                             118 
[1] "DEL PEAK 11(22Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(22Q12.1) MUTATED DEL PEAK 11(22Q12.1) WILD-TYPE 
                            19                            104 
  DEL PEAK 11(22Q12.1) MUTATED DEL PEAK 11(22Q12.1) WILD-TYPE 
                            19                            104 
[1] "DEL PEAK 12(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(22Q13.32) MUTATED DEL PEAK 12(22Q13.32) WILD-TYPE 
                             15                             108 
  DEL PEAK 12(22Q13.32) MUTATED DEL PEAK 12(22Q13.32) WILD-TYPE 
                             15                             108 
[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 123 columns.

Variable 1:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'RPPA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'RPPA_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_MATURE_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=4,	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 123 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=4, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=6, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = DEL PEAK  1(2Q37.1) MUTATION ANALYSIS
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  1(2Q37.1) MUTATED        1      2      2
  DEL PEAK  1(2Q37.1) WILD-TYPE     64     29     25
D1V1, multiclass
        clus
vv       DEL PEAK  1(2Q37.1) MUTATED DEL PEAK  1(2Q37.1) WILD-TYPE
  CLUS_1                           1                            64
  CLUS_2                           2                            29
  CLUS_3                           2                            25
[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
  DEL PEAK  1(2Q37.1) MUTATED        0      4      1      0
  DEL PEAK  1(2Q37.1) WILD-TYPE     39     32     23     24
D1V2, multiclass
        clus
vv       DEL PEAK  1(2Q37.1) MUTATED DEL PEAK  1(2Q37.1) WILD-TYPE
  CLUS_1                           0                            39
  CLUS_2                           4                            32
  CLUS_3                           1                            23
  CLUS_4                           0                            24
[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
  DEL PEAK  1(2Q37.1) MUTATED        1      3      0
  DEL PEAK  1(2Q37.1) WILD-TYPE     26     21     39
D1V3, multiclass
        clus
vv       DEL PEAK  1(2Q37.1) MUTATED DEL PEAK  1(2Q37.1) WILD-TYPE
  CLUS_1                           1                            26
  CLUS_2                           3                            21
  CLUS_3                           0                            39
[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
  DEL PEAK  1(2Q37.1) MUTATED        0      3      0      1
  DEL PEAK  1(2Q37.1) WILD-TYPE     16     20     31     19
D1V4, multiclass
        clus
vv       DEL PEAK  1(2Q37.1) MUTATED DEL PEAK  1(2Q37.1) WILD-TYPE
  CLUS_1                           0                            16
  CLUS_2                           3                            20
  CLUS_3                           0                            31
  CLUS_4                           1                            19
[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
  DEL PEAK  1(2Q37.1) MUTATED        1      1      2      1
  DEL PEAK  1(2Q37.1) WILD-TYPE     44     30     27     13
D1V5, multiclass
        clus
vv       DEL PEAK  1(2Q37.1) MUTATED DEL PEAK  1(2Q37.1) WILD-TYPE
  CLUS_1                           1                            44
  CLUS_2                           1                            30
  CLUS_3                           2                            27
  CLUS_4                           1                            13
[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
  DEL PEAK  1(2Q37.1) MUTATED        1      3      0      1
  DEL PEAK  1(2Q37.1) WILD-TYPE     46     39     20      9
D1V6, multiclass
        clus
vv       DEL PEAK  1(2Q37.1) MUTATED DEL PEAK  1(2Q37.1) WILD-TYPE
  CLUS_1                           1                            46
  CLUS_2                           3                            39
  CLUS_3                           0                            20
  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
  DEL PEAK  1(2Q37.1) MUTATED        2      3      0      0      0
  DEL PEAK  1(2Q37.1) WILD-TYPE     56     58      1      2      1
D1V7, multiclass
        clus
vv       DEL PEAK  1(2Q37.1) MUTATED DEL PEAK  1(2Q37.1) WILD-TYPE
  CLUS_1                           2                            56
  CLUS_2                           3                            58
  CLUS_3                           0                             1
  CLUS_4                           0                             2
  CLUS_5                           0                             1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  1(2Q37.1) MUTATED        0      3      1      1      0      0
  DEL PEAK  1(2Q37.1) WILD-TYPE     27     15     27      6     16     27
D1V8, multiclass
        clus
vv       DEL PEAK  1(2Q37.1) MUTATED DEL PEAK  1(2Q37.1) WILD-TYPE
  CLUS_1                           0                            27
  CLUS_2                           3                            15
  CLUS_3                           1                            27
  CLUS_4                           1                             6
  CLUS_5                           0                            16
  CLUS_6                           0                            27
[1] 6 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
  DEL PEAK  1(2Q37.1) MUTATED        0      3      2
  DEL PEAK  1(2Q37.1) WILD-TYPE     18     56     44
D1V9, multiclass
        clus
vv       DEL PEAK  1(2Q37.1) MUTATED DEL PEAK  1(2Q37.1) WILD-TYPE
  CLUS_1                           0                            18
  CLUS_2                           3                            56
  CLUS_3                           2                            44
[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
  DEL PEAK  1(2Q37.1) MUTATED        0      3      2      0
  DEL PEAK  1(2Q37.1) WILD-TYPE     29     30     31     28
D1V10, multiclass
        clus
vv       DEL PEAK  1(2Q37.1) MUTATED DEL PEAK  1(2Q37.1) WILD-TYPE
  CLUS_1                           0                            29
  CLUS_2                           3                            30
  CLUS_3                           2                            31
  CLUS_4                           0                            28
[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"

Clustering(2) Variable = DEL PEAK  2(3P22.2) MUTATION ANALYSIS
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  2(3P22.2) MUTATED        1     10      3
  DEL PEAK  2(3P22.2) WILD-TYPE     64     21     24
D2V1, multiclass
        clus
vv       DEL PEAK  2(3P22.2) MUTATED DEL PEAK  2(3P22.2) WILD-TYPE
  CLUS_1                           1                            64
  CLUS_2                          10                            21
  CLUS_3                           3                            24
[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
  DEL PEAK  2(3P22.2) MUTATED        0      3     10      1
  DEL PEAK  2(3P22.2) WILD-TYPE     39     33     14     23
D2V2, multiclass
        clus
vv       DEL PEAK  2(3P22.2) MUTATED DEL PEAK  2(3P22.2) WILD-TYPE
  CLUS_1                           0                            39
  CLUS_2                           3                            33
  CLUS_3                          10                            14
  CLUS_4                           1                            23
[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
  DEL PEAK  2(3P22.2) MUTATED        8      1      2
  DEL PEAK  2(3P22.2) WILD-TYPE     19     23     37
D2V3, multiclass
        clus
vv       DEL PEAK  2(3P22.2) MUTATED DEL PEAK  2(3P22.2) WILD-TYPE
  CLUS_1                           8                            19
  CLUS_2                           1                            23
  CLUS_3                           2                            37
[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
  DEL PEAK  2(3P22.2) MUTATED        3      0      0      8
  DEL PEAK  2(3P22.2) WILD-TYPE     13     23     31     12
D2V4, multiclass
        clus
vv       DEL PEAK  2(3P22.2) MUTATED DEL PEAK  2(3P22.2) WILD-TYPE
  CLUS_1                           3                            13
