[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTDLBC-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/DLBC-TP/10668122/DLBC-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/DLBC-TP/10013676/transformed.cor.cli.txt"

nPatients in clinical file=48, in cluster file=28, common to both=28
[1] "Reduce the number of clustering variables from 26 to 24."
[1] 24 28
[1] "AMP PEAK 1(1Q31.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 1(1Q31.1) MUTATED AMP PEAK 1(1Q31.1) WILD-TYPE 
                           9                           19 
  AMP PEAK 1(1Q31.1) MUTATED AMP PEAK 1(1Q31.1) WILD-TYPE 
                           9                           19 
[1] "AMP PEAK 2(2P15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 2(2P15) MUTATED AMP PEAK 2(2P15) WILD-TYPE 
                         8                         20 
  AMP PEAK 2(2P15) MUTATED AMP PEAK 2(2P15) WILD-TYPE 
                         8                         20 
[1] "AMP PEAK 3(3Q27.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 3(3Q27.3) MUTATED AMP PEAK 3(3Q27.3) WILD-TYPE 
                           7                           21 
  AMP PEAK 3(3Q27.3) MUTATED AMP PEAK 3(3Q27.3) WILD-TYPE 
                           7                           21 
[1] "AMP PEAK 4(8Q24.12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 4(8Q24.12) MUTATED AMP PEAK 4(8Q24.12) WILD-TYPE 
                            6                            22 
  AMP PEAK 4(8Q24.12) MUTATED AMP PEAK 4(8Q24.12) WILD-TYPE 
                            6                            22 
[1] "AMP PEAK 5(12Q13.12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 5(12Q13.12) MUTATED AMP PEAK 5(12Q13.12) WILD-TYPE 
                             5                             23 
  AMP PEAK 5(12Q13.12) MUTATED AMP PEAK 5(12Q13.12) WILD-TYPE 
                             5                             23 
[1] "AMP PEAK 6(16P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 6(16P11.2) MUTATED AMP PEAK 6(16P11.2) WILD-TYPE 
                            6                            22 
  AMP PEAK 6(16P11.2) MUTATED AMP PEAK 6(16P11.2) WILD-TYPE 
                            6                            22 
[1] "AMP PEAK 7(XQ27.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 7(XQ27.3) MUTATED AMP PEAK 7(XQ27.3) WILD-TYPE 
                           6                           22 
  AMP PEAK 7(XQ27.3) MUTATED AMP PEAK 7(XQ27.3) WILD-TYPE 
                           6                           22 
[1] "DEL PEAK  1(1P22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE 
                            4                            24 
  DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE 
                            4                            24 
[1] "DEL PEAK  2(1P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                            7                            21 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                            7                            21 
[1] "DEL PEAK  3(1Q43) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                          7                          21 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                          7                          21 
[1] "DEL PEAK  4(2Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE 
                            6                            22 
  DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE 
                            6                            22 
[1] "DEL PEAK  5(6Q14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE 
                            9                            19 
  DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE 
                            9                            19 
[1] "DEL PEAK  6(6Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(6Q23.3) MUTATED DEL PEAK  6(6Q23.3) WILD-TYPE 
                            7                            21 
  DEL PEAK  6(6Q23.3) MUTATED DEL PEAK  6(6Q23.3) WILD-TYPE 
                            7                            21 
[1] "DEL PEAK  8(8P23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(8P23.1) MUTATED DEL PEAK  8(8P23.1) WILD-TYPE 
                            4                            24 
  DEL PEAK  8(8P23.1) MUTATED DEL PEAK  8(8P23.1) WILD-TYPE 
                            4                            24 
[1] "DEL PEAK  9(8Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(8Q12.1) MUTATED DEL PEAK  9(8Q12.1) WILD-TYPE 
                            4                            24 
  DEL PEAK  9(8Q12.1) MUTATED DEL PEAK  9(8Q12.1) WILD-TYPE 
                            4                            24 
[1] "DEL PEAK 10(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE 
                            9                            19 
  DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE 
                            9                            19 
[1] "DEL PEAK 11(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE 
                              5                              23 
  DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE 
                              5                              23 
[1] "DEL PEAK 12(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(13Q14.2) MUTATED DEL PEAK 12(13Q14.2) WILD-TYPE 
                             3                             25 
  DEL PEAK 12(13Q14.2) MUTATED DEL PEAK 12(13Q14.2) WILD-TYPE 
                             3                             25 
[1] "DEL PEAK 13(13Q33.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(13Q33.3) MUTATED DEL PEAK 13(13Q33.3) WILD-TYPE 
                             4                             24 
  DEL PEAK 13(13Q33.3) MUTATED DEL PEAK 13(13Q33.3) WILD-TYPE 
                             4                             24 
[1] "DEL PEAK 14(15Q15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE 
                             8                             20 
  DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE 
                             8                             20 
[1] "DEL PEAK 15(15Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(15Q21.1) MUTATED DEL PEAK 15(15Q21.1) WILD-TYPE 
                             9                             19 
  DEL PEAK 15(15Q21.1) MUTATED DEL PEAK 15(15Q21.1) WILD-TYPE 
                             9                             19 
[1] "DEL PEAK 16(16P13.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(16P13.13) MUTATED DEL PEAK 16(16P13.13) WILD-TYPE 
                              4                              24 
  DEL PEAK 16(16P13.13) MUTATED DEL PEAK 16(16P13.13) WILD-TYPE 
                              4                              24 
[1] "DEL PEAK 17(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE 
                             5                             23 
  DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE 
                             5                             23 
[1] "DEL PEAK 18(17Q24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(17Q24.1) MUTATED DEL PEAK 18(17Q24.1) WILD-TYPE 
                             4                             24 
  DEL PEAK 18(17Q24.1) MUTATED DEL PEAK 18(17Q24.1) WILD-TYPE 
                             4                             24 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
[1] "METHLYATION_CNMF"            "MRNASEQ_CNMF"               
[3] "MRNASEQ_CHIERARCHICAL"       "MIRSEQ_CNMF"                
[5] "MIRSEQ_CHIERARCHICAL"        "MIRSEQ_MATURE_CNMF"         
[7] "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 7 rows and 28 columns.

Variable 1:'METHLYATION_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNASEQ_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MIRSEQ_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MIRSEQ_MATURE_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "METHLYATION_CNMF"            "MRNASEQ_CNMF"               
[3] "MRNASEQ_CHIERARCHICAL"       "MIRSEQ_CNMF"                
[5] "MIRSEQ_CHIERARCHICAL"        "MIRSEQ_MATURE_CNMF"         
[7] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 28 columns, 0 survival variables, and 7 non-survival variables.
METHLYATION_CNMF, nv=2, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=2, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=2, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=8, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=9, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK 1(1Q31.1) MUTATION ANALYSIS
D1V1, binary
                              cls
clus                            0  1
  AMP PEAK 1(1Q31.1) MUTATED    6  3
  AMP PEAK 1(1Q31.1) WILD-TYPE  9 10
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(1Q31.1) MUTATED      6    3
  AMP PEAK 1(1Q31.1) WILD-TYPE    9   10
        clus
vv       AMP PEAK 1(1Q31.1) MUTATED AMP PEAK 1(1Q31.1) WILD-TYPE
  CLUS_1                          6                            9
  CLUS_2                          3                           10
[1] 2 2
[1] FALSE
D1V2, binary
                              cls
clus                            0  1
  AMP PEAK 1(1Q31.1) MUTATED    3  6
  AMP PEAK 1(1Q31.1) WILD-TYPE 12  7
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(1Q31.1) MUTATED      3    6
  AMP PEAK 1(1Q31.1) WILD-TYPE   12    7
        clus
vv       AMP PEAK 1(1Q31.1) MUTATED AMP PEAK 1(1Q31.1) WILD-TYPE
  CLUS_1                          3                           12
  CLUS_2                          6                            7
[1] 2 2
[1] FALSE
                              vv
clus                           CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 1(1Q31.1) MUTATED        2      6      1
  AMP PEAK 1(1Q31.1) WILD-TYPE     11      4      4
D1V3, multiclass
        clus
vv       AMP PEAK 1(1Q31.1) MUTATED AMP PEAK 1(1Q31.1) WILD-TYPE
  CLUS_1                          2                           11
  CLUS_2                          6                            4
  CLUS_3                          1                            4
[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"
D1V4, binary
                              cls
clus                            0  1
  AMP PEAK 1(1Q31.1) MUTATED    2  7
  AMP PEAK 1(1Q31.1) WILD-TYPE 12  6
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(1Q31.1) MUTATED      2    7
  AMP PEAK 1(1Q31.1) WILD-TYPE   12    6
        clus
vv       AMP PEAK 1(1Q31.1) MUTATED AMP PEAK 1(1Q31.1) WILD-TYPE
  CLUS_1                          2                           12
  CLUS_2                          7                            6
[1] 2 2
[1] FALSE
                              vv
clus                           CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  AMP PEAK 1(1Q31.1) MUTATED        0      1      2      2      2      0      2
  AMP PEAK 1(1Q31.1) WILD-TYPE      2      1      3      2      3      3      1
                              vv
clus                           CLUS_8
  AMP PEAK 1(1Q31.1) MUTATED        0
  AMP PEAK 1(1Q31.1) WILD-TYPE      3
D1V5, multiclass
        clus
vv       AMP PEAK 1(1Q31.1) MUTATED AMP PEAK 1(1Q31.1) WILD-TYPE
  CLUS_1                          0                            2
  CLUS_2                          1                            1
  CLUS_3                          2                            3
  CLUS_4                          2                            2
  CLUS_5                          2                            3
  CLUS_6                          0                            3
  CLUS_7                          2                            1
  CLUS_8                          0                            3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 1(1Q31.1) MUTATED        2      3      4
  AMP PEAK 1(1Q31.1) WILD-TYPE      7      6      5
D1V6, multiclass
        clus
vv       AMP PEAK 1(1Q31.1) MUTATED AMP PEAK 1(1Q31.1) WILD-TYPE
  CLUS_1                          2                            7
  CLUS_2                          3                            6
  CLUS_3                          4                            5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  AMP PEAK 1(1Q31.1) MUTATED        0      2      2      1      0      0      2
  AMP PEAK 1(1Q31.1) WILD-TYPE      4      1      2      1      3      2      2
                              vv
clus                           CLUS_8 CLUS_9
  AMP PEAK 1(1Q31.1) MUTATED        2      0
  AMP PEAK 1(1Q31.1) WILD-TYPE      1      2
D1V7, multiclass
        clus
vv       AMP PEAK 1(1Q31.1) MUTATED AMP PEAK 1(1Q31.1) WILD-TYPE
  CLUS_1                          0                            4
  CLUS_2                          2                            1
  CLUS_3                          2                            2
  CLUS_4                          1                            1
  CLUS_5                          0                            3
  CLUS_6                          0                            2
  CLUS_7                          2                            2
  CLUS_8                          2                            1
  CLUS_9                          0                            2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = AMP PEAK 2(2P15) MUTATION ANALYSIS
D2V1, binary
                            cls
clus                          0  1
  AMP PEAK 2(2P15) MUTATED    0  8
  AMP PEAK 2(2P15) WILD-TYPE 15  5
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 2(2P15) MUTATED      0    8
  AMP PEAK 2(2P15) WILD-TYPE   15    5
        clus
vv       AMP PEAK 2(2P15) MUTATED AMP PEAK 2(2P15) WILD-TYPE
  CLUS_1                        0                         15
  CLUS_2                        8                          5
[1] 2 2
[1] FALSE
D2V2, binary
                            cls
clus                          0  1
  AMP PEAK 2(2P15) MUTATED    5  3
  AMP PEAK 2(2P15) WILD-TYPE 10 10
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 2(2P15) MUTATED      5    3
  AMP PEAK 2(2P15) WILD-TYPE   10   10
        clus
vv       AMP PEAK 2(2P15) MUTATED AMP PEAK 2(2P15) WILD-TYPE
  CLUS_1                        5                         10
  CLUS_2                        3                         10
[1] 2 2
[1] FALSE
                            vv
clus                         CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 2(2P15) MUTATED        4      2      2
  AMP PEAK 2(2P15) WILD-TYPE      9      8      3
D2V3, multiclass
        clus
vv       AMP PEAK 2(2P15) MUTATED AMP PEAK 2(2P15) WILD-TYPE
  CLUS_1                        4                          9
  CLUS_2                        2                          8
  CLUS_3                        2                          3
[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"
D2V4, binary
                            cls
clus                          0  1
  AMP PEAK 2(2P15) MUTATED    4  4
  AMP PEAK 2(2P15) WILD-TYPE 10  9
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 2(2P15) MUTATED      4    4
  AMP PEAK 2(2P15) WILD-TYPE   10    9
        clus
vv       AMP PEAK 2(2P15) MUTATED AMP PEAK 2(2P15) WILD-TYPE
  CLUS_1                        4                         10
