[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/11589724/DLBC-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/DLBC-TP/11544213/transformed.cor.cli.txt"

nPatients in clinical file=48, in cluster file=48, common to both=48
[1] "Reduce the number of clustering variables from 41 to 40."
[1] 40 48
[1] "AMP PEAK  1(1Q24.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1Q24.2) MUTATED AMP PEAK  1(1Q24.2) WILD-TYPE 
                           16                            32 
  AMP PEAK  1(1Q24.2) MUTATED AMP PEAK  1(1Q24.2) WILD-TYPE 
                           16                            32 
[1] "AMP PEAK  2(2P16.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                           16                            32 
  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                           16                            32 
[1] "AMP PEAK  3(3Q27.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE 
                           14                            34 
  AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE 
                           14                            34 
[1] "AMP PEAK  4(3Q29) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(3Q29) MUTATED AMP PEAK  4(3Q29) WILD-TYPE 
                         15                          33 
  AMP PEAK  4(3Q29) MUTATED AMP PEAK  4(3Q29) WILD-TYPE 
                         15                          33 
[1] "AMP PEAK  5(5P13.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(5P13.1) MUTATED AMP PEAK  5(5P13.1) WILD-TYPE 
                            8                            40 
  AMP PEAK  5(5P13.1) MUTATED AMP PEAK  5(5P13.1) WILD-TYPE 
                            8                            40 
[1] "AMP PEAK  6(7P22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(7P22.3) MUTATED AMP PEAK  6(7P22.3) WILD-TYPE 
                           16                            32 
  AMP PEAK  6(7P22.3) MUTATED AMP PEAK  6(7P22.3) WILD-TYPE 
                           16                            32 
[1] "AMP PEAK  7(7Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(7Q21.3) MUTATED AMP PEAK  7(7Q21.3) WILD-TYPE 
                           15                            33 
  AMP PEAK  7(7Q21.3) MUTATED AMP PEAK  7(7Q21.3) WILD-TYPE 
                           15                            33 
[1] "AMP PEAK  8(8Q24.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(8Q24.23) MUTATED AMP PEAK  8(8Q24.23) WILD-TYPE 
                            14                             34 
  AMP PEAK  8(8Q24.23) MUTATED AMP PEAK  8(8Q24.23) WILD-TYPE 
                            14                             34 
[1] "AMP PEAK  9(12Q21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(12Q21.1) MUTATED AMP PEAK  9(12Q21.1) WILD-TYPE 
                            14                             34 
  AMP PEAK  9(12Q21.1) MUTATED AMP PEAK  9(12Q21.1) WILD-TYPE 
                            14                             34 
[1] "AMP PEAK 11(16P12.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(16P12.2) MUTATED AMP PEAK 11(16P12.2) WILD-TYPE 
                            10                             38 
  AMP PEAK 11(16P12.2) MUTATED AMP PEAK 11(16P12.2) WILD-TYPE 
                            10                             38 
[1] "AMP PEAK 12(18Q21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(18Q21.2) MUTATED AMP PEAK 12(18Q21.2) WILD-TYPE 
                            16                             32 
  AMP PEAK 12(18Q21.2) MUTATED AMP PEAK 12(18Q21.2) WILD-TYPE 
                            16                             32 
[1] "AMP PEAK 13(19Q13.43) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(19Q13.43) MUTATED AMP PEAK 13(19Q13.43) WILD-TYPE 
                             10                              38 
  AMP PEAK 13(19Q13.43) MUTATED AMP PEAK 13(19Q13.43) WILD-TYPE 
                             10                              38 
[1] "AMP PEAK 14(XQ27.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(XQ27.3) MUTATED AMP PEAK 14(XQ27.3) WILD-TYPE 
                            7                            41 
  AMP PEAK 14(XQ27.3) MUTATED AMP PEAK 14(XQ27.3) WILD-TYPE 
                            7                            41 
[1] "DEL PEAK  1(1P36.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            11                             37 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            11                             37 
[1] "DEL PEAK  2(1P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                           12                            36 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                           12                            36 
[1] "DEL PEAK  3(1Q43) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                         10                          38 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                         10                          38 
[1] "DEL PEAK  4(2Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE 
                            8                            40 
  DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE 
                            8                            40 
[1] "DEL PEAK  5(3P21.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                             8                             40 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                             8                             40 
[1] "DEL PEAK  6(4Q35.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(4Q35.1) MUTATED DEL PEAK  6(4Q35.1) WILD-TYPE 
                           10                            38 
  DEL PEAK  6(4Q35.1) MUTATED DEL PEAK  6(4Q35.1) WILD-TYPE 
                           10                            38 
[1] "DEL PEAK  7(5Q33.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(5Q33.3) MUTATED DEL PEAK  7(5Q33.3) WILD-TYPE 
                            4                            44 
  DEL PEAK  7(5Q33.3) MUTATED DEL PEAK  7(5Q33.3) WILD-TYPE 
                            4                            44 
[1] "DEL PEAK  8(6P21.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(6P21.32) MUTATED DEL PEAK  8(6P21.32) WILD-TYPE 
                             6                             42 
  DEL PEAK  8(6P21.32) MUTATED DEL PEAK  8(6P21.32) WILD-TYPE 
                             6                             42 
[1] "DEL PEAK  9(6Q14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(6Q14.1) MUTATED DEL PEAK  9(6Q14.1) WILD-TYPE 
                           17                            31 
  DEL PEAK  9(6Q14.1) MUTATED DEL PEAK  9(6Q14.1) WILD-TYPE 
                           17                            31 
[1] "DEL PEAK 10(6Q22.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(6Q22.32) MUTATED DEL PEAK 10(6Q22.32) WILD-TYPE 
                            16                             32 
  DEL PEAK 10(6Q22.32) MUTATED DEL PEAK 10(6Q22.32) WILD-TYPE 
                            16                             32 
[1] "DEL PEAK 11(6Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(6Q23.3) MUTATED DEL PEAK 11(6Q23.3) WILD-TYPE 
                           16                            32 
  DEL PEAK 11(6Q23.3) MUTATED DEL PEAK 11(6Q23.3) WILD-TYPE 
                           16                            32 
[1] "DEL PEAK 12(7Q33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(7Q33) MUTATED DEL PEAK 12(7Q33) WILD-TYPE 
                          5                          43 
  DEL PEAK 12(7Q33) MUTATED DEL PEAK 12(7Q33) WILD-TYPE 
                          5                          43 
[1] "DEL PEAK 13(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE 
                           12                            36 
  DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE 
                           12                            36 
[1] "DEL PEAK 14(8Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(8Q12.1) MUTATED DEL PEAK 14(8Q12.1) WILD-TYPE 
                            9                            39 
  DEL PEAK 14(8Q12.1) MUTATED DEL PEAK 14(8Q12.1) WILD-TYPE 
                            9                            39 
[1] "DEL PEAK 15(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                           17                            31 
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                           17                            31 
[1] "DEL PEAK 16(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                              8                              40 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                              8                              40 
[1] "DEL PEAK 17(12P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(12P13.2) MUTATED DEL PEAK 17(12P13.2) WILD-TYPE 
                             8                             40 
  DEL PEAK 17(12P13.2) MUTATED DEL PEAK 17(12P13.2) WILD-TYPE 
                             8                             40 
[1] "DEL PEAK 18(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE 
                             7                             41 
  DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE 
                             7                             41 
[1] "DEL PEAK 19(15Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE 
                            13                             35 
  DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE 
                            13                             35 
[1] "DEL PEAK 20(16P13.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(16P13.13) MUTATED DEL PEAK 20(16P13.13) WILD-TYPE 
                              6                              42 
  DEL PEAK 20(16P13.13) MUTATED DEL PEAK 20(16P13.13) WILD-TYPE 
                              6                              42 
[1] "DEL PEAK 21(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE 
                             5                             43 
  DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE 
                             5                             43 
[1] "DEL PEAK 22(17P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(17P13.1) MUTATED DEL PEAK 22(17P13.1) WILD-TYPE 
                            13                             35 
  DEL PEAK 22(17P13.1) MUTATED DEL PEAK 22(17P13.1) WILD-TYPE 
                            13                             35 
[1] "DEL PEAK 23(17Q24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(17Q24.1) MUTATED DEL PEAK 23(17Q24.1) WILD-TYPE 
                             8                             40 
  DEL PEAK 23(17Q24.1) MUTATED DEL PEAK 23(17Q24.1) WILD-TYPE 
                             8                             40 
[1] "DEL PEAK 24(19P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(19P13.2) MUTATED DEL PEAK 24(19P13.2) WILD-TYPE 
                             4                             44 
  DEL PEAK 24(19P13.2) MUTATED DEL PEAK 24(19P13.2) WILD-TYPE 
                             4                             44 
[1] "DEL PEAK 25(19Q13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(19Q13.2) MUTATED DEL PEAK 25(19Q13.2) WILD-TYPE 
                             5                             43 
  DEL PEAK 25(19Q13.2) MUTATED DEL PEAK 25(19Q13.2) WILD-TYPE 
                             5                             43 
[1] "DEL PEAK 26(22Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(22Q13.31) MUTATED DEL PEAK 26(22Q13.31) WILD-TYPE 
                              7                              41 
  DEL PEAK 26(22Q13.31) MUTATED DEL PEAK 26(22Q13.31) WILD-TYPE 
                              7                              41 
[1] "DEL PEAK 27(XQ28) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(XQ28) MUTATED DEL PEAK 27(XQ28) WILD-TYPE 
                          3                          45 
  DEL PEAK 27(XQ28) MUTATED DEL PEAK 27(XQ28) WILD-TYPE 
                          3                          45 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
[1] "CN_CNMF"                     "METHLYATION_CNMF"           
[3] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
[5] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[7] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 8 rows and 48 columns.

Variable 1:'CN_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MRNASEQ_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MIRSEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_MATURE_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "CN_CNMF"                     "METHLYATION_CNMF"           
[3] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
[5] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[7] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 48 columns, 0 survival variables, and 8 non-survival variables.
CN_CNMF, nv=2, binary=FALSE, numeric=FALSE
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=4, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=2, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=9, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1Q24.2) MUTATION ANALYSIS
D1V1, binary
                               cls
clus                             0  1
  AMP PEAK  1(1Q24.2) MUTATED    5 11
  AMP PEAK  1(1Q24.2) WILD-TYPE 24  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q24.2) MUTATED      5   11
  AMP PEAK  1(1Q24.2) WILD-TYPE   24    8
        clus
vv       AMP PEAK  1(1Q24.2) MUTATED AMP PEAK  1(1Q24.2) WILD-TYPE
  CLUS_1                           5                            24
  CLUS_2                          11                             8
[1] 2 2
[1] FALSE
D1V2, binary
                               cls
clus                             0  1
  AMP PEAK  1(1Q24.2) MUTATED    8  8
  AMP PEAK  1(1Q24.2) WILD-TYPE 16 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q24.2) MUTATED      8    8
  AMP PEAK  1(1Q24.2) WILD-TYPE   16   16
        clus
vv       AMP PEAK  1(1Q24.2) MUTATED AMP PEAK  1(1Q24.2) WILD-TYPE
  CLUS_1                           8                            16
  CLUS_2                           8                            16
[1] 2 2
[1] FALSE
D1V3, binary
                               cls
clus                             0  1
  AMP PEAK  1(1Q24.2) MUTATED    3  5
  AMP PEAK  1(1Q24.2) WILD-TYPE 12  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q24.2) MUTATED      3    5
  AMP PEAK  1(1Q24.2) WILD-TYPE   12    8
        clus
vv       AMP PEAK  1(1Q24.2) MUTATED AMP PEAK  1(1Q24.2) WILD-TYPE
  CLUS_1                           3                            12
  CLUS_2                           5                             8
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  AMP PEAK  1(1Q24.2) MUTATED        2      5      1
  AMP PEAK  1(1Q24.2) WILD-TYPE     11      5      4
D1V4, multiclass
        clus
vv       AMP PEAK  1(1Q24.2) MUTATED AMP PEAK  1(1Q24.2) WILD-TYPE
  CLUS_1                           2                            11
  CLUS_2                           5                             5
  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"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AMP PEAK  1(1Q24.2) MUTATED        5      4      2      5
  AMP PEAK  1(1Q24.2) WILD-TYPE      9      7      8      7
D1V5, multiclass
        clus
vv       AMP PEAK  1(1Q24.2) MUTATED AMP PEAK  1(1Q24.2) WILD-TYPE
  CLUS_1                           5                             9
  CLUS_2                           4                             7
  CLUS_3                           2                             8
  CLUS_4                           5                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AMP PEAK  1(1Q24.2) MUTATED        1      4      4      4      3
  AMP PEAK  1(1Q24.2) WILD-TYPE      8      8      4      8      3
D1V6, multiclass
        clus
vv       AMP PEAK  1(1Q24.2) MUTATED AMP PEAK  1(1Q24.2) WILD-TYPE
  CLUS_1                           1                             8
  CLUS_2                           4                             8
  CLUS_3                           4                             4
  CLUS_4                           4                             8
  CLUS_5                           3                             3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                               cls
clus                             0  1
  AMP PEAK  1(1Q24.2) MUTATED    6  8
  AMP PEAK  1(1Q24.2) WILD-TYPE 13 15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q24.2) MUTATED      6    8
  AMP PEAK  1(1Q24.2) WILD-TYPE   13   15
        clus
vv       AMP PEAK  1(1Q24.2) MUTATED AMP PEAK  1(1Q24.2) WILD-TYPE
  CLUS_1                           6                            13
  CLUS_2                           8                            15
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  AMP PEAK  1(1Q24.2) MUTATED        1      2      2      2      3      1
  AMP PEAK  1(1Q24.2) WILD-TYPE      3      3      4      4      5      2
                               vv
clus                            CLUS_7 CLUS_8 CLUS_9
  AMP PEAK  1(1Q24.2) MUTATED        2      0      1
  AMP PEAK  1(1Q24.2) WILD-TYPE      3      2      2
D1V8, multiclass
        clus
vv       AMP PEAK  1(1Q24.2) MUTATED AMP PEAK  1(1Q24.2) WILD-TYPE
  CLUS_1                           1                             3
  CLUS_2                           2                             3
  CLUS_3                           2                             4
  CLUS_4                           2                             4
  CLUS_5                           3                             5
  CLUS_6                           1                             2
  CLUS_7                           2                             3
  CLUS_8                           0                             2
  CLUS_9                           1                             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(2P16.1) MUTATION ANALYSIS
D2V1, binary
                               cls
clus                             0  1
  AMP PEAK  2(2P16.1) MUTATED    7  9
  AMP PEAK  2(2P16.1) WILD-TYPE 22 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2P16.1) MUTATED      7    9
  AMP PEAK  2(2P16.1) WILD-TYPE   22   10
        clus
vv       AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE
  CLUS_1                           7                            22
  CLUS_2                           9                            10
[1] 2 2
[1] FALSE
D2V2, binary
                               cls
clus                             0  1
  AMP PEAK  2(2P16.1) MUTATED    2 14
  AMP PEAK  2(2P16.1) WILD-TYPE 22 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2P16.1) MUTATED      2   14
  AMP PEAK  2(2P16.1) WILD-TYPE   22   10
        clus
vv       AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE
  CLUS_1                           2                            22
  CLUS_2                          14                            10
[1] 2 2
[1] FALSE
D2V3, binary
                               cls
clus                             0  1
  AMP PEAK  2(2P16.1) MUTATED    5  3
  AMP PEAK  2(2P16.1) WILD-TYPE 10 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2P16.1) MUTATED      5    3
  AMP PEAK  2(2P16.1) WILD-TYPE   10   10
        clus
vv       AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) 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(2P16.1) MUTATED        4      2      2
  AMP PEAK  2(2P16.1) WILD-TYPE      9      8      3
D2V4, multiclass
        clus
vv       AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) 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"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AMP PEAK  2(2P16.1) MUTATED        6      1      2      7
  AMP PEAK  2(2P16.1) WILD-TYPE      8     10      8      5
D2V5, multiclass
        clus
vv       AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE
  CLUS_1                           6                             8
  CLUS_2                           1                            10
  CLUS_3                           2                             8
  CLUS_4                           7                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AMP PEAK  2(2P16.1) MUTATED        1      3      6      2      4
  AMP PEAK  2(2P16.1) WILD-TYPE      8      9      2     10      2
D2V6, multiclass
        clus
vv       AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE
  CLUS_1                           1                             8
  CLUS_2                           3                             9
  CLUS_3                           6                             2
  CLUS_4                           2                            10
  CLUS_5                           4                             2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                               cls
clus                             0  1
  AMP PEAK  2(2P16.1) MUTATED    8  6
  AMP PEAK  2(2P16.1) WILD-TYPE 11 17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2P16.1) MUTATED      8    6
  AMP PEAK  2(2P16.1) WILD-TYPE   11   17
        clus
vv       AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE
  CLUS_1                           8                            11
  CLUS_2                           6                            17
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  AMP PEAK  2(2P16.1) MUTATED        2      0      2      1      3      2
  AMP PEAK  2(2P16.1) WILD-TYPE      2      5      4      5      5      1
                               vv
clus                            CLUS_7 CLUS_8 CLUS_9
  AMP PEAK  2(2P16.1) MUTATED        3      0      1
  AMP PEAK  2(2P16.1) WILD-TYPE      2      2      2
D2V8, multiclass
        clus
vv       AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE
  CLUS_1                           2                             2
  CLUS_2                           0                             5
  CLUS_3                           2                             4
  CLUS_4                           1                             5
  CLUS_5                           3                             5
  CLUS_6                           2                             1
  CLUS_7                           3                             2
  CLUS_8                           0                             2
  CLUS_9                           1                             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 10
  AMP PEAK  3(3Q27.3) WILD-TYPE 25  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(3Q27.3) MUTATED      4   10
  AMP PEAK  3(3Q27.3) WILD-TYPE   25    9
        clus
vv       AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE
  CLUS_1                           4                            25
  CLUS_2                          10                             9
[1] 2 2
[1] FALSE
D3V2, binary
                               cls
clus                             0  1
  AMP PEAK  3(3Q27.3) MUTATED    9  5
  AMP PEAK  3(3Q27.3) WILD-TYPE 15 19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(3Q27.3) MUTATED      9    5
  AMP PEAK  3(3Q27.3) WILD-TYPE   15   19
        clus
vv       AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE
  CLUS_1                           9                            15
  CLUS_2                           5                            19
[1] 2 2
[1] FALSE
D3V3, 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
D3V4, 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"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AMP PEAK  3(3Q27.3) MUTATED        5      4      3      2
  AMP PEAK  3(3Q27.3) WILD-TYPE      9      7      7     10
D3V5, multiclass
        clus
vv       AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE
  CLUS_1                           5                             9
  CLUS_2                           4                             7
  CLUS_3                           3                             7
  CLUS_4                           2                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AMP PEAK  3(3Q27.3) MUTATED        2      3      4      5      0
  AMP PEAK  3(3Q27.3) WILD-TYPE      7      9      4      7      6
D3V6, multiclass
        clus
vv       AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE
  CLUS_1                           2                             7
  CLUS_2                           3                             9
  CLUS_3                           4                             4
  CLUS_4                           5                             7
  CLUS_5                           0                             6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                               cls
clus                             0  1
  AMP PEAK  3(3Q27.3) MUTATED    7  6
  AMP PEAK  3(3Q27.3) WILD-TYPE 12 17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(3Q27.3) MUTATED      7    6
  AMP PEAK  3(3Q27.3) WILD-TYPE   12   17
        clus
vv       AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE
  CLUS_1                           7                            12
  CLUS_2                           6                            17
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  AMP PEAK  3(3Q27.3) MUTATED        1      1      4      2      1      0
  AMP PEAK  3(3Q27.3) WILD-TYPE      3      4      2      4      7      3
                               vv
clus                            CLUS_7 CLUS_8 CLUS_9
  AMP PEAK  3(3Q27.3) MUTATED        2      0      2
  AMP PEAK  3(3Q27.3) WILD-TYPE      3      2      1
D3V8, multiclass
        clus
vv       AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE
  CLUS_1                           1                             3
  CLUS_2                           1                             4
  CLUS_3                           4                             2
  CLUS_4                           2                             4
  CLUS_5                           1                             7
  CLUS_6                           0                             3
  CLUS_7                           2                             3
  CLUS_8                           0                             2