  CLUS_2                           0                            23
  CLUS_3                           0                            31
  CLUS_4                           8                            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
  DEL PEAK  2(3P22.2) MUTATED        9      1      1      3
  DEL PEAK  2(3P22.2) WILD-TYPE     36     30     28     11
D2V5, multiclass
        clus
vv       DEL PEAK  2(3P22.2) MUTATED DEL PEAK  2(3P22.2) WILD-TYPE
  CLUS_1                           9                            36
  CLUS_2                           1                            30
  CLUS_3                           1                            28
  CLUS_4                           3                            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
  DEL PEAK  2(3P22.2) MUTATED       10      1      1      2
  DEL PEAK  2(3P22.2) WILD-TYPE     37     41     19      8
D2V6, multiclass
        clus
vv       DEL PEAK  2(3P22.2) MUTATED DEL PEAK  2(3P22.2) WILD-TYPE
  CLUS_1                          10                            37
  CLUS_2                           1                            41
  CLUS_3                           1                            19
  CLUS_4                           2                             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
  DEL PEAK  2(3P22.2) MUTATED       12      2      0      0      0
  DEL PEAK  2(3P22.2) WILD-TYPE     46     59      1      2      1
D2V7, multiclass
        clus
vv       DEL PEAK  2(3P22.2) MUTATED DEL PEAK  2(3P22.2) WILD-TYPE
  CLUS_1                          12                            46
  CLUS_2                           2                            59
  CLUS_3                           0                             1
  CLUS_4                           0                             2
  CLUS_5                           0                             1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  2(3P22.2) MUTATED        6      0      4      2      1      1
  DEL PEAK  2(3P22.2) WILD-TYPE     21     18     24      5     15     26
D2V8, multiclass
        clus
vv       DEL PEAK  2(3P22.2) MUTATED DEL PEAK  2(3P22.2) WILD-TYPE
  CLUS_1                           6                            21
  CLUS_2                           0                            18
  CLUS_3                           4                            24
  CLUS_4                           2                             5
  CLUS_5                           1                            15
  CLUS_6                           1                            26
[1] 6 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
  DEL PEAK  2(3P22.2) MUTATED        0      2     12
  DEL PEAK  2(3P22.2) WILD-TYPE     18     57     34
D2V9, multiclass
        clus
vv       DEL PEAK  2(3P22.2) MUTATED DEL PEAK  2(3P22.2) WILD-TYPE
  CLUS_1                           0                            18
  CLUS_2                           2                            57
  CLUS_3                          12                            34
[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
  DEL PEAK  2(3P22.2) MUTATED        7      1      5      1
  DEL PEAK  2(3P22.2) WILD-TYPE     22     32     28     27
D2V10, multiclass
        clus
vv       DEL PEAK  2(3P22.2) MUTATED DEL PEAK  2(3P22.2) WILD-TYPE
  CLUS_1                           7                            22
  CLUS_2                           1                            32
  CLUS_3                           5                            28
  CLUS_4                           1                            27
[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"

Clustering(3) Variable = DEL PEAK  3(6P25.2) MUTATION ANALYSIS
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  3(6P25.2) MUTATED        1     20      5
  DEL PEAK  3(6P25.2) WILD-TYPE     64     11     22
D3V1, multiclass
        clus
vv       DEL PEAK  3(6P25.2) MUTATED DEL PEAK  3(6P25.2) WILD-TYPE
  CLUS_1                           1                            64
  CLUS_2                          20                            11
  CLUS_3                           5                            22
[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
  DEL PEAK  3(6P25.2) MUTATED        2      6     15      3
  DEL PEAK  3(6P25.2) WILD-TYPE     37     30      9     21
D3V2, multiclass
        clus
vv       DEL PEAK  3(6P25.2) MUTATED DEL PEAK  3(6P25.2) WILD-TYPE
  CLUS_1                           2                            37
  CLUS_2                           6                            30
  CLUS_3                          15                             9
  CLUS_4                           3                            21
[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
  DEL PEAK  3(6P25.2) MUTATED       15      4      2
  DEL PEAK  3(6P25.2) WILD-TYPE     12     20     37
D3V3, multiclass
        clus
vv       DEL PEAK  3(6P25.2) MUTATED DEL PEAK  3(6P25.2) WILD-TYPE
  CLUS_1                          15                            12
  CLUS_2                           4                            20
  CLUS_3                           2                            37
[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
  DEL PEAK  3(6P25.2) MUTATED        3      4      2     12
  DEL PEAK  3(6P25.2) WILD-TYPE     13     19     29      8
D3V4, multiclass
        clus
vv       DEL PEAK  3(6P25.2) MUTATED DEL PEAK  3(6P25.2) WILD-TYPE
  CLUS_1                           3                            13
  CLUS_2                           4                            19
  CLUS_3                           2                            29
  CLUS_4                          12                             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
  DEL PEAK  3(6P25.2) MUTATED       14      1      4      6
  DEL PEAK  3(6P25.2) WILD-TYPE     31     30     25      8
D3V5, multiclass
        clus
vv       DEL PEAK  3(6P25.2) MUTATED DEL PEAK  3(6P25.2) WILD-TYPE
  CLUS_1                          14                            31
  CLUS_2                           1                            30
  CLUS_3                           4                            25
  CLUS_4                           6                             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
  DEL PEAK  3(6P25.2) MUTATED       15      4      0      6
  DEL PEAK  3(6P25.2) WILD-TYPE     32     38     20      4
D3V6, multiclass
        clus
vv       DEL PEAK  3(6P25.2) MUTATED DEL PEAK  3(6P25.2) WILD-TYPE
  CLUS_1                          15                            32
  CLUS_2                           4                            38
  CLUS_3                           0                            20
  CLUS_4                           6                             4
[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
  DEL PEAK  3(6P25.2) MUTATED       20      5      0      1      0
  DEL PEAK  3(6P25.2) WILD-TYPE     38     56      1      1      1
D3V7, multiclass
        clus
vv       DEL PEAK  3(6P25.2) MUTATED DEL PEAK  3(6P25.2) WILD-TYPE
  CLUS_1                          20                            38
  CLUS_2                           5                            56
  CLUS_3                           0                             1
  CLUS_4                           1                             1
  CLUS_5                           0                             1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  3(6P25.2) MUTATED       10      3      8      3      0      2
  DEL PEAK  3(6P25.2) WILD-TYPE     17     15     20      4     16     25
D3V8, multiclass
        clus
vv       DEL PEAK  3(6P25.2) MUTATED DEL PEAK  3(6P25.2) WILD-TYPE
  CLUS_1                          10                            17
  CLUS_2                           3                            15
  CLUS_3                           8                            20
  CLUS_4                           3                             4
  CLUS_5                           0                            16
  CLUS_6                           2                            25
[1] 6 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
  DEL PEAK  3(6P25.2) MUTATED        1      5     20
  DEL PEAK  3(6P25.2) WILD-TYPE     17     54     26
D3V9, multiclass
        clus
vv       DEL PEAK  3(6P25.2) MUTATED DEL PEAK  3(6P25.2) WILD-TYPE
  CLUS_1                           1                            17
  CLUS_2                           5                            54