  CLUS_2                        4                          9
[1] 2 2
[1] FALSE
                            vv
clus                         CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  AMP PEAK 2(2P15) MUTATED        1      0      2      0      4      0      0
  AMP PEAK 2(2P15) WILD-TYPE      1      2      3      4      1      3      3
                            vv
clus                         CLUS_8
  AMP PEAK 2(2P15) MUTATED        1
  AMP PEAK 2(2P15) WILD-TYPE      2
D2V5, multiclass
        clus
vv       AMP PEAK 2(2P15) MUTATED AMP PEAK 2(2P15) WILD-TYPE
  CLUS_1                        1                          1
  CLUS_2                        0                          2
  CLUS_3                        2                          3
  CLUS_4                        0                          4
  CLUS_5                        4                          1
  CLUS_6                        0                          3
  CLUS_7                        0                          3
  CLUS_8                        1                          2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                            vv
clus                         CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 2(2P15) MUTATED        3      1      4
  AMP PEAK 2(2P15) WILD-TYPE      6      8      5
D2V6, multiclass
        clus
vv       AMP PEAK 2(2P15) MUTATED AMP PEAK 2(2P15) WILD-TYPE
  CLUS_1                        3                          6
  CLUS_2                        1                          8
  CLUS_3                        4                          5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                            vv
clus                         CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  AMP PEAK 2(2P15) MUTATED        1      0      2      0      2      0      3
  AMP PEAK 2(2P15) WILD-TYPE      3      3      2      2      1      2      1
                            vv
clus                         CLUS_8 CLUS_9
  AMP PEAK 2(2P15) MUTATED        0      0
  AMP PEAK 2(2P15) WILD-TYPE      3      2
D2V7, multiclass
        clus
vv       AMP PEAK 2(2P15) MUTATED AMP PEAK 2(2P15) WILD-TYPE
  CLUS_1                        1                          3
  CLUS_2                        0                          3
  CLUS_3                        2                          2
  CLUS_4                        0                          2
  CLUS_5                        2                          1
  CLUS_6                        0                          2
  CLUS_7                        3                          1
  CLUS_8                        0                          3
  CLUS_9                        0                          2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = AMP PEAK 3(3Q27.3) MUTATION ANALYSIS
D3V1, binary
                              cls
clus                            0  1
  AMP PEAK 3(3Q27.3) MUTATED    4  3
  AMP PEAK 3(3Q27.3) WILD-TYPE 11 10
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 3(3Q27.3) MUTATED      4    3
  AMP PEAK 3(3Q27.3) WILD-TYPE   11   10
        clus
vv       AMP PEAK 3(3Q27.3) MUTATED AMP PEAK 3(3Q27.3) WILD-TYPE
  CLUS_1                          4                           11
  CLUS_2                          3                           10
[1] 2 2
[1] FALSE
D3V2, binary
                              cls
clus                            0  1
  AMP PEAK 3(3Q27.3) MUTATED    5  2
  AMP PEAK 3(3Q27.3) WILD-TYPE 10 11
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 3(3Q27.3) MUTATED      5    2
  AMP PEAK 3(3Q27.3) WILD-TYPE   10   11
        clus
vv       AMP PEAK 3(3Q27.3) MUTATED AMP PEAK 3(3Q27.3) WILD-TYPE
  CLUS_1                          5                           10
  CLUS_2                          2                           11
[1] 2 2
[1] FALSE
                              vv
clus                           CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 3(3Q27.3) MUTATED        3      2      2
  AMP PEAK 3(3Q27.3) WILD-TYPE     10      8      3
D3V3, multiclass
        clus
vv       AMP PEAK 3(3Q27.3) MUTATED AMP PEAK 3(3Q27.3) WILD-TYPE
  CLUS_1                          3                           10
  CLUS_2                          2                            8
  CLUS_3                          2                            3
[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"
D3V4, binary
                              cls
clus                            0  1
  AMP PEAK 3(3Q27.3) MUTATED    5  2
  AMP PEAK 3(3Q27.3) WILD-TYPE  9 11
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 3(3Q27.3) MUTATED      5    2
  AMP PEAK 3(3Q27.3) WILD-TYPE    9   11
        clus
vv       AMP PEAK 3(3Q27.3) MUTATED AMP PEAK 3(3Q27.3) WILD-TYPE
  CLUS_1                          5                            9
  CLUS_2                          2                           11
[1] 2 2
[1] FALSE
                              vv
clus                           CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  AMP PEAK 3(3Q27.3) MUTATED        0      0      3      2      0      2      0
  AMP PEAK 3(3Q27.3) WILD-TYPE      2      2      2      2      5      1      3
                              vv
clus                           CLUS_8
  AMP PEAK 3(3Q27.3) MUTATED        0
  AMP PEAK 3(3Q27.3) WILD-TYPE      3
D3V5, multiclass
        clus
vv       AMP PEAK 3(3Q27.3) MUTATED AMP PEAK 3(3Q27.3) WILD-TYPE
  CLUS_1                          0                            2
  CLUS_2                          0                            2
  CLUS_3                          3                            2
  CLUS_4                          2                            2
  CLUS_5                          0                            5
  CLUS_6                          2                            1
  CLUS_7                          0                            3
  CLUS_8                          0                            3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 3(3Q27.3) MUTATED        4      2      1
  AMP PEAK 3(3Q27.3) WILD-TYPE      5      7      8
D3V6, multiclass
        clus
vv       AMP PEAK 3(3Q27.3) MUTATED AMP PEAK 3(3Q27.3) WILD-TYPE
  CLUS_1                          4                            5
  CLUS_2                          2                            7
  CLUS_3                          1                            8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  AMP PEAK 3(3Q27.3) MUTATED        1      0      2      2      0      2      0
  AMP PEAK 3(3Q27.3) WILD-TYPE      3      3      2      0      3      0      4
                              vv
clus                           CLUS_8 CLUS_9
  AMP PEAK 3(3Q27.3) MUTATED        0      0
  AMP PEAK 3(3Q27.3) WILD-TYPE      3      2
D3V7, multiclass
        clus
vv       AMP PEAK 3(3Q27.3) MUTATED AMP PEAK 3(3Q27.3) WILD-TYPE
  CLUS_1                          1                            3
  CLUS_2                          0                            3
  CLUS_3                          2                            2
  CLUS_4                          2                            0
  CLUS_5                          0                            3
  CLUS_6                          2                            0
  CLUS_7                          0                            4
  CLUS_8                          0                            3
  CLUS_9                          0                            2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = AMP PEAK 4(8Q24.12) MUTATION ANALYSIS
D4V1, binary
                               cls
clus                             0  1
  AMP PEAK 4(8Q24.12) MUTATED    2  4
  AMP PEAK 4(8Q24.12) WILD-TYPE 13  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 4(8Q24.12) MUTATED      2    4
  AMP PEAK 4(8Q24.12) WILD-TYPE   13    9
        clus
vv       AMP PEAK 4(8Q24.12) MUTATED AMP PEAK 4(8Q24.12) WILD-TYPE
  CLUS_1                           2                            13
  CLUS_2                           4                             9
[1] 2 2
[1] FALSE
D4V2, binary
                               cls
clus                             0  1
  AMP PEAK 4(8Q24.12) MUTATED    3  3
  AMP PEAK 4(8Q24.12) WILD-TYPE 12 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 4(8Q24.12) MUTATED      3    3
  AMP PEAK 4(8Q24.12) WILD-TYPE   12   10
        clus
vv       AMP PEAK 4(8Q24.12) MUTATED AMP PEAK 4(8Q24.12) WILD-TYPE
  CLUS_1                           3                            12
  CLUS_2                           3                            10
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 4(8Q24.12) MUTATED        4      2      0
  AMP PEAK 4(8Q24.12) WILD-TYPE      9      8      5
D4V3, multiclass
        clus
vv       AMP PEAK 4(8Q24.12) MUTATED AMP PEAK 4(8Q24.12) WILD-TYPE
  CLUS_1                           4                             9
  CLUS_2                           2                             8
  CLUS_3                           0                             5
[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"
D4V4, binary
                               cls
clus                             0  1
  AMP PEAK 4(8Q24.12) MUTATED    3  3
  AMP PEAK 4(8Q24.12) WILD-TYPE 11 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 4(8Q24.12) MUTATED      3    3
  AMP PEAK 4(8Q24.12) WILD-TYPE   11   10
        clus
vv       AMP PEAK 4(8Q24.12) MUTATED AMP PEAK 4(8Q24.12) WILD-TYPE
  CLUS_1                           3                            11
  CLUS_2                           3                            10
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  AMP PEAK 4(8Q24.12) MUTATED        1      0      0      1      3      1
  AMP PEAK 4(8Q24.12) WILD-TYPE      1      2      5      3      2      2
                               vv
clus                            CLUS_7 CLUS_8
  AMP PEAK 4(8Q24.12) MUTATED        0      0
  AMP PEAK 4(8Q24.12) WILD-TYPE      3      3
D4V5, multiclass
        clus
vv       AMP PEAK 4(8Q24.12) MUTATED AMP PEAK 4(8Q24.12) WILD-TYPE
  CLUS_1                           1                             1
  CLUS_2                           0                             2
  CLUS_3                           0                             5
  CLUS_4                           1                             3
  CLUS_5                           3                             2
  CLUS_6                           1                             2
  CLUS_7                           0                             3
  CLUS_8                           0                             3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 4(8Q24.12) MUTATED        1      1      4
  AMP PEAK 4(8Q24.12) WILD-TYPE      8      8      5
D4V6, multiclass
        clus
vv       AMP PEAK 4(8Q24.12) MUTATED AMP PEAK 4(8Q24.12) WILD-TYPE
  CLUS_1                           1                             8
  CLUS_2                           1                             8
  CLUS_3                           4                             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  AMP PEAK 4(8Q24.12) MUTATED        1      0      0      1      1      1
  AMP PEAK 4(8Q24.12) WILD-TYPE      3      3      4      1      2      1
                               vv
clus                            CLUS_7 CLUS_8 CLUS_9
  AMP PEAK 4(8Q24.12) MUTATED        2      0      0
  AMP PEAK 4(8Q24.12) WILD-TYPE      2      3      2
D4V7, multiclass
        clus
vv       AMP PEAK 4(8Q24.12) MUTATED AMP PEAK 4(8Q24.12) WILD-TYPE
  CLUS_1                           1                             3
  CLUS_2                           0                             3
  CLUS_3                           0                             4
  CLUS_4                           1                             1
  CLUS_5                           1                             2
  CLUS_6                           1                             1
  CLUS_7                           2                             2
  CLUS_8                           0                             3
  CLUS_9                           0                             2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = AMP PEAK 5(12Q13.12) MUTATION ANALYSIS
D5V1, binary
                                cls
clus                              0  1
  AMP PEAK 5(12Q13.12) MUTATED    1  4
  AMP PEAK 5(12Q13.12) WILD-TYPE 14  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 5(12Q13.12) MUTATED      1    4
  AMP PEAK 5(12Q13.12) WILD-TYPE   14    9
        clus
vv       AMP PEAK 5(12Q13.12) MUTATED AMP PEAK 5(12Q13.12) WILD-TYPE
  CLUS_1                            1                             14
  CLUS_2                            4                              9
[1] 2 2
[1] FALSE
D5V2, binary
                                cls
clus                              0  1
  AMP PEAK 5(12Q13.12) MUTATED    3  2
  AMP PEAK 5(12Q13.12) WILD-TYPE 12 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 5(12Q13.12) MUTATED      3    2
  AMP PEAK 5(12Q13.12) WILD-TYPE   12   11
        clus
vv       AMP PEAK 5(12Q13.12) MUTATED AMP PEAK 5(12Q13.12) WILD-TYPE
  CLUS_1                            3                             12
  CLUS_2                            2                             11
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 5(12Q13.12) MUTATED        3      0      2
  AMP PEAK 5(12Q13.12) WILD-TYPE     10     10      3
D5V3, multiclass
        clus
vv       AMP PEAK 5(12Q13.12) MUTATED AMP PEAK 5(12Q13.12) WILD-TYPE
  CLUS_1                            3                             10
  CLUS_2                            0                             10
  CLUS_3                            2                              3
[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"
D5V4, binary
                                cls
clus                              0  1
  AMP PEAK 5(12Q13.12) MUTATED    4  1
  AMP PEAK 5(12Q13.12) WILD-TYPE 10 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 5(12Q13.12) MUTATED      4    1
  AMP PEAK 5(12Q13.12) WILD-TYPE   10   12
        clus
vv       AMP PEAK 5(12Q13.12) MUTATED AMP PEAK 5(12Q13.12) WILD-TYPE
  CLUS_1                            4                             10
  CLUS_2                            1                             12
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  AMP PEAK 5(12Q13.12) MUTATED        0      1      2      0      2      0
  AMP PEAK 5(12Q13.12) WILD-TYPE      2      1      3      4      3      3
                                vv
clus                             CLUS_7 CLUS_8
  AMP PEAK 5(12Q13.12) MUTATED        0      0
  AMP PEAK 5(12Q13.12) WILD-TYPE      3      3
D5V5, multiclass
        clus
vv       AMP PEAK 5(12Q13.12) MUTATED AMP PEAK 5(12Q13.12) WILD-TYPE
  CLUS_1                            0                              2
  CLUS_2                            1                              1
  CLUS_3                            2                              3
  CLUS_4                            0                              4
  CLUS_5                            2                              3