  CLUS_9                           2                             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(4) Variable = AMP PEAK  4(3Q29) MUTATION ANALYSIS
D4V1, binary
                             cls
clus                           0  1
  AMP PEAK  4(3Q29) MUTATED    4 11
  AMP PEAK  4(3Q29) WILD-TYPE 25  8
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(3Q29) MUTATED      4   11
  AMP PEAK  4(3Q29) WILD-TYPE   25    8
        clus
vv       AMP PEAK  4(3Q29) MUTATED AMP PEAK  4(3Q29) WILD-TYPE
  CLUS_1                         4                          25
  CLUS_2                        11                           8
[1] 2 2
[1] FALSE
D4V2, binary
                             cls
clus                           0  1
  AMP PEAK  4(3Q29) MUTATED   10  5
  AMP PEAK  4(3Q29) WILD-TYPE 14 19
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(3Q29) MUTATED     10    5
  AMP PEAK  4(3Q29) WILD-TYPE   14   19
        clus
vv       AMP PEAK  4(3Q29) MUTATED AMP PEAK  4(3Q29) WILD-TYPE
  CLUS_1                        10                          14
  CLUS_2                         5                          19
[1] 2 2
[1] FALSE
D4V3, binary
                             cls
clus                           0  1
  AMP PEAK  4(3Q29) MUTATED    4  2
  AMP PEAK  4(3Q29) WILD-TYPE 11 11
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(3Q29) MUTATED      4    2
  AMP PEAK  4(3Q29) WILD-TYPE   11   11
        clus
vv       AMP PEAK  4(3Q29) MUTATED AMP PEAK  4(3Q29) 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  4(3Q29) MUTATED        3      2      1
  AMP PEAK  4(3Q29) WILD-TYPE     10      8      4
D4V4, multiclass
        clus
vv       AMP PEAK  4(3Q29) MUTATED AMP PEAK  4(3Q29) WILD-TYPE
  CLUS_1                         3                          10
  CLUS_2                         2                           8
  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"
                             vv
clus                          CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AMP PEAK  4(3Q29) MUTATED        4      4      4      3
  AMP PEAK  4(3Q29) WILD-TYPE     10      7      6      9
D4V5, multiclass
        clus
vv       AMP PEAK  4(3Q29) MUTATED AMP PEAK  4(3Q29) WILD-TYPE
  CLUS_1                         4                          10
  CLUS_2                         4                           7
  CLUS_3                         4                           6
  CLUS_4                         3                           9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AMP PEAK  4(3Q29) MUTATED        2      4      3      6      0
  AMP PEAK  4(3Q29) WILD-TYPE      7      8      5      6      6
D4V6, multiclass
        clus
vv       AMP PEAK  4(3Q29) MUTATED AMP PEAK  4(3Q29) WILD-TYPE
  CLUS_1                         2                           7
  CLUS_2                         4                           8
  CLUS_3                         3                           5
  CLUS_4                         6                           6
  CLUS_5                         0                           6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                             cls
clus                           0  1
  AMP PEAK  4(3Q29) MUTATED    6  7
  AMP PEAK  4(3Q29) WILD-TYPE 13 16
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(3Q29) MUTATED      6    7
  AMP PEAK  4(3Q29) WILD-TYPE   13   16
        clus
vv       AMP PEAK  4(3Q29) MUTATED AMP PEAK  4(3Q29) WILD-TYPE
  CLUS_1                         6                          13
  CLUS_2                         7                          16
[1] 2 2
[1] FALSE
                             vv
clus                          CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  AMP PEAK  4(3Q29) MUTATED        1      1      3      2      1      0      2
  AMP PEAK  4(3Q29) WILD-TYPE      3      4      3      4      7      3      3
                             vv
clus                          CLUS_8 CLUS_9
  AMP PEAK  4(3Q29) MUTATED        0      3
  AMP PEAK  4(3Q29) WILD-TYPE      2      0
D4V8, multiclass
        clus
vv       AMP PEAK  4(3Q29) MUTATED AMP PEAK  4(3Q29) WILD-TYPE
  CLUS_1                         1                           3
  CLUS_2                         1                           4
  CLUS_3                         3                           3
  CLUS_4                         2                           4
  CLUS_5                         1                           7
  CLUS_6                         0                           3
  CLUS_7                         2                           3
  CLUS_8                         0                           2
  CLUS_9                         3                           0
[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(5P13.1) MUTATION ANALYSIS
D5V1, binary
                               cls
clus                             0  1
  AMP PEAK  5(5P13.1) MUTATED    5  3
  AMP PEAK  5(5P13.1) WILD-TYPE 24 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(5P13.1) MUTATED      5    3
  AMP PEAK  5(5P13.1) WILD-TYPE   24   16
        clus
vv       AMP PEAK  5(5P13.1) MUTATED AMP PEAK  5(5P13.1) WILD-TYPE
  CLUS_1                           5                            24
  CLUS_2                           3                            16
[1] 2 2
[1] FALSE
D5V2, binary
                               cls
clus                             0  1
  AMP PEAK  5(5P13.1) MUTATED    3  5
  AMP PEAK  5(5P13.1) WILD-TYPE 21 19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(5P13.1) MUTATED      3    5
  AMP PEAK  5(5P13.1) WILD-TYPE   21   19
        clus
vv       AMP PEAK  5(5P13.1) MUTATED AMP PEAK  5(5P13.1) WILD-TYPE
  CLUS_1                           3                            21
  CLUS_2                           5                            19
[1] 2 2
[1] FALSE
D5V3, binary
                               cls
clus                             0  1
  AMP PEAK  5(5P13.1) MUTATED    1  1
  AMP PEAK  5(5P13.1) WILD-TYPE 14 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(5P13.1) MUTATED      1    1
  AMP PEAK  5(5P13.1) WILD-TYPE   14   12
        clus
vv       AMP PEAK  5(5P13.1) MUTATED AMP PEAK  5(5P13.1) WILD-TYPE
  CLUS_1                           1                            14
  CLUS_2                           1                            12
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  AMP PEAK  5(5P13.1) MUTATED        2      0      0
  AMP PEAK  5(5P13.1) WILD-TYPE     11     10      5
D5V4, multiclass
[1] "Remove cluster labels:"      "AMP PEAK  5(5P13.1) MUTATED"
clus
  AMP PEAK  5(5P13.1) MUTATED AMP PEAK  5(5P13.1) WILD-TYPE 
                            2                            26 
                   TCGA-FA-8693                    TCGA-FA-A4BB 
"AMP PEAK  5(5P13.1) WILD-TYPE" "AMP PEAK  5(5P13.1) WILD-TYPE" 
                   TCGA-FA-A4XK                    TCGA-FA-A6HN 
"AMP PEAK  5(5P13.1) WILD-TYPE" "AMP PEAK  5(5P13.1) WILD-TYPE" 
                   TCGA-FA-A6HO                    TCGA-FF-8042 
"AMP PEAK  5(5P13.1) WILD-TYPE" "AMP PEAK  5(5P13.1) WILD-TYPE" 
                   TCGA-FF-8043                    TCGA-FF-8046 
"AMP PEAK  5(5P13.1) WILD-TYPE" "AMP PEAK  5(5P13.1) WILD-TYPE" 
                   TCGA-FF-8047                    TCGA-FF-8061 
"AMP PEAK  5(5P13.1) WILD-TYPE" "AMP PEAK  5(5P13.1) WILD-TYPE" 
                   TCGA-FF-8062                    TCGA-FM-8000 
"AMP PEAK  5(5P13.1) WILD-TYPE" "AMP PEAK  5(5P13.1) WILD-TYPE" 
                   TCGA-G8-6324                    TCGA-G8-6325 
"AMP PEAK  5(5P13.1) WILD-TYPE" "AMP PEAK  5(5P13.1) WILD-TYPE" 
                   TCGA-G8-6326                    TCGA-G8-6906 
"AMP PEAK  5(5P13.1) WILD-TYPE" "AMP PEAK  5(5P13.1) WILD-TYPE" 
                   TCGA-G8-6907                    TCGA-G8-6914 
"AMP PEAK  5(5P13.1) WILD-TYPE" "AMP PEAK  5(5P13.1) WILD-TYPE" 
                   TCGA-GR-7351                    TCGA-GR-7353 
"AMP PEAK  5(5P13.1) WILD-TYPE" "AMP PEAK  5(5P13.1) WILD-TYPE" 
                   TCGA-GR-A4D4                    TCGA-GR-A4D5 
"AMP PEAK  5(5P13.1) WILD-TYPE" "AMP PEAK  5(5P13.1) WILD-TYPE" 
                   TCGA-GR-A4D6                    TCGA-GR-A4D9 
"AMP PEAK  5(5P13.1) WILD-TYPE" "AMP PEAK  5(5P13.1) WILD-TYPE" 
                   TCGA-RQ-A68N                    TCGA-RQ-A6JB 
"AMP PEAK  5(5P13.1) WILD-TYPE" "AMP PEAK  5(5P13.1) WILD-TYPE" 
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AMP PEAK  5(5P13.1) MUTATED        2      1      1      4
  AMP PEAK  5(5P13.1) WILD-TYPE     12     10      9      8
D5V5, multiclass
        clus
vv       AMP PEAK  5(5P13.1) MUTATED AMP PEAK  5(5P13.1) WILD-TYPE
  CLUS_1                           2                            12
  CLUS_2                           1                            10
  CLUS_3                           1                             9
  CLUS_4                           4                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AMP PEAK  5(5P13.1) MUTATED        0      3      2      2      1
  AMP PEAK  5(5P13.1) WILD-TYPE      9      9      6     10      5
D5V6, multiclass
        clus
vv       AMP PEAK  5(5P13.1) MUTATED AMP PEAK  5(5P13.1) WILD-TYPE
  CLUS_1                           0                             9
  CLUS_2                           3                             9
  CLUS_3                           2                             6
  CLUS_4                           2                            10
  CLUS_5                           1                             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                               cls
clus                             0  1
  AMP PEAK  5(5P13.1) MUTATED    2  4
  AMP PEAK  5(5P13.1) WILD-TYPE 17 19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(5P13.1) MUTATED      2    4
  AMP PEAK  5(5P13.1) WILD-TYPE   17   19
        clus
vv       AMP PEAK  5(5P13.1) MUTATED AMP PEAK  5(5P13.1) WILD-TYPE
  CLUS_1                           2                            17
  CLUS_2                           4                            19
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  AMP PEAK  5(5P13.1) MUTATED        1      0      1      0      1      2
  AMP PEAK  5(5P13.1) WILD-TYPE      3      5      5      6      7      1
                               vv
clus                            CLUS_7 CLUS_8 CLUS_9
  AMP PEAK  5(5P13.1) MUTATED        0      0      1
  AMP PEAK  5(5P13.1) WILD-TYPE      5      2      2
D5V8, multiclass
        clus
vv       AMP PEAK  5(5P13.1) MUTATED AMP PEAK  5(5P13.1) WILD-TYPE
  CLUS_1                           1                             3
  CLUS_2                           0                             5
  CLUS_3                           1                             5
  CLUS_4                           0                             6
  CLUS_5                           1                             7
  CLUS_6                           2                             1
  CLUS_7                           0                             5
  CLUS_8                           0                             2
  CLUS_9                           1                             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(7P22.3) MUTATION ANALYSIS
D6V1, binary
                               cls
clus                             0  1
  AMP PEAK  6(7P22.3) MUTATED    3 13
  AMP PEAK  6(7P22.3) WILD-TYPE 26  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P22.3) MUTATED      3   13
  AMP PEAK  6(7P22.3) WILD-TYPE   26    6
        clus
vv       AMP PEAK  6(7P22.3) MUTATED AMP PEAK  6(7P22.3) WILD-TYPE
  CLUS_1                           3                            26
  CLUS_2                          13                             6
[1] 2 2
[1] FALSE
D6V2, binary
                               cls
clus                             0  1
  AMP PEAK  6(7P22.3) MUTATED   10  6
  AMP PEAK  6(7P22.3) WILD-TYPE 14 18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P22.3) MUTATED     10    6
  AMP PEAK  6(7P22.3) WILD-TYPE   14   18
        clus
vv       AMP PEAK  6(7P22.3) MUTATED AMP PEAK  6(7P22.3) WILD-TYPE
  CLUS_1                          10                            14
  CLUS_2                           6                            18
[1] 2 2
[1] FALSE
D6V3, binary
                               cls
clus                             0  1
  AMP PEAK  6(7P22.3) MUTATED    5  4
  AMP PEAK  6(7P22.3) WILD-TYPE 10  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P22.3) MUTATED      5    4
  AMP PEAK  6(7P22.3) WILD-TYPE   10    9
        clus
vv       AMP PEAK  6(7P22.3) MUTATED AMP PEAK  6(7P22.3) WILD-TYPE
  CLUS_1                           5                            10
  CLUS_2                           4                             9
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  AMP PEAK  6(7P22.3) MUTATED        3      4      2
  AMP PEAK  6(7P22.3) WILD-TYPE     10      6      3
D6V4, multiclass
        clus
vv       AMP PEAK  6(7P22.3) MUTATED AMP PEAK  6(7P22.3) 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"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AMP PEAK  6(7P22.3) MUTATED        4      3      4      4
  AMP PEAK  6(7P22.3) WILD-TYPE     10      8      6      8
D6V5, multiclass
        clus
vv       AMP PEAK  6(7P22.3) MUTATED AMP PEAK  6(7P22.3) WILD-TYPE
  CLUS_1                           4                            10
  CLUS_2                           3                             8
  CLUS_3                           4                             6
  CLUS_4                           4                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AMP PEAK  6(7P22.3) MUTATED        2      3      3      5      2
  AMP PEAK  6(7P22.3) WILD-TYPE      7      9      5      7      4
D6V6, multiclass
        clus
vv       AMP PEAK  6(7P22.3) MUTATED AMP PEAK  6(7P22.3) WILD-TYPE
  CLUS_1                           2                             7
  CLUS_2                           3                             9
  CLUS_3                           3                             5
  CLUS_4                           5                             7
  CLUS_5                           2                             4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                               cls
clus                             0  1
  AMP PEAK  6(7P22.3) MUTATED    6  7
  AMP PEAK  6(7P22.3) WILD-TYPE 13 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P22.3) MUTATED      6    7
  AMP PEAK  6(7P22.3) WILD-TYPE   13   16
        clus
vv       AMP PEAK  6(7P22.3) MUTATED AMP PEAK  6(7P22.3) WILD-TYPE
  CLUS_1                           6                            13
  CLUS_2                           7                            16
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  AMP PEAK  6(7P22.3) MUTATED        1      0      2      2      2      0
  AMP PEAK  6(7P22.3) WILD-TYPE      3      5      4      4      6      3
                               vv
clus                            CLUS_7 CLUS_8 CLUS_9
  AMP PEAK  6(7P22.3) MUTATED        3      0      3
  AMP PEAK  6(7P22.3) WILD-TYPE      2      2      0
D6V8, multiclass
        clus
vv       AMP PEAK  6(7P22.3) MUTATED AMP PEAK  6(7P22.3) WILD-TYPE
  CLUS_1                           1                             3
  CLUS_2                           0                             5
  CLUS_3                           2                             4
  CLUS_4                           2                             4
  CLUS_5                           2                             6
  CLUS_6                           0                             3
  CLUS_7                           3                             2
  CLUS_8                           0                             2
  CLUS_9                           3                             0
[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(7Q21.3) MUTATION ANALYSIS
D7V1, binary
                               cls
clus                             0  1
  AMP PEAK  7(7Q21.3) MUTATED    2 13
  AMP PEAK  7(7Q21.3) WILD-TYPE 27  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7Q21.3) MUTATED      2   13
  AMP PEAK  7(7Q21.3) WILD-TYPE   27    6
        clus
vv       AMP PEAK  7(7Q21.3) MUTATED AMP PEAK  7(7Q21.3) WILD-TYPE
  CLUS_1                           2                            27
  CLUS_2                          13                             6
[1] 2 2
[1] FALSE
D7V2, binary
                               cls
clus                             0  1
  AMP PEAK  7(7Q21.3) MUTATED    7  8
  AMP PEAK  7(7Q21.3) WILD-TYPE 17 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7Q21.3) MUTATED      7    8
  AMP PEAK  7(7Q21.3) WILD-TYPE   17   16
        clus
vv       AMP PEAK  7(7Q21.3) MUTATED AMP PEAK  7(7Q21.3) WILD-TYPE
  CLUS_1                           7                            17
  CLUS_2                           8                            16
[1] 2 2
[1] FALSE
D7V3, binary
                               cls
clus                             0  1
  AMP PEAK  7(7Q21.3) MUTATED    3  4
  AMP PEAK  7(7Q21.3) WILD-TYPE 12  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7Q21.3) MUTATED      3    4
  AMP PEAK  7(7Q21.3) WILD-TYPE   12    9
        clus
vv       AMP PEAK  7(7Q21.3) MUTATED AMP PEAK  7(7Q21.3) WILD-TYPE
  CLUS_1                           3                            12
  CLUS_2                           4                             9
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  AMP PEAK  7(7Q21.3) MUTATED        1      4      2
  AMP PEAK  7(7Q21.3) WILD-TYPE     12      6      3
D7V4, multiclass
        clus
vv       AMP PEAK  7(7Q21.3) MUTATED AMP PEAK  7(7Q21.3) WILD-TYPE
  CLUS_1                           1                            12
  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"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AMP PEAK  7(7Q21.3) MUTATED        4      2      5      4
  AMP PEAK  7(7Q21.3) WILD-TYPE     10      9      5      8
D7V5, multiclass
        clus
vv       AMP PEAK  7(7Q21.3) MUTATED AMP PEAK  7(7Q21.3) WILD-TYPE
  CLUS_1                           4                            10
  CLUS_2                           2                             9
  CLUS_3                           5                             5
  CLUS_4                           4                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AMP PEAK  7(7Q21.3) MUTATED        2      3      3      5      2
  AMP PEAK  7(7Q21.3) WILD-TYPE      7      9      5      7      4
D7V6, multiclass
        clus
vv       AMP PEAK  7(7Q21.3) MUTATED AMP PEAK  7(7Q21.3) WILD-TYPE
  CLUS_1                           2                             7
  CLUS_2                           3                             9
  CLUS_3                           3                             5
  CLUS_4                           5                             7
  CLUS_5                           2                             4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                               cls
clus                             0  1
  AMP PEAK  7(7Q21.3) MUTATED    6  6
  AMP PEAK  7(7Q21.3) WILD-TYPE 13 17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7Q21.3) MUTATED      6    6
  AMP PEAK  7(7Q21.3) WILD-TYPE   13   17
        clus
vv       AMP PEAK  7(7Q21.3) MUTATED AMP PEAK  7(7Q21.3) WILD-TYPE
  CLUS_1                           6                            13
  CLUS_2                           6                            17
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  AMP PEAK  7(7Q21.3) MUTATED        1      0      2      2      2      0
  AMP PEAK  7(7Q21.3) WILD-TYPE      3      5      4      4      6      3
                               vv
clus                            CLUS_7 CLUS_8 CLUS_9
  AMP PEAK  7(7Q21.3) MUTATED        3      0      2
  AMP PEAK  7(7Q21.3) WILD-TYPE      2      2      1
D7V8, multiclass
        clus
vv       AMP PEAK  7(7Q21.3) MUTATED AMP PEAK  7(7Q21.3) WILD-TYPE
  CLUS_1                           1                             3
  CLUS_2                           0                             5
  CLUS_3                           2                             4
  CLUS_4                           2                             4
  CLUS_5                           2                             6
  CLUS_6                           0                             3
  CLUS_7                           3                             2
  CLUS_8                           0                             2
  CLUS_9                           2                             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(8) Variable = AMP PEAK  8(8Q24.23) MUTATION ANALYSIS
D8V1, binary
                                cls
clus                              0  1
  AMP PEAK  8(8Q24.23) MUTATED    8  6
  AMP PEAK  8(8Q24.23) WILD-TYPE 21 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8Q24.23) MUTATED      8    6
  AMP PEAK  8(8Q24.23) WILD-TYPE   21   13
        clus
vv       AMP PEAK  8(8Q24.23) MUTATED AMP PEAK  8(8Q24.23) WILD-TYPE
  CLUS_1                            8                             21
  CLUS_2                            6                             13
[1] 2 2
[1] FALSE
D8V2, binary
                                cls
clus                              0  1
  AMP PEAK  8(8Q24.23) MUTATED    8  6
  AMP PEAK  8(8Q24.23) WILD-TYPE 16 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8Q24.23) MUTATED      8    6
  AMP PEAK  8(8Q24.23) WILD-TYPE   16   18
        clus
vv       AMP PEAK  8(8Q24.23) MUTATED AMP PEAK  8(8Q24.23) WILD-TYPE
  CLUS_1                            8                             16
  CLUS_2                            6                             18
[1] 2 2
[1] FALSE
D8V3, binary
                                cls
clus                              0  1
  AMP PEAK  8(8Q24.23) MUTATED    2  3
  AMP PEAK  8(8Q24.23) WILD-TYPE 13 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8Q24.23) MUTATED      2    3
  AMP PEAK  8(8Q24.23) WILD-TYPE   13   10
        clus
vv       AMP PEAK  8(8Q24.23) MUTATED AMP PEAK  8(8Q24.23) WILD-TYPE
  CLUS_1                            2                             13
  CLUS_2                            3                             10
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  AMP PEAK  8(8Q24.23) MUTATED        3      2      0
  AMP PEAK  8(8Q24.23) WILD-TYPE     10      8      5
D8V4, multiclass
        clus
vv       AMP PEAK  8(8Q24.23) MUTATED AMP PEAK  8(8Q24.23) WILD-TYPE
  CLUS_1                            3                             10
  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"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AMP PEAK  8(8Q24.23) MUTATED        2      4      4      4
  AMP PEAK  8(8Q24.23) WILD-TYPE     12      7      6      8
D8V5, multiclass
        clus
vv       AMP PEAK  8(8Q24.23) MUTATED AMP PEAK  8(8Q24.23) WILD-TYPE
  CLUS_1                            2                             12
  CLUS_2                            4                              7
  CLUS_3                            4                              6
  CLUS_4                            4                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AMP PEAK  8(8Q24.23) MUTATED        1      3      1      6      3
  AMP PEAK  8(8Q24.23) WILD-TYPE      8      9      7      6      3
D8V6, multiclass
        clus
vv       AMP PEAK  8(8Q24.23) MUTATED AMP PEAK  8(8Q24.23) WILD-TYPE
  CLUS_1                            1                              8
  CLUS_2                            3                              9
  CLUS_3                            1                              7
  CLUS_4                            6                              6
  CLUS_5                            3                              3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                                cls
clus                              0  1
  AMP PEAK  8(8Q24.23) MUTATED    4  7
  AMP PEAK  8(8Q24.23) WILD-TYPE 15 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8Q24.23) MUTATED      4    7
  AMP PEAK  8(8Q24.23) WILD-TYPE   15   16
        clus
vv       AMP PEAK  8(8Q24.23) MUTATED AMP PEAK  8(8Q24.23) WILD-TYPE
  CLUS_1                            4                             15
  CLUS_2                            7                             16
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  AMP PEAK  8(8Q24.23) MUTATED        0      1      2      1      4      1
  AMP PEAK  8(8Q24.23) WILD-TYPE      4      4      4      5      4      2
                                vv
clus                             CLUS_7 CLUS_8 CLUS_9
  AMP PEAK  8(8Q24.23) MUTATED        0      0      2
  AMP PEAK  8(8Q24.23) WILD-TYPE      5      2      1
D8V8, multiclass
        clus
vv       AMP PEAK  8(8Q24.23) MUTATED AMP PEAK  8(8Q24.23) WILD-TYPE
  CLUS_1                            0                              4
  CLUS_2                            1                              4
  CLUS_3                            2                              4
  CLUS_4                            1                              5
  CLUS_5                            4                              4
  CLUS_6                            1                              2
  CLUS_7                            0                              5
  CLUS_8                            0                              2
  CLUS_9                            2                              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(9) Variable = AMP PEAK  9(12Q21.1) MUTATION ANALYSIS
D9V1, binary
                                cls
clus                              0  1
  AMP PEAK  9(12Q21.1) MUTATED    7  7
  AMP PEAK  9(12Q21.1) WILD-TYPE 22 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(12Q21.1) MUTATED      7    7
  AMP PEAK  9(12Q21.1) WILD-TYPE   22   12
        clus
vv       AMP PEAK  9(12Q21.1) MUTATED AMP PEAK  9(12Q21.1) WILD-TYPE
  CLUS_1                            7                             22