  CLUS_3                          20                            26
[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
  DEL PEAK  3(6P25.2) MUTATED       11      3     10      2
  DEL PEAK  3(6P25.2) WILD-TYPE     18     30     23     26
D3V10, multiclass
        clus
vv       DEL PEAK  3(6P25.2) MUTATED DEL PEAK  3(6P25.2) WILD-TYPE
  CLUS_1                          11                            18
  CLUS_2                           3                            30
  CLUS_3                          10                            23
  CLUS_4                           2                            26
[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"

Clustering(4) Variable = DEL PEAK  4(6Q21) MUTATION ANALYSIS
                             vv
clus                          CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  4(6Q21) MUTATED        0     18      2
  DEL PEAK  4(6Q21) WILD-TYPE     65     13     25
D4V1, multiclass
        clus
vv       DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE
  CLUS_1                         0                          65
  CLUS_2                        18                          13
  CLUS_3                         2                          25
[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
  DEL PEAK  4(6Q21) MUTATED        1      3     16      0
  DEL PEAK  4(6Q21) WILD-TYPE     38     33      8     24
D4V2, multiclass
        clus
vv       DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE
  CLUS_1                         1                          38
  CLUS_2                         3                          33
  CLUS_3                        16                           8
  CLUS_4                         0                          24
[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
  DEL PEAK  4(6Q21) MUTATED       13      1      1
  DEL PEAK  4(6Q21) WILD-TYPE     14     23     38
D4V3, multiclass
        clus
vv       DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE
  CLUS_1                        13                          14
  CLUS_2                         1                          23
  CLUS_3                         1                          38
[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
  DEL PEAK  4(6Q21) MUTATED        2      1      1     11
  DEL PEAK  4(6Q21) WILD-TYPE     14     22     30      9
D4V4, multiclass
        clus
vv       DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE
  CLUS_1                         2                          14
  CLUS_2                         1                          22
  CLUS_3                         1                          30
  CLUS_4                        11                           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
  DEL PEAK  4(6Q21) MUTATED       13      0      0      7
  DEL PEAK  4(6Q21) WILD-TYPE     32     31     29      7
D4V5, multiclass
        clus
vv       DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE
  CLUS_1                        13                          32
  CLUS_2                         0                          31
  CLUS_3                         0                          29
  CLUS_4                         7                           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
  DEL PEAK  4(6Q21) MUTATED       14      0      1      5
  DEL PEAK  4(6Q21) WILD-TYPE     33     42     19      5
D4V6, multiclass
        clus
vv       DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE
  CLUS_1                        14                          33
  CLUS_2                         0                          42
  CLUS_3                         1                          19
  CLUS_4                         5                           5
[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
  DEL PEAK  4(6Q21) MUTATED       18      1      0      1      0
  DEL PEAK  4(6Q21) WILD-TYPE     40     60      1      1      1
D4V7, multiclass
        clus
vv       DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE
  CLUS_1                        18                          40
  CLUS_2                         1                          60
  CLUS_3                         0                           1
  CLUS_4                         1                           1
  CLUS_5                         0                           1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  4(6Q21) MUTATED        9      0      7      3      1      0
  DEL PEAK  4(6Q21) WILD-TYPE     18     18     21      4     15     27
D4V8, multiclass
        clus
vv       DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE
  CLUS_1                         9                          18
  CLUS_2                         0                          18
  CLUS_3                         7                          21
  CLUS_4                         3                           4
  CLUS_5                         1                          15
  CLUS_6                         0                          27
[1] 6 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
  DEL PEAK  4(6Q21) MUTATED        0      0     20
  DEL PEAK  4(6Q21) WILD-TYPE     18     59     26
D4V9, multiclass
        clus
vv       DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE
  CLUS_1                         0                          18
  CLUS_2                         0                          59
  CLUS_3                        20                          26
[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
  DEL PEAK  4(6Q21) MUTATED       10      1      9      0
  DEL PEAK  4(6Q21) WILD-TYPE     19     32     24     28
D4V10, multiclass
        clus
vv       DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE
  CLUS_1                        10                          19
  CLUS_2                         1                          32
  CLUS_3                         9                          24
  CLUS_4                         0                          28
[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"

Clustering(5) Variable = DEL PEAK  5(7Q36.3) MUTATION ANALYSIS
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  5(7Q36.3) MUTATED        0      1      2
  DEL PEAK  5(7Q36.3) WILD-TYPE     65     30     25
D5V1, multiclass
        clus
vv       DEL PEAK  5(7Q36.3) MUTATED DEL PEAK  5(7Q36.3) WILD-TYPE
  CLUS_1                           0                            65
  CLUS_2                           1                            30
  CLUS_3                           2                            25
[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
  DEL PEAK  5(7Q36.3) MUTATED        0      1      2      0
  DEL PEAK  5(7Q36.3) WILD-TYPE     39     35     22     24
D5V2, multiclass
        clus
vv       DEL PEAK  5(7Q36.3) MUTATED DEL PEAK  5(7Q36.3) WILD-TYPE
  CLUS_1                           0                            39
  CLUS_2                           1                            35
  CLUS_3                           2                            22
  CLUS_4                           0                            24
[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
  DEL PEAK  5(7Q36.3) MUTATED        3      0      0
  DEL PEAK  5(7Q36.3) WILD-TYPE     24     24     39
D5V3, multiclass
        clus
vv       DEL PEAK  5(7Q36.3) MUTATED DEL PEAK  5(7Q36.3) WILD-TYPE
  CLUS_1                           3                            24
  CLUS_2                           0                            24
  CLUS_3                           0                            39
[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
  DEL PEAK  5(7Q36.3) MUTATED        0      1      0      2
  DEL PEAK  5(7Q36.3) WILD-TYPE     16     22     31     18
D5V4, multiclass
        clus
vv       DEL PEAK  5(7Q36.3) MUTATED DEL PEAK  5(7Q36.3) WILD-TYPE
  CLUS_1                           0                            16
  CLUS_2                           1                            22
  CLUS_3                           0                            31
  CLUS_4                           2                            18
[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
  DEL PEAK  5(7Q36.3) MUTATED        0      0      0      3
  DEL PEAK  5(7Q36.3) WILD-TYPE     45     31     29     11
D5V5, multiclass
        clus
vv       DEL PEAK  5(7Q36.3) MUTATED DEL PEAK  5(7Q36.3) WILD-TYPE
  CLUS_1                           0                            45
  CLUS_2                           0                            31