  CLUS_6                            0                              3
  CLUS_7                            0                              3
  CLUS_8                            0                              3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 5(12Q13.12) MUTATED        2      1      2
  AMP PEAK 5(12Q13.12) WILD-TYPE      7      8      7
D5V6, multiclass
        clus
vv       AMP PEAK 5(12Q13.12) MUTATED AMP PEAK 5(12Q13.12) WILD-TYPE
  CLUS_1                            2                              7
  CLUS_2                            1                              8
  CLUS_3                            2                              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  AMP PEAK 5(12Q13.12) MUTATED        1      1      1      0      1      0
  AMP PEAK 5(12Q13.12) WILD-TYPE      3      2      3      2      2      2
                                vv
clus                             CLUS_7 CLUS_8 CLUS_9
  AMP PEAK 5(12Q13.12) MUTATED        1      0      0
  AMP PEAK 5(12Q13.12) WILD-TYPE      3      3      2
D5V7, multiclass
        clus
vv       AMP PEAK 5(12Q13.12) MUTATED AMP PEAK 5(12Q13.12) WILD-TYPE
  CLUS_1                            1                              3
  CLUS_2                            1                              2
  CLUS_3                            1                              3
  CLUS_4                            0                              2
  CLUS_5                            1                              2
  CLUS_6                            0                              2
  CLUS_7                            1                              3
  CLUS_8                            0                              3
  CLUS_9                            0                              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = AMP PEAK 6(16P11.2) MUTATION ANALYSIS
D6V1, binary
                               cls
clus                             0  1
  AMP PEAK 6(16P11.2) MUTATED    1  5
  AMP PEAK 6(16P11.2) WILD-TYPE 14  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(16P11.2) MUTATED      1    5
  AMP PEAK 6(16P11.2) WILD-TYPE   14    8
        clus
vv       AMP PEAK 6(16P11.2) MUTATED AMP PEAK 6(16P11.2) WILD-TYPE
  CLUS_1                           1                            14
  CLUS_2                           5                             8
[1] 2 2
[1] FALSE
D6V2, binary
                               cls
clus                             0  1
  AMP PEAK 6(16P11.2) MUTATED    5  1
  AMP PEAK 6(16P11.2) WILD-TYPE 10 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(16P11.2) MUTATED      5    1
  AMP PEAK 6(16P11.2) WILD-TYPE   10   12
        clus
vv       AMP PEAK 6(16P11.2) MUTATED AMP PEAK 6(16P11.2) WILD-TYPE
  CLUS_1                           5                            10
  CLUS_2                           1                            12
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 6(16P11.2) MUTATED        3      1      2
  AMP PEAK 6(16P11.2) WILD-TYPE     10      9      3
D6V3, multiclass
        clus
vv       AMP PEAK 6(16P11.2) MUTATED AMP PEAK 6(16P11.2) WILD-TYPE
  CLUS_1                           3                            10
  CLUS_2                           1                             9
  CLUS_3                           2                             3
[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"
D6V4, binary
                               cls
clus                             0  1
  AMP PEAK 6(16P11.2) MUTATED    4  2
  AMP PEAK 6(16P11.2) WILD-TYPE 10 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(16P11.2) MUTATED      4    2
  AMP PEAK 6(16P11.2) WILD-TYPE   10   11
        clus
vv       AMP PEAK 6(16P11.2) MUTATED AMP PEAK 6(16P11.2) WILD-TYPE
  CLUS_1                           4                            10
  CLUS_2                           2                            11
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  AMP PEAK 6(16P11.2) MUTATED        0      0      2      0      2      1
  AMP PEAK 6(16P11.2) WILD-TYPE      2      2      3      4      3      2
                               vv
clus                            CLUS_7 CLUS_8
  AMP PEAK 6(16P11.2) MUTATED        0      1
  AMP PEAK 6(16P11.2) WILD-TYPE      3      2
D6V5, multiclass
        clus
vv       AMP PEAK 6(16P11.2) MUTATED AMP PEAK 6(16P11.2) WILD-TYPE
  CLUS_1                           0                             2
  CLUS_2                           0                             2
  CLUS_3                           2                             3
  CLUS_4                           0                             4
  CLUS_5                           2                             3
  CLUS_6                           1                             2
  CLUS_7                           0                             3
  CLUS_8                           1                             2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 6(16P11.2) MUTATED        3      1      2
  AMP PEAK 6(16P11.2) WILD-TYPE      6      8      7
D6V6, multiclass
        clus
vv       AMP PEAK 6(16P11.2) MUTATED AMP PEAK 6(16P11.2) WILD-TYPE
  CLUS_1                           3                             6
  CLUS_2                           1                             8
  CLUS_3                           2                             7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  AMP PEAK 6(16P11.2) MUTATED        1      0      1      0      1      1
  AMP PEAK 6(16P11.2) WILD-TYPE      3      3      3      2      2      1
                               vv
clus                            CLUS_7 CLUS_8 CLUS_9
  AMP PEAK 6(16P11.2) MUTATED        2      0      0
  AMP PEAK 6(16P11.2) WILD-TYPE      2      3      2
D6V7, multiclass
        clus
vv       AMP PEAK 6(16P11.2) MUTATED AMP PEAK 6(16P11.2) WILD-TYPE
  CLUS_1                           1                             3
  CLUS_2                           0                             3
  CLUS_3                           1                             3
  CLUS_4                           0                             2
  CLUS_5                           1                             2
  CLUS_6                           1                             1
  CLUS_7                           2                             2
  CLUS_8                           0                             3
  CLUS_9                           0                             2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = AMP PEAK 7(XQ27.3) MUTATION ANALYSIS
D7V1, binary
                              cls
clus                            0  1
  AMP PEAK 7(XQ27.3) MUTATED    1  5
  AMP PEAK 7(XQ27.3) WILD-TYPE 14  8
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 7(XQ27.3) MUTATED      1    5
  AMP PEAK 7(XQ27.3) WILD-TYPE   14    8
        clus
vv       AMP PEAK 7(XQ27.3) MUTATED AMP PEAK 7(XQ27.3) WILD-TYPE
  CLUS_1                          1                           14
  CLUS_2                          5                            8
[1] 2 2
[1] FALSE
D7V2, binary
                              cls
clus                            0  1
  AMP PEAK 7(XQ27.3) MUTATED    4  2
  AMP PEAK 7(XQ27.3) WILD-TYPE 11 11
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 7(XQ27.3) MUTATED      4    2
  AMP PEAK 7(XQ27.3) WILD-TYPE   11   11
        clus
vv       AMP PEAK 7(XQ27.3) MUTATED AMP PEAK 7(XQ27.3) WILD-TYPE
  CLUS_1                          4                           11
  CLUS_2                          2                           11
[1] 2 2
[1] FALSE
                              vv
clus                           CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 7(XQ27.3) MUTATED        4      1      1
  AMP PEAK 7(XQ27.3) WILD-TYPE      9      9      4
D7V3, multiclass
        clus
vv       AMP PEAK 7(XQ27.3) MUTATED AMP PEAK 7(XQ27.3) WILD-TYPE
  CLUS_1                          4                            9
  CLUS_2                          1                            9
  CLUS_3                          1                            4
[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"
D7V4, binary
                              cls
clus                            0  1
  AMP PEAK 7(XQ27.3) MUTATED    4  2
  AMP PEAK 7(XQ27.3) WILD-TYPE 10 11
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 7(XQ27.3) MUTATED      4    2
  AMP PEAK 7(XQ27.3) WILD-TYPE   10   11
        clus
vv       AMP PEAK 7(XQ27.3) MUTATED AMP PEAK 7(XQ27.3) WILD-TYPE
  CLUS_1                          4                           10
  CLUS_2                          2                           11
[1] 2 2
[1] FALSE
                              vv
clus                           CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  AMP PEAK 7(XQ27.3) MUTATED        0      0      2      1      2      1      0
  AMP PEAK 7(XQ27.3) WILD-TYPE      2      2      3      3      3      2      3
                              vv
clus                           CLUS_8
  AMP PEAK 7(XQ27.3) MUTATED        0
  AMP PEAK 7(XQ27.3) WILD-TYPE      3
D7V5, multiclass
        clus
vv       AMP PEAK 7(XQ27.3) MUTATED AMP PEAK 7(XQ27.3) WILD-TYPE
  CLUS_1                          0                            2
  CLUS_2                          0                            2
  CLUS_3                          2                            3
  CLUS_4                          1                            3
  CLUS_5                          2                            3
  CLUS_6                          1                            2
  CLUS_7                          0                            3
  CLUS_8                          0                            3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 7(XQ27.3) MUTATED        2      1      3
  AMP PEAK 7(XQ27.3) WILD-TYPE      7      8      6
D7V6, multiclass
        clus
vv       AMP PEAK 7(XQ27.3) MUTATED AMP PEAK 7(XQ27.3) WILD-TYPE
  CLUS_1                          2                            7
  CLUS_2                          1                            8
  CLUS_3                          3                            6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  AMP PEAK 7(XQ27.3) MUTATED        1      1      1      0      1      1      1
  AMP PEAK 7(XQ27.3) WILD-TYPE      3      2      3      2      2      1      3
                              vv
clus                           CLUS_8 CLUS_9
  AMP PEAK 7(XQ27.3) MUTATED        0      0
  AMP PEAK 7(XQ27.3) WILD-TYPE      3      2
D7V7, multiclass
        clus
vv       AMP PEAK 7(XQ27.3) MUTATED AMP PEAK 7(XQ27.3) WILD-TYPE
  CLUS_1                          1                            3
  CLUS_2                          1                            2
  CLUS_3                          1                            3
  CLUS_4                          0                            2
  CLUS_5                          1                            2
  CLUS_6                          1                            1
  CLUS_7                          1                            3
  CLUS_8                          0                            3
  CLUS_9                          0                            2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = DEL PEAK  1(1P22.1) MUTATION ANALYSIS
D8V1, binary
                               cls
clus                             0  1
  DEL PEAK  1(1P22.1) MUTATED    3  1
  DEL PEAK  1(1P22.1) WILD-TYPE 12 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  1(1P22.1) MUTATED      3    1
  DEL PEAK  1(1P22.1) WILD-TYPE   12   12
        clus
vv       DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE
  CLUS_1                           3                            12
  CLUS_2                           1                            12
[1] 2 2
[1] FALSE
D8V2, binary
                               cls
clus                             0  1
  DEL PEAK  1(1P22.1) MUTATED    2  2
  DEL PEAK  1(1P22.1) WILD-TYPE 13 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  1(1P22.1) MUTATED      2    2
  DEL PEAK  1(1P22.1) WILD-TYPE   13   11
        clus
vv       DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE
  CLUS_1                           2                            13
  CLUS_2                           2                            11
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  1(1P22.1) MUTATED        2      2      0
  DEL PEAK  1(1P22.1) WILD-TYPE     11      8      5
D8V3, multiclass
        clus
vv       DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE
  CLUS_1                           2                            11
  CLUS_2                           2                             8
  CLUS_3                           0                             5
[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"
D8V4, binary
                               cls
clus                             0  1
  DEL PEAK  1(1P22.1) MUTATED    1  3
  DEL PEAK  1(1P22.1) WILD-TYPE 13 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  1(1P22.1) MUTATED      1    3
  DEL PEAK  1(1P22.1) WILD-TYPE   13   10
        clus
vv       DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE
  CLUS_1                           1                            13
  CLUS_2                           3                            10
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  1(1P22.1) MUTATED        0      0      1      1      1      0
  DEL PEAK  1(1P22.1) WILD-TYPE      2      2      4      3      4      3
                               vv
clus                            CLUS_7 CLUS_8
  DEL PEAK  1(1P22.1) MUTATED        1      0
  DEL PEAK  1(1P22.1) WILD-TYPE      2      3
D8V5, multiclass
        clus
vv       DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE
  CLUS_1                           0                             2
  CLUS_2                           0                             2
  CLUS_3                           1                             4
  CLUS_4                           1                             3
  CLUS_5                           1                             4
  CLUS_6                           0                             3
  CLUS_7                           1                             2
  CLUS_8                           0                             3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  1(1P22.1) MUTATED        1      1      2
  DEL PEAK  1(1P22.1) WILD-TYPE      8      8      7
D8V6, multiclass
        clus
vv       DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE
  CLUS_1                           1                             8
  CLUS_2                           1                             8
  CLUS_3                           2                             7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  1(1P22.1) MUTATED        1      0      0      1      0      0
  DEL PEAK  1(1P22.1) WILD-TYPE      3      3      4      1      3      2
                               vv
clus                            CLUS_7 CLUS_8 CLUS_9
  DEL PEAK  1(1P22.1) MUTATED        1      1      0
  DEL PEAK  1(1P22.1) WILD-TYPE      3      2      2
D8V7, multiclass
        clus