  CLUS_2                            7                             12
[1] 2 2
[1] FALSE
D9V2, binary
                                cls
clus                              0  1
  AMP PEAK  9(12Q21.1) MUTATED    3 11
  AMP PEAK  9(12Q21.1) WILD-TYPE 21 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(12Q21.1) MUTATED      3   11
  AMP PEAK  9(12Q21.1) WILD-TYPE   21   13
        clus
vv       AMP PEAK  9(12Q21.1) MUTATED AMP PEAK  9(12Q21.1) WILD-TYPE
  CLUS_1                            3                             21
  CLUS_2                           11                             13
[1] 2 2
[1] FALSE
D9V3, binary
                                cls
clus                              0  1
  AMP PEAK  9(12Q21.1) MUTATED    3  2
  AMP PEAK  9(12Q21.1) WILD-TYPE 12 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(12Q21.1) MUTATED      3    2
  AMP PEAK  9(12Q21.1) WILD-TYPE   12   11
        clus
vv       AMP PEAK  9(12Q21.1) MUTATED AMP PEAK  9(12Q21.1) 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  9(12Q21.1) MUTATED        3      0      2
  AMP PEAK  9(12Q21.1) WILD-TYPE     10     10      3
D9V4, multiclass
        clus
vv       AMP PEAK  9(12Q21.1) MUTATED AMP PEAK  9(12Q21.1) 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"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AMP PEAK  9(12Q21.1) MUTATED        5      2      4      3
  AMP PEAK  9(12Q21.1) WILD-TYPE      9      9      6      9
D9V5, multiclass
        clus
vv       AMP PEAK  9(12Q21.1) MUTATED AMP PEAK  9(12Q21.1) WILD-TYPE
  CLUS_1                            5                              9
  CLUS_2                            2                              9
  CLUS_3                            4                              6
  CLUS_4                            3                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AMP PEAK  9(12Q21.1) MUTATED        0      3      5      4      2
  AMP PEAK  9(12Q21.1) WILD-TYPE      9      9      3      8      4
D9V6, multiclass
        clus
vv       AMP PEAK  9(12Q21.1) MUTATED AMP PEAK  9(12Q21.1) WILD-TYPE
  CLUS_1                            0                              9
  CLUS_2                            3                              9
  CLUS_3                            5                              3
  CLUS_4                            4                              8
  CLUS_5                            2                              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                                cls
clus                              0  1
  AMP PEAK  9(12Q21.1) MUTATED    7  5
  AMP PEAK  9(12Q21.1) WILD-TYPE 12 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(12Q21.1) MUTATED      7    5
  AMP PEAK  9(12Q21.1) WILD-TYPE   12   18
        clus
vv       AMP PEAK  9(12Q21.1) MUTATED AMP PEAK  9(12Q21.1) WILD-TYPE
  CLUS_1                            7                             12
  CLUS_2                            5                             18
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  AMP PEAK  9(12Q21.1) MUTATED        1      1      3      3      2      1
  AMP PEAK  9(12Q21.1) WILD-TYPE      3      4      3      3      6      2
                                vv
clus                             CLUS_7 CLUS_8 CLUS_9
  AMP PEAK  9(12Q21.1) MUTATED        0      0      1
  AMP PEAK  9(12Q21.1) WILD-TYPE      5      2      2
D9V8, multiclass
        clus
vv       AMP PEAK  9(12Q21.1) MUTATED AMP PEAK  9(12Q21.1) WILD-TYPE
  CLUS_1                            1                              3
  CLUS_2                            1                              4
  CLUS_3                            3                              3
  CLUS_4                            3                              3
  CLUS_5                            2                              6
  CLUS_6                            1                              2
  CLUS_7                            0                              5
  CLUS_8                            0                              2
  CLUS_9                            1                              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 = AMP PEAK 11(16P12.2) MUTATION ANALYSIS
D10V1, binary
                                cls
clus                              0  1
  AMP PEAK 11(16P12.2) MUTATED    2  8
  AMP PEAK 11(16P12.2) WILD-TYPE 27 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(16P12.2) MUTATED      2    8
  AMP PEAK 11(16P12.2) WILD-TYPE   27   11
        clus
vv       AMP PEAK 11(16P12.2) MUTATED AMP PEAK 11(16P12.2) WILD-TYPE
  CLUS_1                            2                             27
  CLUS_2                            8                             11
[1] 2 2
[1] FALSE
D10V2, binary
                                cls
clus                              0  1
  AMP PEAK 11(16P12.2) MUTATED    2  8
  AMP PEAK 11(16P12.2) WILD-TYPE 22 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(16P12.2) MUTATED      2    8
  AMP PEAK 11(16P12.2) WILD-TYPE   22   16
        clus
vv       AMP PEAK 11(16P12.2) MUTATED AMP PEAK 11(16P12.2) WILD-TYPE
  CLUS_1                            2                             22
  CLUS_2                            8                             16
[1] 2 2
[1] FALSE
D10V3, binary
                                cls
clus                              0  1
  AMP PEAK 11(16P12.2) MUTATED    5  1
  AMP PEAK 11(16P12.2) WILD-TYPE 10 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(16P12.2) MUTATED      5    1
  AMP PEAK 11(16P12.2) WILD-TYPE   10   12
        clus
vv       AMP PEAK 11(16P12.2) MUTATED AMP PEAK 11(16P12.2) 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 11(16P12.2) MUTATED        3      1      2
  AMP PEAK 11(16P12.2) WILD-TYPE     10      9      3
D10V4, multiclass
        clus
vv       AMP PEAK 11(16P12.2) MUTATED AMP PEAK 11(16P12.2) 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"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AMP PEAK 11(16P12.2) MUTATED        4      1      0      5
  AMP PEAK 11(16P12.2) WILD-TYPE     10     10     10      7
D10V5, multiclass
        clus
vv       AMP PEAK 11(16P12.2) MUTATED AMP PEAK 11(16P12.2) WILD-TYPE
  CLUS_1                            4                             10
  CLUS_2                            1                             10
  CLUS_3                            0                             10
  CLUS_4                            5                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AMP PEAK 11(16P12.2) MUTATED        1      3      4      0      2
  AMP PEAK 11(16P12.2) WILD-TYPE      8      9      4     12      4
D10V6, multiclass
        clus
vv       AMP PEAK 11(16P12.2) MUTATED AMP PEAK 11(16P12.2) WILD-TYPE
  CLUS_1                            1                              8
  CLUS_2                            3                              9
  CLUS_3                            4                              4
  CLUS_4                            0                             12
  CLUS_5                            2                              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                                cls
clus                              0  1
  AMP PEAK 11(16P12.2) MUTATED    4  4
  AMP PEAK 11(16P12.2) WILD-TYPE 15 19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(16P12.2) MUTATED      4    4
  AMP PEAK 11(16P12.2) WILD-TYPE   15   19
        clus
vv       AMP PEAK 11(16P12.2) MUTATED AMP PEAK 11(16P12.2) WILD-TYPE
  CLUS_1                            4                             15
  CLUS_2                            4                             19
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  AMP PEAK 11(16P12.2) MUTATED        1      0      2      0      2      1
  AMP PEAK 11(16P12.2) WILD-TYPE      3      5      4      6      6      2
                                vv
clus                             CLUS_7 CLUS_8 CLUS_9
  AMP PEAK 11(16P12.2) MUTATED        2      0      0
  AMP PEAK 11(16P12.2) WILD-TYPE      3      2      3
D10V8, multiclass
        clus
vv       AMP PEAK 11(16P12.2) MUTATED AMP PEAK 11(16P12.2) WILD-TYPE
  CLUS_1                            1                              3
  CLUS_2                            0                              5
  CLUS_3                            2                              4
  CLUS_4                            0                              6
  CLUS_5                            2                              6
  CLUS_6                            1                              2
  CLUS_7                            2                              3
  CLUS_8                            0                              2
  CLUS_9                            0                              3
[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 = AMP PEAK 12(18Q21.2) MUTATION ANALYSIS
D11V1, binary
                                cls
clus                              0  1
  AMP PEAK 12(18Q21.2) MUTATED    6 10
  AMP PEAK 12(18Q21.2) WILD-TYPE 23  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(18Q21.2) MUTATED      6   10
  AMP PEAK 12(18Q21.2) WILD-TYPE   23    9
        clus
vv       AMP PEAK 12(18Q21.2) MUTATED AMP PEAK 12(18Q21.2) WILD-TYPE
  CLUS_1                            6                             23
  CLUS_2                           10                              9
[1] 2 2
[1] FALSE
D11V2, binary
                                cls
clus                              0  1
  AMP PEAK 12(18Q21.2) MUTATED    7  9
  AMP PEAK 12(18Q21.2) WILD-TYPE 17 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(18Q21.2) MUTATED      7    9
  AMP PEAK 12(18Q21.2) WILD-TYPE   17   15
        clus
vv       AMP PEAK 12(18Q21.2) MUTATED AMP PEAK 12(18Q21.2) WILD-TYPE
  CLUS_1                            7                             17
  CLUS_2                            9                             15
[1] 2 2
[1] FALSE
D11V3, binary
                                cls
clus                              0  1
  AMP PEAK 12(18Q21.2) MUTATED    4  2
  AMP PEAK 12(18Q21.2) WILD-TYPE 11 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(18Q21.2) MUTATED      4    2
  AMP PEAK 12(18Q21.2) WILD-TYPE   11   11
        clus
vv       AMP PEAK 12(18Q21.2) MUTATED AMP PEAK 12(18Q21.2) 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 12(18Q21.2) MUTATED        3      2      1
  AMP PEAK 12(18Q21.2) WILD-TYPE     10      8      4
D11V4, multiclass
        clus
vv       AMP PEAK 12(18Q21.2) MUTATED AMP PEAK 12(18Q21.2) WILD-TYPE
  CLUS_1                            3                             10
  CLUS_2                            2                              8
  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"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AMP PEAK 12(18Q21.2) MUTATED        5      3      6      2
  AMP PEAK 12(18Q21.2) WILD-TYPE      9      8      4     10
D11V5, multiclass
        clus
vv       AMP PEAK 12(18Q21.2) MUTATED AMP PEAK 12(18Q21.2) WILD-TYPE
  CLUS_1                            5                              9
  CLUS_2                            3                              8
  CLUS_3                            6                              4
  CLUS_4                            2                             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AMP PEAK 12(18Q21.2) MUTATED        1      2      4      8      1
  AMP PEAK 12(18Q21.2) WILD-TYPE      8     10      4      4      5
D11V6, multiclass
        clus
vv       AMP PEAK 12(18Q21.2) MUTATED AMP PEAK 12(18Q21.2) WILD-TYPE
  CLUS_1                            1                              8
  CLUS_2                            2                             10
  CLUS_3                            4                              4
  CLUS_4                            8                              4
  CLUS_5                            1                              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                                cls
clus                              0  1
  AMP PEAK 12(18Q21.2) MUTATED    8  6
  AMP PEAK 12(18Q21.2) WILD-TYPE 11 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(18Q21.2) MUTATED      8    6
  AMP PEAK 12(18Q21.2) WILD-TYPE   11   17
        clus
vv       AMP PEAK 12(18Q21.2) MUTATED AMP PEAK 12(18Q21.2) WILD-TYPE
  CLUS_1                            8                             11
  CLUS_2                            6                             17
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  AMP PEAK 12(18Q21.2) MUTATED        1      0      4      4      2      0
  AMP PEAK 12(18Q21.2) WILD-TYPE      3      5      2      2      6      3
                                vv
clus                             CLUS_7 CLUS_8 CLUS_9
  AMP PEAK 12(18Q21.2) MUTATED        1      0      2
  AMP PEAK 12(18Q21.2) WILD-TYPE      4      2      1
D11V8, multiclass
        clus
vv       AMP PEAK 12(18Q21.2) MUTATED AMP PEAK 12(18Q21.2) WILD-TYPE
  CLUS_1                            1                              3
  CLUS_2                            0                              5
  CLUS_3                            4                              2
  CLUS_4                            4                              2
  CLUS_5                            2                              6
  CLUS_6                            0                              3
  CLUS_7                            1                              4
  CLUS_8                            0                              2
  CLUS_9                            2                              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 = AMP PEAK 13(19Q13.43) MUTATION ANALYSIS
D12V1, binary
                                 cls
clus                               0  1
  AMP PEAK 13(19Q13.43) MUTATED    6  4
  AMP PEAK 13(19Q13.43) WILD-TYPE 23 15
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(19Q13.43) MUTATED      6    4
  AMP PEAK 13(19Q13.43) WILD-TYPE   23   15
        clus
vv       AMP PEAK 13(19Q13.43) MUTATED AMP PEAK 13(19Q13.43) WILD-TYPE
  CLUS_1                             6                              23
  CLUS_2                             4                              15
[1] 2 2
[1] FALSE
D12V2, binary
                                 cls
clus                               0  1
  AMP PEAK 13(19Q13.43) MUTATED    3  7
  AMP PEAK 13(19Q13.43) WILD-TYPE 21 17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(19Q13.43) MUTATED      3    7
  AMP PEAK 13(19Q13.43) WILD-TYPE   21   17
        clus
vv       AMP PEAK 13(19Q13.43) MUTATED AMP PEAK 13(19Q13.43) WILD-TYPE
  CLUS_1                             3                              21
  CLUS_2                             7                              17
[1] 2 2
[1] FALSE
D12V3, binary
                                 cls
clus                               0  1
  AMP PEAK 13(19Q13.43) MUTATED    1  2
  AMP PEAK 13(19Q13.43) WILD-TYPE 14 11
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(19Q13.43) MUTATED      1    2
  AMP PEAK 13(19Q13.43) WILD-TYPE   14   11
        clus
vv       AMP PEAK 13(19Q13.43) MUTATED AMP PEAK 13(19Q13.43) WILD-TYPE
  CLUS_1                             1                              14
  CLUS_2                             2                              11
[1] 2 2
[1] FALSE
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 13(19Q13.43) MUTATED        2      1      0
  AMP PEAK 13(19Q13.43) WILD-TYPE     11      9      5
D12V4, multiclass
        clus
vv       AMP PEAK 13(19Q13.43) MUTATED AMP PEAK 13(19Q13.43) WILD-TYPE
  CLUS_1                             2                              11
  CLUS_2                             1                               9
  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"
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AMP PEAK 13(19Q13.43) MUTATED        1      2      4      3
  AMP PEAK 13(19Q13.43) WILD-TYPE     13      9      6      9
D12V5, multiclass
        clus
vv       AMP PEAK 13(19Q13.43) MUTATED AMP PEAK 13(19Q13.43) WILD-TYPE
  CLUS_1                             1                              13
  CLUS_2                             2                               9
  CLUS_3                             4                               6
  CLUS_4                             3                               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AMP PEAK 13(19Q13.43) MUTATED        0      4      1      4      1
  AMP PEAK 13(19Q13.43) WILD-TYPE      9      8      7      8      5
D12V6, multiclass
        clus
vv       AMP PEAK 13(19Q13.43) MUTATED AMP PEAK 13(19Q13.43) WILD-TYPE
  CLUS_1                             0                               9
  CLUS_2                             4                               8
  CLUS_3                             1                               7
  CLUS_4                             4                               8
  CLUS_5                             1                               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                                 cls
clus                               0  1
  AMP PEAK 13(19Q13.43) MUTATED    3  5
  AMP PEAK 13(19Q13.43) WILD-TYPE 16 18
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(19Q13.43) MUTATED      3    5
  AMP PEAK 13(19Q13.43) WILD-TYPE   16   18
        clus
vv       AMP PEAK 13(19Q13.43) MUTATED AMP PEAK 13(19Q13.43) WILD-TYPE
  CLUS_1                             3                              16
  CLUS_2                             5                              18
[1] 2 2
[1] FALSE
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  AMP PEAK 13(19Q13.43) MUTATED        1      1      0      3      0      2
  AMP PEAK 13(19Q13.43) WILD-TYPE      3      4      6      3      8      1
                                 vv
clus                              CLUS_7 CLUS_8 CLUS_9
  AMP PEAK 13(19Q13.43) MUTATED        0      0      1
  AMP PEAK 13(19Q13.43) WILD-TYPE      5      2      2
D12V8, multiclass
        clus
vv       AMP PEAK 13(19Q13.43) MUTATED AMP PEAK 13(19Q13.43) WILD-TYPE
  CLUS_1                             1                               3
  CLUS_2                             1                               4
  CLUS_3                             0                               6
  CLUS_4                             3                               3
  CLUS_5                             0                               8
  CLUS_6                             2                               1
  CLUS_7                             0                               5
  CLUS_8                             0                               2
  CLUS_9                             1                               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 = AMP PEAK 14(XQ27.3) MUTATION ANALYSIS
D13V1, binary
                               cls
clus                             0  1
  AMP PEAK 14(XQ27.3) MUTATED    2  5
  AMP PEAK 14(XQ27.3) WILD-TYPE 27 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(XQ27.3) MUTATED      2    5
  AMP PEAK 14(XQ27.3) WILD-TYPE   27   14
        clus
vv       AMP PEAK 14(XQ27.3) MUTATED AMP PEAK 14(XQ27.3) WILD-TYPE
  CLUS_1                           2                            27
  CLUS_2                           5                            14
[1] 2 2
[1] FALSE
D13V2, binary
                               cls
clus                             0  1
  AMP PEAK 14(XQ27.3) MUTATED    1  6
  AMP PEAK 14(XQ27.3) WILD-TYPE 23 18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(XQ27.3) MUTATED      1    6
  AMP PEAK 14(XQ27.3) WILD-TYPE   23   18
        clus
vv       AMP PEAK 14(XQ27.3) MUTATED AMP PEAK 14(XQ27.3) WILD-TYPE
  CLUS_1                           1                            23
  CLUS_2                           6                            18
[1] 2 2
[1] FALSE
D13V3, binary
                               cls
clus                             0  1
  AMP PEAK 14(XQ27.3) MUTATED    4  2
  AMP PEAK 14(XQ27.3) WILD-TYPE 11 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(XQ27.3) MUTATED      4    2
  AMP PEAK 14(XQ27.3) WILD-TYPE   11   11
        clus
vv       AMP PEAK 14(XQ27.3) MUTATED AMP PEAK 14(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 14(XQ27.3) MUTATED        4      1      1
  AMP PEAK 14(XQ27.3) WILD-TYPE      9      9      4
D13V4, multiclass
        clus
vv       AMP PEAK 14(XQ27.3) MUTATED AMP PEAK 14(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"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AMP PEAK 14(XQ27.3) MUTATED        4      1      0      2
  AMP PEAK 14(XQ27.3) WILD-TYPE     10     10     10     10
D13V5, multiclass
        clus
vv       AMP PEAK 14(XQ27.3) MUTATED AMP PEAK 14(XQ27.3) WILD-TYPE
  CLUS_1                           4                            10
  CLUS_2                           1                            10
  CLUS_3                           0                            10
  CLUS_4                           2                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AMP PEAK 14(XQ27.3) MUTATED        1      1      3      0      2
  AMP PEAK 14(XQ27.3) WILD-TYPE      8     11      5     12      4
D13V6, multiclass
        clus
vv       AMP PEAK 14(XQ27.3) MUTATED AMP PEAK 14(XQ27.3) WILD-TYPE
  CLUS_1                           1                             8
  CLUS_2                           1                            11
  CLUS_3                           3                             5
  CLUS_4                           0                            12
  CLUS_5                           2                             4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                               cls
clus                             0  1
  AMP PEAK 14(XQ27.3) MUTATED    4  3
  AMP PEAK 14(XQ27.3) WILD-TYPE 15 20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(XQ27.3) MUTATED      4    3
  AMP PEAK 14(XQ27.3) WILD-TYPE   15   20
        clus
vv       AMP PEAK 14(XQ27.3) MUTATED AMP PEAK 14(XQ27.3) WILD-TYPE
  CLUS_1                           4                            15
  CLUS_2                           3                            20
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  AMP PEAK 14(XQ27.3) MUTATED        0      1      3      0      2      1
  AMP PEAK 14(XQ27.3) WILD-TYPE      4      4      3      6      6      2
                               vv
clus                            CLUS_7 CLUS_8 CLUS_9
  AMP PEAK 14(XQ27.3) MUTATED        0      0      0
  AMP PEAK 14(XQ27.3) WILD-TYPE      5      2      3
D13V8, multiclass
        clus
vv       AMP PEAK 14(XQ27.3) MUTATED AMP PEAK 14(XQ27.3) WILD-TYPE
  CLUS_1                           0                             4
  CLUS_2                           1                             4
  CLUS_3                           3                             3
  CLUS_4                           0                             6
  CLUS_5                           2                             6
  CLUS_6                           1                             2
  CLUS_7                           0                             5
  CLUS_8                           0                             2
  CLUS_9                           0                             3
[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  1(1P36.32) MUTATION ANALYSIS
D14V1, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.32) MUTATED    3  8
  DEL PEAK  1(1P36.32) WILD-TYPE 26 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED      3    8
  DEL PEAK  1(1P36.32) WILD-TYPE   26   11
        clus
vv       DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  CLUS_1                            3                             26
  CLUS_2                            8                             11
[1] 2 2
[1] FALSE
D14V2, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.32) MUTATED    5  6
  DEL PEAK  1(1P36.32) WILD-TYPE 19 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED      5    6
  DEL PEAK  1(1P36.32) WILD-TYPE   19   18
        clus
vv       DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  CLUS_1                            5                             19
  CLUS_2                            6                             18
[1] 2 2
[1] FALSE
D14V3, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.32) MUTATED    3  3
  DEL PEAK  1(1P36.32) WILD-TYPE 12 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED      3    3
  DEL PEAK  1(1P36.32) WILD-TYPE   12   10
        clus
vv       DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) 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  1(1P36.32) MUTATED        3      3      0
  DEL PEAK  1(1P36.32) WILD-TYPE     10      7      5
D14V4, multiclass
        clus
vv       DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) 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"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK  1(1P36.32) MUTATED        3      1      3      4
  DEL PEAK  1(1P36.32) WILD-TYPE     11     10      7      8
D14V5, multiclass
        clus
vv       DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  CLUS_1                            3                             11
  CLUS_2                            1                             10
  CLUS_3                            3                              7
  CLUS_4                            4                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK  1(1P36.32) MUTATED        1      2      3      3      2
  DEL PEAK  1(1P36.32) WILD-TYPE      8     10      5      9      4
D14V6, multiclass
        clus
vv       DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  CLUS_1                            1                              8
  CLUS_2                            2                             10
  CLUS_3                            3                              5
  CLUS_4                            3                              9
  CLUS_5                            2                              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.32) MUTATED    4  6
  DEL PEAK  1(1P36.32) WILD-TYPE 15 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED      4    6