  CLUS_3                           0                            29
  CLUS_4                           3                            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
  DEL PEAK  5(7Q36.3) MUTATED        0      0      1      2
  DEL PEAK  5(7Q36.3) WILD-TYPE     47     42     19      8
D5V6, multiclass
        clus
vv       DEL PEAK  5(7Q36.3) MUTATED DEL PEAK  5(7Q36.3) WILD-TYPE
  CLUS_1                           0                            47
  CLUS_2                           0                            42
  CLUS_3                           1                            19
  CLUS_4                           2                             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
  DEL PEAK  5(7Q36.3) MUTATED        2      1      0      0      0
  DEL PEAK  5(7Q36.3) WILD-TYPE     56     60      1      2      1
D5V7, multiclass
        clus
vv       DEL PEAK  5(7Q36.3) MUTATED DEL PEAK  5(7Q36.3) WILD-TYPE
  CLUS_1                           2                            56
  CLUS_2                           1                            60
  CLUS_3                           0                             1
  CLUS_4                           0                             2
  CLUS_5                           0                             1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  5(7Q36.3) MUTATED        0      0      1      1      1      0
  DEL PEAK  5(7Q36.3) WILD-TYPE     27     18     27      6     15     27
D5V8, multiclass
        clus
vv       DEL PEAK  5(7Q36.3) MUTATED DEL PEAK  5(7Q36.3) WILD-TYPE
  CLUS_1                           0                            27
  CLUS_2                           0                            18
  CLUS_3                           1                            27
  CLUS_4                           1                             6
  CLUS_5                           1                            15
  CLUS_6                           0                            27
[1] 6 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
  DEL PEAK  5(7Q36.3) MUTATED        0      0      3
  DEL PEAK  5(7Q36.3) WILD-TYPE     18     59     43
D5V9, multiclass
        clus
vv       DEL PEAK  5(7Q36.3) MUTATED DEL PEAK  5(7Q36.3) WILD-TYPE
  CLUS_1                           0                            18
  CLUS_2                           0                            59
  CLUS_3                           3                            43
[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
  DEL PEAK  5(7Q36.3) MUTATED        0      1      2      0
  DEL PEAK  5(7Q36.3) WILD-TYPE     29     32     31     28
D5V10, multiclass
        clus
vv       DEL PEAK  5(7Q36.3) MUTATED DEL PEAK  5(7Q36.3) WILD-TYPE
  CLUS_1                           0                            29
  CLUS_2                           1                            32
  CLUS_3                           2                            31
  CLUS_4                           0                            28
[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"

Clustering(6) Variable = DEL PEAK  6(9P21.3) MUTATION ANALYSIS
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  6(9P21.3) MUTATED        2      6      3
  DEL PEAK  6(9P21.3) WILD-TYPE     63     25     24
D6V1, multiclass
        clus
vv       DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE
  CLUS_1                           2                            63
  CLUS_2                           6                            25
  CLUS_3                           3                            24
[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
  DEL PEAK  6(9P21.3) MUTATED        0      8      2      1
  DEL PEAK  6(9P21.3) WILD-TYPE     39     28     22     23
D6V2, multiclass
        clus
vv       DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE
  CLUS_1                           0                            39
  CLUS_2                           8                            28
  CLUS_3                           2                            22
  CLUS_4                           1                            23
[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
  DEL PEAK  6(9P21.3) MUTATED        5      3      1
  DEL PEAK  6(9P21.3) WILD-TYPE     22     21     38
D6V3, multiclass
        clus
vv       DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE
  CLUS_1                           5                            22
  CLUS_2                           3                            21
  CLUS_3                           1                            38
[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
  DEL PEAK  6(9P21.3) MUTATED        0      3      0      6
  DEL PEAK  6(9P21.3) WILD-TYPE     16     20     31     14
D6V4, multiclass
        clus
vv       DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE
  CLUS_1                           0                            16
  CLUS_2                           3                            20
  CLUS_3                           0                            31
  CLUS_4                           6                            14
[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
  DEL PEAK  6(9P21.3) MUTATED        1      0      3      6
  DEL PEAK  6(9P21.3) WILD-TYPE     44     31     26      8
D6V5, multiclass
        clus
vv       DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE
  CLUS_1                           1                            44
  CLUS_2                           0                            31
  CLUS_3                           3                            26
  CLUS_4                           6                             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
  DEL PEAK  6(9P21.3) MUTATED        1      0      3      6
  DEL PEAK  6(9P21.3) WILD-TYPE     46     42     17      4
D6V6, multiclass
        clus
vv       DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE
  CLUS_1                           1                            46
  CLUS_2                           0                            42
  CLUS_3                           3                            17
  CLUS_4                           6                             4
[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
  DEL PEAK  6(9P21.3) MUTATED        7      4      0      0      0
  DEL PEAK  6(9P21.3) WILD-TYPE     51     57      1      2      1
D6V7, multiclass
        clus
vv       DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE
  CLUS_1                           7                            51
  CLUS_2                           4                            57
  CLUS_3                           0                             1
  CLUS_4                           0                             2
  CLUS_5                           0                             1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  6(9P21.3) MUTATED        0      0      3      4      3      1
  DEL PEAK  6(9P21.3) WILD-TYPE     27     18     25      3     13     26
D6V8, multiclass
        clus
vv       DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE
  CLUS_1                           0                            27
  CLUS_2                           0                            18
  CLUS_3                           3                            25
  CLUS_4                           4                             3
  CLUS_5                           3                            13
  CLUS_6                           1                            26
[1] 6 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
  DEL PEAK  6(9P21.3) MUTATED        0      4      7
  DEL PEAK  6(9P21.3) WILD-TYPE     18     55     39
D6V9, multiclass
        clus
vv       DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE
  CLUS_1                           0                            18
  CLUS_2                           4                            55
  CLUS_3                           7                            39
[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
  DEL PEAK  6(9P21.3) MUTATED        0      3      7      1
  DEL PEAK  6(9P21.3) WILD-TYPE     29     30     26     27
D6V10, multiclass
        clus
vv       DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE
  CLUS_1                           0                            29
  CLUS_2                           3                            30
  CLUS_3                           7                            26
  CLUS_4                           1                            27