vv       DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE
  CLUS_1                           1                             3
  CLUS_2                           0                             3
  CLUS_3                           0                             4
  CLUS_4                           1                             1
  CLUS_5                           0                             3
  CLUS_6                           0                             2
  CLUS_7                           1                             3
  CLUS_8                           1                             2
  CLUS_9                           0                             2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = DEL PEAK  2(1P13.1) MUTATION ANALYSIS
D9V1, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.1) MUTATED    5  2
  DEL PEAK  2(1P13.1) WILD-TYPE 10 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED      5    2
  DEL PEAK  2(1P13.1) WILD-TYPE   10   11
        clus
vv       DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  CLUS_1                           5                            10
  CLUS_2                           2                            11
[1] 2 2
[1] FALSE
D9V2, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.1) MUTATED    3  4
  DEL PEAK  2(1P13.1) WILD-TYPE 12  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED      3    4
  DEL PEAK  2(1P13.1) WILD-TYPE   12    9
        clus
vv       DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  CLUS_1                           3                            12
  CLUS_2                           4                             9
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  2(1P13.1) MUTATED        3      4      0
  DEL PEAK  2(1P13.1) WILD-TYPE     10      6      5
D9V3, multiclass
        clus
vv       DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  CLUS_1                           3                            10
  CLUS_2                           4                             6
  CLUS_3                           0                             5
[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"
D9V4, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.1) MUTATED    1  6
  DEL PEAK  2(1P13.1) WILD-TYPE 13  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED      1    6
  DEL PEAK  2(1P13.1) WILD-TYPE   13    7
        clus
vv       DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  CLUS_1                           1                            13
  CLUS_2                           6                             7
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  2(1P13.1) MUTATED        0      0      1      3      1      0
  DEL PEAK  2(1P13.1) WILD-TYPE      2      2      4      1      4      3
                               vv
clus                            CLUS_7 CLUS_8
  DEL PEAK  2(1P13.1) MUTATED        1      1
  DEL PEAK  2(1P13.1) WILD-TYPE      2      2
D9V5, multiclass
        clus
vv       DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  CLUS_1                           0                             2
  CLUS_2                           0                             2
  CLUS_3                           1                             4
  CLUS_4                           3                             1
  CLUS_5                           1                             4
  CLUS_6                           0                             3
  CLUS_7                           1                             2
  CLUS_8                           1                             2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  2(1P13.1) MUTATED        1      4      2
  DEL PEAK  2(1P13.1) WILD-TYPE      8      5      7
D9V6, multiclass
        clus
vv       DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  CLUS_1                           1                             8
  CLUS_2                           4                             5
  CLUS_3                           2                             7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  2(1P13.1) MUTATED        1      1      0      2      1      0
  DEL PEAK  2(1P13.1) WILD-TYPE      3      2      4      0      2      2
                               vv
clus                            CLUS_7 CLUS_8 CLUS_9
  DEL PEAK  2(1P13.1) MUTATED        1      1      0
  DEL PEAK  2(1P13.1) WILD-TYPE      3      2      2
D9V7, multiclass
        clus
vv       DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  CLUS_1                           1                             3
  CLUS_2                           1                             2
  CLUS_3                           0                             4
  CLUS_4                           2                             0
  CLUS_5                           1                             2
  CLUS_6                           0                             2
  CLUS_7                           1                             3
  CLUS_8                           1                             2
  CLUS_9                           0                             2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = DEL PEAK  3(1Q43) MUTATION ANALYSIS
D10V1, binary
                             cls
clus                           0  1
  DEL PEAK  3(1Q43) MUTATED    2  5
  DEL PEAK  3(1Q43) WILD-TYPE 13  8
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q43) MUTATED      2    5
  DEL PEAK  3(1Q43) WILD-TYPE   13    8
        clus
vv       DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  CLUS_1                         2                          13
  CLUS_2                         5                           8
[1] 2 2
[1] FALSE
D10V2, binary
                             cls
clus                           0  1
  DEL PEAK  3(1Q43) MUTATED    4  3
  DEL PEAK  3(1Q43) WILD-TYPE 11 10
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q43) MUTATED      4    3
  DEL PEAK  3(1Q43) WILD-TYPE   11   10
        clus
vv       DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  CLUS_1                         4                          11
  CLUS_2                         3                          10
[1] 2 2
[1] FALSE
                             vv
clus                          CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  3(1Q43) MUTATED        3      3      1
  DEL PEAK  3(1Q43) WILD-TYPE     10      7      4
D10V3, multiclass
        clus
vv       DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  CLUS_1                         3                          10
  CLUS_2                         3                           7
  CLUS_3                         1                           4
[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"
D10V4, binary
                             cls
clus                           0  1
  DEL PEAK  3(1Q43) MUTATED    4  3
  DEL PEAK  3(1Q43) WILD-TYPE 10 10
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q43) MUTATED      4    3
  DEL PEAK  3(1Q43) WILD-TYPE   10   10
        clus
vv       DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  CLUS_1                         4                          10
  CLUS_2                         3                          10
[1] 2 2
[1] FALSE
                             vv
clus                          CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  DEL PEAK  3(1Q43) MUTATED        0      0      2      2      1      1      1
  DEL PEAK  3(1Q43) WILD-TYPE      2      2      3      2      4      2      2
                             vv
clus                          CLUS_8
  DEL PEAK  3(1Q43) MUTATED        0
  DEL PEAK  3(1Q43) WILD-TYPE      3
D10V5, multiclass
        clus
vv       DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  CLUS_1                         0                           2
  CLUS_2                         0                           2
  CLUS_3                         2                           3
  CLUS_4                         2                           2
  CLUS_5                         1                           4
  CLUS_6                         1                           2
  CLUS_7                         1                           2
  CLUS_8                         0                           3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  3(1Q43) MUTATED        2      2      3
  DEL PEAK  3(1Q43) WILD-TYPE      7      7      6
D10V6, multiclass
        clus
vv       DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  CLUS_1                         2                           7
  CLUS_2                         2                           7
  CLUS_3                         3                           6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  DEL PEAK  3(1Q43) MUTATED        1      1      1      1      0      1      1
  DEL PEAK  3(1Q43) WILD-TYPE      3      2      3      1      3      1      3
                             vv
clus                          CLUS_8 CLUS_9
  DEL PEAK  3(1Q43) MUTATED        1      0
  DEL PEAK  3(1Q43) WILD-TYPE      2      2
D10V7, multiclass
        clus
vv       DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  CLUS_1                         1                           3
  CLUS_2                         1                           2
  CLUS_3                         1                           3
  CLUS_4                         1                           1
  CLUS_5                         0                           3
  CLUS_6                         1                           1
  CLUS_7                         1                           3
  CLUS_8                         1                           2
  CLUS_9                         0                           2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = DEL PEAK  4(2Q23.1) MUTATION ANALYSIS
D11V1, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q23.1) MUTATED    3  3
  DEL PEAK  4(2Q23.1) WILD-TYPE 12 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q23.1) MUTATED      3    3
  DEL PEAK  4(2Q23.1) WILD-TYPE   12   10
        clus
vv       DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE
  CLUS_1                           3                            12
  CLUS_2                           3                            10
[1] 2 2
[1] FALSE
D11V2, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q23.1) MUTATED    3  3
  DEL PEAK  4(2Q23.1) WILD-TYPE 12 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q23.1) MUTATED      3    3
  DEL PEAK  4(2Q23.1) WILD-TYPE   12   10
        clus
vv       DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE
  CLUS_1                           3                            12
  CLUS_2                           3                            10
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  4(2Q23.1) MUTATED        3      3      0
  DEL PEAK  4(2Q23.1) WILD-TYPE     10      7      5
D11V3, multiclass
        clus
vv       DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE
  CLUS_1                           3                            10
  CLUS_2                           3                             7
  CLUS_3                           0                             5
[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"
D11V4, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q23.1) MUTATED    2  3
  DEL PEAK  4(2Q23.1) WILD-TYPE 12 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q23.1) MUTATED      2    3
  DEL PEAK  4(2Q23.1) WILD-TYPE   12   10
        clus
vv       DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE
  CLUS_1                           2                            12
  CLUS_2                           3                            10
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  4(2Q23.1) MUTATED        0      0      1      1      1      0
  DEL PEAK  4(2Q23.1) WILD-TYPE      2      2      4      3      4      3
                               vv
clus                            CLUS_7 CLUS_8
  DEL PEAK  4(2Q23.1) MUTATED        1      1
  DEL PEAK  4(2Q23.1) WILD-TYPE      2      2
D11V5, multiclass
        clus
vv       DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE
  CLUS_1                           0                             2
  CLUS_2                           0                             2
  CLUS_3                           1                             4
  CLUS_4                           1                             3
  CLUS_5                           1                             4
  CLUS_6                           0                             3
  CLUS_7                           1                             2
  CLUS_8                           1                             2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  4(2Q23.1) MUTATED        1      2      2
  DEL PEAK  4(2Q23.1) WILD-TYPE      8      7      7
D11V6, multiclass
        clus
vv       DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE
  CLUS_1                           1                             8
  CLUS_2                           2                             7
  CLUS_3                           2                             7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  4(2Q23.1) MUTATED        1      0      0      1      0      0
  DEL PEAK  4(2Q23.1) WILD-TYPE      3      3      4      1      3      2
                               vv
clus                            CLUS_7 CLUS_8 CLUS_9
  DEL PEAK  4(2Q23.1) MUTATED        1      1      1
  DEL PEAK  4(2Q23.1) WILD-TYPE      3      2      1
D11V7, multiclass
        clus
vv       DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE
  CLUS_1                           1                             3
  CLUS_2                           0                             3
  CLUS_3                           0                             4
  CLUS_4                           1                             1
  CLUS_5                           0                             3
  CLUS_6                           0                             2
  CLUS_7                           1                             3
  CLUS_8                           1                             2
  CLUS_9                           1                             1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = DEL PEAK  5(6Q14.1) MUTATION ANALYSIS
D12V1, binary
                               cls
clus                             0  1
  DEL PEAK  5(6Q14.1) MUTATED    4  5
  DEL PEAK  5(6Q14.1) WILD-TYPE 11  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(6Q14.1) MUTATED      4    5
  DEL PEAK  5(6Q14.1) WILD-TYPE   11    8
        clus
vv       DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE
  CLUS_1                           4                            11
  CLUS_2                           5                             8
[1] 2 2
[1] FALSE
D12V2, binary
                               cls
clus                             0  1
  DEL PEAK  5(6Q14.1) MUTATED    6  3
  DEL PEAK  5(6Q14.1) WILD-TYPE  9 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(6Q14.1) MUTATED      6    3
  DEL PEAK  5(6Q14.1) WILD-TYPE    9   10
        clus
vv       DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE
