[1] "ofn"        "-oTLAML-TB"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LAML-TB/22541002/LAML-TB.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LAML-TB/22529563/transformed.cor.cli.txt"

nPatients in clinical file=200, in cluster file=191, common to both=191
[1]  16 191
[1] "AMP PEAK 1(1P33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 1(1P33) MUTATED AMP PEAK 1(1P33) WILD-TYPE 
                         7                        184 
  AMP PEAK 1(1P33) MUTATED AMP PEAK 1(1P33) WILD-TYPE 
                         7                        184 
[1] "AMP PEAK 2(11Q23.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 2(11Q23.3) MUTATED AMP PEAK 2(11Q23.3) WILD-TYPE 
                           17                           174 
  AMP PEAK 2(11Q23.3) MUTATED AMP PEAK 2(11Q23.3) WILD-TYPE 
                           17                           174 
[1] "AMP PEAK 3(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 3(20Q11.21) MUTATED AMP PEAK 3(20Q11.21) WILD-TYPE 
                             3                            188 
  AMP PEAK 3(20Q11.21) MUTATED AMP PEAK 3(20Q11.21) WILD-TYPE 
                             3                            188 
[1] "AMP PEAK 4(21Q22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 4(21Q22.2) MUTATED AMP PEAK 4(21Q22.2) WILD-TYPE 
                           14                           177 
  AMP PEAK 4(21Q22.2) MUTATED AMP PEAK 4(21Q22.2) WILD-TYPE 
                           14                           177 
[1] "DEL PEAK  1(3P13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(3P13) MUTATED DEL PEAK  1(3P13) WILD-TYPE 
                          8                         183 
  DEL PEAK  1(3P13) MUTATED DEL PEAK  1(3P13) WILD-TYPE 
                          8                         183 
[1] "DEL PEAK  2(5Q31.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(5Q31.2) MUTATED DEL PEAK  2(5Q31.2) WILD-TYPE 
                           18                           173 
  DEL PEAK  2(5Q31.2) MUTATED DEL PEAK  2(5Q31.2) WILD-TYPE 
                           18                           173 
[1] "DEL PEAK  3(7P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(7P12.1) MUTATED DEL PEAK  3(7P12.1) WILD-TYPE 
                           16                           175 
  DEL PEAK  3(7P12.1) MUTATED DEL PEAK  3(7P12.1) WILD-TYPE 
                           16                           175 
[1] "DEL PEAK  4(7Q32.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(7Q32.3) MUTATED DEL PEAK  4(7Q32.3) WILD-TYPE 
                           23                           168 
  DEL PEAK  4(7Q32.3) MUTATED DEL PEAK  4(7Q32.3) WILD-TYPE 
                           23                           168 
[1] "DEL PEAK  5(9Q21.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(9Q21.32) MUTATED DEL PEAK  5(9Q21.32) WILD-TYPE 
                             5                            186 
  DEL PEAK  5(9Q21.32) MUTATED DEL PEAK  5(9Q21.32) WILD-TYPE 
                             5                            186 
[1] "DEL PEAK  6(12P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(12P13.2) MUTATED DEL PEAK  6(12P13.2) WILD-TYPE 
                            10                            181 
  DEL PEAK  6(12P13.2) MUTATED DEL PEAK  6(12P13.2) WILD-TYPE 
                            10                            181 
[1] "DEL PEAK  7(12Q21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(12Q21.33) MUTATED DEL PEAK  7(12Q21.33) WILD-TYPE 
                              3                             188 
  DEL PEAK  7(12Q21.33) MUTATED DEL PEAK  7(12Q21.33) WILD-TYPE 
                              3                             188 
[1] "DEL PEAK  8(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(16Q23.1) MUTATED DEL PEAK  8(16Q23.1) WILD-TYPE 
                             9                            182 
  DEL PEAK  8(16Q23.1) MUTATED DEL PEAK  8(16Q23.1) WILD-TYPE 
                             9                            182 
[1] "DEL PEAK  9(17P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(17P13.2) MUTATED DEL PEAK  9(17P13.2) WILD-TYPE 
                            15                            176 
  DEL PEAK  9(17P13.2) MUTATED DEL PEAK  9(17P13.2) WILD-TYPE 
                            15                            176 
[1] "DEL PEAK 10(17Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(17Q11.2) MUTATED DEL PEAK 10(17Q11.2) WILD-TYPE 
                            13                            178 
  DEL PEAK 10(17Q11.2) MUTATED DEL PEAK 10(17Q11.2) WILD-TYPE 
                            13                            178 
[1] "DEL PEAK 11(18P11.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(18P11.21) MUTATED DEL PEAK 11(18P11.21) WILD-TYPE 
                              9                             182 
  DEL PEAK 11(18P11.21) MUTATED DEL PEAK 11(18P11.21) WILD-TYPE 
                              9                             182 
[1] "DEL PEAK 12(20Q13.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(20Q13.13) MUTATED DEL PEAK 12(20Q13.13) WILD-TYPE 
                              4                             187 
  DEL PEAK 12(20Q13.13) MUTATED DEL PEAK 12(20Q13.13) WILD-TYPE 
                              4                             187 
[1] "data2feature, selection=ALL"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "MRNASEQ_CNMF"         
[4] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 

Input Data has 6 rows and 191 columns.