[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"

Clustering(7) Variable = DEL PEAK  7(9Q22.33) MUTATION ANALYSIS
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  7(9Q22.33) MUTATED        1      1      1
  DEL PEAK  7(9Q22.33) WILD-TYPE     64     30     26
D7V1, multiclass
        clus
vv       DEL PEAK  7(9Q22.33) MUTATED DEL PEAK  7(9Q22.33) WILD-TYPE
  CLUS_1                            1                             64
  CLUS_2                            1                             30
  CLUS_3                            1                             26
[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
  DEL PEAK  7(9Q22.33) MUTATED        0      1      2      0
  DEL PEAK  7(9Q22.33) WILD-TYPE     39     35     22     24
D7V2, multiclass
        clus
vv       DEL PEAK  7(9Q22.33) MUTATED DEL PEAK  7(9Q22.33) WILD-TYPE
  CLUS_1                            0                             39
  CLUS_2                            1                             35
  CLUS_3                            2                             22
  CLUS_4                            0                             24
[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
  DEL PEAK  7(9Q22.33) MUTATED        3      0      0
  DEL PEAK  7(9Q22.33) WILD-TYPE     24     24     39
D7V3, multiclass
        clus
vv       DEL PEAK  7(9Q22.33) MUTATED DEL PEAK  7(9Q22.33) WILD-TYPE
  CLUS_1                            3                             24
  CLUS_2                            0                             24
  CLUS_3                            0                             39
[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
  DEL PEAK  7(9Q22.33) MUTATED        0      0      0      3
  DEL PEAK  7(9Q22.33) WILD-TYPE     16     23     31     17
D7V4, multiclass
        clus
vv       DEL PEAK  7(9Q22.33) MUTATED DEL PEAK  7(9Q22.33) WILD-TYPE
  CLUS_1                            0                             16
  CLUS_2                            0                             23
  CLUS_3                            0                             31
  CLUS_4                            3                             17
[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
  DEL PEAK  7(9Q22.33) MUTATED        1      0      0      2
  DEL PEAK  7(9Q22.33) WILD-TYPE     44     31     29     12
D7V5, multiclass
        clus
vv       DEL PEAK  7(9Q22.33) MUTATED DEL PEAK  7(9Q22.33) WILD-TYPE
  CLUS_1                            1                             44
  CLUS_2                            0                             31
  CLUS_3                            0                             29
  CLUS_4                            2                             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
  DEL PEAK  7(9Q22.33) MUTATED        1      0      0      2
  DEL PEAK  7(9Q22.33) WILD-TYPE     46     42     20      8
D7V6, multiclass
        clus
vv       DEL PEAK  7(9Q22.33) MUTATED DEL PEAK  7(9Q22.33) WILD-TYPE
  CLUS_1                            1                             46
  CLUS_2                            0                             42
  CLUS_3                            0                             20
  CLUS_4                            2                              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
  DEL PEAK  7(9Q22.33) MUTATED        3      0      0      0      0
  DEL PEAK  7(9Q22.33) WILD-TYPE     55     61      1      2      1
D7V7, multiclass
        clus
vv       DEL PEAK  7(9Q22.33) MUTATED DEL PEAK  7(9Q22.33) WILD-TYPE
  CLUS_1                            3                             55
  CLUS_2                            0                             61
  CLUS_3                            0                              1
  CLUS_4                            0                              2
  CLUS_5                            0                              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  7(9Q22.33) MUTATED        0      0      2      1      0      0
  DEL PEAK  7(9Q22.33) WILD-TYPE     27     18     26      6     16     27
D7V8, multiclass
        clus
vv       DEL PEAK  7(9Q22.33) MUTATED DEL PEAK  7(9Q22.33) WILD-TYPE
  CLUS_1                            0                             27
  CLUS_2                            0                             18
  CLUS_3                            2                             26
  CLUS_4                            1                              6
  CLUS_5                            0                             16
  CLUS_6                            0                             27
[1] 6 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
  DEL PEAK  7(9Q22.33) MUTATED        0      0      3
  DEL PEAK  7(9Q22.33) WILD-TYPE     18     59     43
D7V9, multiclass
        clus
vv       DEL PEAK  7(9Q22.33) MUTATED DEL PEAK  7(9Q22.33) WILD-TYPE
  CLUS_1                            0                             18
  CLUS_2                            0                             59
  CLUS_3                            3                             43
[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
  DEL PEAK  7(9Q22.33) MUTATED        0      0      3      0
  DEL PEAK  7(9Q22.33) WILD-TYPE     29     33     30     28
D7V10, multiclass
        clus
vv       DEL PEAK  7(9Q22.33) MUTATED DEL PEAK  7(9Q22.33) WILD-TYPE
  CLUS_1                            0                             29
  CLUS_2                            0                             33
  CLUS_3                            3                             30
  CLUS_4                            0                             28
[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"

Clustering(8) Variable = DEL PEAK  8(10Q26.3) MUTATION ANALYSIS
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  8(10Q26.3) MUTATED        2      2      2
  DEL PEAK  8(10Q26.3) WILD-TYPE     63     29     25
D8V1, multiclass
        clus
vv       DEL PEAK  8(10Q26.3) MUTATED DEL PEAK  8(10Q26.3) WILD-TYPE
  CLUS_1                            2                             63
  CLUS_2                            2                             29
  CLUS_3                            2                             25
[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
  DEL PEAK  8(10Q26.3) MUTATED        0      3      3      0
  DEL PEAK  8(10Q26.3) WILD-TYPE     39     33     21     24
D8V2, multiclass
        clus
vv       DEL PEAK  8(10Q26.3) MUTATED DEL PEAK  8(10Q26.3) WILD-TYPE
  CLUS_1                            0                             39
  CLUS_2                            3                             33
  CLUS_3                            3                             21
  CLUS_4                            0                             24
[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
  DEL PEAK  8(10Q26.3) MUTATED        3      2      0
  DEL PEAK  8(10Q26.3) WILD-TYPE     24     22     39
D8V3, multiclass
        clus
vv       DEL PEAK  8(10Q26.3) MUTATED DEL PEAK  8(10Q26.3) WILD-TYPE
  CLUS_1                            3                             24
  CLUS_2                            2                             22
  CLUS_3                            0                             39
[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
  DEL PEAK  8(10Q26.3) MUTATED        0      4      0      1
  DEL PEAK  8(10Q26.3) WILD-TYPE     16     19     31     19
D8V4, multiclass
        clus
vv       DEL PEAK  8(10Q26.3) MUTATED DEL PEAK  8(10Q26.3) WILD-TYPE
  CLUS_1                            0                             16
  CLUS_2                            4                             19
  CLUS_3                            0                             31
  CLUS_4                            1                             19
[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
  DEL PEAK  8(10Q26.3) MUTATED        1      0      3      2
  DEL PEAK  8(10Q26.3) WILD-TYPE     44     31     26     12
D8V5, multiclass
        clus
vv       DEL PEAK  8(10Q26.3) MUTATED DEL PEAK  8(10Q26.3) WILD-TYPE
  CLUS_1                            1                             44
  CLUS_2                            0                             31
  CLUS_3                            3                             26
  CLUS_4                            2                             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
  DEL PEAK  8(10Q26.3) MUTATED        2      1      3      0
  DEL PEAK  8(10Q26.3) WILD-TYPE     45     41     17     10