  CLUS_1                           6                             9
  CLUS_2                           3                            10
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  5(6Q14.1) MUTATED        4      2      3
  DEL PEAK  5(6Q14.1) WILD-TYPE      9      8      2
D12V3, multiclass
        clus
vv       DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE
  CLUS_1                           4                             9
  CLUS_2                           2                             8
  CLUS_3                           3                             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V4, binary
                               cls
clus                             0  1
  DEL PEAK  5(6Q14.1) MUTATED    7  2
  DEL PEAK  5(6Q14.1) WILD-TYPE  7 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(6Q14.1) MUTATED      7    2
  DEL PEAK  5(6Q14.1) WILD-TYPE    7   11
        clus
vv       DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE
  CLUS_1                           7                             7
  CLUS_2                           2                            11
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  5(6Q14.1) MUTATED        0      1      3      1      0      2
  DEL PEAK  5(6Q14.1) WILD-TYPE      2      1      2      3      5      1
                               vv
clus                            CLUS_7 CLUS_8
  DEL PEAK  5(6Q14.1) MUTATED        2      0
  DEL PEAK  5(6Q14.1) WILD-TYPE      1      3
D12V5, multiclass
        clus
vv       DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE
  CLUS_1                           0                             2
  CLUS_2                           1                             1
  CLUS_3                           3                             2
  CLUS_4                           1                             3
  CLUS_5                           0                             5
  CLUS_6                           2                             1
  CLUS_7                           2                             1
  CLUS_8                           0                             3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  5(6Q14.1) MUTATED        4      2      3
  DEL PEAK  5(6Q14.1) WILD-TYPE      5      7      6
D12V6, multiclass
        clus
vv       DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE
  CLUS_1                           4                             5
  CLUS_2                           2                             7
  CLUS_3                           3                             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  5(6Q14.1) MUTATED        2      1      2      1      0      1
  DEL PEAK  5(6Q14.1) WILD-TYPE      2      2      2      1      3      1
                               vv
clus                            CLUS_7 CLUS_8 CLUS_9
  DEL PEAK  5(6Q14.1) MUTATED        0      2      0
  DEL PEAK  5(6Q14.1) WILD-TYPE      4      1      2
D12V7, multiclass
        clus
vv       DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE
  CLUS_1                           2                             2
  CLUS_2                           1                             2
  CLUS_3                           2                             2
  CLUS_4                           1                             1
  CLUS_5                           0                             3
  CLUS_6                           1                             1
  CLUS_7                           0                             4
  CLUS_8                           2                             1
  CLUS_9                           0                             2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = DEL PEAK  6(6Q23.3) MUTATION ANALYSIS
D13V1, binary
                               cls
clus                             0  1
  DEL PEAK  6(6Q23.3) MUTATED    2  5
  DEL PEAK  6(6Q23.3) WILD-TYPE 13  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(6Q23.3) MUTATED      2    5
  DEL PEAK  6(6Q23.3) WILD-TYPE   13    8
        clus
vv       DEL PEAK  6(6Q23.3) MUTATED DEL PEAK  6(6Q23.3) WILD-TYPE
  CLUS_1                           2                            13
  CLUS_2                           5                             8
[1] 2 2
[1] FALSE
D13V2, binary
                               cls
clus                             0  1
  DEL PEAK  6(6Q23.3) MUTATED    6  1
  DEL PEAK  6(6Q23.3) WILD-TYPE  9 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(6Q23.3) MUTATED      6    1
  DEL PEAK  6(6Q23.3) WILD-TYPE    9   12
        clus
vv       DEL PEAK  6(6Q23.3) MUTATED DEL PEAK  6(6Q23.3) WILD-TYPE
  CLUS_1                           6                             9
  CLUS_2                           1                            12
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  6(6Q23.3) MUTATED        4      0      3
  DEL PEAK  6(6Q23.3) WILD-TYPE      9     10      2
D13V3, multiclass
        clus
vv       DEL PEAK  6(6Q23.3) MUTATED DEL PEAK  6(6Q23.3) WILD-TYPE
  CLUS_1                           4                             9
  CLUS_2                           0                            10
  CLUS_3                           3                             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V4, binary
                               cls
clus                             0  1
  DEL PEAK  6(6Q23.3) MUTATED    5  2
  DEL PEAK  6(6Q23.3) WILD-TYPE  9 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(6Q23.3) MUTATED      5    2
  DEL PEAK  6(6Q23.3) WILD-TYPE    9   11
        clus
vv       DEL PEAK  6(6Q23.3) MUTATED DEL PEAK  6(6Q23.3) WILD-TYPE
  CLUS_1                           5                             9
  CLUS_2                           2                            11
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  6(6Q23.3) MUTATED        0      1      3      0      0      0
  DEL PEAK  6(6Q23.3) WILD-TYPE      2      1      2      4      5      3
                               vv
clus                            CLUS_7 CLUS_8
  DEL PEAK  6(6Q23.3) MUTATED        2      1
  DEL PEAK  6(6Q23.3) WILD-TYPE      1      2
D13V5, multiclass
        clus
vv       DEL PEAK  6(6Q23.3) MUTATED DEL PEAK  6(6Q23.3) WILD-TYPE
  CLUS_1                           0                             2
  CLUS_2                           1                             1
  CLUS_3                           3                             2
  CLUS_4                           0                             4
  CLUS_5                           0                             5
  CLUS_6                           0                             3
  CLUS_7                           2                             1
  CLUS_8                           1                             2
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  6(6Q23.3) MUTATED        3      2      2
  DEL PEAK  6(6Q23.3) WILD-TYPE      6      7      7
D13V6, multiclass
        clus
vv       DEL PEAK  6(6Q23.3) MUTATED DEL PEAK  6(6Q23.3) WILD-TYPE
  CLUS_1                           3                             6
  CLUS_2                           2                             7
  CLUS_3                           2                             7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  6(6Q23.3) MUTATED        1      1      2      0      1      0
  DEL PEAK  6(6Q23.3) WILD-TYPE      3      2      2      2      2      2
                               vv
clus                            CLUS_7 CLUS_8 CLUS_9
  DEL PEAK  6(6Q23.3) MUTATED        0      2      0
  DEL PEAK  6(6Q23.3) WILD-TYPE      4      1      2
D13V7, multiclass
        clus
vv       DEL PEAK  6(6Q23.3) MUTATED DEL PEAK  6(6Q23.3) WILD-TYPE
  CLUS_1                           1                             3
  CLUS_2                           1                             2
  CLUS_3                           2                             2
  CLUS_4                           0                             2
  CLUS_5                           1                             2
  CLUS_6                           0                             2
  CLUS_7                           0                             4
  CLUS_8                           2                             1
  CLUS_9                           0                             2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = DEL PEAK  8(8P23.1) MUTATION ANALYSIS
D14V1, binary
                               cls
clus                             0  1
  DEL PEAK  8(8P23.1) MUTATED    2  2
  DEL PEAK  8(8P23.1) WILD-TYPE 13 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(8P23.1) MUTATED      2    2
  DEL PEAK  8(8P23.1) WILD-TYPE   13   11
        clus
vv       DEL PEAK  8(8P23.1) MUTATED DEL PEAK  8(8P23.1) WILD-TYPE
  CLUS_1                           2                            13
  CLUS_2                           2                            11
[1] 2 2
[1] FALSE
D14V2, binary
                               cls
clus                             0  1
  DEL PEAK  8(8P23.1) MUTATED    1  3
  DEL PEAK  8(8P23.1) WILD-TYPE 14 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(8P23.1) MUTATED      1    3
  DEL PEAK  8(8P23.1) WILD-TYPE   14   10
        clus
vv       DEL PEAK  8(8P23.1) MUTATED DEL PEAK  8(8P23.1) WILD-TYPE
  CLUS_1                           1                            14
  CLUS_2                           3                            10
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  8(8P23.1) MUTATED        1      3      0
  DEL PEAK  8(8P23.1) WILD-TYPE     12      7      5
D14V3, multiclass
        clus
vv       DEL PEAK  8(8P23.1) MUTATED DEL PEAK  8(8P23.1) WILD-TYPE
  CLUS_1                           1                            12
  CLUS_2                           3                             7
  CLUS_3                           0                             5
[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"
D14V4, binary
                               cls
clus                             0  1
  DEL PEAK  8(8P23.1) MUTATED    1  3
  DEL PEAK  8(8P23.1) WILD-TYPE 13 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(8P23.1) MUTATED      1    3
  DEL PEAK  8(8P23.1) WILD-TYPE   13   10
        clus
vv       DEL PEAK  8(8P23.1) MUTATED DEL PEAK  8(8P23.1) WILD-TYPE
  CLUS_1                           1                            13
  CLUS_2                           3                            10
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  8(8P23.1) MUTATED        0      0      1      2      0      0
  DEL PEAK  8(8P23.1) WILD-TYPE      2      2      4      2      5      3
                               vv
clus                            CLUS_7 CLUS_8
  DEL PEAK  8(8P23.1) MUTATED        1      0
  DEL PEAK  8(8P23.1) WILD-TYPE      2      3
D14V5, multiclass
        clus
vv       DEL PEAK  8(8P23.1) MUTATED DEL PEAK  8(8P23.1) WILD-TYPE
  CLUS_1                           0                             2
  CLUS_2                           0                             2
  CLUS_3                           1                             4
  CLUS_4                           2                             2
  CLUS_5                           0                             5
  CLUS_6                           0                             3
  CLUS_7                           1                             2
  CLUS_8                           0                             3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  8(8P23.1) MUTATED        1      2      1
  DEL PEAK  8(8P23.1) WILD-TYPE      8      7      8
D14V6, multiclass
        clus
vv       DEL PEAK  8(8P23.1) MUTATED DEL PEAK  8(8P23.1) WILD-TYPE
  CLUS_1                           1                             8
  CLUS_2                           2                             7
  CLUS_3                           1                             8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  8(8P23.1) MUTATED        1      0      0      2      0      0
  DEL PEAK  8(8P23.1) WILD-TYPE      3      3      4      0      3      2
                               vv
clus                            CLUS_7 CLUS_8 CLUS_9
  DEL PEAK  8(8P23.1) MUTATED        0      1      0
  DEL PEAK  8(8P23.1) WILD-TYPE      4      2      2
D14V7, multiclass
        clus
vv       DEL PEAK  8(8P23.1) MUTATED DEL PEAK  8(8P23.1) WILD-TYPE
  CLUS_1                           1                             3
  CLUS_2                           0                             3
  CLUS_3                           0                             4
  CLUS_4                           2                             0
  CLUS_5                           0                             3
  CLUS_6                           0                             2
  CLUS_7                           0                             4
  CLUS_8                           1                             2
  CLUS_9                           0                             2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = DEL PEAK  9(8Q12.1) MUTATION ANALYSIS
D15V1, binary
                               cls
clus                             0  1
  DEL PEAK  9(8Q12.1) MUTATED    2  2
  DEL PEAK  9(8Q12.1) WILD-TYPE 13 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(8Q12.1) MUTATED      2    2
  DEL PEAK  9(8Q12.1) WILD-TYPE   13   11
        clus
vv       DEL PEAK  9(8Q12.1) MUTATED DEL PEAK  9(8Q12.1) WILD-TYPE
  CLUS_1                           2                            13
  CLUS_2                           2                            11
[1] 2 2
[1] FALSE
D15V2, binary
                               cls
clus                             0  1
  DEL PEAK  9(8Q12.1) MUTATED    1  3
  DEL PEAK  9(8Q12.1) WILD-TYPE 14 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(8Q12.1) MUTATED      1    3
  DEL PEAK  9(8Q12.1) WILD-TYPE   14   10
        clus
vv       DEL PEAK  9(8Q12.1) MUTATED DEL PEAK  9(8Q12.1) WILD-TYPE
  CLUS_1                           1                            14
  CLUS_2                           3                            10
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  9(8Q12.1) MUTATED        1      3      0
  DEL PEAK  9(8Q12.1) WILD-TYPE     12      7      5
D15V3, multiclass
        clus
vv       DEL PEAK  9(8Q12.1) MUTATED DEL PEAK  9(8Q12.1) WILD-TYPE
  CLUS_1                           1                            12
  CLUS_2                           3                             7
  CLUS_3                           0                             5
[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"
D15V4, binary
                               cls
clus                             0  1
  DEL PEAK  9(8Q12.1) MUTATED    1  3
  DEL PEAK  9(8Q12.1) WILD-TYPE 13 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(8Q12.1) MUTATED      1    3
  DEL PEAK  9(8Q12.1) WILD-TYPE   13   10
        clus
vv       DEL PEAK  9(8Q12.1) MUTATED DEL PEAK  9(8Q12.1) WILD-TYPE
  CLUS_1                           1                            13
  CLUS_2                           3                            10