  DEL PEAK  1(1P36.32) WILD-TYPE   15   17
        clus
vv       DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  CLUS_1                            4                             15
  CLUS_2                            6                             17
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  1(1P36.32) MUTATED        1      0      1      1      2      2
  DEL PEAK  1(1P36.32) WILD-TYPE      3      5      5      5      6      1
                                vv
clus                             CLUS_7 CLUS_8 CLUS_9
  DEL PEAK  1(1P36.32) MUTATED        1      0      2
  DEL PEAK  1(1P36.32) WILD-TYPE      4      2      1
D14V8, multiclass
        clus
vv       DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  CLUS_1                            1                              3
  CLUS_2                            0                              5
  CLUS_3                            1                              5
  CLUS_4                            1                              5
  CLUS_5                            2                              6
  CLUS_6                            2                              1
  CLUS_7                            1                              4
  CLUS_8                            0                              2
  CLUS_9                            2                              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(15) Variable = DEL PEAK  2(1P13.1) MUTATION ANALYSIS
D15V1, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.1) MUTATED    6  6
  DEL PEAK  2(1P13.1) WILD-TYPE 23 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED      6    6
  DEL PEAK  2(1P13.1) WILD-TYPE   23   13
        clus
vv       DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  CLUS_1                           6                            23
  CLUS_2                           6                            13
[1] 2 2
[1] FALSE
D15V2, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.1) MUTATED    5  7
  DEL PEAK  2(1P13.1) WILD-TYPE 19 17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED      5    7
  DEL PEAK  2(1P13.1) WILD-TYPE   19   17
        clus
vv       DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  CLUS_1                           5                            19
  CLUS_2                           7                            17
[1] 2 2
[1] FALSE
D15V3, 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
D15V4, 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"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK  2(1P13.1) MUTATED        2      3      4      3
  DEL PEAK  2(1P13.1) WILD-TYPE     12      8      6      9
D15V5, multiclass
        clus
vv       DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  CLUS_1                           2                            12
  CLUS_2                           3                             8
  CLUS_3                           4                             6
  CLUS_4                           3                             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK  2(1P13.1) MUTATED        1      4      2      4      1
  DEL PEAK  2(1P13.1) WILD-TYPE      8      8      6      8      5
D15V6, multiclass
        clus
vv       DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  CLUS_1                           1                             8
  CLUS_2                           4                             8
  CLUS_3                           2                             6
  CLUS_4                           4                             8
  CLUS_5                           1                             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.1) MUTATED    4  6
  DEL PEAK  2(1P13.1) WILD-TYPE 15 17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED      4    6
  DEL PEAK  2(1P13.1) WILD-TYPE   15   17
        clus
vv       DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  CLUS_1                           4                            15
  CLUS_2                           6                            17
[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        1      1      1      3      1      2
  DEL PEAK  2(1P13.1) WILD-TYPE      3      4      5      3      7      1
                               vv
clus                            CLUS_7 CLUS_8 CLUS_9
  DEL PEAK  2(1P13.1) MUTATED        1      0      0
  DEL PEAK  2(1P13.1) WILD-TYPE      4      2      3
D15V8, multiclass
        clus
vv       DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  CLUS_1                           1                             3
  CLUS_2                           1                             4
  CLUS_3                           1                             5
  CLUS_4                           3                             3
  CLUS_5                           1                             7
  CLUS_6                           2                             1
  CLUS_7                           1                             4
  CLUS_8                           0                             2
  CLUS_9                           0                             3
[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  3(1Q43) MUTATION ANALYSIS
D16V1, binary
                             cls
clus                           0  1
  DEL PEAK  3(1Q43) MUTATED    3  7
  DEL PEAK  3(1Q43) WILD-TYPE 26 12
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q43) MUTATED      3    7
  DEL PEAK  3(1Q43) WILD-TYPE   26   12
        clus
vv       DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  CLUS_1                         3                          26
  CLUS_2                         7                          12
[1] 2 2
[1] FALSE
D16V2, binary
                             cls
clus                           0  1
  DEL PEAK  3(1Q43) MUTATED    4  6
  DEL PEAK  3(1Q43) WILD-TYPE 20 18
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q43) MUTATED      4    6
  DEL PEAK  3(1Q43) WILD-TYPE   20   18
        clus
vv       DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  CLUS_1                         4                          20
  CLUS_2                         6                          18
[1] 2 2
[1] FALSE
D16V3, 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
D16V4, 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"
                             vv
clus                          CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK  3(1Q43) MUTATED        4      3      1      2
  DEL PEAK  3(1Q43) WILD-TYPE     10      8      9     10
D16V5, multiclass
        clus
vv       DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  CLUS_1                         4                          10
  CLUS_2                         3                           8
  CLUS_3                         1                           9
  CLUS_4                         2                          10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK  3(1Q43) MUTATED        1      3      2      2      2
  DEL PEAK  3(1Q43) WILD-TYPE      8      9      6     10      4
D16V6, multiclass
        clus
vv       DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  CLUS_1                         1                           8
  CLUS_2                         3                           9
  CLUS_3                         2                           6
  CLUS_4                         2                          10
  CLUS_5                         2                           4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                             cls
clus                           0  1
  DEL PEAK  3(1Q43) MUTATED    4  4
  DEL PEAK  3(1Q43) WILD-TYPE 15 19
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q43) MUTATED      4    4
  DEL PEAK  3(1Q43) WILD-TYPE   15   19
        clus
vv       DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  CLUS_1                         4                          15
  CLUS_2                         4                          19
[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      2      2      1      3      0      0
  DEL PEAK  3(1Q43) WILD-TYPE      4      3      4      5      5      3      5
                             vv
clus                          CLUS_8 CLUS_9
  DEL PEAK  3(1Q43) MUTATED        0      0
  DEL PEAK  3(1Q43) WILD-TYPE      2      3
D16V8, multiclass
        clus
vv       DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  CLUS_1                         0                           4
  CLUS_2                         2                           3
  CLUS_3                         2                           4
  CLUS_4                         1                           5
  CLUS_5                         3                           5
  CLUS_6                         0                           3
  CLUS_7                         0                           5
  CLUS_8                         0                           2
  CLUS_9                         0                           3
[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  4(2Q23.1) MUTATION ANALYSIS
D17V1, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q23.1) MUTATED    3  5
  DEL PEAK  4(2Q23.1) WILD-TYPE 26 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q23.1) MUTATED      3    5
  DEL PEAK  4(2Q23.1) WILD-TYPE   26   14
        clus
vv       DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE
  CLUS_1                           3                            26
  CLUS_2                           5                            14
[1] 2 2
[1] FALSE
D17V2, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q23.1) MUTATED    4  4
  DEL PEAK  4(2Q23.1) WILD-TYPE 20 20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q23.1) MUTATED      4    4
  DEL PEAK  4(2Q23.1) WILD-TYPE   20   20
        clus
vv       DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE
  CLUS_1                           4                            20
  CLUS_2                           4                            20
[1] 2 2
[1] FALSE
D17V3, 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
D17V4, 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"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK  4(2Q23.1) MUTATED        1      2      2      2
  DEL PEAK  4(2Q23.1) WILD-TYPE     13      9      8     10
D17V5, multiclass
        clus
vv       DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE
  CLUS_1                           1                            13
  CLUS_2                           2                             9
  CLUS_3                           2                             8
  CLUS_4                           2                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK  4(2Q23.1) MUTATED        0      2      1      2      2
  DEL PEAK  4(2Q23.1) WILD-TYPE      9     10      7     10      4
D17V6, multiclass
        clus
vv       DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE
  CLUS_1                           0                             9
  CLUS_2                           2                            10
  CLUS_3                           1                             7
  CLUS_4                           2                            10
  CLUS_5                           2                             4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q23.1) MUTATED    2  4
  DEL PEAK  4(2Q23.1) WILD-TYPE 17 19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q23.1) MUTATED      2    4
  DEL PEAK  4(2Q23.1) WILD-TYPE   17   19
        clus
vv       DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE
  CLUS_1                           2                            17
  CLUS_2                           4                            19
[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      2      0
  DEL PEAK  4(2Q23.1) WILD-TYPE      4      5      5      5      6      3
                               vv
clus                            CLUS_7 CLUS_8 CLUS_9
  DEL PEAK  4(2Q23.1) MUTATED        0      1      1
  DEL PEAK  4(2Q23.1) WILD-TYPE      5      1      2
D17V8, multiclass
        clus
vv       DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE
  CLUS_1                           0                             4
  CLUS_2                           0                             5
  CLUS_3                           1                             5
  CLUS_4                           1                             5
  CLUS_5                           2                             6
  CLUS_6                           0                             3
  CLUS_7                           0                             5
  CLUS_8                           1                             1
  CLUS_9                           1                             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  5(3P21.31) MUTATION ANALYSIS
D18V1, binary
                                cls
clus                              0  1
  DEL PEAK  5(3P21.31) MUTATED    6  2
  DEL PEAK  5(3P21.31) WILD-TYPE 23 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3P21.31) MUTATED      6    2
  DEL PEAK  5(3P21.31) WILD-TYPE   23   17
        clus
vv       DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  CLUS_1                            6                             23
  CLUS_2                            2                             17
[1] 2 2
[1] FALSE
D18V2, binary
                                cls
clus                              0  1
  DEL PEAK  5(3P21.31) MUTATED    3  5
  DEL PEAK  5(3P21.31) WILD-TYPE 21 19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3P21.31) MUTATED      3    5
  DEL PEAK  5(3P21.31) WILD-TYPE   21   19
        clus
vv       DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  CLUS_1                            3                             21
  CLUS_2                            5                             19
[1] 2 2
[1] FALSE
D18V3, binary
                                cls
clus                              0  1
  DEL PEAK  5(3P21.31) MUTATED    2  0
  DEL PEAK  5(3P21.31) WILD-TYPE 13 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3P21.31) MUTATED      2    0
  DEL PEAK  5(3P21.31) WILD-TYPE   13   13
        clus
vv       DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  CLUS_1                            2                             13
  CLUS_2                            0                             13
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  5(3P21.31) MUTATED        1      0      1
  DEL PEAK  5(3P21.31) WILD-TYPE     12     10      4
D18V4, multiclass
[1] "Remove cluster labels:"       "DEL PEAK  5(3P21.31) MUTATED"
clus
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                             2                             26 
                    TCGA-FA-A4BB                     TCGA-FA-A4XK 
"DEL PEAK  5(3P21.31) WILD-TYPE" "DEL PEAK  5(3P21.31) WILD-TYPE" 
                    TCGA-FA-A6HN                     TCGA-FA-A6HO 
"DEL PEAK  5(3P21.31) WILD-TYPE" "DEL PEAK  5(3P21.31) WILD-TYPE" 
                    TCGA-FF-8041                     TCGA-FF-8042 
"DEL PEAK  5(3P21.31) WILD-TYPE" "DEL PEAK  5(3P21.31) WILD-TYPE" 
                    TCGA-FF-8043                     TCGA-FF-8046 
"DEL PEAK  5(3P21.31) WILD-TYPE" "DEL PEAK  5(3P21.31) WILD-TYPE" 
                    TCGA-FF-8047                     TCGA-FF-8061 
"DEL PEAK  5(3P21.31) WILD-TYPE" "DEL PEAK  5(3P21.31) WILD-TYPE" 
                    TCGA-FF-8062                     TCGA-FM-8000 
"DEL PEAK  5(3P21.31) WILD-TYPE" "DEL PEAK  5(3P21.31) WILD-TYPE" 
                    TCGA-G8-6324                     TCGA-G8-6325 
"DEL PEAK  5(3P21.31) WILD-TYPE" "DEL PEAK  5(3P21.31) WILD-TYPE" 
                    TCGA-G8-6326                     TCGA-G8-6906 
"DEL PEAK  5(3P21.31) WILD-TYPE" "DEL PEAK  5(3P21.31) WILD-TYPE" 
                    TCGA-G8-6907                     TCGA-G8-6909 
"DEL PEAK  5(3P21.31) WILD-TYPE" "DEL PEAK  5(3P21.31) WILD-TYPE" 
                    TCGA-G8-6914                     TCGA-GR-7351 
"DEL PEAK  5(3P21.31) WILD-TYPE" "DEL PEAK  5(3P21.31) WILD-TYPE" 
                    TCGA-GR-7353                     TCGA-GR-A4D4 
"DEL PEAK  5(3P21.31) WILD-TYPE" "DEL PEAK  5(3P21.31) WILD-TYPE" 
                    TCGA-GR-A4D5                     TCGA-GR-A4D6 
"DEL PEAK  5(3P21.31) WILD-TYPE" "DEL PEAK  5(3P21.31) WILD-TYPE" 
                    TCGA-GR-A4D9                     TCGA-RQ-A68N 
"DEL PEAK  5(3P21.31) WILD-TYPE" "DEL PEAK  5(3P21.31) WILD-TYPE" 
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK  5(3P21.31) MUTATED        3      2      3      0
  DEL PEAK  5(3P21.31) WILD-TYPE     11      9      7     12
D18V5, multiclass
        clus
vv       DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  CLUS_1                            3                             11
  CLUS_2                            2                              9
  CLUS_3                            3                              7
  CLUS_4                            0                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK  5(3P21.31) MUTATED        1      2      2      3      0
  DEL PEAK  5(3P21.31) WILD-TYPE      8     10      6      9      6
D18V6, multiclass
        clus
vv       DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  CLUS_1                            1                              8
  CLUS_2                            2                             10
  CLUS_3                            2                              6
  CLUS_4                            3                              9
  CLUS_5                            0                              6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                                cls
clus                              0  1
  DEL PEAK  5(3P21.31) MUTATED    5  2
  DEL PEAK  5(3P21.31) WILD-TYPE 14 21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3P21.31) MUTATED      5    2
  DEL PEAK  5(3P21.31) WILD-TYPE   14   21
        clus
vv       DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  CLUS_1                            5                             14
  CLUS_2                            2                             21
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  5(3P21.31) MUTATED        1      1      1      3      0      0
  DEL PEAK  5(3P21.31) WILD-TYPE      3      4      5      3      8      3
                                vv
clus                             CLUS_7 CLUS_8 CLUS_9
  DEL PEAK  5(3P21.31) MUTATED        1      0      0
  DEL PEAK  5(3P21.31) WILD-TYPE      4      2      3
D18V8, multiclass
        clus
vv       DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  CLUS_1                            1                              3
  CLUS_2                            1                              4
  CLUS_3                            1                              5
  CLUS_4                            3                              3
  CLUS_5                            0                              8
  CLUS_6                            0                              3
  CLUS_7                            1                              4
  CLUS_8                            0                              2
  CLUS_9                            0                              3
[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  6(4Q35.1) MUTATION ANALYSIS
D19V1, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q35.1) MUTATED    5  5
  DEL PEAK  6(4Q35.1) WILD-TYPE 24 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q35.1) MUTATED      5    5
  DEL PEAK  6(4Q35.1) WILD-TYPE   24   14
        clus
vv       DEL PEAK  6(4Q35.1) MUTATED DEL PEAK  6(4Q35.1) WILD-TYPE
  CLUS_1                           5                            24
  CLUS_2                           5                            14
[1] 2 2
[1] FALSE
D19V2, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q35.1) MUTATED    4  6
  DEL PEAK  6(4Q35.1) WILD-TYPE 20 18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q35.1) MUTATED      4    6
  DEL PEAK  6(4Q35.1) WILD-TYPE   20   18
        clus
vv       DEL PEAK  6(4Q35.1) MUTATED DEL PEAK  6(4Q35.1) WILD-TYPE
  CLUS_1                           4                            20
  CLUS_2                           6                            18
[1] 2 2
[1] FALSE
D19V3, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q35.1) MUTATED    2  3
  DEL PEAK  6(4Q35.1) WILD-TYPE 13 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q35.1) MUTATED      2    3
  DEL PEAK  6(4Q35.1) WILD-TYPE   13   10
        clus
vv       DEL PEAK  6(4Q35.1) MUTATED DEL PEAK  6(4Q35.1) 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  6(4Q35.1) MUTATED        2      3      0
  DEL PEAK  6(4Q35.1) WILD-TYPE     11      7      5
D19V4, multiclass
        clus
vv       DEL PEAK  6(4Q35.1) MUTATED DEL PEAK  6(4Q35.1) WILD-TYPE
  CLUS_1                           2                            11
  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"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK  6(4Q35.1) MUTATED        1      2      3      4
  DEL PEAK  6(4Q35.1) WILD-TYPE     13      9      7      8
D19V5, multiclass
        clus
vv       DEL PEAK  6(4Q35.1) MUTATED DEL PEAK  6(4Q35.1) WILD-TYPE
  CLUS_1                           1                            13
  CLUS_2                           2                             9
  CLUS_3                           3                             7
  CLUS_4                           4                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK  6(4Q35.1) MUTATED        1      2      0      4      3
  DEL PEAK  6(4Q35.1) WILD-TYPE      8     10      8      8      3
D19V6, multiclass
        clus
vv       DEL PEAK  6(4Q35.1) MUTATED DEL PEAK  6(4Q35.1) WILD-TYPE
  CLUS_1                           1                             8
  CLUS_2                           2                            10
  CLUS_3                           0                             8
  CLUS_4                           4                             8
  CLUS_5                           3                             3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q35.1) MUTATED    2  7
  DEL PEAK  6(4Q35.1) WILD-TYPE 17 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q35.1) MUTATED      2    7
  DEL PEAK  6(4Q35.1) WILD-TYPE   17   16
        clus
vv       DEL PEAK  6(4Q35.1) MUTATED DEL PEAK  6(4Q35.1) WILD-TYPE
  CLUS_1                           2                            17
  CLUS_2                           7                            16
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  6(4Q35.1) MUTATED        0      2      1      2      4      0
  DEL PEAK  6(4Q35.1) WILD-TYPE      4      3      5      4      4      3
                               vv
clus                            CLUS_7 CLUS_8 CLUS_9
  DEL PEAK  6(4Q35.1) MUTATED        0      0      0
  DEL PEAK  6(4Q35.1) WILD-TYPE      5      2      3
D19V8, multiclass
        clus
vv       DEL PEAK  6(4Q35.1) MUTATED DEL PEAK  6(4Q35.1) WILD-TYPE
  CLUS_1                           0                             4
  CLUS_2                           2                             3
  CLUS_3                           1                             5
  CLUS_4                           2                             4
  CLUS_5                           4                             4
  CLUS_6                           0                             3
  CLUS_7                           0                             5
  CLUS_8                           0                             2
  CLUS_9                           0                             3
[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  7(5Q33.3) MUTATION ANALYSIS
D20V1, binary
                               cls
clus                             0  1
  DEL PEAK  7(5Q33.3) MUTATED    1  3
  DEL PEAK  7(5Q33.3) WILD-TYPE 28 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(5Q33.3) MUTATED      1    3
  DEL PEAK  7(5Q33.3) WILD-TYPE   28   16
        clus
vv       DEL PEAK  7(5Q33.3) MUTATED DEL PEAK  7(5Q33.3) WILD-TYPE
  CLUS_1                           1                            28
  CLUS_2                           3                            16
[1] 2 2
[1] FALSE
D20V2, binary
                               cls
clus                             0  1
  DEL PEAK  7(5Q33.3) MUTATED    1  3
  DEL PEAK  7(5Q33.3) WILD-TYPE 23 21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(5Q33.3) MUTATED      1    3
  DEL PEAK  7(5Q33.3) WILD-TYPE   23   21
        clus
vv       DEL PEAK  7(5Q33.3) MUTATED DEL PEAK  7(5Q33.3) WILD-TYPE
  CLUS_1                           1                            23
  CLUS_2                           3                            21
[1] 2 2
[1] FALSE
D20V3, binary
                               cls
clus                             0  1
  DEL PEAK  7(5Q33.3) MUTATED    2  1
  DEL PEAK  7(5Q33.3) WILD-TYPE 13 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(5Q33.3) MUTATED      2    1
  DEL PEAK  7(5Q33.3) WILD-TYPE   13   12
        clus
vv       DEL PEAK  7(5Q33.3) MUTATED DEL PEAK  7(5Q33.3) 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  7(5Q33.3) MUTATED        0      1      2
  DEL PEAK  7(5Q33.3) WILD-TYPE     13      9      3
D20V4, multiclass
        clus
vv       DEL PEAK  7(5Q33.3) MUTATED DEL PEAK  7(5Q33.3) WILD-TYPE
  CLUS_1                           0                            13
  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"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK  7(5Q33.3) MUTATED        3      0      0      1
  DEL PEAK  7(5Q33.3) WILD-TYPE     11     11     10     11
D20V5, multiclass
        clus
vv       DEL PEAK  7(5Q33.3) MUTATED DEL PEAK  7(5Q33.3) WILD-TYPE
  CLUS_1                           3                            11
  CLUS_2                           0                            11
  CLUS_3                           0                            10
  CLUS_4                           1                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK  7(5Q33.3) MUTATED        0      0      3      0      1