Variable 1:'CN_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MIRSEQ_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
NULL
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 191 columns, 0 survival variables, and 6 non-survival variables.
[1] "* survival variables: "
NULL
[1] "* non-survival variables: "
[1] "CN_CNMF"               "METHLYATION_CNMF"      "MRNASEQ_CNMF"         
[4] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 
CN_CNMF, nv=4, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=5, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=6, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK 1(1P33) MUTATION ANALYSIS
                            vv
clus                         CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AMP PEAK 1(1P33) MUTATED        1      2      3      1
  AMP PEAK 1(1P33) WILD-TYPE     48     42     52     42
D1V1, multiclass
        clus
vv       AMP PEAK 1(1P33) MUTATED AMP PEAK 1(1P33) WILD-TYPE
  CLUS_1                        1                         48
  CLUS_2                        2                         42
  CLUS_3                        3                         52
  CLUS_4                        1                         42
[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(1P33) MUTATED        0      1      6      0      0
  AMP PEAK 1(1P33) WILD-TYPE     23     24     54     35     42
D1V2, multiclass
        clus
vv       AMP PEAK 1(1P33) MUTATED AMP PEAK 1(1P33) WILD-TYPE
  CLUS_1                        0                         23
  CLUS_2                        1                         24
  CLUS_3                        6                         54
  CLUS_4                        0                         35
  CLUS_5                        0                         42
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                            vv
clus                         CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 1(1P33) MUTATED        5      1      0
  AMP PEAK 1(1P33) WILD-TYPE     66     49     45
D1V3, multiclass
        clus
vv       AMP PEAK 1(1P33) MUTATED AMP PEAK 1(1P33) WILD-TYPE
  CLUS_1                        5                         66
  CLUS_2                        1                         49
  CLUS_3                        0                         45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                            vv
clus                         CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  AMP PEAK 1(1P33) MUTATED        0      1      0      5      0      0
  AMP PEAK 1(1P33) WILD-TYPE     16     12     14     50     26     42
D1V4, multiclass
        clus
vv       AMP PEAK 1(1P33) MUTATED AMP PEAK 1(1P33) WILD-TYPE
  CLUS_1                        0                         16
  CLUS_2                        1                         12
  CLUS_3                        0                         14
  CLUS_4                        5                         50
  CLUS_5                        0                         26
  CLUS_6                        0                         42
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                            vv
clus                         CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AMP PEAK 1(1P33) MUTATED        1      1      1      0      4
  AMP PEAK 1(1P33) WILD-TYPE     56     30     38     33     15
D1V5, multiclass
        clus
vv       AMP PEAK 1(1P33) MUTATED AMP PEAK 1(1P33) WILD-TYPE
  CLUS_1                        1                         56
  CLUS_2                        1                         30
  CLUS_3                        1                         38
  CLUS_4                        0                         33
  CLUS_5                        4                         15
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                            vv
clus                         CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 1(1P33) MUTATED        0      3      4
  AMP PEAK 1(1P33) WILD-TYPE     67     31     74
D1V6, multiclass
        clus
vv       AMP PEAK 1(1P33) MUTATED AMP PEAK 1(1P33) WILD-TYPE
  CLUS_1                        0                         67
  CLUS_2                        3                         31
  CLUS_3                        4                         74
[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"

Clustering(2) Variable = AMP PEAK 2(11Q23.3) MUTATION ANALYSIS
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AMP PEAK 2(11Q23.3) MUTATED        1      7      6      3
  AMP PEAK 2(11Q23.3) WILD-TYPE     48     37     49     40
D2V1, multiclass
        clus
vv       AMP PEAK 2(11Q23.3) MUTATED AMP PEAK 2(11Q23.3) WILD-TYPE
  CLUS_1                           1                            48
  CLUS_2                           7                            37
  CLUS_3                           6                            49
  CLUS_4                           3                            40
[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(11Q23.3) MUTATED        0      0     13      1      3
  AMP PEAK 2(11Q23.3) WILD-TYPE     23     25     47     34     39
D2V2, multiclass
        clus
vv       AMP PEAK 2(11Q23.3) MUTATED AMP PEAK 2(11Q23.3) WILD-TYPE
  CLUS_1                           0                            23
  CLUS_2                           0                            25
  CLUS_3                          13                            47
  CLUS_4                           1                            34
  CLUS_5                           3                            39
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 2(11Q23.3) MUTATED        9      5      2
  AMP PEAK 2(11Q23.3) WILD-TYPE     62     45     43
D2V3, multiclass
        clus
vv       AMP PEAK 2(11Q23.3) MUTATED AMP PEAK 2(11Q23.3) WILD-TYPE
  CLUS_1                           9                            62
  CLUS_2                           5                            45
  CLUS_3                           2                            43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  AMP PEAK 2(11Q23.3) MUTATED        0      3      0      8      2      3
  AMP PEAK 2(11Q23.3) WILD-TYPE     16     10     14     47     24     39
D2V4, multiclass
        clus
vv       AMP PEAK 2(11Q23.3) MUTATED AMP PEAK 2(11Q23.3) WILD-TYPE
  CLUS_1                           0                            16
  CLUS_2                           3                            10
  CLUS_3                           0                            14
  CLUS_4                           8                            47
  CLUS_5                           2                            24