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  9(8Q12.1) MUTATED        0      0      1      1      1      0
  DEL PEAK  9(8Q12.1) WILD-TYPE      2      2      4      3      4      3
                               vv
clus                            CLUS_7 CLUS_8
  DEL PEAK  9(8Q12.1) MUTATED        1      0
  DEL PEAK  9(8Q12.1) WILD-TYPE      2      3
D15V5, multiclass
        clus
vv       DEL PEAK  9(8Q12.1) MUTATED DEL PEAK  9(8Q12.1) WILD-TYPE
  CLUS_1                           0                             2
  CLUS_2                           0                             2
  CLUS_3                           1                             4
  CLUS_4                           1                             3
  CLUS_5                           1                             4
  CLUS_6                           0                             3
  CLUS_7                           1                             2
  CLUS_8                           0                             3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  9(8Q12.1) MUTATED        1      1      2
  DEL PEAK  9(8Q12.1) WILD-TYPE      8      8      7
D15V6, multiclass
        clus
vv       DEL PEAK  9(8Q12.1) MUTATED DEL PEAK  9(8Q12.1) WILD-TYPE
  CLUS_1                           1                             8
  CLUS_2                           1                             8
  CLUS_3                           2                             7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  9(8Q12.1) MUTATED        1      0      0      1      0      0
  DEL PEAK  9(8Q12.1) WILD-TYPE      3      3      4      1      3      2
                               vv
clus                            CLUS_7 CLUS_8 CLUS_9
  DEL PEAK  9(8Q12.1) MUTATED        1      1      0
  DEL PEAK  9(8Q12.1) WILD-TYPE      3      2      2
D15V7, multiclass
        clus
vv       DEL PEAK  9(8Q12.1) MUTATED DEL PEAK  9(8Q12.1) WILD-TYPE
  CLUS_1                           1                             3
  CLUS_2                           0                             3
  CLUS_3                           0                             4
  CLUS_4                           1                             1
  CLUS_5                           0                             3
  CLUS_6                           0                             2
  CLUS_7                           1                             3
  CLUS_8                           1                             2
  CLUS_9                           0                             2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = DEL PEAK 10(9P21.3) MUTATION ANALYSIS
D16V1, binary
                               cls
clus                             0  1
  DEL PEAK 10(9P21.3) MUTATED    2  7
  DEL PEAK 10(9P21.3) WILD-TYPE 13  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(9P21.3) MUTATED      2    7
  DEL PEAK 10(9P21.3) WILD-TYPE   13    6
        clus
vv       DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE
  CLUS_1                           2                            13
  CLUS_2                           7                             6
[1] 2 2
[1] FALSE
D16V2, binary
                               cls
clus                             0  1
  DEL PEAK 10(9P21.3) MUTATED    7  2
  DEL PEAK 10(9P21.3) WILD-TYPE  8 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(9P21.3) MUTATED      7    2
  DEL PEAK 10(9P21.3) WILD-TYPE    8   11
        clus
vv       DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE
  CLUS_1                           7                             8
  CLUS_2                           2                            11
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 10(9P21.3) MUTATED        4      2      3
  DEL PEAK 10(9P21.3) WILD-TYPE      9      8      2
D16V3, multiclass
        clus
vv       DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE
  CLUS_1                           4                             9
  CLUS_2                           2                             8
  CLUS_3                           3                             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V4, binary
                               cls
clus                             0  1
  DEL PEAK 10(9P21.3) MUTATED    6  3
  DEL PEAK 10(9P21.3) WILD-TYPE  8 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(9P21.3) MUTATED      6    3
  DEL PEAK 10(9P21.3) WILD-TYPE    8   10
        clus
vv       DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE
  CLUS_1                           6                             8
  CLUS_2                           3                            10
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 10(9P21.3) MUTATED        0      0      4      1      0      1
  DEL PEAK 10(9P21.3) WILD-TYPE      2      2      1      3      5      2
                               vv
clus                            CLUS_7 CLUS_8
  DEL PEAK 10(9P21.3) MUTATED        3      0
  DEL PEAK 10(9P21.3) WILD-TYPE      0      3
D16V5, multiclass
        clus
vv       DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE
  CLUS_1                           0                             2
  CLUS_2                           0                             2
  CLUS_3                           4                             1
  CLUS_4                           1                             3
  CLUS_5                           0                             5
  CLUS_6                           1                             2
  CLUS_7                           3                             0
  CLUS_8                           0                             3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 10(9P21.3) MUTATED        4      1      4
  DEL PEAK 10(9P21.3) WILD-TYPE      5      8      5
D16V6, multiclass
        clus
vv       DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE
  CLUS_1                           4                             5
  CLUS_2                           1                             8
  CLUS_3                           4                             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 10(9P21.3) MUTATED        1      0      3      1      0      1
  DEL PEAK 10(9P21.3) WILD-TYPE      3      3      1      1      3      1
                               vv
clus                            CLUS_7 CLUS_8 CLUS_9
  DEL PEAK 10(9P21.3) MUTATED        0      3      0
  DEL PEAK 10(9P21.3) WILD-TYPE      4      0      2
D16V7, multiclass
        clus
vv       DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE
  CLUS_1                           1                             3
  CLUS_2                           0                             3
  CLUS_3                           3                             1
  CLUS_4                           1                             1
  CLUS_5                           0                             3
  CLUS_6                           1                             1
  CLUS_7                           0                             4
  CLUS_8                           3                             0
  CLUS_9                           0                             2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = DEL PEAK 11(10Q23.31) MUTATION ANALYSIS
D17V1, binary
                                 cls
clus                               0  1
  DEL PEAK 11(10Q23.31) MUTATED    3  2
  DEL PEAK 11(10Q23.31) WILD-TYPE 12 11
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 11(10Q23.31) MUTATED      3    2
  DEL PEAK 11(10Q23.31) WILD-TYPE   12   11
        clus
vv       DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE
  CLUS_1                             3                              12
  CLUS_2                             2                              11
[1] 2 2
[1] FALSE
D17V2, binary
                                 cls
clus                               0  1
  DEL PEAK 11(10Q23.31) MUTATED    2  3
  DEL PEAK 11(10Q23.31) WILD-TYPE 13 10
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 11(10Q23.31) MUTATED      2    3
  DEL PEAK 11(10Q23.31) WILD-TYPE   13   10
        clus
vv       DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE
  CLUS_1                             2                              13
  CLUS_2                             3                              10
[1] 2 2
[1] FALSE
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 11(10Q23.31) MUTATED        0      3      2
  DEL PEAK 11(10Q23.31) WILD-TYPE     13      7      3
D17V3, multiclass
        clus
vv       DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE
  CLUS_1                             0                              13
  CLUS_2                             3                               7
  CLUS_3                             2                               3
[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"
D17V4, binary
                                 cls
clus                               0  1
  DEL PEAK 11(10Q23.31) MUTATED    2  3
  DEL PEAK 11(10Q23.31) WILD-TYPE 12 10
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 11(10Q23.31) MUTATED      2    3
  DEL PEAK 11(10Q23.31) WILD-TYPE   12   10
        clus
vv       DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE
  CLUS_1                             2                              12
  CLUS_2                             3                              10
[1] 2 2
[1] FALSE
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 11(10Q23.31) MUTATED        0      0      1      1      2      1
  DEL PEAK 11(10Q23.31) WILD-TYPE      2      2      4      3      3      2
                                 vv
clus                              CLUS_7 CLUS_8
  DEL PEAK 11(10Q23.31) MUTATED        0      0
  DEL PEAK 11(10Q23.31) WILD-TYPE      3      3
D17V5, multiclass
        clus
vv       DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE
  CLUS_1                             0                               2
  CLUS_2                             0                               2
  CLUS_3                             1                               4
  CLUS_4                             1                               3
  CLUS_5                             2                               3
  CLUS_6                             1                               2
  CLUS_7                             0                               3
  CLUS_8                             0                               3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 11(10Q23.31) MUTATED        2      1      2
  DEL PEAK 11(10Q23.31) WILD-TYPE      7      8      7
D17V6, multiclass
        clus
vv       DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE
  CLUS_1                             2                               7
  CLUS_2                             1                               8
  CLUS_3                             2                               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 11(10Q23.31) MUTATED        0      0      1      1      0      1
  DEL PEAK 11(10Q23.31) WILD-TYPE      4      3      3      1      3      1
                                 vv
clus                              CLUS_7 CLUS_8 CLUS_9
  DEL PEAK 11(10Q23.31) MUTATED        2      0      0
  DEL PEAK 11(10Q23.31) WILD-TYPE      2      3      2
D17V7, multiclass
        clus
vv       DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE
  CLUS_1                             0                               4
  CLUS_2                             0                               3
  CLUS_3                             1                               3
  CLUS_4                             1                               1
  CLUS_5                             0                               3
  CLUS_6                             1                               1
  CLUS_7                             2                               2
  CLUS_8                             0                               3
  CLUS_9                             0                               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = DEL PEAK 12(13Q14.2) MUTATION ANALYSIS
D18V1, binary
                                cls
clus                              0  1
  DEL PEAK 12(13Q14.2) MUTATED    1  2
  DEL PEAK 12(13Q14.2) WILD-TYPE 14 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(13Q14.2) MUTATED      1    2
  DEL PEAK 12(13Q14.2) WILD-TYPE   14   11
        clus
vv       DEL PEAK 12(13Q14.2) MUTATED DEL PEAK 12(13Q14.2) WILD-TYPE
  CLUS_1                            1                             14
  CLUS_2                            2                             11
[1] 2 2
[1] FALSE
D18V2, binary
                                cls
clus                              0  1
  DEL PEAK 12(13Q14.2) MUTATED    2  1
  DEL PEAK 12(13Q14.2) WILD-TYPE 13 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(13Q14.2) MUTATED      2    1
  DEL PEAK 12(13Q14.2) WILD-TYPE   13   12
        clus
vv       DEL PEAK 12(13Q14.2) MUTATED DEL PEAK 12(13Q14.2) WILD-TYPE
  CLUS_1                            2                             13
  CLUS_2                            1                             12
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 12(13Q14.2) MUTATED        1      1      1
  DEL PEAK 12(13Q14.2) WILD-TYPE     12      9      4
D18V3, multiclass
        clus
vv       DEL PEAK 12(13Q14.2) MUTATED DEL PEAK 12(13Q14.2) WILD-TYPE
  CLUS_1                            1                             12
  CLUS_2                            1                              9
  CLUS_3                            1                              4
[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"
D18V4, binary
                                cls
clus                              0  1
  DEL PEAK 12(13Q14.2) MUTATED    2  1
  DEL PEAK 12(13Q14.2) WILD-TYPE 12 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(13Q14.2) MUTATED      2    1
  DEL PEAK 12(13Q14.2) WILD-TYPE   12   12
        clus
vv       DEL PEAK 12(13Q14.2) MUTATED DEL PEAK 12(13Q14.2) WILD-TYPE
  CLUS_1                            2                             12
  CLUS_2                            1                             12
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 12(13Q14.2) MUTATED        0      0      0      0      2      1
  DEL PEAK 12(13Q14.2) WILD-TYPE      2      2      5      4      3      2
                                vv
clus                             CLUS_7 CLUS_8
  DEL PEAK 12(13Q14.2) MUTATED        0      0
  DEL PEAK 12(13Q14.2) WILD-TYPE      3      3
D18V5, multiclass
        clus
vv       DEL PEAK 12(13Q14.2) MUTATED DEL PEAK 12(13Q14.2) WILD-TYPE
  CLUS_1                            0                              2
  CLUS_2                            0                              2
  CLUS_3                            0                              5
  CLUS_4                            0                              4
  CLUS_5                            2                              3
  CLUS_6                            1                              2
  CLUS_7                            0                              3