  DEL PEAK  7(5Q33.3) WILD-TYPE      9     12      5     12      5
D20V6, multiclass
        clus
vv       DEL PEAK  7(5Q33.3) MUTATED DEL PEAK  7(5Q33.3) WILD-TYPE
  CLUS_1                           0                             9
  CLUS_2                           0                            12
  CLUS_3                           3                             5
  CLUS_4                           0                            12
  CLUS_5                           1                             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                               cls
clus                             0  1
  DEL PEAK  7(5Q33.3) MUTATED    3  1
  DEL PEAK  7(5Q33.3) WILD-TYPE 16 22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(5Q33.3) MUTATED      3    1
  DEL PEAK  7(5Q33.3) WILD-TYPE   16   22
        clus
vv       DEL PEAK  7(5Q33.3) MUTATED DEL PEAK  7(5Q33.3) WILD-TYPE
  CLUS_1                           3                            16
  CLUS_2                           1                            22
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  7(5Q33.3) MUTATED        0      0      2      0      1      0
  DEL PEAK  7(5Q33.3) WILD-TYPE      4      5      4      6      7      3
                               vv
clus                            CLUS_7 CLUS_8 CLUS_9
  DEL PEAK  7(5Q33.3) MUTATED        1      0      0
  DEL PEAK  7(5Q33.3) WILD-TYPE      4      2      3
D20V8, multiclass
        clus
vv       DEL PEAK  7(5Q33.3) MUTATED DEL PEAK  7(5Q33.3) WILD-TYPE
  CLUS_1                           0                             4
  CLUS_2                           0                             5
  CLUS_3                           2                             4
  CLUS_4                           0                             6
  CLUS_5                           1                             7
  CLUS_6                           0                             3
  CLUS_7                           1                             4
  CLUS_8                           0                             2
  CLUS_9                           0                             3
[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  8(6P21.32) MUTATION ANALYSIS
D21V1, binary
                                cls
clus                              0  1
  DEL PEAK  8(6P21.32) MUTATED    4  2
  DEL PEAK  8(6P21.32) WILD-TYPE 25 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(6P21.32) MUTATED      4    2
  DEL PEAK  8(6P21.32) WILD-TYPE   25   17
        clus
vv       DEL PEAK  8(6P21.32) MUTATED DEL PEAK  8(6P21.32) WILD-TYPE
  CLUS_1                            4                             25
  CLUS_2                            2                             17
[1] 2 2
[1] FALSE
D21V2, binary
                                cls
clus                              0  1
  DEL PEAK  8(6P21.32) MUTATED    3  3
  DEL PEAK  8(6P21.32) WILD-TYPE 21 21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(6P21.32) MUTATED      3    3
  DEL PEAK  8(6P21.32) WILD-TYPE   21   21
        clus
vv       DEL PEAK  8(6P21.32) MUTATED DEL PEAK  8(6P21.32) WILD-TYPE
  CLUS_1                            3                             21
  CLUS_2                            3                             21
[1] 2 2
[1] FALSE
D21V3, binary
                                cls
clus                              0  1
  DEL PEAK  8(6P21.32) MUTATED    1  2
  DEL PEAK  8(6P21.32) WILD-TYPE 14 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(6P21.32) MUTATED      1    2
  DEL PEAK  8(6P21.32) WILD-TYPE   14   11
        clus
vv       DEL PEAK  8(6P21.32) MUTATED DEL PEAK  8(6P21.32) WILD-TYPE
  CLUS_1                            1                             14
  CLUS_2                            2                             11
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  8(6P21.32) MUTATED        1      1      1
  DEL PEAK  8(6P21.32) WILD-TYPE     12      9      4
D21V4, multiclass
        clus
vv       DEL PEAK  8(6P21.32) MUTATED DEL PEAK  8(6P21.32) 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"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK  8(6P21.32) MUTATED        1      2      2      1
  DEL PEAK  8(6P21.32) WILD-TYPE     13      9      8     11
D21V5, multiclass
        clus
vv       DEL PEAK  8(6P21.32) MUTATED DEL PEAK  8(6P21.32) WILD-TYPE
  CLUS_1                            1                             13
  CLUS_2                            2                              9
  CLUS_3                            2                              8
  CLUS_4                            1                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK  8(6P21.32) MUTATED        0      3      1      2      0
  DEL PEAK  8(6P21.32) WILD-TYPE      9      9      7     10      6
D21V6, multiclass
        clus
vv       DEL PEAK  8(6P21.32) MUTATED DEL PEAK  8(6P21.32) WILD-TYPE
  CLUS_1                            0                              9
  CLUS_2                            3                              9
  CLUS_3                            1                              7
  CLUS_4                            2                             10
  CLUS_5                            0                              6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                                cls
clus                              0  1
  DEL PEAK  8(6P21.32) MUTATED    3  2
  DEL PEAK  8(6P21.32) WILD-TYPE 16 21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(6P21.32) MUTATED      3    2
  DEL PEAK  8(6P21.32) WILD-TYPE   16   21
        clus
vv       DEL PEAK  8(6P21.32) MUTATED DEL PEAK  8(6P21.32) WILD-TYPE
  CLUS_1                            3                             16
  CLUS_2                            2                             21
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  8(6P21.32) MUTATED        0      2      2      1      0      0
  DEL PEAK  8(6P21.32) WILD-TYPE      4      3      4      5      8      3
                                vv
clus                             CLUS_7 CLUS_8 CLUS_9
  DEL PEAK  8(6P21.32) MUTATED        0      0      0
  DEL PEAK  8(6P21.32) WILD-TYPE      5      2      3
D21V8, multiclass
        clus
vv       DEL PEAK  8(6P21.32) MUTATED DEL PEAK  8(6P21.32) WILD-TYPE
  CLUS_1                            0                              4
  CLUS_2                            2                              3
  CLUS_3                            2                              4
  CLUS_4                            1                              5
  CLUS_5                            0                              8
  CLUS_6                            0                              3
  CLUS_7                            0                              5
  CLUS_8                            0                              2
  CLUS_9                            0                              3
[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  9(6Q14.1) MUTATION ANALYSIS
D22V1, binary
                               cls
clus                             0  1
  DEL PEAK  9(6Q14.1) MUTATED    8  9
  DEL PEAK  9(6Q14.1) WILD-TYPE 21 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(6Q14.1) MUTATED      8    9
  DEL PEAK  9(6Q14.1) WILD-TYPE   21   10
        clus
vv       DEL PEAK  9(6Q14.1) MUTATED DEL PEAK  9(6Q14.1) WILD-TYPE
  CLUS_1                           8                            21
  CLUS_2                           9                            10
[1] 2 2
[1] FALSE
D22V2, binary
                               cls
clus                             0  1
  DEL PEAK  9(6Q14.1) MUTATED    7 10
  DEL PEAK  9(6Q14.1) WILD-TYPE 17 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(6Q14.1) MUTATED      7   10
  DEL PEAK  9(6Q14.1) WILD-TYPE   17   14
        clus
vv       DEL PEAK  9(6Q14.1) MUTATED DEL PEAK  9(6Q14.1) WILD-TYPE
  CLUS_1                           7                            17
  CLUS_2                          10                            14
[1] 2 2
[1] FALSE
D22V3, binary
                               cls
clus                             0  1
  DEL PEAK  9(6Q14.1) MUTATED    6  3
  DEL PEAK  9(6Q14.1) WILD-TYPE  9 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(6Q14.1) MUTATED      6    3
  DEL PEAK  9(6Q14.1) WILD-TYPE    9   10
        clus
vv       DEL PEAK  9(6Q14.1) MUTATED DEL PEAK  9(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  9(6Q14.1) MUTATED        4      2      3
  DEL PEAK  9(6Q14.1) WILD-TYPE      9      8      2
D22V4, multiclass
        clus
vv       DEL PEAK  9(6Q14.1) MUTATED DEL PEAK  9(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"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK  9(6Q14.1) MUTATED        8      2      4      3
  DEL PEAK  9(6Q14.1) WILD-TYPE      6      9      6      9
D22V5, multiclass
        clus
vv       DEL PEAK  9(6Q14.1) MUTATED DEL PEAK  9(6Q14.1) WILD-TYPE
  CLUS_1                           8                             6
  CLUS_2                           2                             9
  CLUS_3                           4                             6
  CLUS_4                           3                             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK  9(6Q14.1) MUTATED        5      3      4      5      0
  DEL PEAK  9(6Q14.1) WILD-TYPE      4      9      4      7      6
D22V6, multiclass
        clus
vv       DEL PEAK  9(6Q14.1) MUTATED DEL PEAK  9(6Q14.1) WILD-TYPE
  CLUS_1                           5                             4
  CLUS_2                           3                             9
  CLUS_3                           4                             4
  CLUS_4                           5                             7
  CLUS_5                           0                             6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                               cls
clus                             0  1
  DEL PEAK  9(6Q14.1) MUTATED   11  3
  DEL PEAK  9(6Q14.1) WILD-TYPE  8 20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(6Q14.1) MUTATED     11    3
  DEL PEAK  9(6Q14.1) WILD-TYPE    8   20
        clus
vv       DEL PEAK  9(6Q14.1) MUTATED DEL PEAK  9(6Q14.1) WILD-TYPE
  CLUS_1                          11                             8
  CLUS_2                           3                            20
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  9(6Q14.1) MUTATED        1      1      5      3      3      1
  DEL PEAK  9(6Q14.1) WILD-TYPE      3      4      1      3      5      2
                               vv
clus                            CLUS_7 CLUS_8 CLUS_9
  DEL PEAK  9(6Q14.1) MUTATED        0      0      0
  DEL PEAK  9(6Q14.1) WILD-TYPE      5      2      3
D22V8, multiclass
        clus
vv       DEL PEAK  9(6Q14.1) MUTATED DEL PEAK  9(6Q14.1) WILD-TYPE
  CLUS_1                           1                             3
  CLUS_2                           1                             4
  CLUS_3                           5                             1
  CLUS_4                           3                             3
  CLUS_5                           3                             5
  CLUS_6                           1                             2
  CLUS_7                           0                             5
  CLUS_8                           0                             2
  CLUS_9                           0                             3
[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 10(6Q22.32) MUTATION ANALYSIS
D23V1, binary
                                cls
clus                              0  1
  DEL PEAK 10(6Q22.32) MUTATED    9  7
  DEL PEAK 10(6Q22.32) WILD-TYPE 20 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(6Q22.32) MUTATED      9    7
  DEL PEAK 10(6Q22.32) WILD-TYPE   20   12
        clus
vv       DEL PEAK 10(6Q22.32) MUTATED DEL PEAK 10(6Q22.32) WILD-TYPE
  CLUS_1                            9                             20
  CLUS_2                            7                             12
[1] 2 2
[1] FALSE
D23V2, binary
                                cls
clus                              0  1
  DEL PEAK 10(6Q22.32) MUTATED    4 12
  DEL PEAK 10(6Q22.32) WILD-TYPE 20 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(6Q22.32) MUTATED      4   12
  DEL PEAK 10(6Q22.32) WILD-TYPE   20   12
        clus
vv       DEL PEAK 10(6Q22.32) MUTATED DEL PEAK 10(6Q22.32) WILD-TYPE
  CLUS_1                            4                             20
  CLUS_2                           12                             12
[1] 2 2
[1] FALSE
D23V3, binary
                                cls
clus                              0  1
  DEL PEAK 10(6Q22.32) MUTATED    5  2
  DEL PEAK 10(6Q22.32) WILD-TYPE 10 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(6Q22.32) MUTATED      5    2
  DEL PEAK 10(6Q22.32) WILD-TYPE   10   11
        clus
vv       DEL PEAK 10(6Q22.32) MUTATED DEL PEAK 10(6Q22.32) WILD-TYPE
  CLUS_1                            5                             10
  CLUS_2                            2                             11
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 10(6Q22.32) MUTATED        4      1      2
  DEL PEAK 10(6Q22.32) WILD-TYPE      9      9      3
D23V4, multiclass
        clus
vv       DEL PEAK 10(6Q22.32) MUTATED DEL PEAK 10(6Q22.32) WILD-TYPE
  CLUS_1                            4                              9
  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"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK 10(6Q22.32) MUTATED        6      2      5      3
  DEL PEAK 10(6Q22.32) WILD-TYPE      8      9      5      9
D23V5, multiclass
        clus
vv       DEL PEAK 10(6Q22.32) MUTATED DEL PEAK 10(6Q22.32) WILD-TYPE
  CLUS_1                            6                              8
  CLUS_2                            2                              9
  CLUS_3                            5                              5
  CLUS_4                            3                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK 10(6Q22.32) MUTATED        3      4      4      5      0
  DEL PEAK 10(6Q22.32) WILD-TYPE      6      8      4      7      6
D23V6, multiclass
        clus
vv       DEL PEAK 10(6Q22.32) MUTATED DEL PEAK 10(6Q22.32) WILD-TYPE
  CLUS_1                            3                              6
  CLUS_2                            4                              8
  CLUS_3                            4                              4
  CLUS_4                            5                              7
  CLUS_5                            0                              6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                                cls
clus                              0  1
  DEL PEAK 10(6Q22.32) MUTATED    9  4
  DEL PEAK 10(6Q22.32) WILD-TYPE 10 19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(6Q22.32) MUTATED      9    4
  DEL PEAK 10(6Q22.32) WILD-TYPE   10   19
        clus
vv       DEL PEAK 10(6Q22.32) MUTATED DEL PEAK 10(6Q22.32) WILD-TYPE
  CLUS_1                            9                             10
  CLUS_2                            4                             19
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 10(6Q22.32) MUTATED        2      1      3      4      1      2
  DEL PEAK 10(6Q22.32) WILD-TYPE      2      4      3      2      7      1
                                vv
clus                             CLUS_7 CLUS_8 CLUS_9
  DEL PEAK 10(6Q22.32) MUTATED        0      0      0
  DEL PEAK 10(6Q22.32) WILD-TYPE      5      2      3
D23V8, multiclass
        clus
vv       DEL PEAK 10(6Q22.32) MUTATED DEL PEAK 10(6Q22.32) WILD-TYPE
  CLUS_1                            2                              2
  CLUS_2                            1                              4
  CLUS_3                            3                              3
  CLUS_4                            4                              2
  CLUS_5                            1                              7
  CLUS_6                            2                              1
  CLUS_7                            0                              5
  CLUS_8                            0                              2
  CLUS_9                            0                              3
[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 11(6Q23.3) MUTATION ANALYSIS
D24V1, binary
                               cls
clus                             0  1
  DEL PEAK 11(6Q23.3) MUTATED   10  6
  DEL PEAK 11(6Q23.3) WILD-TYPE 19 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6Q23.3) MUTATED     10    6
  DEL PEAK 11(6Q23.3) WILD-TYPE   19   13
        clus
vv       DEL PEAK 11(6Q23.3) MUTATED DEL PEAK 11(6Q23.3) WILD-TYPE
  CLUS_1                          10                            19
  CLUS_2                           6                            13
[1] 2 2
[1] FALSE
D24V2, binary
                               cls
clus                             0  1
  DEL PEAK 11(6Q23.3) MUTATED    4 12
  DEL PEAK 11(6Q23.3) WILD-TYPE 20 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6Q23.3) MUTATED      4   12
  DEL PEAK 11(6Q23.3) WILD-TYPE   20   12
        clus
vv       DEL PEAK 11(6Q23.3) MUTATED DEL PEAK 11(6Q23.3) WILD-TYPE
  CLUS_1                           4                            20
  CLUS_2                          12                            12
[1] 2 2
[1] FALSE
D24V3, binary
                               cls
clus                             0  1
  DEL PEAK 11(6Q23.3) MUTATED    6  1
  DEL PEAK 11(6Q23.3) WILD-TYPE  9 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6Q23.3) MUTATED      6    1
  DEL PEAK 11(6Q23.3) WILD-TYPE    9   12
        clus
vv       DEL PEAK 11(6Q23.3) MUTATED DEL PEAK 11(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 11(6Q23.3) MUTATED        4      0      3
  DEL PEAK 11(6Q23.3) WILD-TYPE      9     10      2
D24V4, multiclass
        clus
vv       DEL PEAK 11(6Q23.3) MUTATED DEL PEAK 11(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"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK 11(6Q23.3) MUTATED        7      1      4      4
  DEL PEAK 11(6Q23.3) WILD-TYPE      7     10      6      8
D24V5, multiclass
        clus
vv       DEL PEAK 11(6Q23.3) MUTATED DEL PEAK 11(6Q23.3) WILD-TYPE
  CLUS_1                           7                             7
  CLUS_2                           1                            10
  CLUS_3                           4                             6
  CLUS_4                           4                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK 11(6Q23.3) MUTATED        3      3      5      5      0
  DEL PEAK 11(6Q23.3) WILD-TYPE      6      9      3      7      6
D24V6, multiclass
        clus
vv       DEL PEAK 11(6Q23.3) MUTATED DEL PEAK 11(6Q23.3) WILD-TYPE
  CLUS_1                           3                             6
  CLUS_2                           3                             9
  CLUS_3                           5                             3
  CLUS_4                           5                             7
  CLUS_5                           0                             6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                               cls
clus                             0  1
  DEL PEAK 11(6Q23.3) MUTATED   10  4
  DEL PEAK 11(6Q23.3) WILD-TYPE  9 19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6Q23.3) MUTATED     10    4
  DEL PEAK 11(6Q23.3) WILD-TYPE    9   19
        clus
vv       DEL PEAK 11(6Q23.3) MUTATED DEL PEAK 11(6Q23.3) WILD-TYPE
  CLUS_1                          10                             9
  CLUS_2                           4                            19
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 11(6Q23.3) MUTATED        2      1      4      3      1      2
  DEL PEAK 11(6Q23.3) WILD-TYPE      2      4      2      3      7      1
                               vv
clus                            CLUS_7 CLUS_8 CLUS_9
  DEL PEAK 11(6Q23.3) MUTATED        1      0      0
  DEL PEAK 11(6Q23.3) WILD-TYPE      4      2      3
D24V8, multiclass
        clus
vv       DEL PEAK 11(6Q23.3) MUTATED DEL PEAK 11(6Q23.3) WILD-TYPE
  CLUS_1                           2                             2
  CLUS_2                           1                             4
  CLUS_3                           4                             2
  CLUS_4                           3                             3
  CLUS_5                           1                             7
  CLUS_6                           2                             1
  CLUS_7                           1                             4
  CLUS_8                           0                             2
  CLUS_9                           0                             3
[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(25) Variable = DEL PEAK 12(7Q33) MUTATION ANALYSIS
D25V1, binary
                             cls
clus                           0  1
  DEL PEAK 12(7Q33) MUTATED    2  3
  DEL PEAK 12(7Q33) WILD-TYPE 27 16
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(7Q33) MUTATED      2    3
  DEL PEAK 12(7Q33) WILD-TYPE   27   16
        clus
vv       DEL PEAK 12(7Q33) MUTATED DEL PEAK 12(7Q33) WILD-TYPE
  CLUS_1                         2                          27
  CLUS_2                         3                          16
[1] 2 2
[1] FALSE
D25V2, binary
                             cls
clus                           0  1
  DEL PEAK 12(7Q33) MUTATED    3  2
  DEL PEAK 12(7Q33) WILD-TYPE 21 22
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(7Q33) MUTATED      3    2
  DEL PEAK 12(7Q33) WILD-TYPE   21   22
        clus
vv       DEL PEAK 12(7Q33) MUTATED DEL PEAK 12(7Q33) WILD-TYPE
  CLUS_1                         3                          21
  CLUS_2                         2                          22
[1] 2 2
[1] FALSE
D25V3, binary
                             cls
clus                           0  1
  DEL PEAK 12(7Q33) MUTATED    0  1
  DEL PEAK 12(7Q33) WILD-TYPE 15 12
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(7Q33) MUTATED      0    1
  DEL PEAK 12(7Q33) WILD-TYPE   15   12
        clus
vv       DEL PEAK 12(7Q33) MUTATED DEL PEAK 12(7Q33) WILD-TYPE
  CLUS_1                         0                          15
  CLUS_2                         1                          12
[1] 2 2
[1] FALSE
                             vv
clus                          CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 12(7Q33) MUTATED        0      1      0
  DEL PEAK 12(7Q33) WILD-TYPE     13      9      5
D25V4, multiclass
[1] "Remove cluster labels:"    "DEL PEAK 12(7Q33) MUTATED"
clus
  DEL PEAK 12(7Q33) MUTATED DEL PEAK 12(7Q33) WILD-TYPE 
                          1                          27 
                 TCGA-FA-8693                  TCGA-FA-A4BB 
"DEL PEAK 12(7Q33) WILD-TYPE" "DEL PEAK 12(7Q33) WILD-TYPE" 
                 TCGA-FA-A4XK                  TCGA-FA-A6HN 
"DEL PEAK 12(7Q33) WILD-TYPE" "DEL PEAK 12(7Q33) WILD-TYPE" 
                 TCGA-FA-A6HO                  TCGA-FF-8041 
"DEL PEAK 12(7Q33) WILD-TYPE" "DEL PEAK 12(7Q33) WILD-TYPE" 
                 TCGA-FF-8042                  TCGA-FF-8043 
"DEL PEAK 12(7Q33) WILD-TYPE" "DEL PEAK 12(7Q33) WILD-TYPE" 
                 TCGA-FF-8046                  TCGA-FF-8047 
"DEL PEAK 12(7Q33) WILD-TYPE" "DEL PEAK 12(7Q33) WILD-TYPE" 
                 TCGA-FF-8061                  TCGA-FF-8062 
"DEL PEAK 12(7Q33) WILD-TYPE" "DEL PEAK 12(7Q33) WILD-TYPE" 
                 TCGA-FM-8000                  TCGA-G8-6324 
"DEL PEAK 12(7Q33) WILD-TYPE" "DEL PEAK 12(7Q33) WILD-TYPE" 
                 TCGA-G8-6325                  TCGA-G8-6326 
"DEL PEAK 12(7Q33) WILD-TYPE" "DEL PEAK 12(7Q33) WILD-TYPE" 
                 TCGA-G8-6906                  TCGA-G8-6907 
"DEL PEAK 12(7Q33) WILD-TYPE" "DEL PEAK 12(7Q33) WILD-TYPE" 
                 TCGA-G8-6909                  TCGA-G8-6914 
"DEL PEAK 12(7Q33) WILD-TYPE" "DEL PEAK 12(7Q33) WILD-TYPE" 
                 TCGA-GR-7351                  TCGA-GR-A4D4 
"DEL PEAK 12(7Q33) WILD-TYPE" "DEL PEAK 12(7Q33) WILD-TYPE" 
                 TCGA-GR-A4D5                  TCGA-GR-A4D6 
"DEL PEAK 12(7Q33) WILD-TYPE" "DEL PEAK 12(7Q33) WILD-TYPE" 
                 TCGA-GR-A4D9                  TCGA-RQ-A68N 
"DEL PEAK 12(7Q33) WILD-TYPE" "DEL PEAK 12(7Q33) WILD-TYPE" 
                 TCGA-RQ-A6JB 
"DEL PEAK 12(7Q33) WILD-TYPE" 
                             vv
clus                          CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK 12(7Q33) MUTATED        1      0      2      2
  DEL PEAK 12(7Q33) WILD-TYPE     13     11      8     10
D25V5, multiclass
        clus
vv       DEL PEAK 12(7Q33) MUTATED DEL PEAK 12(7Q33) WILD-TYPE
  CLUS_1                         1                          13
  CLUS_2                         0                          11
  CLUS_3                         2                           8
  CLUS_4                         2                          10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK 12(7Q33) MUTATED        0      0      1      3      1
  DEL PEAK 12(7Q33) WILD-TYPE      9     12      7      9      5
D25V6, multiclass
        clus
vv       DEL PEAK 12(7Q33) MUTATED DEL PEAK 12(7Q33) WILD-TYPE
  CLUS_1                         0                           9
  CLUS_2                         0                          12
  CLUS_3                         1                           7
  CLUS_4                         3                           9
  CLUS_5                         1                           5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                             cls
clus                           0  1
  DEL PEAK 12(7Q33) MUTATED    3  2
  DEL PEAK 12(7Q33) WILD-TYPE 16 21
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(7Q33) MUTATED      3    2
  DEL PEAK 12(7Q33) WILD-TYPE   16   21
        clus
vv       DEL PEAK 12(7Q33) MUTATED DEL PEAK 12(7Q33) WILD-TYPE
  CLUS_1                         3                          16
  CLUS_2                         2                          21