D8V6, multiclass
        clus
vv       DEL PEAK  8(10Q26.3) MUTATED DEL PEAK  8(10Q26.3) WILD-TYPE
  CLUS_1                            2                             45
  CLUS_2                            1                             41
  CLUS_3                            3                             17
  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
  DEL PEAK  8(10Q26.3) MUTATED        2      4      0      0      0
  DEL PEAK  8(10Q26.3) WILD-TYPE     56     57      1      2      1
D8V7, multiclass
        clus
vv       DEL PEAK  8(10Q26.3) MUTATED DEL PEAK  8(10Q26.3) WILD-TYPE
  CLUS_1                            2                             56
  CLUS_2                            4                             57
  CLUS_3                            0                              1
  CLUS_4                            0                              2
  CLUS_5                            0                              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  8(10Q26.3) MUTATED        2      1      0      0      3      0
  DEL PEAK  8(10Q26.3) WILD-TYPE     25     17     28      7     13     27
D8V8, multiclass
        clus
vv       DEL PEAK  8(10Q26.3) MUTATED DEL PEAK  8(10Q26.3) WILD-TYPE
  CLUS_1                            2                             25
  CLUS_2                            1                             17
  CLUS_3                            0                             28
  CLUS_4                            0                              7
  CLUS_5                            3                             13
  CLUS_6                            0                             27
[1] 6 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
  DEL PEAK  8(10Q26.3) MUTATED        0      3      3
  DEL PEAK  8(10Q26.3) WILD-TYPE     18     56     43
D8V9, multiclass
        clus
vv       DEL PEAK  8(10Q26.3) MUTATED DEL PEAK  8(10Q26.3) WILD-TYPE
  CLUS_1                            0                             18
  CLUS_2                            3                             56
  CLUS_3                            3                             43
[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
  DEL PEAK  8(10Q26.3) MUTATED        2      4      0      0
  DEL PEAK  8(10Q26.3) WILD-TYPE     27     29     33     28
D8V10, multiclass
        clus
vv       DEL PEAK  8(10Q26.3) MUTATED DEL PEAK  8(10Q26.3) WILD-TYPE
  CLUS_1                            2                             27
  CLUS_2                            4                             29
  CLUS_3                            0                             33
  CLUS_4                            0                             28
[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"

Clustering(9) Variable = DEL PEAK  9(11Q22.1) MUTATION ANALYSIS
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  9(11Q22.1) MUTATED        0      7      0
  DEL PEAK  9(11Q22.1) WILD-TYPE     65     24     27
D9V1, multiclass
        clus
vv       DEL PEAK  9(11Q22.1) MUTATED DEL PEAK  9(11Q22.1) WILD-TYPE
  CLUS_1                            0                             65
  CLUS_2                            7                             24
  CLUS_3                            0                             27
[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
  DEL PEAK  9(11Q22.1) MUTATED        0      0      7      0
  DEL PEAK  9(11Q22.1) WILD-TYPE     39     36     17     24
D9V2, multiclass
        clus
vv       DEL PEAK  9(11Q22.1) MUTATED DEL PEAK  9(11Q22.1) WILD-TYPE
  CLUS_1                            0                             39
  CLUS_2                            0                             36
  CLUS_3                            7                             17
  CLUS_4                            0                             24
[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
  DEL PEAK  9(11Q22.1) MUTATED        4      1      0
  DEL PEAK  9(11Q22.1) WILD-TYPE     23     23     39
D9V3, multiclass
        clus
vv       DEL PEAK  9(11Q22.1) MUTATED DEL PEAK  9(11Q22.1) WILD-TYPE
  CLUS_1                            4                             23
  CLUS_2                            1                             23
  CLUS_3                            0                             39
[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
  DEL PEAK  9(11Q22.1) MUTATED        1      0      0      4
  DEL PEAK  9(11Q22.1) WILD-TYPE     15     23     31     16
D9V4, multiclass
        clus
vv       DEL PEAK  9(11Q22.1) MUTATED DEL PEAK  9(11Q22.1) WILD-TYPE
  CLUS_1                            1                             15
  CLUS_2                            0                             23
  CLUS_3                            0                             31
  CLUS_4                            4                             16
[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
  DEL PEAK  9(11Q22.1) MUTATED        6      0      0      1
  DEL PEAK  9(11Q22.1) WILD-TYPE     39     31     29     13
D9V5, multiclass
        clus
vv       DEL PEAK  9(11Q22.1) MUTATED DEL PEAK  9(11Q22.1) WILD-TYPE
  CLUS_1                            6                             39
  CLUS_2                            0                             31
  CLUS_3                            0                             29
  CLUS_4                            1                             13
[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
  DEL PEAK  9(11Q22.1) MUTATED        7      0      0      0
  DEL PEAK  9(11Q22.1) WILD-TYPE     40     42     20     10
D9V6, multiclass
        clus
vv       DEL PEAK  9(11Q22.1) MUTATED DEL PEAK  9(11Q22.1) WILD-TYPE
  CLUS_1                            7                             40
  CLUS_2                            0                             42
  CLUS_3                            0                             20
  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
  DEL PEAK  9(11Q22.1) MUTATED        7      0      0      0      0
  DEL PEAK  9(11Q22.1) WILD-TYPE     51     61      1      2      1
D9V7, multiclass
        clus
vv       DEL PEAK  9(11Q22.1) MUTATED DEL PEAK  9(11Q22.1) WILD-TYPE
  CLUS_1                            7                             51
  CLUS_2                            0                             61
  CLUS_3                            0                              1
  CLUS_4                            0                              2
  CLUS_5                            0                              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  9(11Q22.1) MUTATED        4      0      3      0      0      0
  DEL PEAK  9(11Q22.1) WILD-TYPE     23     18     25      7     16     27
D9V8, multiclass
        clus
vv       DEL PEAK  9(11Q22.1) MUTATED DEL PEAK  9(11Q22.1) WILD-TYPE
  CLUS_1                            4                             23
  CLUS_2                            0                             18
  CLUS_3                            3                             25
  CLUS_4                            0                              7
  CLUS_5                            0                             16
  CLUS_6                            0                             27
[1] 6 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
  DEL PEAK  9(11Q22.1) MUTATED        0      0      7
  DEL PEAK  9(11Q22.1) WILD-TYPE     18     59     39
D9V9, multiclass
        clus
vv       DEL PEAK  9(11Q22.1) MUTATED DEL PEAK  9(11Q22.1) WILD-TYPE
  CLUS_1                            0                             18
  CLUS_2                            0                             59
  CLUS_3                            7                             39
[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
  DEL PEAK  9(11Q22.1) MUTATED        5      0      2      0
  DEL PEAK  9(11Q22.1) WILD-TYPE     24     33     31     28
D9V10, multiclass
        clus
vv       DEL PEAK  9(11Q22.1) MUTATED DEL PEAK  9(11Q22.1) WILD-TYPE
  CLUS_1                            5                             24
  CLUS_2                            0                             33
  CLUS_3                            2                             31
  CLUS_4                            0                             28
[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"

Clustering(10) Variable = DEL PEAK 10(19P13.11) MUTATION ANALYSIS
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 10(19P13.11) MUTATED        1      2      2