  CLUS_8                            0                              3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 12(13Q14.2) MUTATED        1      0      2
  DEL PEAK 12(13Q14.2) WILD-TYPE      8      9      7
D18V6, multiclass
        clus
vv       DEL PEAK 12(13Q14.2) MUTATED DEL PEAK 12(13Q14.2) WILD-TYPE
  CLUS_1                            1                              8
  CLUS_2                            0                              9
  CLUS_3                            2                              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 12(13Q14.2) MUTATED        0      0      0      0      0      1
  DEL PEAK 12(13Q14.2) WILD-TYPE      4      3      4      2      3      1
                                vv
clus                             CLUS_7 CLUS_8 CLUS_9
  DEL PEAK 12(13Q14.2) MUTATED        2      0      0
  DEL PEAK 12(13Q14.2) WILD-TYPE      2      3      2
D18V7, multiclass
        clus
vv       DEL PEAK 12(13Q14.2) MUTATED DEL PEAK 12(13Q14.2) WILD-TYPE
  CLUS_1                            0                              4
  CLUS_2                            0                              3
  CLUS_3                            0                              4
  CLUS_4                            0                              2
  CLUS_5                            0                              3
  CLUS_6                            1                              1
  CLUS_7                            2                              2
  CLUS_8                            0                              3
  CLUS_9                            0                              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = DEL PEAK 13(13Q33.3) MUTATION ANALYSIS
D19V1, binary
                                cls
clus                              0  1
  DEL PEAK 13(13Q33.3) MUTATED    2  2
  DEL PEAK 13(13Q33.3) WILD-TYPE 13 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(13Q33.3) MUTATED      2    2
  DEL PEAK 13(13Q33.3) WILD-TYPE   13   11
        clus
vv       DEL PEAK 13(13Q33.3) MUTATED DEL PEAK 13(13Q33.3) WILD-TYPE
  CLUS_1                            2                             13
  CLUS_2                            2                             11
[1] 2 2
[1] FALSE
D19V2, binary
                                cls
clus                              0  1
  DEL PEAK 13(13Q33.3) MUTATED    4  0
  DEL PEAK 13(13Q33.3) WILD-TYPE 11 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(13Q33.3) MUTATED      4    0
  DEL PEAK 13(13Q33.3) WILD-TYPE   11   13
        clus
vv       DEL PEAK 13(13Q33.3) MUTATED DEL PEAK 13(13Q33.3) WILD-TYPE
  CLUS_1                            4                             11
  CLUS_2                            0                             13
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 13(13Q33.3) MUTATED        3      0      1
  DEL PEAK 13(13Q33.3) WILD-TYPE     10     10      4
D19V3, multiclass
        clus
vv       DEL PEAK 13(13Q33.3) MUTATED DEL PEAK 13(13Q33.3) WILD-TYPE
  CLUS_1                            3                             10
  CLUS_2                            0                             10
  CLUS_3                            1                              4
[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"
D19V4, binary
                                cls
clus                              0  1
  DEL PEAK 13(13Q33.3) MUTATED    3  0
  DEL PEAK 13(13Q33.3) WILD-TYPE 11 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(13Q33.3) MUTATED      3    0
  DEL PEAK 13(13Q33.3) WILD-TYPE   11   13
        clus
vv       DEL PEAK 13(13Q33.3) MUTATED DEL PEAK 13(13Q33.3) WILD-TYPE
  CLUS_1                            3                             11
  CLUS_2                            0                             13
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 13(13Q33.3) MUTATED        0      0      0      0      1      2
  DEL PEAK 13(13Q33.3) WILD-TYPE      2      2      5      4      4      1
                                vv
clus                             CLUS_7 CLUS_8
  DEL PEAK 13(13Q33.3) MUTATED        0      0
  DEL PEAK 13(13Q33.3) WILD-TYPE      3      3
D19V5, multiclass
        clus
vv       DEL PEAK 13(13Q33.3) MUTATED DEL PEAK 13(13Q33.3) WILD-TYPE
  CLUS_1                            0                              2
  CLUS_2                            0                              2
  CLUS_3                            0                              5
  CLUS_4                            0                              4
  CLUS_5                            1                              4
  CLUS_6                            2                              1
  CLUS_7                            0                              3
  CLUS_8                            0                              3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 13(13Q33.3) MUTATED        1      0      2
  DEL PEAK 13(13Q33.3) WILD-TYPE      8      9      7
D19V6, multiclass
        clus
vv       DEL PEAK 13(13Q33.3) MUTATED DEL PEAK 13(13Q33.3) WILD-TYPE
  CLUS_1                            1                              8
  CLUS_2                            0                              9
  CLUS_3                            2                              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 13(13Q33.3) MUTATED        0      0      0      0      0      2
  DEL PEAK 13(13Q33.3) WILD-TYPE      4      3      4      2      3      0
                                vv
clus                             CLUS_7 CLUS_8 CLUS_9
  DEL PEAK 13(13Q33.3) MUTATED        1      0      0
  DEL PEAK 13(13Q33.3) WILD-TYPE      3      3      2
D19V7, multiclass
        clus
vv       DEL PEAK 13(13Q33.3) MUTATED DEL PEAK 13(13Q33.3) WILD-TYPE
  CLUS_1                            0                              4
  CLUS_2                            0                              3
  CLUS_3                            0                              4
  CLUS_4                            0                              2
  CLUS_5                            0                              3
  CLUS_6                            2                              0
  CLUS_7                            1                              3
  CLUS_8                            0                              3
  CLUS_9                            0                              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = DEL PEAK 14(15Q15.1) MUTATION ANALYSIS
D20V1, binary
                                cls
clus                              0  1
  DEL PEAK 14(15Q15.1) MUTATED    6  2
  DEL PEAK 14(15Q15.1) WILD-TYPE  9 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(15Q15.1) MUTATED      6    2
  DEL PEAK 14(15Q15.1) WILD-TYPE    9   11
        clus
vv       DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE
  CLUS_1                            6                              9
  CLUS_2                            2                             11
[1] 2 2
[1] FALSE
D20V2, binary
                                cls
clus                              0  1
  DEL PEAK 14(15Q15.1) MUTATED    4  4
  DEL PEAK 14(15Q15.1) WILD-TYPE 11  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(15Q15.1) MUTATED      4    4
  DEL PEAK 14(15Q15.1) WILD-TYPE   11    9
        clus
vv       DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE
  CLUS_1                            4                             11
  CLUS_2                            4                              9
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 14(15Q15.1) MUTATED        3      4      1
  DEL PEAK 14(15Q15.1) WILD-TYPE     10      6      4
D20V3, multiclass
        clus
vv       DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE
  CLUS_1                            3                             10
  CLUS_2                            4                              6
  CLUS_3                            1                              4
[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"
D20V4, binary
                                cls
clus                              0  1
  DEL PEAK 14(15Q15.1) MUTATED    3  4
  DEL PEAK 14(15Q15.1) WILD-TYPE 11  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(15Q15.1) MUTATED      3    4
  DEL PEAK 14(15Q15.1) WILD-TYPE   11    9
        clus
vv       DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE
  CLUS_1                            3                             11
  CLUS_2                            4                              9
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 14(15Q15.1) MUTATED        1      0      0      2      3      1
  DEL PEAK 14(15Q15.1) WILD-TYPE      1      2      5      2      2      2
                                vv
clus                             CLUS_7 CLUS_8
  DEL PEAK 14(15Q15.1) MUTATED        0      0
  DEL PEAK 14(15Q15.1) WILD-TYPE      3      3
D20V5, multiclass
        clus
vv       DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE
  CLUS_1                            1                              1
  CLUS_2                            0                              2
  CLUS_3                            0                              5
  CLUS_4                            2                              2
  CLUS_5                            3                              2
  CLUS_6                            1                              2
  CLUS_7                            0                              3
  CLUS_8                            0                              3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 14(15Q15.1) MUTATED        2      2      3
  DEL PEAK 14(15Q15.1) WILD-TYPE      7      7      6
D20V6, multiclass
        clus
vv       DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE
  CLUS_1                            2                              7
  CLUS_2                            2                              7
  CLUS_3                            3                              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 14(15Q15.1) MUTATED        1      0      0      2      0      1
  DEL PEAK 14(15Q15.1) WILD-TYPE      3      3      4      0      3      1
                                vv
clus                             CLUS_7 CLUS_8 CLUS_9
  DEL PEAK 14(15Q15.1) MUTATED        3      0      0
  DEL PEAK 14(15Q15.1) WILD-TYPE      1      3      2
D20V7, multiclass
        clus
vv       DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE
  CLUS_1                            1                              3
  CLUS_2                            0                              3
  CLUS_3                            0                              4
  CLUS_4                            2                              0
  CLUS_5                            0                              3
  CLUS_6                            1                              1
  CLUS_7                            3                              1
  CLUS_8                            0                              3
  CLUS_9                            0                              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = DEL PEAK 15(15Q21.1) MUTATION ANALYSIS
D21V1, binary
                                cls
clus                              0  1
  DEL PEAK 15(15Q21.1) MUTATED    6  3
  DEL PEAK 15(15Q21.1) WILD-TYPE  9 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(15Q21.1) MUTATED      6    3
  DEL PEAK 15(15Q21.1) WILD-TYPE    9   10
        clus
vv       DEL PEAK 15(15Q21.1) MUTATED DEL PEAK 15(15Q21.1) WILD-TYPE
  CLUS_1                            6                              9
  CLUS_2                            3                             10
[1] 2 2
[1] FALSE
D21V2, binary
                                cls
clus                              0  1
  DEL PEAK 15(15Q21.1) MUTATED    5  4
  DEL PEAK 15(15Q21.1) WILD-TYPE 10  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(15Q21.1) MUTATED      5    4
  DEL PEAK 15(15Q21.1) WILD-TYPE   10    9
        clus
vv       DEL PEAK 15(15Q21.1) MUTATED DEL PEAK 15(15Q21.1) WILD-TYPE
  CLUS_1                            5                             10
  CLUS_2                            4                              9
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 15(15Q21.1) MUTATED        3      4      2
  DEL PEAK 15(15Q21.1) WILD-TYPE     10      6      3
D21V3, multiclass
        clus
vv       DEL PEAK 15(15Q21.1) MUTATED DEL PEAK 15(15Q21.1) WILD-TYPE
  CLUS_1                            3                             10
  CLUS_2                            4                              6
  CLUS_3                            2                              3
[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"
D21V4, binary
                                cls
clus                              0  1
  DEL PEAK 15(15Q21.1) MUTATED    4  4
  DEL PEAK 15(15Q21.1) WILD-TYPE 10  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(15Q21.1) MUTATED      4    4
  DEL PEAK 15(15Q21.1) WILD-TYPE   10    9
        clus
vv       DEL PEAK 15(15Q21.1) MUTATED DEL PEAK 15(15Q21.1) WILD-TYPE
  CLUS_1                            4                             10
  CLUS_2                            4                              9
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 15(15Q21.1) MUTATED        1      0      1      2      3      1
  DEL PEAK 15(15Q21.1) WILD-TYPE      1      2      4      2      2      2
                                vv
clus                             CLUS_7 CLUS_8
  DEL PEAK 15(15Q21.1) MUTATED        0      0
  DEL PEAK 15(15Q21.1) WILD-TYPE      3      3
D21V5, multiclass
        clus
vv       DEL PEAK 15(15Q21.1) MUTATED DEL PEAK 15(15Q21.1) WILD-TYPE
  CLUS_1                            1                              1
  CLUS_2                            0                              2
  CLUS_3                            1                              4
  CLUS_4                            2                              2
  CLUS_5                            3                              2
  CLUS_6                            1                              2
  CLUS_7                            0                              3
  CLUS_8                            0                              3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 15(15Q21.1) MUTATED        3      2      3
  DEL PEAK 15(15Q21.1) WILD-TYPE      6      7      6
D21V6, multiclass
        clus
vv       DEL PEAK 15(15Q21.1) MUTATED DEL PEAK 15(15Q21.1) WILD-TYPE
  CLUS_1                            3                              6
  CLUS_2                            2                              7
  CLUS_3                            3                              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 15(15Q21.1) MUTATED        1      0      1      2      0      1
  DEL PEAK 15(15Q21.1) WILD-TYPE      3      3      3      0      3      1
                                vv
clus                             CLUS_7 CLUS_8 CLUS_9
  DEL PEAK 15(15Q21.1) MUTATED        3      0      0
  DEL PEAK 15(15Q21.1) WILD-TYPE      1      3      2
D21V7, multiclass