[1] 2 2
[1] FALSE
                             vv
clus                          CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  DEL PEAK 12(7Q33) MUTATED        0      0      3      1      1      0      0
  DEL PEAK 12(7Q33) WILD-TYPE      4      5      3      5      7      3      5
                             vv
clus                          CLUS_8 CLUS_9
  DEL PEAK 12(7Q33) MUTATED        0      0
  DEL PEAK 12(7Q33) WILD-TYPE      2      3
D25V8, multiclass
        clus
vv       DEL PEAK 12(7Q33) MUTATED DEL PEAK 12(7Q33) WILD-TYPE
  CLUS_1                         0                           4
  CLUS_2                         0                           5
  CLUS_3                         3                           3
  CLUS_4                         1                           5
  CLUS_5                         1                           7
  CLUS_6                         0                           3
  CLUS_7                         0                           5
  CLUS_8                         0                           2
  CLUS_9                         0                           3
[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(26) Variable = DEL PEAK 13(8P23.2) MUTATION ANALYSIS
D26V1, binary
                               cls
clus                             0  1
  DEL PEAK 13(8P23.2) MUTATED    3  9
  DEL PEAK 13(8P23.2) WILD-TYPE 26 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(8P23.2) MUTATED      3    9
  DEL PEAK 13(8P23.2) WILD-TYPE   26   10
        clus
vv       DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE
  CLUS_1                           3                            26
  CLUS_2                           9                            10
[1] 2 2
[1] FALSE
D26V2, binary
                               cls
clus                             0  1
  DEL PEAK 13(8P23.2) MUTATED    5  7
  DEL PEAK 13(8P23.2) WILD-TYPE 19 17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(8P23.2) MUTATED      5    7
  DEL PEAK 13(8P23.2) WILD-TYPE   19   17
        clus
vv       DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE
  CLUS_1                           5                            19
  CLUS_2                           7                            17
[1] 2 2
[1] FALSE
D26V3, binary
                               cls
clus                             0  1
  DEL PEAK 13(8P23.2) MUTATED    1  3
  DEL PEAK 13(8P23.2) WILD-TYPE 14 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(8P23.2) MUTATED      1    3
  DEL PEAK 13(8P23.2) WILD-TYPE   14   10
        clus
vv       DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) 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 13(8P23.2) MUTATED        1      3      0
  DEL PEAK 13(8P23.2) WILD-TYPE     12      7      5
D26V4, multiclass
        clus
vv       DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) 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"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK 13(8P23.2) MUTATED        4      4      1      3
  DEL PEAK 13(8P23.2) WILD-TYPE     10      7      9      9
D26V5, multiclass
        clus
vv       DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE
  CLUS_1                           4                            10
  CLUS_2                           4                             7
  CLUS_3                           1                             9
  CLUS_4                           3                             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK 13(8P23.2) MUTATED        0      5      4      2      1
  DEL PEAK 13(8P23.2) WILD-TYPE      9      7      4     10      5
D26V6, multiclass
        clus
vv       DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE
  CLUS_1                           0                             9
  CLUS_2                           5                             7
  CLUS_3                           4                             4
  CLUS_4                           2                            10
  CLUS_5                           1                             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                               cls
clus                             0  1
  DEL PEAK 13(8P23.2) MUTATED    5  4
  DEL PEAK 13(8P23.2) WILD-TYPE 14 19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(8P23.2) MUTATED      5    4
  DEL PEAK 13(8P23.2) WILD-TYPE   14   19
        clus
vv       DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE
  CLUS_1                           5                            14
  CLUS_2                           4                            19
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 13(8P23.2) MUTATED        2      1      2      1      2      0
  DEL PEAK 13(8P23.2) WILD-TYPE      2      4      4      5      6      3
                               vv
clus                            CLUS_7 CLUS_8 CLUS_9
  DEL PEAK 13(8P23.2) MUTATED        1      0      0
  DEL PEAK 13(8P23.2) WILD-TYPE      4      2      3
D26V8, multiclass
        clus
vv       DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE
  CLUS_1                           2                             2
  CLUS_2                           1                             4
  CLUS_3                           2                             4
  CLUS_4                           1                             5
  CLUS_5                           2                             6
  CLUS_6                           0                             3
  CLUS_7                           1                             4
  CLUS_8                           0                             2
  CLUS_9                           0                             3
[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(27) Variable = DEL PEAK 14(8Q12.1) MUTATION ANALYSIS
D27V1, binary
                               cls
clus                             0  1
  DEL PEAK 14(8Q12.1) MUTATED    3  6
  DEL PEAK 14(8Q12.1) WILD-TYPE 26 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8Q12.1) MUTATED      3    6
  DEL PEAK 14(8Q12.1) WILD-TYPE   26   13
        clus
vv       DEL PEAK 14(8Q12.1) MUTATED DEL PEAK 14(8Q12.1) WILD-TYPE
  CLUS_1                           3                            26
  CLUS_2                           6                            13
[1] 2 2
[1] FALSE
D27V2, binary
                               cls
clus                             0  1
  DEL PEAK 14(8Q12.1) MUTATED    3  6
  DEL PEAK 14(8Q12.1) WILD-TYPE 21 18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8Q12.1) MUTATED      3    6
  DEL PEAK 14(8Q12.1) WILD-TYPE   21   18
        clus
vv       DEL PEAK 14(8Q12.1) MUTATED DEL PEAK 14(8Q12.1) WILD-TYPE
  CLUS_1                           3                            21
  CLUS_2                           6                            18
[1] 2 2
[1] FALSE
D27V3, binary
                               cls
clus                             0  1
  DEL PEAK 14(8Q12.1) MUTATED    1  3
  DEL PEAK 14(8Q12.1) WILD-TYPE 14 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8Q12.1) MUTATED      1    3
  DEL PEAK 14(8Q12.1) WILD-TYPE   14   10
        clus
vv       DEL PEAK 14(8Q12.1) MUTATED DEL PEAK 14(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 14(8Q12.1) MUTATED        1      3      0
  DEL PEAK 14(8Q12.1) WILD-TYPE     12      7      5
D27V4, multiclass
        clus
vv       DEL PEAK 14(8Q12.1) MUTATED DEL PEAK 14(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"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK 14(8Q12.1) MUTATED        1      2      3      3
  DEL PEAK 14(8Q12.1) WILD-TYPE     13      9      7      9
D27V5, multiclass
        clus
vv       DEL PEAK 14(8Q12.1) MUTATED DEL PEAK 14(8Q12.1) WILD-TYPE
  CLUS_1                           1                            13
  CLUS_2                           2                             9
  CLUS_3                           3                             7
  CLUS_4                           3                             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK 14(8Q12.1) MUTATED        0      3      1      3      2
  DEL PEAK 14(8Q12.1) WILD-TYPE      9      9      7      9      4
D27V6, multiclass
        clus
vv       DEL PEAK 14(8Q12.1) MUTATED DEL PEAK 14(8Q12.1) WILD-TYPE
  CLUS_1                           0                             9
  CLUS_2                           3                             9
  CLUS_3                           1                             7
  CLUS_4                           3                             9
  CLUS_5                           2                             4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                               cls
clus                             0  1
  DEL PEAK 14(8Q12.1) MUTATED    3  4
  DEL PEAK 14(8Q12.1) WILD-TYPE 16 19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8Q12.1) MUTATED      3    4
  DEL PEAK 14(8Q12.1) WILD-TYPE   16   19
        clus
vv       DEL PEAK 14(8Q12.1) MUTATED DEL PEAK 14(8Q12.1) WILD-TYPE
  CLUS_1                           3                            16
  CLUS_2                           4                            19
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 14(8Q12.1) MUTATED        0      1      1      3      2      0
  DEL PEAK 14(8Q12.1) WILD-TYPE      4      4      5      3      6      3
                               vv
clus                            CLUS_7 CLUS_8 CLUS_9
  DEL PEAK 14(8Q12.1) MUTATED        0      0      0
  DEL PEAK 14(8Q12.1) WILD-TYPE      5      2      3
D27V8, multiclass
        clus
vv       DEL PEAK 14(8Q12.1) MUTATED DEL PEAK 14(8Q12.1) WILD-TYPE
  CLUS_1                           0                             4
  CLUS_2                           1                             4
  CLUS_3                           1                             5
  CLUS_4                           3                             3
  CLUS_5                           2                             6
  CLUS_6                           0                             3
  CLUS_7                           0                             5
  CLUS_8                           0                             2
  CLUS_9                           0                             3
[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(28) Variable = DEL PEAK 15(9P21.3) MUTATION ANALYSIS
D28V1, binary
                               cls
clus                             0  1
  DEL PEAK 15(9P21.3) MUTATED    8  9
  DEL PEAK 15(9P21.3) WILD-TYPE 21 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P21.3) MUTATED      8    9
  DEL PEAK 15(9P21.3) WILD-TYPE   21   10
        clus
vv       DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  CLUS_1                           8                            21
  CLUS_2                           9                            10
[1] 2 2
[1] FALSE
D28V2, binary
                               cls
clus                             0  1
  DEL PEAK 15(9P21.3) MUTATED    4 13
  DEL PEAK 15(9P21.3) WILD-TYPE 20 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P21.3) MUTATED      4   13
  DEL PEAK 15(9P21.3) WILD-TYPE   20   11
        clus
vv       DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  CLUS_1                           4                            20
  CLUS_2                          13                            11
[1] 2 2
[1] FALSE
D28V3, binary
                               cls
clus                             0  1
  DEL PEAK 15(9P21.3) MUTATED    7  2
  DEL PEAK 15(9P21.3) WILD-TYPE  8 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P21.3) MUTATED      7    2
  DEL PEAK 15(9P21.3) WILD-TYPE    8   11
        clus
vv       DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(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 15(9P21.3) MUTATED        4      2      3
  DEL PEAK 15(9P21.3) WILD-TYPE      9      8      2
D28V4, multiclass
        clus
vv       DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(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"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK 15(9P21.3) MUTATED        7      1      7      2
  DEL PEAK 15(9P21.3) WILD-TYPE      7     10      3     10
D28V5, multiclass
        clus
vv       DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  CLUS_1                           7                             7
  CLUS_2                           1                            10
  CLUS_3                           7                             3
  CLUS_4                           2                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK 15(9P21.3) MUTATED        3      1      4      8      1
  DEL PEAK 15(9P21.3) WILD-TYPE      6     11      4      4      5
D28V6, multiclass
        clus
vv       DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  CLUS_1                           3                             6
  CLUS_2                           1                            11
  CLUS_3                           4                             4
  CLUS_4                           8                             4
  CLUS_5                           1                             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                               cls
clus                             0  1
  DEL PEAK 15(9P21.3) MUTATED   10  5
  DEL PEAK 15(9P21.3) WILD-TYPE  9 18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P21.3) MUTATED     10    5
  DEL PEAK 15(9P21.3) WILD-TYPE    9   18
        clus
vv       DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  CLUS_1                          10                             9
  CLUS_2                           5                            18
[1] 2 2
[1] FALSE
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 15(9P21.3) MUTATED        0      0      2      5      4      1
  DEL PEAK 15(9P21.3) WILD-TYPE      4      5      4      1      4      2
                               vv
clus                            CLUS_7 CLUS_8 CLUS_9
  DEL PEAK 15(9P21.3) MUTATED        2      0      1
  DEL PEAK 15(9P21.3) WILD-TYPE      3      2      2
D28V8, multiclass
        clus
vv       DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  CLUS_1                           0                             4
  CLUS_2                           0                             5
  CLUS_3                           2                             4
  CLUS_4                           5                             1
  CLUS_5                           4                             4
  CLUS_6                           1                             2
  CLUS_7                           2                             3
  CLUS_8                           0                             2
  CLUS_9                           1                             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(29) Variable = DEL PEAK 16(10Q23.31) MUTATION ANALYSIS
D29V1, binary
                                 cls
clus                               0  1
  DEL PEAK 16(10Q23.31) MUTATED    3  5
  DEL PEAK 16(10Q23.31) WILD-TYPE 26 14
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED      3    5
  DEL PEAK 16(10Q23.31) WILD-TYPE   26   14
        clus
vv       DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  CLUS_1                             3                              26
  CLUS_2                             5                              14
[1] 2 2
[1] FALSE
D29V2, binary
                                 cls
clus                               0  1
  DEL PEAK 16(10Q23.31) MUTATED    4  4
  DEL PEAK 16(10Q23.31) WILD-TYPE 20 20
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED      4    4
  DEL PEAK 16(10Q23.31) WILD-TYPE   20   20
        clus
vv       DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  CLUS_1                             4                              20
  CLUS_2                             4                              20
[1] 2 2
[1] FALSE
D29V3, binary
                                 cls
clus                               0  1
  DEL PEAK 16(10Q23.31) MUTATED    2  3
  DEL PEAK 16(10Q23.31) WILD-TYPE 13 10
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED      2    3
  DEL PEAK 16(10Q23.31) WILD-TYPE   13   10
        clus
vv       DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(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 16(10Q23.31) MUTATED        0      3      2
  DEL PEAK 16(10Q23.31) WILD-TYPE     13      7      3
D29V4, multiclass
        clus
vv       DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(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"
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK 16(10Q23.31) MUTATED        2      1      0      5
  DEL PEAK 16(10Q23.31) WILD-TYPE     12     10     10      7
D29V5, multiclass
        clus
vv       DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  CLUS_1                             2                              12
  CLUS_2                             1                              10
  CLUS_3                             0                              10
  CLUS_4                             5                               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK 16(10Q23.31) MUTATED        1      2      2      1      2
  DEL PEAK 16(10Q23.31) WILD-TYPE      8     10      6     11      4
D29V6, multiclass
        clus
vv       DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  CLUS_1                             1                               8
  CLUS_2                             2                              10
  CLUS_3                             2                               6
  CLUS_4                             1                              11
  CLUS_5                             2                               4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                                 cls
clus                               0  1
  DEL PEAK 16(10Q23.31) MUTATED    2  5
  DEL PEAK 16(10Q23.31) WILD-TYPE 17 18
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED      2    5
  DEL PEAK 16(10Q23.31) WILD-TYPE   17   18
        clus
vv       DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  CLUS_1                             2                              17
  CLUS_2                             5                              18
[1] 2 2
[1] FALSE
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 16(10Q23.31) MUTATED        0      0      1      0      2      0
  DEL PEAK 16(10Q23.31) WILD-TYPE      4      5      5      6      6      3
                                 vv
clus                              CLUS_7 CLUS_8 CLUS_9
  DEL PEAK 16(10Q23.31) MUTATED        4      0      0
  DEL PEAK 16(10Q23.31) WILD-TYPE      1      2      3
D29V8, multiclass
        clus
vv       DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  CLUS_1                             0                               4
  CLUS_2                             0                               5
  CLUS_3                             1                               5
  CLUS_4                             0                               6
  CLUS_5                             2                               6
  CLUS_6                             0                               3
  CLUS_7                             4                               1
  CLUS_8                             0                               2
  CLUS_9                             0                               3
[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(30) Variable = DEL PEAK 17(12P13.2) MUTATION ANALYSIS
D30V1, binary
                                cls
clus                              0  1
  DEL PEAK 17(12P13.2) MUTATED    2  6
  DEL PEAK 17(12P13.2) WILD-TYPE 27 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(12P13.2) MUTATED      2    6
  DEL PEAK 17(12P13.2) WILD-TYPE   27   13
        clus
vv       DEL PEAK 17(12P13.2) MUTATED DEL PEAK 17(12P13.2) WILD-TYPE
  CLUS_1                            2                             27
  CLUS_2                            6                             13
[1] 2 2
[1] FALSE
D30V2, binary
                                cls
clus                              0  1
  DEL PEAK 17(12P13.2) MUTATED    3  5
  DEL PEAK 17(12P13.2) WILD-TYPE 21 19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(12P13.2) MUTATED      3    5
  DEL PEAK 17(12P13.2) WILD-TYPE   21   19
        clus
vv       DEL PEAK 17(12P13.2) MUTATED DEL PEAK 17(12P13.2) WILD-TYPE
  CLUS_1                            3                             21
  CLUS_2                            5                             19
[1] 2 2
[1] FALSE
D30V3, binary
                                cls
clus                              0  1
  DEL PEAK 17(12P13.2) MUTATED    3  2
  DEL PEAK 17(12P13.2) WILD-TYPE 12 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(12P13.2) MUTATED      3    2
  DEL PEAK 17(12P13.2) WILD-TYPE   12   11
        clus
vv       DEL PEAK 17(12P13.2) MUTATED DEL PEAK 17(12P13.2) WILD-TYPE
  CLUS_1                            3                             12
  CLUS_2                            2                             11
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 17(12P13.2) MUTATED        2      2      1
  DEL PEAK 17(12P13.2) WILD-TYPE     11      8      4
D30V4, multiclass
        clus
vv       DEL PEAK 17(12P13.2) MUTATED DEL PEAK 17(12P13.2) WILD-TYPE
  CLUS_1                            2                             11
  CLUS_2                            2                              8
  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"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK 17(12P13.2) MUTATED        1      2      2      3
  DEL PEAK 17(12P13.2) WILD-TYPE     13      9      8      9
D30V5, multiclass
        clus
vv       DEL PEAK 17(12P13.2) MUTATED DEL PEAK 17(12P13.2) WILD-TYPE
  CLUS_1                            1                             13
  CLUS_2                            2                              9
  CLUS_3                            2                              8
  CLUS_4                            3                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK 17(12P13.2) MUTATED        1      3      1      2      1
  DEL PEAK 17(12P13.2) WILD-TYPE      8      9      7     10      5
D30V6, multiclass
        clus
vv       DEL PEAK 17(12P13.2) MUTATED DEL PEAK 17(12P13.2) WILD-TYPE
  CLUS_1                            1                              8
  CLUS_2                            3                              9
  CLUS_3                            1                              7
  CLUS_4                            2                             10
  CLUS_5                            1                              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                                cls
clus                              0  1
  DEL PEAK 17(12P13.2) MUTATED    2  3
  DEL PEAK 17(12P13.2) WILD-TYPE 17 20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(12P13.2) MUTATED      2    3
  DEL PEAK 17(12P13.2) WILD-TYPE   17   20
        clus
vv       DEL PEAK 17(12P13.2) MUTATED DEL PEAK 17(12P13.2) WILD-TYPE
  CLUS_1                            2                             17
  CLUS_2                            3                             20
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 17(12P13.2) MUTATED        0      0      1      1      1      0
  DEL PEAK 17(12P13.2) WILD-TYPE      4      5      5      5      7      3
                                vv
clus                             CLUS_7 CLUS_8 CLUS_9
  DEL PEAK 17(12P13.2) MUTATED        2      0      0
  DEL PEAK 17(12P13.2) WILD-TYPE      3      2      3
D30V8, multiclass
        clus
vv       DEL PEAK 17(12P13.2) MUTATED DEL PEAK 17(12P13.2) WILD-TYPE
  CLUS_1                            0                              4
  CLUS_2                            0                              5
  CLUS_3                            1                              5
  CLUS_4                            1                              5
  CLUS_5                            1                              7
  CLUS_6                            0                              3
  CLUS_7                            2                              3
  CLUS_8                            0                              2
  CLUS_9                            0                              3
[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(31) Variable = DEL PEAK 18(13Q14.2) MUTATION ANALYSIS
D31V1, binary
                                cls
clus                              0  1
  DEL PEAK 18(13Q14.2) MUTATED    2  5
  DEL PEAK 18(13Q14.2) WILD-TYPE 27 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(13Q14.2) MUTATED      2    5
  DEL PEAK 18(13Q14.2) WILD-TYPE   27   14
        clus
vv       DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE
  CLUS_1                            2                             27
  CLUS_2                            5                             14
[1] 2 2
[1] FALSE
D31V2, binary
                                cls
clus                              0  1
  DEL PEAK 18(13Q14.2) MUTATED    2  5
  DEL PEAK 18(13Q14.2) WILD-TYPE 22 19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(13Q14.2) MUTATED      2    5
  DEL PEAK 18(13Q14.2) WILD-TYPE   22   19
        clus
vv       DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE
  CLUS_1                            2                             22
  CLUS_2                            5                             19
[1] 2 2
[1] FALSE
D31V3, binary
                                cls
clus                              0  1
  DEL PEAK 18(13Q14.2) MUTATED    2  1
  DEL PEAK 18(13Q14.2) WILD-TYPE 13 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(13Q14.2) MUTATED      2    1
  DEL PEAK 18(13Q14.2) WILD-TYPE   13   12
        clus
vv       DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(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 18(13Q14.2) MUTATED        1      1      1
  DEL PEAK 18(13Q14.2) WILD-TYPE     12      9      4
D31V4, multiclass