  DEL PEAK 10(19P13.11) WILD-TYPE     64     29     25
D10V1, multiclass
        clus
vv       DEL PEAK 10(19P13.11) MUTATED DEL PEAK 10(19P13.11) WILD-TYPE
  CLUS_1                             1                              64
  CLUS_2                             2                              29
  CLUS_3                             2                              25
[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
  DEL PEAK 10(19P13.11) MUTATED        0      4      1      0
  DEL PEAK 10(19P13.11) WILD-TYPE     39     32     23     24
D10V2, multiclass
        clus
vv       DEL PEAK 10(19P13.11) MUTATED DEL PEAK 10(19P13.11) WILD-TYPE
  CLUS_1                             0                              39
  CLUS_2                             4                              32
  CLUS_3                             1                              23
  CLUS_4                             0                              24
[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
  DEL PEAK 10(19P13.11) MUTATED        2      1      0
  DEL PEAK 10(19P13.11) WILD-TYPE     25     23     39
D10V3, multiclass
        clus
vv       DEL PEAK 10(19P13.11) MUTATED DEL PEAK 10(19P13.11) WILD-TYPE
  CLUS_1                             2                              25
  CLUS_2                             1                              23
  CLUS_3                             0                              39
[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
  DEL PEAK 10(19P13.11) MUTATED        0      1      0      2
  DEL PEAK 10(19P13.11) WILD-TYPE     16     22     31     18
D10V4, multiclass
        clus
vv       DEL PEAK 10(19P13.11) MUTATED DEL PEAK 10(19P13.11) WILD-TYPE
  CLUS_1                             0                              16
  CLUS_2                             1                              22
  CLUS_3                             0                              31
  CLUS_4                             2                              18
[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
  DEL PEAK 10(19P13.11) MUTATED        0      0      2      3
  DEL PEAK 10(19P13.11) WILD-TYPE     45     31     27     11
D10V5, multiclass
        clus
vv       DEL PEAK 10(19P13.11) MUTATED DEL PEAK 10(19P13.11) WILD-TYPE
  CLUS_1                             0                              45
  CLUS_2                             0                              31
  CLUS_3                             2                              27
  CLUS_4                             3                              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
  DEL PEAK 10(19P13.11) MUTATED        0      0      2      3
  DEL PEAK 10(19P13.11) WILD-TYPE     47     42     18      7
D10V6, multiclass
        clus
vv       DEL PEAK 10(19P13.11) MUTATED DEL PEAK 10(19P13.11) WILD-TYPE
  CLUS_1                             0                              47
  CLUS_2                             0                              42
  CLUS_3                             2                              18
  CLUS_4                             3                               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK 10(19P13.11) MUTATED        3      2      0      0      0
  DEL PEAK 10(19P13.11) WILD-TYPE     55     59      1      2      1
D10V7, multiclass
        clus
vv       DEL PEAK 10(19P13.11) MUTATED DEL PEAK 10(19P13.11) WILD-TYPE
  CLUS_1                             3                              55
  CLUS_2                             2                              59
  CLUS_3                             0                               1
  CLUS_4                             0                               2
  CLUS_5                             0                               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 10(19P13.11) MUTATED        0      0      1      2      2      0
  DEL PEAK 10(19P13.11) WILD-TYPE     27     18     27      5     14     27
D10V8, multiclass
        clus
vv       DEL PEAK 10(19P13.11) MUTATED DEL PEAK 10(19P13.11) WILD-TYPE
  CLUS_1                             0                              27
  CLUS_2                             0                              18
  CLUS_3                             1                              27
  CLUS_4                             2                               5
  CLUS_5                             2                              14
  CLUS_6                             0                              27
[1] 6 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
  DEL PEAK 10(19P13.11) MUTATED        0      2      3
  DEL PEAK 10(19P13.11) WILD-TYPE     18     57     43
D10V9, multiclass
        clus
vv       DEL PEAK 10(19P13.11) MUTATED DEL PEAK 10(19P13.11) WILD-TYPE
  CLUS_1                             0                              18
  CLUS_2                             2                              57
  CLUS_3                             3                              43
[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
  DEL PEAK 10(19P13.11) MUTATED        0      2      3      0
  DEL PEAK 10(19P13.11) WILD-TYPE     29     31     30     28
D10V10, multiclass
        clus
vv       DEL PEAK 10(19P13.11) MUTATED DEL PEAK 10(19P13.11) WILD-TYPE
  CLUS_1                             0                              29
  CLUS_2                             2                              31
  CLUS_3                             3                              30
  CLUS_4                             0                              28
[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"

Clustering(11) Variable = DEL PEAK 11(22Q12.1) MUTATION ANALYSIS
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 11(22Q12.1) MUTATED        0      4     15
  DEL PEAK 11(22Q12.1) WILD-TYPE     65     27     12
D11V1, multiclass
        clus
vv       DEL PEAK 11(22Q12.1) MUTATED DEL PEAK 11(22Q12.1) WILD-TYPE
  CLUS_1                            0                             65
  CLUS_2                            4                             27
  CLUS_3                           15                             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
  DEL PEAK 11(22Q12.1) MUTATED        1      9      3      6
  DEL PEAK 11(22Q12.1) WILD-TYPE     38     27     21     18
D11V2, multiclass
        clus
vv       DEL PEAK 11(22Q12.1) MUTATED DEL PEAK 11(22Q12.1) WILD-TYPE
  CLUS_1                            1                             38
  CLUS_2                            9                             27
  CLUS_3                            3                             21
  CLUS_4                            6                             18
[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
  DEL PEAK 11(22Q12.1) MUTATED        4      8      2
  DEL PEAK 11(22Q12.1) WILD-TYPE     23     16     37
D11V3, multiclass
        clus
vv       DEL PEAK 11(22Q12.1) MUTATED DEL PEAK 11(22Q12.1) WILD-TYPE
  CLUS_1                            4                             23
  CLUS_2                            8                             16
  CLUS_3                            2                             37
[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
  DEL PEAK 11(22Q12.1) MUTATED        4      6      1      3
  DEL PEAK 11(22Q12.1) WILD-TYPE     12     17     30     17
D11V4, multiclass
        clus
vv       DEL PEAK 11(22Q12.1) MUTATED DEL PEAK 11(22Q12.1) WILD-TYPE
  CLUS_1                            4                             12
  CLUS_2                            6                             17
  CLUS_3                            1                             30
  CLUS_4                            3                             17
[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
  DEL PEAK 11(22Q12.1) MUTATED        2      5      8      4
  DEL PEAK 11(22Q12.1) WILD-TYPE     43     26     21     10
D11V5, multiclass
        clus
vv       DEL PEAK 11(22Q12.1) MUTATED DEL PEAK 11(22Q12.1) WILD-TYPE
  CLUS_1                            2                             43
  CLUS_2                            5                             26
  CLUS_3                            8                             21
  CLUS_4                            4                             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
  DEL PEAK 11(22Q12.1) MUTATED        3      9      4      3
  DEL PEAK 11(22Q12.1) WILD-TYPE     44     33     16      7
D11V6, multiclass
        clus