        clus
vv       DEL PEAK 15(15Q21.1) MUTATED DEL PEAK 15(15Q21.1) WILD-TYPE
  CLUS_1                            1                              3
  CLUS_2                            0                              3
  CLUS_3                            1                              3
  CLUS_4                            2                              0
  CLUS_5                            0                              3
  CLUS_6                            1                              1
  CLUS_7                            3                              1
  CLUS_8                            0                              3
  CLUS_9                            0                              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = DEL PEAK 16(16P13.13) MUTATION ANALYSIS
D22V1, binary
                                 cls
clus                               0  1
  DEL PEAK 16(16P13.13) MUTATED    1  3
  DEL PEAK 16(16P13.13) WILD-TYPE 14 10
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(16P13.13) MUTATED      1    3
  DEL PEAK 16(16P13.13) WILD-TYPE   14   10
        clus
vv       DEL PEAK 16(16P13.13) MUTATED DEL PEAK 16(16P13.13) WILD-TYPE
  CLUS_1                             1                              14
  CLUS_2                             3                              10
[1] 2 2
[1] FALSE
D22V2, binary
                                 cls
clus                               0  1
  DEL PEAK 16(16P13.13) MUTATED    1  3
  DEL PEAK 16(16P13.13) WILD-TYPE 14 10
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(16P13.13) MUTATED      1    3
  DEL PEAK 16(16P13.13) WILD-TYPE   14   10
        clus
vv       DEL PEAK 16(16P13.13) MUTATED DEL PEAK 16(16P13.13) WILD-TYPE
  CLUS_1                             1                              14
  CLUS_2                             3                              10
[1] 2 2
[1] FALSE
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 16(16P13.13) MUTATED        2      2      0
  DEL PEAK 16(16P13.13) WILD-TYPE     11      8      5
D22V3, multiclass
        clus
vv       DEL PEAK 16(16P13.13) MUTATED DEL PEAK 16(16P13.13) WILD-TYPE
  CLUS_1                             2                              11
  CLUS_2                             2                               8
  CLUS_3                             0                               5
[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"
D22V4, binary
                                 cls
clus                               0  1
  DEL PEAK 16(16P13.13) MUTATED    1  3
  DEL PEAK 16(16P13.13) WILD-TYPE 13 10
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(16P13.13) MUTATED      1    3
  DEL PEAK 16(16P13.13) WILD-TYPE   13   10
        clus
vv       DEL PEAK 16(16P13.13) MUTATED DEL PEAK 16(16P13.13) WILD-TYPE
  CLUS_1                             1                              13
  CLUS_2                             3                              10
[1] 2 2
[1] FALSE
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 16(16P13.13) MUTATED        0      0      0      1      3      0
  DEL PEAK 16(16P13.13) WILD-TYPE      2      2      5      3      2      3
                                 vv
clus                              CLUS_7 CLUS_8
  DEL PEAK 16(16P13.13) MUTATED        0      0
  DEL PEAK 16(16P13.13) WILD-TYPE      3      3
D22V5, multiclass
        clus
vv       DEL PEAK 16(16P13.13) MUTATED DEL PEAK 16(16P13.13) WILD-TYPE
  CLUS_1                             0                               2
  CLUS_2                             0                               2
  CLUS_3                             0                               5
  CLUS_4                             1                               3
  CLUS_5                             3                               2
  CLUS_6                             0                               3
  CLUS_7                             0                               3
  CLUS_8                             0                               3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 16(16P13.13) MUTATED        0      1      3
  DEL PEAK 16(16P13.13) WILD-TYPE      9      8      6
D22V6, multiclass
        clus
vv       DEL PEAK 16(16P13.13) MUTATED DEL PEAK 16(16P13.13) WILD-TYPE
  CLUS_1                             0                               9
  CLUS_2                             1                               8
  CLUS_3                             3                               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 16(16P13.13) MUTATED        0      0      0      1      1      0
  DEL PEAK 16(16P13.13) WILD-TYPE      4      3      4      1      2      2
                                 vv
clus                              CLUS_7 CLUS_8 CLUS_9
  DEL PEAK 16(16P13.13) MUTATED        2      0      0
  DEL PEAK 16(16P13.13) WILD-TYPE      2      3      2
D22V7, multiclass
        clus
vv       DEL PEAK 16(16P13.13) MUTATED DEL PEAK 16(16P13.13) WILD-TYPE
  CLUS_1                             0                               4
  CLUS_2                             0                               3
  CLUS_3                             0                               4
  CLUS_4                             1                               1
  CLUS_5                             1                               2
  CLUS_6                             0                               2
  CLUS_7                             2                               2
  CLUS_8                             0                               3
  CLUS_9                             0                               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = DEL PEAK 17(16Q23.1) MUTATION ANALYSIS
D23V1, binary
                                cls
clus                              0  1
  DEL PEAK 17(16Q23.1) MUTATED    3  2
  DEL PEAK 17(16Q23.1) WILD-TYPE 12 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(16Q23.1) MUTATED      3    2
  DEL PEAK 17(16Q23.1) WILD-TYPE   12   11
        clus
vv       DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE
  CLUS_1                            3                             12
  CLUS_2                            2                             11
[1] 2 2
[1] FALSE
D23V2, binary
                                cls
clus                              0  1
  DEL PEAK 17(16Q23.1) MUTATED    2  3
  DEL PEAK 17(16Q23.1) WILD-TYPE 13 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(16Q23.1) MUTATED      2    3
  DEL PEAK 17(16Q23.1) WILD-TYPE   13   10
        clus
vv       DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE
  CLUS_1                            2                             13
  CLUS_2                            3                             10
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 17(16Q23.1) MUTATED        1      3      1
  DEL PEAK 17(16Q23.1) WILD-TYPE     12      7      4
D23V3, multiclass
        clus
vv       DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE
  CLUS_1                            1                             12
  CLUS_2                            3                              7
  CLUS_3                            1                              4
[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"
D23V4, binary
                                cls
clus                              0  1
  DEL PEAK 17(16Q23.1) MUTATED    2  3
  DEL PEAK 17(16Q23.1) WILD-TYPE 12 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(16Q23.1) MUTATED      2    3
  DEL PEAK 17(16Q23.1) WILD-TYPE   12   10
        clus
vv       DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE
  CLUS_1                            2                             12
  CLUS_2                            3                             10
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 17(16Q23.1) MUTATED        0      0      0      2      1      1
  DEL PEAK 17(16Q23.1) WILD-TYPE      2      2      5      2      4      2
                                vv
clus                             CLUS_7 CLUS_8
  DEL PEAK 17(16Q23.1) MUTATED        1      0
  DEL PEAK 17(16Q23.1) WILD-TYPE      2      3
D23V5, multiclass
        clus
vv       DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE
  CLUS_1                            0                              2
  CLUS_2                            0                              2
  CLUS_3                            0                              5
  CLUS_4                            2                              2
  CLUS_5                            1                              4
  CLUS_6                            1                              2
  CLUS_7                            1                              2
  CLUS_8                            0                              3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 17(16Q23.1) MUTATED        1      2      2
  DEL PEAK 17(16Q23.1) WILD-TYPE      8      7      7
D23V6, multiclass
        clus
vv       DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE
  CLUS_1                            1                              8
  CLUS_2                            2                              7
  CLUS_3                            2                              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 17(16Q23.1) MUTATED        0      1      0      1      0      1
  DEL PEAK 17(16Q23.1) WILD-TYPE      4      2      4      1      3      1
                                vv
clus                             CLUS_7 CLUS_8 CLUS_9
  DEL PEAK 17(16Q23.1) MUTATED        1      1      0
  DEL PEAK 17(16Q23.1) WILD-TYPE      3      2      2
D23V7, multiclass
        clus
vv       DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE
  CLUS_1                            0                              4
  CLUS_2                            1                              2
  CLUS_3                            0                              4
  CLUS_4                            1                              1
  CLUS_5                            0                              3
  CLUS_6                            1                              1
  CLUS_7                            1                              3
  CLUS_8                            1                              2
  CLUS_9                            0                              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = DEL PEAK 18(17Q24.1) MUTATION ANALYSIS
D24V1, binary
                                cls
clus                              0  1
  DEL PEAK 18(17Q24.1) MUTATED    0  4
  DEL PEAK 18(17Q24.1) WILD-TYPE 15  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(17Q24.1) MUTATED      0    4
  DEL PEAK 18(17Q24.1) WILD-TYPE   15    9
        clus
vv       DEL PEAK 18(17Q24.1) MUTATED DEL PEAK 18(17Q24.1) WILD-TYPE
  CLUS_1                            0                             15
  CLUS_2                            4                              9
[1] 2 2
[1] FALSE
D24V2, binary
                                cls
clus                              0  1
  DEL PEAK 18(17Q24.1) MUTATED    2  2
  DEL PEAK 18(17Q24.1) WILD-TYPE 13 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(17Q24.1) MUTATED      2    2
  DEL PEAK 18(17Q24.1) WILD-TYPE   13   11
        clus
vv       DEL PEAK 18(17Q24.1) MUTATED DEL PEAK 18(17Q24.1) WILD-TYPE
  CLUS_1                            2                             13
  CLUS_2                            2                             11
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 18(17Q24.1) MUTATED        0      2      2
  DEL PEAK 18(17Q24.1) WILD-TYPE     13      8      3
D24V3, multiclass
        clus
vv       DEL PEAK 18(17Q24.1) MUTATED DEL PEAK 18(17Q24.1) WILD-TYPE
  CLUS_1                            0                             13
  CLUS_2                            2                              8
  CLUS_3                            2                              3
[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"
D24V4, binary
                                cls
clus                              0  1
  DEL PEAK 18(17Q24.1) MUTATED    2  2
  DEL PEAK 18(17Q24.1) WILD-TYPE 12 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(17Q24.1) MUTATED      2    2
  DEL PEAK 18(17Q24.1) WILD-TYPE   12   11
        clus
vv       DEL PEAK 18(17Q24.1) MUTATED DEL PEAK 18(17Q24.1) WILD-TYPE
  CLUS_1                            2                             12
  CLUS_2                            2                             11
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 18(17Q24.1) MUTATED        0      0      2      0      2      0
  DEL PEAK 18(17Q24.1) WILD-TYPE      2      2      3      4      3      3
                                vv
clus                             CLUS_7 CLUS_8
  DEL PEAK 18(17Q24.1) MUTATED        0      0
  DEL PEAK 18(17Q24.1) WILD-TYPE      3      3
D24V5, multiclass
        clus
vv       DEL PEAK 18(17Q24.1) MUTATED DEL PEAK 18(17Q24.1) WILD-TYPE
  CLUS_1                            0                              2
  CLUS_2                            0                              2
  CLUS_3                            2                              3
  CLUS_4                            0                              4
  CLUS_5                            2                              3
  CLUS_6                            0                              3
  CLUS_7                            0                              3
  CLUS_8                            0                              3
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 18(17Q24.1) MUTATED        2      0      2
  DEL PEAK 18(17Q24.1) WILD-TYPE      7      9      7
D24V6, multiclass
        clus
vv       DEL PEAK 18(17Q24.1) MUTATED DEL PEAK 18(17Q24.1) WILD-TYPE
  CLUS_1                            2                              7
  CLUS_2                            0                              9
  CLUS_3                            2                              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 18(17Q24.1) MUTATED        0      0      2      0      0      0
  DEL PEAK 18(17Q24.1) WILD-TYPE      4      3      2      2      3      2
                                vv
clus                             CLUS_7 CLUS_8 CLUS_9
  DEL PEAK 18(17Q24.1) MUTATED        2      0      0
  DEL PEAK 18(17Q24.1) WILD-TYPE      2      3      2
D24V7, multiclass
        clus
vv       DEL PEAK 18(17Q24.1) MUTATED DEL PEAK 18(17Q24.1) WILD-TYPE
  CLUS_1                            0                              4
  CLUS_2                            0                              3
  CLUS_3                            2                              2
  CLUS_4                            0                              2
  CLUS_5                            0                              3
  CLUS_6                            0                              2
  CLUS_7                            2                              2
  CLUS_8                            0                              3
  CLUS_9                            0                              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