        clus
vv       DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(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"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK 18(13Q14.2) MUTATED        2      1      0      4
  DEL PEAK 18(13Q14.2) WILD-TYPE     12     10     10      8
D31V5, multiclass
        clus
vv       DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE
  CLUS_1                            2                             12
  CLUS_2                            1                             10
  CLUS_3                            0                             10
  CLUS_4                            4                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK 18(13Q14.2) MUTATED        1      2      2      0      2
  DEL PEAK 18(13Q14.2) WILD-TYPE      8     10      6     12      4
D31V6, multiclass
        clus
vv       DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE
  CLUS_1                            1                              8
  CLUS_2                            2                             10
  CLUS_3                            2                              6
  CLUS_4                            0                             12
  CLUS_5                            2                              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                                cls
clus                              0  1
  DEL PEAK 18(13Q14.2) MUTATED    2  3
  DEL PEAK 18(13Q14.2) WILD-TYPE 17 20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(13Q14.2) MUTATED      2    3
  DEL PEAK 18(13Q14.2) WILD-TYPE   17   20
        clus
vv       DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE
  CLUS_1                            2                             17
  CLUS_2                            3                             20
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 18(13Q14.2) MUTATED        1      0      1      0      1      0
  DEL PEAK 18(13Q14.2) WILD-TYPE      3      5      5      6      7      3
                                vv
clus                             CLUS_7 CLUS_8 CLUS_9
  DEL PEAK 18(13Q14.2) MUTATED        2      0      0
  DEL PEAK 18(13Q14.2) WILD-TYPE      3      2      3
D31V8, multiclass
        clus
vv       DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE
  CLUS_1                            1                              3
  CLUS_2                            0                              5
  CLUS_3                            1                              5
  CLUS_4                            0                              6
  CLUS_5                            1                              7
  CLUS_6                            0                              3
  CLUS_7                            2                              3
  CLUS_8                            0                              2
  CLUS_9                            0                              3
[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(32) Variable = DEL PEAK 19(15Q21.1) MUTATION ANALYSIS
D32V1, binary
                                cls
clus                              0  1
  DEL PEAK 19(15Q21.1) MUTATED    7  6
  DEL PEAK 19(15Q21.1) WILD-TYPE 22 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(15Q21.1) MUTATED      7    6
  DEL PEAK 19(15Q21.1) WILD-TYPE   22   13
        clus
vv       DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE
  CLUS_1                            7                             22
  CLUS_2                            6                             13
[1] 2 2
[1] FALSE
D32V2, binary
                                cls
clus                              0  1
  DEL PEAK 19(15Q21.1) MUTATED    8  5
  DEL PEAK 19(15Q21.1) WILD-TYPE 16 19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(15Q21.1) MUTATED      8    5
  DEL PEAK 19(15Q21.1) WILD-TYPE   16   19
        clus
vv       DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE
  CLUS_1                            8                             16
  CLUS_2                            5                             19
[1] 2 2
[1] FALSE
D32V3, binary
                                cls
clus                              0  1
  DEL PEAK 19(15Q21.1) MUTATED    5  4
  DEL PEAK 19(15Q21.1) WILD-TYPE 10  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(15Q21.1) MUTATED      5    4
  DEL PEAK 19(15Q21.1) WILD-TYPE   10    9
        clus
vv       DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(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 19(15Q21.1) MUTATED        3      4      2
  DEL PEAK 19(15Q21.1) WILD-TYPE     10      6      3
D32V4, multiclass
        clus
vv       DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(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"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK 19(15Q21.1) MUTATED        2      3      2      5
  DEL PEAK 19(15Q21.1) WILD-TYPE     12      8      8      7
D32V5, multiclass
        clus
vv       DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE
  CLUS_1                            2                             12
  CLUS_2                            3                              8
  CLUS_3                            2                              8
  CLUS_4                            5                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK 19(15Q21.1) MUTATED        2      3      1      3      3
  DEL PEAK 19(15Q21.1) WILD-TYPE      7      9      7      9      3
D32V6, multiclass
        clus
vv       DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE
  CLUS_1                            2                              7
  CLUS_2                            3                              9
  CLUS_3                            1                              7
  CLUS_4                            3                              9
  CLUS_5                            3                              3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                                cls
clus                              0  1
  DEL PEAK 19(15Q21.1) MUTATED    4  7
  DEL PEAK 19(15Q21.1) WILD-TYPE 15 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(15Q21.1) MUTATED      4    7
  DEL PEAK 19(15Q21.1) WILD-TYPE   15   16
        clus
vv       DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE
  CLUS_1                            4                             15
  CLUS_2                            7                             16
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 19(15Q21.1) MUTATED        1      1      1      2      2      0
  DEL PEAK 19(15Q21.1) WILD-TYPE      3      4      5      4      6      3
                                vv
clus                             CLUS_7 CLUS_8 CLUS_9
  DEL PEAK 19(15Q21.1) MUTATED        4      0      0
  DEL PEAK 19(15Q21.1) WILD-TYPE      1      2      3
D32V8, multiclass
        clus
vv       DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE
  CLUS_1                            1                              3
  CLUS_2                            1                              4
  CLUS_3                            1                              5
  CLUS_4                            2                              4
  CLUS_5                            2                              6
  CLUS_6                            0                              3
  CLUS_7                            4                              1
  CLUS_8                            0                              2
  CLUS_9                            0                              3
[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(33) Variable = DEL PEAK 20(16P13.13) MUTATION ANALYSIS
D33V1, binary
                                 cls
clus                               0  1
  DEL PEAK 20(16P13.13) MUTATED    2  4
  DEL PEAK 20(16P13.13) WILD-TYPE 27 15
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(16P13.13) MUTATED      2    4
  DEL PEAK 20(16P13.13) WILD-TYPE   27   15
        clus
vv       DEL PEAK 20(16P13.13) MUTATED DEL PEAK 20(16P13.13) WILD-TYPE
  CLUS_1                             2                              27
  CLUS_2                             4                              15
[1] 2 2
[1] FALSE
D33V2, binary
                                 cls
clus                               0  1
  DEL PEAK 20(16P13.13) MUTATED    2  4
  DEL PEAK 20(16P13.13) WILD-TYPE 22 20
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(16P13.13) MUTATED      2    4
  DEL PEAK 20(16P13.13) WILD-TYPE   22   20
        clus
vv       DEL PEAK 20(16P13.13) MUTATED DEL PEAK 20(16P13.13) WILD-TYPE
  CLUS_1                             2                              22
  CLUS_2                             4                              20
[1] 2 2
[1] FALSE
D33V3, binary
                                 cls
clus                               0  1
  DEL PEAK 20(16P13.13) MUTATED    1  3
  DEL PEAK 20(16P13.13) WILD-TYPE 14 10
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(16P13.13) MUTATED      1    3
  DEL PEAK 20(16P13.13) WILD-TYPE   14   10
        clus
vv       DEL PEAK 20(16P13.13) MUTATED DEL PEAK 20(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 20(16P13.13) MUTATED        2      2      0
  DEL PEAK 20(16P13.13) WILD-TYPE     11      8      5
D33V4, multiclass
        clus
vv       DEL PEAK 20(16P13.13) MUTATED DEL PEAK 20(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"
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK 20(16P13.13) MUTATED        1      2      0      3
  DEL PEAK 20(16P13.13) WILD-TYPE     13      9     10      9
D33V5, multiclass
        clus
vv       DEL PEAK 20(16P13.13) MUTATED DEL PEAK 20(16P13.13) WILD-TYPE
  CLUS_1                             1                              13
  CLUS_2                             2                               9
  CLUS_3                             0                              10
  CLUS_4                             3                               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK 20(16P13.13) MUTATED        0      2      1      0      3
  DEL PEAK 20(16P13.13) WILD-TYPE      9     10      7     12      3
D33V6, multiclass
        clus
vv       DEL PEAK 20(16P13.13) MUTATED DEL PEAK 20(16P13.13) WILD-TYPE
  CLUS_1                             0                               9
  CLUS_2                             2                              10
  CLUS_3                             1                               7
  CLUS_4                             0                              12
  CLUS_5                             3                               3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                                 cls
clus                               0  1
  DEL PEAK 20(16P13.13) MUTATED    1  3
  DEL PEAK 20(16P13.13) WILD-TYPE 18 20
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(16P13.13) MUTATED      1    3
  DEL PEAK 20(16P13.13) WILD-TYPE   18   20
        clus
vv       DEL PEAK 20(16P13.13) MUTATED DEL PEAK 20(16P13.13) WILD-TYPE
  CLUS_1                             1                              18
  CLUS_2                             3                              20
[1] 2 2
[1] FALSE
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 20(16P13.13) MUTATED        1      0      0      0      1      1
  DEL PEAK 20(16P13.13) WILD-TYPE      3      5      6      6      7      2
                                 vv
clus                              CLUS_7 CLUS_8 CLUS_9
  DEL PEAK 20(16P13.13) MUTATED        1      0      0
  DEL PEAK 20(16P13.13) WILD-TYPE      4      2      3
D33V8, multiclass
        clus
vv       DEL PEAK 20(16P13.13) MUTATED DEL PEAK 20(16P13.13) WILD-TYPE
  CLUS_1                             1                               3
  CLUS_2                             0                               5
  CLUS_3                             0                               6
  CLUS_4                             0                               6
  CLUS_5                             1                               7
  CLUS_6                             1                               2
  CLUS_7                             1                               4
  CLUS_8                             0                               2
  CLUS_9                             0                               3
[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(34) Variable = DEL PEAK 21(16Q23.1) MUTATION ANALYSIS
D34V1, binary
                                cls
clus                              0  1
  DEL PEAK 21(16Q23.1) MUTATED    1  4
  DEL PEAK 21(16Q23.1) WILD-TYPE 28 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(16Q23.1) MUTATED      1    4
  DEL PEAK 21(16Q23.1) WILD-TYPE   28   15
        clus
vv       DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE
  CLUS_1                            1                             28
  CLUS_2                            4                             15
[1] 2 2
[1] FALSE
D34V2, binary
                                cls
clus                              0  1
  DEL PEAK 21(16Q23.1) MUTATED    3  2
  DEL PEAK 21(16Q23.1) WILD-TYPE 21 22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(16Q23.1) MUTATED      3    2
  DEL PEAK 21(16Q23.1) WILD-TYPE   21   22
        clus
vv       DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE
  CLUS_1                            3                             21
  CLUS_2                            2                             22
[1] 2 2
[1] FALSE
D34V3, binary
                                cls
clus                              0  1
  DEL PEAK 21(16Q23.1) MUTATED    2  3
  DEL PEAK 21(16Q23.1) WILD-TYPE 13 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(16Q23.1) MUTATED      2    3
  DEL PEAK 21(16Q23.1) WILD-TYPE   13   10
        clus
vv       DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(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 21(16Q23.1) MUTATED        1      3      1
  DEL PEAK 21(16Q23.1) WILD-TYPE     12      7      4
D34V4, multiclass
        clus
vv       DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(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"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK 21(16Q23.1) MUTATED        0      2      0      3
  DEL PEAK 21(16Q23.1) WILD-TYPE     14      9     10      9
D34V5, multiclass
        clus
vv       DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE
  CLUS_1                            0                             14
  CLUS_2                            2                              9
  CLUS_3                            0                             10
  CLUS_4                            3                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK 21(16Q23.1) MUTATED        1      2      0      0      2
  DEL PEAK 21(16Q23.1) WILD-TYPE      8     10      8     12      4
D34V6, multiclass
        clus
vv       DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE
  CLUS_1                            1                              8
  CLUS_2                            2                             10
  CLUS_3                            0                              8
  CLUS_4                            0                             12
  CLUS_5                            2                              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                                cls
clus                              0  1
  DEL PEAK 21(16Q23.1) MUTATED    0  4
  DEL PEAK 21(16Q23.1) WILD-TYPE 19 19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(16Q23.1) MUTATED      0    4
  DEL PEAK 21(16Q23.1) WILD-TYPE   19   19
        clus
vv       DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE
  CLUS_1                            0                             19
  CLUS_2                            4                             19
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 21(16Q23.1) MUTATED        0      1      0      0      2      0
  DEL PEAK 21(16Q23.1) WILD-TYPE      4      4      6      6      6      3
                                vv
clus                             CLUS_7 CLUS_8 CLUS_9
  DEL PEAK 21(16Q23.1) MUTATED        1      0      0
  DEL PEAK 21(16Q23.1) WILD-TYPE      4      2      3
D34V8, multiclass
        clus
vv       DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE
  CLUS_1                            0                              4
  CLUS_2                            1                              4
  CLUS_3                            0                              6
  CLUS_4                            0                              6
  CLUS_5                            2                              6
  CLUS_6                            0                              3
  CLUS_7                            1                              4
  CLUS_8                            0                              2
  CLUS_9                            0                              3
[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(35) Variable = DEL PEAK 22(17P13.1) MUTATION ANALYSIS
D35V1, binary
                                cls
clus                              0  1
  DEL PEAK 22(17P13.1) MUTATED    3 10
  DEL PEAK 22(17P13.1) WILD-TYPE 26  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(17P13.1) MUTATED      3   10
  DEL PEAK 22(17P13.1) WILD-TYPE   26    9
        clus
vv       DEL PEAK 22(17P13.1) MUTATED DEL PEAK 22(17P13.1) WILD-TYPE
  CLUS_1                            3                             26
  CLUS_2                           10                              9
[1] 2 2
[1] FALSE
D35V2, binary
                                cls
clus                              0  1
  DEL PEAK 22(17P13.1) MUTATED    5  8
  DEL PEAK 22(17P13.1) WILD-TYPE 19 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(17P13.1) MUTATED      5    8
  DEL PEAK 22(17P13.1) WILD-TYPE   19   16
        clus
vv       DEL PEAK 22(17P13.1) MUTATED DEL PEAK 22(17P13.1) WILD-TYPE
  CLUS_1                            5                             19
  CLUS_2                            8                             16
[1] 2 2
[1] FALSE
D35V3, binary
                                cls
clus                              0  1
  DEL PEAK 22(17P13.1) MUTATED    3  2
  DEL PEAK 22(17P13.1) WILD-TYPE 12 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(17P13.1) MUTATED      3    2
  DEL PEAK 22(17P13.1) WILD-TYPE   12   11
        clus
vv       DEL PEAK 22(17P13.1) MUTATED DEL PEAK 22(17P13.1) WILD-TYPE
  CLUS_1                            3                             12
  CLUS_2                            2                             11
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 22(17P13.1) MUTATED        2      2      1
  DEL PEAK 22(17P13.1) WILD-TYPE     11      8      4
D35V4, multiclass
        clus
vv       DEL PEAK 22(17P13.1) MUTATED DEL PEAK 22(17P13.1) WILD-TYPE
  CLUS_1                            2                             11
  CLUS_2                            2                              8
  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"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK 22(17P13.1) MUTATED        4      2      2      5
  DEL PEAK 22(17P13.1) WILD-TYPE     10      9      8      7
D35V5, multiclass
        clus
vv       DEL PEAK 22(17P13.1) MUTATED DEL PEAK 22(17P13.1) WILD-TYPE
  CLUS_1                            4                             10
  CLUS_2                            2                              9
  CLUS_3                            2                              8
  CLUS_4                            5                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK 22(17P13.1) MUTATED        1      3      4      3      2
  DEL PEAK 22(17P13.1) WILD-TYPE      8      9      4      9      4
D35V6, multiclass
        clus
vv       DEL PEAK 22(17P13.1) MUTATED DEL PEAK 22(17P13.1) WILD-TYPE
  CLUS_1                            1                              8
  CLUS_2                            3                              9
  CLUS_3                            4                              4
  CLUS_4                            3                              9
  CLUS_5                            2                              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                                cls
clus                              0  1
  DEL PEAK 22(17P13.1) MUTATED    5  5
  DEL PEAK 22(17P13.1) WILD-TYPE 14 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(17P13.1) MUTATED      5    5
  DEL PEAK 22(17P13.1) WILD-TYPE   14   18
        clus
vv       DEL PEAK 22(17P13.1) MUTATED DEL PEAK 22(17P13.1) WILD-TYPE
  CLUS_1                            5                             14
  CLUS_2                            5                             18
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 22(17P13.1) MUTATED        2      0      3      1      2      0
  DEL PEAK 22(17P13.1) WILD-TYPE      2      5      3      5      6      3
                                vv
clus                             CLUS_7 CLUS_8 CLUS_9
  DEL PEAK 22(17P13.1) MUTATED        1      0      1
  DEL PEAK 22(17P13.1) WILD-TYPE      4      2      2
D35V8, multiclass
        clus
vv       DEL PEAK 22(17P13.1) MUTATED DEL PEAK 22(17P13.1) WILD-TYPE
  CLUS_1                            2                              2
  CLUS_2                            0                              5
  CLUS_3                            3                              3
  CLUS_4                            1                              5
  CLUS_5                            2                              6
  CLUS_6                            0                              3
  CLUS_7                            1                              4
  CLUS_8                            0                              2
  CLUS_9                            1                              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(36) Variable = DEL PEAK 23(17Q24.1) MUTATION ANALYSIS
D36V1, binary
                                cls
clus                              0  1
  DEL PEAK 23(17Q24.1) MUTATED    3  5
  DEL PEAK 23(17Q24.1) WILD-TYPE 26 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(17Q24.1) MUTATED      3    5
  DEL PEAK 23(17Q24.1) WILD-TYPE   26   14
        clus
vv       DEL PEAK 23(17Q24.1) MUTATED DEL PEAK 23(17Q24.1) WILD-TYPE
  CLUS_1                            3                             26
  CLUS_2                            5                             14
[1] 2 2
[1] FALSE
D36V2, binary
                                cls
clus                              0  1
  DEL PEAK 23(17Q24.1) MUTATED    1  7
  DEL PEAK 23(17Q24.1) WILD-TYPE 23 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(17Q24.1) MUTATED      1    7
  DEL PEAK 23(17Q24.1) WILD-TYPE   23   17
        clus
vv       DEL PEAK 23(17Q24.1) MUTATED DEL PEAK 23(17Q24.1) WILD-TYPE
  CLUS_1                            1                             23
  CLUS_2                            7                             17
[1] 2 2
[1] FALSE
D36V3, binary
                                cls
clus                              0  1
  DEL PEAK 23(17Q24.1) MUTATED    2  2
  DEL PEAK 23(17Q24.1) WILD-TYPE 13 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(17Q24.1) MUTATED      2    2
  DEL PEAK 23(17Q24.1) WILD-TYPE   13   11
        clus
vv       DEL PEAK 23(17Q24.1) MUTATED DEL PEAK 23(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 23(17Q24.1) MUTATED        0      2      2
  DEL PEAK 23(17Q24.1) WILD-TYPE     13      8      3
D36V4, multiclass
        clus
vv       DEL PEAK 23(17Q24.1) MUTATED DEL PEAK 23(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"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK 23(17Q24.1) MUTATED        4      1      1      2
  DEL PEAK 23(17Q24.1) WILD-TYPE     10     10      9     10
D36V5, multiclass
        clus
vv       DEL PEAK 23(17Q24.1) MUTATED DEL PEAK 23(17Q24.1) WILD-TYPE
  CLUS_1                            4                             10
  CLUS_2                            1                             10
  CLUS_3                            1                              9
  CLUS_4                            2                             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK 23(17Q24.1) MUTATED        0      1      4      1      2
  DEL PEAK 23(17Q24.1) WILD-TYPE      9     11      4     11      4
D36V6, multiclass
        clus
vv       DEL PEAK 23(17Q24.1) MUTATED DEL PEAK 23(17Q24.1) WILD-TYPE
  CLUS_1                            0                              9
  CLUS_2                            1                             11
  CLUS_3                            4                              4
  CLUS_4                            1                             11
  CLUS_5                            2                              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                                cls
clus                              0  1
  DEL PEAK 23(17Q24.1) MUTATED    5  2
  DEL PEAK 23(17Q24.1) WILD-TYPE 14 21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(17Q24.1) MUTATED      5    2
  DEL PEAK 23(17Q24.1) WILD-TYPE   14   21
        clus
vv       DEL PEAK 23(17Q24.1) MUTATED DEL PEAK 23(17Q24.1) WILD-TYPE
  CLUS_1                            5                             14
  CLUS_2                            2                             21
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 23(17Q24.1) MUTATED        1      0      2      1      0      0
  DEL PEAK 23(17Q24.1) WILD-TYPE      3      5      4      5      8      3
                                vv
clus                             CLUS_7 CLUS_8 CLUS_9
  DEL PEAK 23(17Q24.1) MUTATED        3      0      0
  DEL PEAK 23(17Q24.1) WILD-TYPE      2      2      3
D36V8, multiclass
        clus
vv       DEL PEAK 23(17Q24.1) MUTATED DEL PEAK 23(17Q24.1) WILD-TYPE
  CLUS_1                            1                              3
  CLUS_2                            0                              5
  CLUS_3                            2                              4