vv       DEL PEAK 11(22Q12.1) MUTATED DEL PEAK 11(22Q12.1) WILD-TYPE
  CLUS_1                            3                             44
  CLUS_2                            9                             33
  CLUS_3                            4                             16
  CLUS_4                            3                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK 11(22Q12.1) MUTATED        7     11      1      0      0
  DEL PEAK 11(22Q12.1) WILD-TYPE     51     50      0      2      1
D11V7, multiclass
        clus
vv       DEL PEAK 11(22Q12.1) MUTATED DEL PEAK 11(22Q12.1) WILD-TYPE
  CLUS_1                            7                             51
  CLUS_2                           11                             50
  CLUS_3                            1                              0
  CLUS_4                            0                              2
  CLUS_5                            0                              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 11(22Q12.1) MUTATED        3      5      3      2      3      3
  DEL PEAK 11(22Q12.1) WILD-TYPE     24     13     25      5     13     24
D11V8, multiclass
        clus
vv       DEL PEAK 11(22Q12.1) MUTATED DEL PEAK 11(22Q12.1) WILD-TYPE
  CLUS_1                            3                             24
  CLUS_2                            5                             13
  CLUS_3                            3                             25
  CLUS_4                            2                              5
  CLUS_5                            3                             13
  CLUS_6                            3                             24
[1] 6 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
  DEL PEAK 11(22Q12.1) MUTATED        1     10      8
  DEL PEAK 11(22Q12.1) WILD-TYPE     17     49     38
D11V9, multiclass
        clus
vv       DEL PEAK 11(22Q12.1) MUTATED DEL PEAK 11(22Q12.1) WILD-TYPE
  CLUS_1                            1                             17
  CLUS_2                           10                             49
  CLUS_3                            8                             38
[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
  DEL PEAK 11(22Q12.1) MUTATED        3      8      5      3
  DEL PEAK 11(22Q12.1) WILD-TYPE     26     25     28     25
D11V10, multiclass
        clus
vv       DEL PEAK 11(22Q12.1) MUTATED DEL PEAK 11(22Q12.1) WILD-TYPE
  CLUS_1                            3                             26
  CLUS_2                            8                             25
  CLUS_3                            5                             28
  CLUS_4                            3                             25
[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"

Clustering(12) Variable = DEL PEAK 12(22Q13.32) MUTATION ANALYSIS
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 12(22Q13.32) MUTATED        1      4     10
  DEL PEAK 12(22Q13.32) WILD-TYPE     64     27     17
D12V1, multiclass
        clus
vv       DEL PEAK 12(22Q13.32) MUTATED DEL PEAK 12(22Q13.32) WILD-TYPE
  CLUS_1                             1                              64
  CLUS_2                             4                              27
  CLUS_3                            10                              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 CLUS_4
  DEL PEAK 12(22Q13.32) MUTATED        1      6      3      5
  DEL PEAK 12(22Q13.32) WILD-TYPE     38     30     21     19
D12V2, multiclass
        clus
vv       DEL PEAK 12(22Q13.32) MUTATED DEL PEAK 12(22Q13.32) WILD-TYPE
  CLUS_1                             1                              38
  CLUS_2                             6                              30
  CLUS_3                             3                              21
  CLUS_4                             5                              19
[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
  DEL PEAK 12(22Q13.32) MUTATED        5      5      1
  DEL PEAK 12(22Q13.32) WILD-TYPE     22     19     38
D12V3, multiclass
        clus
vv       DEL PEAK 12(22Q13.32) MUTATED DEL PEAK 12(22Q13.32) WILD-TYPE
  CLUS_1                             5                              22
  CLUS_2                             5                              19
  CLUS_3                             1                              38
[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
  DEL PEAK 12(22Q13.32) MUTATED        4      2      1      4
  DEL PEAK 12(22Q13.32) WILD-TYPE     12     21     30     16
D12V4, multiclass
        clus
vv       DEL PEAK 12(22Q13.32) MUTATED DEL PEAK 12(22Q13.32) WILD-TYPE
  CLUS_1                             4                              12
  CLUS_2                             2                              21
  CLUS_3                             1                              30
  CLUS_4                             4                              16
[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
  DEL PEAK 12(22Q13.32) MUTATED        2      4      5      4
  DEL PEAK 12(22Q13.32) WILD-TYPE     43     27     24     10
D12V5, multiclass
        clus
vv       DEL PEAK 12(22Q13.32) MUTATED DEL PEAK 12(22Q13.32) WILD-TYPE
  CLUS_1                             2                              43
  CLUS_2                             4                              27
  CLUS_3                             5                              24
  CLUS_4                             4                              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
  DEL PEAK 12(22Q13.32) MUTATED        3      4      4      4
  DEL PEAK 12(22Q13.32) WILD-TYPE     44     38     16      6
D12V6, multiclass
        clus
vv       DEL PEAK 12(22Q13.32) MUTATED DEL PEAK 12(22Q13.32) WILD-TYPE
  CLUS_1                             3                              44
  CLUS_2                             4                              38
  CLUS_3                             4                              16
  CLUS_4                             4                               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
  DEL PEAK 12(22Q13.32) MUTATED        8      6      1      0      0
  DEL PEAK 12(22Q13.32) WILD-TYPE     50     55      0      2      1
D12V7, multiclass
        clus
vv       DEL PEAK 12(22Q13.32) MUTATED DEL PEAK 12(22Q13.32) WILD-TYPE
  CLUS_1                             8                              50
  CLUS_2                             6                              55
  CLUS_3                             1                               0
  CLUS_4                             0                               2
  CLUS_5                             0                               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 12(22Q13.32) MUTATED        4      0      3      2      3      3
  DEL PEAK 12(22Q13.32) WILD-TYPE     23     18     25      5     13     24
D12V8, multiclass
        clus
vv       DEL PEAK 12(22Q13.32) MUTATED DEL PEAK 12(22Q13.32) WILD-TYPE
  CLUS_1                             4                              23
  CLUS_2                             0                              18
  CLUS_3                             3                              25
  CLUS_4                             2                               5
  CLUS_5                             3                              13
  CLUS_6                             3                              24
[1] 6 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
  DEL PEAK 12(22Q13.32) MUTATED        1      5      9
  DEL PEAK 12(22Q13.32) WILD-TYPE     17     54     37
D12V9, multiclass
        clus
vv       DEL PEAK 12(22Q13.32) MUTATED DEL PEAK 12(22Q13.32) WILD-TYPE
  CLUS_1                             1                              17
  CLUS_2                             5                              54
  CLUS_3                             9                              37
[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
  DEL PEAK 12(22Q13.32) MUTATED        4      3      5      3
  DEL PEAK 12(22Q13.32) WILD-TYPE     25     30     28     25
D12V10, multiclass
        clus
vv       DEL PEAK 12(22Q13.32) MUTATED DEL PEAK 12(22Q13.32) WILD-TYPE
  CLUS_1                             4                              25
  CLUS_2                             3                              30
  CLUS_3                             5                              28
  CLUS_4                             3                              25
[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"