  CLUS_6                           3                            39
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AMP PEAK 2(11Q23.3) MUTATED        4      2      4      3      4
  AMP PEAK 2(11Q23.3) WILD-TYPE     53     29     35     30     15
D2V5, multiclass
        clus
vv       AMP PEAK 2(11Q23.3) MUTATED AMP PEAK 2(11Q23.3) WILD-TYPE
  CLUS_1                           4                            53
  CLUS_2                           2                            29
  CLUS_3                           4                            35
  CLUS_4                           3                            30
  CLUS_5                           4                            15
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 2(11Q23.3) MUTATED        3      4     10
  AMP PEAK 2(11Q23.3) WILD-TYPE     64     30     68
D2V6, multiclass
        clus
vv       AMP PEAK 2(11Q23.3) MUTATED AMP PEAK 2(11Q23.3) WILD-TYPE
  CLUS_1                           3                            64
  CLUS_2                           4                            30
  CLUS_3                          10                            68
[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"

Clustering(3) Variable = AMP PEAK 3(20Q11.21) MUTATION ANALYSIS
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AMP PEAK 3(20Q11.21) MUTATED        0      2      1      0
  AMP PEAK 3(20Q11.21) WILD-TYPE     49     42     54     43
D3V1, multiclass
        clus
vv       AMP PEAK 3(20Q11.21) MUTATED AMP PEAK 3(20Q11.21) WILD-TYPE
  CLUS_1                            0                             49
  CLUS_2                            2                             42
  CLUS_3                            1                             54
  CLUS_4                            0                             43
[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(20Q11.21) MUTATED        0      0      3      0      0
  AMP PEAK 3(20Q11.21) WILD-TYPE     23     25     57     35     42
D3V2, multiclass
        clus
vv       AMP PEAK 3(20Q11.21) MUTATED AMP PEAK 3(20Q11.21) WILD-TYPE
  CLUS_1                            0                             23
  CLUS_2                            0                             25
  CLUS_3                            3                             57
  CLUS_4                            0                             35
  CLUS_5                            0                             42
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 3(20Q11.21) MUTATED        2      0      0
  AMP PEAK 3(20Q11.21) WILD-TYPE     69     50     45
D3V3, multiclass
[1] "Remove cluster labels:"       "AMP PEAK 3(20Q11.21) MUTATED"
clus
  AMP PEAK 3(20Q11.21) MUTATED AMP PEAK 3(20Q11.21) WILD-TYPE 
                             2                            164 
                    TCGA-AB-2803                     TCGA-AB-2805 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2806                     TCGA-AB-2807 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2808                     TCGA-AB-2810 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2811                     TCGA-AB-2812 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2813                     TCGA-AB-2814 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2815                     TCGA-AB-2816 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2817                     TCGA-AB-2818 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2819                     TCGA-AB-2820 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2821                     TCGA-AB-2822 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2823                     TCGA-AB-2824 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2825                     TCGA-AB-2826 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2828                     TCGA-AB-2830 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2832                     TCGA-AB-2834 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2835                     TCGA-AB-2836 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2837                     TCGA-AB-2838 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2839                     TCGA-AB-2840 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2841                     TCGA-AB-2842 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2844                     TCGA-AB-2845 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2846                     TCGA-AB-2848 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2849                     TCGA-AB-2851 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2853                     TCGA-AB-2854 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2855                     TCGA-AB-2856 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2857                     TCGA-AB-2858 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2859                     TCGA-AB-2860 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2861                     TCGA-AB-2862 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2863                     TCGA-AB-2865 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2866                     TCGA-AB-2867 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2869                     TCGA-AB-2870 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2871                     TCGA-AB-2872 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2873                     TCGA-AB-2874 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2875                     TCGA-AB-2877 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2879                     TCGA-AB-2880 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2881                     TCGA-AB-2882 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2884                     TCGA-AB-2885 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2886                     TCGA-AB-2887 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2888                     TCGA-AB-2889 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2890                     TCGA-AB-2895 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2896                     TCGA-AB-2897 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2898                     TCGA-AB-2899 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2900                     TCGA-AB-2901 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2903                     TCGA-AB-2908 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2909                     TCGA-AB-2910 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2911                     