  CLUS_4                            1                              5
  CLUS_5                            0                              8
  CLUS_6                            0                              3
  CLUS_7                            3                              2
  CLUS_8                            0                              2
  CLUS_9                            0                              3
[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(37) Variable = DEL PEAK 24(19P13.2) MUTATION ANALYSIS
D37V1, binary
                                cls
clus                              0  1
  DEL PEAK 24(19P13.2) MUTATED    2  2
  DEL PEAK 24(19P13.2) WILD-TYPE 27 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(19P13.2) MUTATED      2    2
  DEL PEAK 24(19P13.2) WILD-TYPE   27   17
        clus
vv       DEL PEAK 24(19P13.2) MUTATED DEL PEAK 24(19P13.2) WILD-TYPE
  CLUS_1                            2                             27
  CLUS_2                            2                             17
[1] 2 2
[1] FALSE
D37V2, binary
                                cls
clus                              0  1
  DEL PEAK 24(19P13.2) MUTATED    2  2
  DEL PEAK 24(19P13.2) WILD-TYPE 22 22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(19P13.2) MUTATED      2    2
  DEL PEAK 24(19P13.2) WILD-TYPE   22   22
        clus
vv       DEL PEAK 24(19P13.2) MUTATED DEL PEAK 24(19P13.2) WILD-TYPE
  CLUS_1                            2                             22
  CLUS_2                            2                             22
[1] 2 2
[1] FALSE
D37V3, binary
                                cls
clus                              0  1
  DEL PEAK 24(19P13.2) MUTATED    2  0
  DEL PEAK 24(19P13.2) WILD-TYPE 13 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(19P13.2) MUTATED      2    0
  DEL PEAK 24(19P13.2) WILD-TYPE   13   13
        clus
vv       DEL PEAK 24(19P13.2) MUTATED DEL PEAK 24(19P13.2) WILD-TYPE
  CLUS_1                            2                             13
  CLUS_2                            0                             13
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 24(19P13.2) MUTATED        1      0      1
  DEL PEAK 24(19P13.2) WILD-TYPE     12     10      4
D37V4, multiclass
[1] "Remove cluster labels:"       "DEL PEAK 24(19P13.2) MUTATED"
clus
  DEL PEAK 24(19P13.2) MUTATED DEL PEAK 24(19P13.2) WILD-TYPE 
                             2                             26 
                    TCGA-FA-8693                     TCGA-FA-A4BB 
"DEL PEAK 24(19P13.2) WILD-TYPE" "DEL PEAK 24(19P13.2) WILD-TYPE" 
                    TCGA-FA-A4XK                     TCGA-FA-A6HN 
"DEL PEAK 24(19P13.2) WILD-TYPE" "DEL PEAK 24(19P13.2) WILD-TYPE" 
                    TCGA-FA-A6HO                     TCGA-FF-8041 
"DEL PEAK 24(19P13.2) WILD-TYPE" "DEL PEAK 24(19P13.2) WILD-TYPE" 
                    TCGA-FF-8042                     TCGA-FF-8043 
"DEL PEAK 24(19P13.2) WILD-TYPE" "DEL PEAK 24(19P13.2) WILD-TYPE" 
                    TCGA-FF-8046                     TCGA-FF-8047 
"DEL PEAK 24(19P13.2) WILD-TYPE" "DEL PEAK 24(19P13.2) WILD-TYPE" 
                    TCGA-FF-8061                     TCGA-FF-8062 
"DEL PEAK 24(19P13.2) WILD-TYPE" "DEL PEAK 24(19P13.2) WILD-TYPE" 
                    TCGA-FM-8000                     TCGA-G8-6324 
"DEL PEAK 24(19P13.2) WILD-TYPE" "DEL PEAK 24(19P13.2) WILD-TYPE" 
                    TCGA-G8-6325                     TCGA-G8-6326 
"DEL PEAK 24(19P13.2) WILD-TYPE" "DEL PEAK 24(19P13.2) WILD-TYPE" 
                    TCGA-G8-6906                     TCGA-G8-6907 
"DEL PEAK 24(19P13.2) WILD-TYPE" "DEL PEAK 24(19P13.2) WILD-TYPE" 
                    TCGA-G8-6909                     TCGA-G8-6914 
"DEL PEAK 24(19P13.2) WILD-TYPE" "DEL PEAK 24(19P13.2) WILD-TYPE" 
                    TCGA-GR-7351                     TCGA-GR-7353 
"DEL PEAK 24(19P13.2) WILD-TYPE" "DEL PEAK 24(19P13.2) WILD-TYPE" 
                    TCGA-GR-A4D5                     TCGA-GR-A4D6 
"DEL PEAK 24(19P13.2) WILD-TYPE" "DEL PEAK 24(19P13.2) WILD-TYPE" 
                    TCGA-GR-A4D9                     TCGA-RQ-A6JB 
"DEL PEAK 24(19P13.2) WILD-TYPE" "DEL PEAK 24(19P13.2) WILD-TYPE" 
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK 24(19P13.2) MUTATED        1      1      1      1
  DEL PEAK 24(19P13.2) WILD-TYPE     13     10      9     11
D37V5, multiclass
        clus
vv       DEL PEAK 24(19P13.2) MUTATED DEL PEAK 24(19P13.2) WILD-TYPE
  CLUS_1                            1                             13
  CLUS_2                            1                             10
  CLUS_3                            1                              9
  CLUS_4                            1                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK 24(19P13.2) MUTATED        2      0      1      1      0
  DEL PEAK 24(19P13.2) WILD-TYPE      7     12      7     11      6
D37V6, multiclass
        clus
vv       DEL PEAK 24(19P13.2) MUTATED DEL PEAK 24(19P13.2) WILD-TYPE
  CLUS_1                            2                              7
  CLUS_2                            0                             12
  CLUS_3                            1                              7
  CLUS_4                            1                             11
  CLUS_5                            0                              6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                                cls
clus                              0  1
  DEL PEAK 24(19P13.2) MUTATED    2  2
  DEL PEAK 24(19P13.2) WILD-TYPE 17 21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(19P13.2) MUTATED      2    2
  DEL PEAK 24(19P13.2) WILD-TYPE   17   21
        clus
vv       DEL PEAK 24(19P13.2) MUTATED DEL PEAK 24(19P13.2) WILD-TYPE
  CLUS_1                            2                             17
  CLUS_2                            2                             21
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 24(19P13.2) MUTATED        0      0      1      1      0      0
  DEL PEAK 24(19P13.2) WILD-TYPE      4      5      5      5      8      3
                                vv
clus                             CLUS_7 CLUS_8 CLUS_9
  DEL PEAK 24(19P13.2) MUTATED        1      0      1
  DEL PEAK 24(19P13.2) WILD-TYPE      4      2      2
D37V8, multiclass
        clus
vv       DEL PEAK 24(19P13.2) MUTATED DEL PEAK 24(19P13.2) WILD-TYPE
  CLUS_1                            0                              4
  CLUS_2                            0                              5
  CLUS_3                            1                              5
  CLUS_4                            1                              5
  CLUS_5                            0                              8
  CLUS_6                            0                              3
  CLUS_7                            1                              4
  CLUS_8                            0                              2
  CLUS_9                            1                              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(38) Variable = DEL PEAK 25(19Q13.2) MUTATION ANALYSIS
D38V1, binary
                                cls
clus                              0  1
  DEL PEAK 25(19Q13.2) MUTATED    3  2
  DEL PEAK 25(19Q13.2) WILD-TYPE 26 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(19Q13.2) MUTATED      3    2
  DEL PEAK 25(19Q13.2) WILD-TYPE   26   17
        clus
vv       DEL PEAK 25(19Q13.2) MUTATED DEL PEAK 25(19Q13.2) WILD-TYPE
  CLUS_1                            3                             26
  CLUS_2                            2                             17
[1] 2 2
[1] FALSE
D38V2, binary
                                cls
clus                              0  1
  DEL PEAK 25(19Q13.2) MUTATED    1  4
  DEL PEAK 25(19Q13.2) WILD-TYPE 23 20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(19Q13.2) MUTATED      1    4
  DEL PEAK 25(19Q13.2) WILD-TYPE   23   20
        clus
vv       DEL PEAK 25(19Q13.2) MUTATED DEL PEAK 25(19Q13.2) WILD-TYPE
  CLUS_1                            1                             23
  CLUS_2                            4                             20
[1] 2 2
[1] FALSE
D38V3, binary
                                cls
clus                              0  1
  DEL PEAK 25(19Q13.2) MUTATED    2  0
  DEL PEAK 25(19Q13.2) WILD-TYPE 13 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(19Q13.2) MUTATED      2    0
  DEL PEAK 25(19Q13.2) WILD-TYPE   13   13
        clus
vv       DEL PEAK 25(19Q13.2) MUTATED DEL PEAK 25(19Q13.2) WILD-TYPE
  CLUS_1                            2                             13
  CLUS_2                            0                             13
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 25(19Q13.2) MUTATED        1      0      1
  DEL PEAK 25(19Q13.2) WILD-TYPE     12     10      4
D38V4, multiclass
[1] "Remove cluster labels:"       "DEL PEAK 25(19Q13.2) MUTATED"
clus
  DEL PEAK 25(19Q13.2) MUTATED DEL PEAK 25(19Q13.2) WILD-TYPE 
                             2                             26 
                    TCGA-FA-8693                     TCGA-FA-A4BB 
"DEL PEAK 25(19Q13.2) WILD-TYPE" "DEL PEAK 25(19Q13.2) WILD-TYPE" 
                    TCGA-FA-A4XK                     TCGA-FA-A6HN 
"DEL PEAK 25(19Q13.2) WILD-TYPE" "DEL PEAK 25(19Q13.2) WILD-TYPE" 
                    TCGA-FA-A6HO                     TCGA-FF-8041 
"DEL PEAK 25(19Q13.2) WILD-TYPE" "DEL PEAK 25(19Q13.2) WILD-TYPE" 
                    TCGA-FF-8043                     TCGA-FF-8046 
"DEL PEAK 25(19Q13.2) WILD-TYPE" "DEL PEAK 25(19Q13.2) WILD-TYPE" 
                    TCGA-FF-8047                     TCGA-FF-8061 
"DEL PEAK 25(19Q13.2) WILD-TYPE" "DEL PEAK 25(19Q13.2) WILD-TYPE" 
                    TCGA-FF-8062                     TCGA-FM-8000 
"DEL PEAK 25(19Q13.2) WILD-TYPE" "DEL PEAK 25(19Q13.2) WILD-TYPE" 
                    TCGA-G8-6324                     TCGA-G8-6325 
"DEL PEAK 25(19Q13.2) WILD-TYPE" "DEL PEAK 25(19Q13.2) WILD-TYPE" 
                    TCGA-G8-6326                     TCGA-G8-6906 
"DEL PEAK 25(19Q13.2) WILD-TYPE" "DEL PEAK 25(19Q13.2) WILD-TYPE" 
                    TCGA-G8-6907                     TCGA-G8-6909 
"DEL PEAK 25(19Q13.2) WILD-TYPE" "DEL PEAK 25(19Q13.2) WILD-TYPE" 
                    TCGA-G8-6914                     TCGA-GR-7351 
"DEL PEAK 25(19Q13.2) WILD-TYPE" "DEL PEAK 25(19Q13.2) WILD-TYPE" 
                    TCGA-GR-7353                     TCGA-GR-A4D4 
"DEL PEAK 25(19Q13.2) WILD-TYPE" "DEL PEAK 25(19Q13.2) WILD-TYPE" 
                    TCGA-GR-A4D5                     TCGA-GR-A4D6 
"DEL PEAK 25(19Q13.2) WILD-TYPE" "DEL PEAK 25(19Q13.2) WILD-TYPE" 
                    TCGA-RQ-A68N                     TCGA-RQ-A6JB 
"DEL PEAK 25(19Q13.2) WILD-TYPE" "DEL PEAK 25(19Q13.2) WILD-TYPE" 
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK 25(19Q13.2) MUTATED        2      1      1      1
  DEL PEAK 25(19Q13.2) WILD-TYPE     12     10      9     11
D38V5, multiclass
        clus
vv       DEL PEAK 25(19Q13.2) MUTATED DEL PEAK 25(19Q13.2) WILD-TYPE
  CLUS_1                            2                             12
  CLUS_2                            1                             10
  CLUS_3                            1                              9
  CLUS_4                            1                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK 25(19Q13.2) MUTATED        2      1      0      2      0
  DEL PEAK 25(19Q13.2) WILD-TYPE      7     11      8     10      6
D38V6, multiclass
        clus
vv       DEL PEAK 25(19Q13.2) MUTATED DEL PEAK 25(19Q13.2) WILD-TYPE
  CLUS_1                            2                              7
  CLUS_2                            1                             11
  CLUS_3                            0                              8
  CLUS_4                            2                             10
  CLUS_5                            0                              6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                                cls
clus                              0  1
  DEL PEAK 25(19Q13.2) MUTATED    2  1
  DEL PEAK 25(19Q13.2) WILD-TYPE 17 22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(19Q13.2) MUTATED      2    1
  DEL PEAK 25(19Q13.2) WILD-TYPE   17   22
        clus
vv       DEL PEAK 25(19Q13.2) MUTATED DEL PEAK 25(19Q13.2) WILD-TYPE
  CLUS_1                            2                             17
  CLUS_2                            1                             22
[1] 2 2
[1] FALSE
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 25(19Q13.2) MUTATED        0      0      0      1      1      0
  DEL PEAK 25(19Q13.2) WILD-TYPE      4      5      6      5      7      3
                                vv
clus                             CLUS_7 CLUS_8 CLUS_9
  DEL PEAK 25(19Q13.2) MUTATED        0      0      1
  DEL PEAK 25(19Q13.2) WILD-TYPE      5      2      2
D38V8, multiclass
        clus
vv       DEL PEAK 25(19Q13.2) MUTATED DEL PEAK 25(19Q13.2) WILD-TYPE
  CLUS_1                            0                              4
  CLUS_2                            0                              5
  CLUS_3                            0                              6
  CLUS_4                            1                              5
  CLUS_5                            1                              7
  CLUS_6                            0                              3
  CLUS_7                            0                              5
  CLUS_8                            0                              2
  CLUS_9                            1                              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(39) Variable = DEL PEAK 26(22Q13.31) MUTATION ANALYSIS
D39V1, binary
                                 cls
clus                               0  1
  DEL PEAK 26(22Q13.31) MUTATED    2  5
  DEL PEAK 26(22Q13.31) WILD-TYPE 27 14
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(22Q13.31) MUTATED      2    5
  DEL PEAK 26(22Q13.31) WILD-TYPE   27   14
        clus
vv       DEL PEAK 26(22Q13.31) MUTATED DEL PEAK 26(22Q13.31) WILD-TYPE
  CLUS_1                             2                              27
  CLUS_2                             5                              14
[1] 2 2
[1] FALSE
D39V2, binary
                                 cls
clus                               0  1
  DEL PEAK 26(22Q13.31) MUTATED    3  4
  DEL PEAK 26(22Q13.31) WILD-TYPE 21 20
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(22Q13.31) MUTATED      3    4
  DEL PEAK 26(22Q13.31) WILD-TYPE   21   20
        clus
vv       DEL PEAK 26(22Q13.31) MUTATED DEL PEAK 26(22Q13.31) WILD-TYPE
  CLUS_1                             3                              21
  CLUS_2                             4                              20
[1] 2 2
[1] FALSE
D39V3, binary
                                 cls
clus                               0  1
  DEL PEAK 26(22Q13.31) MUTATED    2  1
  DEL PEAK 26(22Q13.31) WILD-TYPE 13 12
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(22Q13.31) MUTATED      2    1
  DEL PEAK 26(22Q13.31) WILD-TYPE   13   12
        clus
vv       DEL PEAK 26(22Q13.31) MUTATED DEL PEAK 26(22Q13.31) 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 26(22Q13.31) MUTATED        2      1      0
  DEL PEAK 26(22Q13.31) WILD-TYPE     11      9      5
D39V4, multiclass
        clus
vv       DEL PEAK 26(22Q13.31) MUTATED DEL PEAK 26(22Q13.31) WILD-TYPE
  CLUS_1                             2                              11
  CLUS_2                             1                               9
  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"
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK 26(22Q13.31) MUTATED        2      1      2      2
  DEL PEAK 26(22Q13.31) WILD-TYPE     12     10      8     10
D39V5, multiclass
        clus
vv       DEL PEAK 26(22Q13.31) MUTATED DEL PEAK 26(22Q13.31) WILD-TYPE
  CLUS_1                             2                              12
  CLUS_2                             1                              10
  CLUS_3                             2                               8
  CLUS_4                             2                              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK 26(22Q13.31) MUTATED        1      1      2      2      1
  DEL PEAK 26(22Q13.31) WILD-TYPE      8     11      6     10      5
D39V6, multiclass
        clus
vv       DEL PEAK 26(22Q13.31) MUTATED DEL PEAK 26(22Q13.31) WILD-TYPE
  CLUS_1                             1                               8
  CLUS_2                             1                              11
  CLUS_3                             2                               6
  CLUS_4                             2                              10
  CLUS_5                             1                               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                                 cls
clus                               0  1
  DEL PEAK 26(22Q13.31) MUTATED    3  3
  DEL PEAK 26(22Q13.31) WILD-TYPE 16 20
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(22Q13.31) MUTATED      3    3
  DEL PEAK 26(22Q13.31) WILD-TYPE   16   20
        clus
vv       DEL PEAK 26(22Q13.31) MUTATED DEL PEAK 26(22Q13.31) WILD-TYPE
  CLUS_1                             3                              16
  CLUS_2                             3                              20
[1] 2 2
[1] FALSE
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 26(22Q13.31) MUTATED        1      0      0      1      2      1
  DEL PEAK 26(22Q13.31) WILD-TYPE      3      5      6      5      6      2
                                 vv
clus                              CLUS_7 CLUS_8 CLUS_9
  DEL PEAK 26(22Q13.31) MUTATED        0      0      1
  DEL PEAK 26(22Q13.31) WILD-TYPE      5      2      2
D39V8, multiclass
        clus
vv       DEL PEAK 26(22Q13.31) MUTATED DEL PEAK 26(22Q13.31) WILD-TYPE
  CLUS_1                             1                               3
  CLUS_2                             0                               5
  CLUS_3                             0                               6
  CLUS_4                             1                               5
  CLUS_5                             2                               6
  CLUS_6                             1                               2
  CLUS_7                             0                               5
  CLUS_8                             0                               2
  CLUS_9                             1                               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(40) Variable = DEL PEAK 27(XQ28) MUTATION ANALYSIS
D40V1, binary
                             cls
clus                           0  1
  DEL PEAK 27(XQ28) MUTATED    0  3
  DEL PEAK 27(XQ28) WILD-TYPE 29 16
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 27(XQ28) MUTATED      0    3
  DEL PEAK 27(XQ28) WILD-TYPE   29   16
        clus
vv       DEL PEAK 27(XQ28) MUTATED DEL PEAK 27(XQ28) WILD-TYPE
  CLUS_1                         0                          29
  CLUS_2                         3                          16
[1] 2 2
[1] FALSE
D40V2, binary
                             cls
clus                           0  1
  DEL PEAK 27(XQ28) MUTATED    0  3
  DEL PEAK 27(XQ28) WILD-TYPE 24 21
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 27(XQ28) MUTATED      0    3
  DEL PEAK 27(XQ28) WILD-TYPE   24   21
        clus
vv       DEL PEAK 27(XQ28) MUTATED DEL PEAK 27(XQ28) WILD-TYPE
  CLUS_1                         0                          24
  CLUS_2                         3                          21
[1] 2 2
[1] FALSE
D40V3, binary
                             cls
clus                           0  1
  DEL PEAK 27(XQ28) MUTATED    0  1
  DEL PEAK 27(XQ28) WILD-TYPE 15 12
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 27(XQ28) MUTATED      0    1
  DEL PEAK 27(XQ28) WILD-TYPE   15   12
        clus
vv       DEL PEAK 27(XQ28) MUTATED DEL PEAK 27(XQ28) WILD-TYPE
  CLUS_1                         0                          15
  CLUS_2                         1                          12
[1] 2 2
[1] FALSE
                             vv
clus                          CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 27(XQ28) MUTATED        0      1      0
  DEL PEAK 27(XQ28) WILD-TYPE     13      9      5
D40V4, multiclass
[1] "Remove cluster labels:"    "DEL PEAK 27(XQ28) MUTATED"
clus
  DEL PEAK 27(XQ28) MUTATED DEL PEAK 27(XQ28) WILD-TYPE 
                          1                          27 
                 TCGA-FA-8693                  TCGA-FA-A4BB 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-FA-A4XK                  TCGA-FA-A6HN 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-FA-A6HO                  TCGA-FF-8041 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-FF-8042                  TCGA-FF-8043 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-FF-8046                  TCGA-FF-8061 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-FF-8062                  TCGA-FM-8000 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-G8-6324                  TCGA-G8-6325 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-G8-6326                  TCGA-G8-6906 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-G8-6907                  TCGA-G8-6909 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-G8-6914                  TCGA-GR-7351 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-GR-7353                  TCGA-GR-A4D4 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-GR-A4D5                  TCGA-GR-A4D6 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-GR-A4D9                  TCGA-RQ-A68N 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-RQ-A6JB 
"DEL PEAK 27(XQ28) WILD-TYPE" 
                             vv
clus                          CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK 27(XQ28) MUTATED        1      0      0      2
  DEL PEAK 27(XQ28) WILD-TYPE     13     11     10     10
D40V5, multiclass
        clus
vv       DEL PEAK 27(XQ28) MUTATED DEL PEAK 27(XQ28) WILD-TYPE
  CLUS_1                         1                          13
  CLUS_2                         0                          11
  CLUS_3                         0                          10
  CLUS_4                         2                          10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK 27(XQ28) MUTATED        0      1      1      0      1
  DEL PEAK 27(XQ28) WILD-TYPE      9     11      7     12      5
D40V6, multiclass
        clus
vv       DEL PEAK 27(XQ28) MUTATED DEL PEAK 27(XQ28) WILD-TYPE
  CLUS_1                         0                           9
  CLUS_2                         1                          11
  CLUS_3                         1                           7
  CLUS_4                         0                          12
  CLUS_5                         1                           5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                             cls
clus                           0  1
  DEL PEAK 27(XQ28) MUTATED    1  1
  DEL PEAK 27(XQ28) WILD-TYPE 18 22
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 27(XQ28) MUTATED      1    1
  DEL PEAK 27(XQ28) WILD-TYPE   18   22
        clus
vv       DEL PEAK 27(XQ28) MUTATED DEL PEAK 27(XQ28) WILD-TYPE
  CLUS_1                         1                          18
  CLUS_2                         1                          22
[1] 2 2
[1] FALSE
                             vv
clus                          CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  DEL PEAK 27(XQ28) MUTATED        0      0      0      0      2      0      0
  DEL PEAK 27(XQ28) WILD-TYPE      4      5      6      6      6      3      5
                             vv
clus                          CLUS_8 CLUS_9
  DEL PEAK 27(XQ28) MUTATED        0      0
  DEL PEAK 27(XQ28) WILD-TYPE      2      3
D40V8, multiclass
[1] "Remove cluster labels:"    "DEL PEAK 27(XQ28) MUTATED"
clus
  DEL PEAK 27(XQ28) MUTATED DEL PEAK 27(XQ28) WILD-TYPE 
                          2                          40 
                 TCGA-FA-8693                  TCGA-FA-A4BB 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-FA-A4XK                  TCGA-FA-A6HN 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-FA-A7DS                  TCGA-FA-A82F 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-FA-A86F                  TCGA-FF-8041 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-FF-8042                  TCGA-FF-8043 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-FF-8046                  TCGA-FF-8061 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-FF-8062                  TCGA-FF-A7CR 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-FF-A7CW                  TCGA-FF-A7CX 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-FM-8000                  TCGA-G8-6324 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-G8-6325                  TCGA-G8-6326 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-G8-6906                  TCGA-G8-6907 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-G8-6909                  TCGA-G8-6914 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-GR-7353                  TCGA-GR-A4D4 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-GR-A4D5                  TCGA-GR-A4D6 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-GS-A9TQ                  TCGA-GS-A9TT 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-GS-A9TU                  TCGA-GS-A9TV 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-GS-A9TW                  TCGA-GS-A9TX 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-GS-A9U3                  TCGA-GS-A9U4 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-RQ-A68N                  TCGA-RQ-A6JB 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
                 TCGA-RQ-AAAT                  TCGA-VB-A8QN 
"DEL PEAK 27(XQ28) WILD-TYPE" "DEL PEAK 27(XQ28) WILD-TYPE" 