TCGA-AB-2912 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2913                     TCGA-AB-2914 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2915                     TCGA-AB-2916 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2917                     TCGA-AB-2919 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2920                     TCGA-AB-2921 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2924                     TCGA-AB-2925 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2927                     TCGA-AB-2928 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2929                     TCGA-AB-2930 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2931                     TCGA-AB-2932 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2933                     TCGA-AB-2934 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2935                     TCGA-AB-2936 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2937                     TCGA-AB-2938 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2939                     TCGA-AB-2940 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2941                     TCGA-AB-2942 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2943                     TCGA-AB-2944 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2946                     TCGA-AB-2948 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2949                     TCGA-AB-2950 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2952                     TCGA-AB-2954 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2955                     TCGA-AB-2956 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2959                     TCGA-AB-2963 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2964                     TCGA-AB-2965 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2966                     TCGA-AB-2967 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2969                     TCGA-AB-2970 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2971                     TCGA-AB-2972 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2973                     TCGA-AB-2975 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2976                     TCGA-AB-2977 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2978                     TCGA-AB-2980 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2982                     TCGA-AB-2983 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2984                     TCGA-AB-2985 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2986                     TCGA-AB-2987 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2988                     TCGA-AB-2990 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2991                     TCGA-AB-2992 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2993                     TCGA-AB-2994 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2995                     TCGA-AB-2996 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2998                     TCGA-AB-2999 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3000                     TCGA-AB-3001 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3002                     TCGA-AB-3005 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3006                     TCGA-AB-3007 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3008                     TCGA-AB-3009 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3011                     TCGA-AB-3012 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  AMP PEAK 3(20Q11.21) MUTATED        0      0      0      2      0      0
  AMP PEAK 3(20Q11.21) WILD-TYPE     16     13     14     53     26     42
D3V4, multiclass
[1] "Remove cluster labels:"       "AMP PEAK 3(20Q11.21) MUTATED"
clus
  AMP PEAK 3(20Q11.21) MUTATED AMP PEAK 3(20Q11.21) WILD-TYPE 
                             2                            164 
                    TCGA-AB-2803                     TCGA-AB-2805 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2806                     TCGA-AB-2807 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2808                     TCGA-AB-2810 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2811                     TCGA-AB-2812 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2813                     TCGA-AB-2814 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2815                     TCGA-AB-2816 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2817                     TCGA-AB-2818 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2819                     TCGA-AB-2820 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2821                     TCGA-AB-2822 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2823                     TCGA-AB-2824 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2825                     TCGA-AB-2826 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2828                     TCGA-AB-2830 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2832                     TCGA-AB-2834 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2835                     TCGA-AB-2836 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2837                     TCGA-AB-2838 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2839                     TCGA-AB-2840 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2841                     TCGA-AB-2842 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2844                     TCGA-AB-2845 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2846                     TCGA-AB-2848 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2849                     TCGA-AB-2851 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2853                     TCGA-AB-2854 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2855                     TCGA-AB-2856 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2857                     TCGA-AB-2858 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2859                     TCGA-AB-2860 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2861                     TCGA-AB-2862 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2863                     TCGA-AB-2865 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2866                     TCGA-AB-2867 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2869                     TCGA-AB-2870 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2871                     TCGA-AB-2872 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2873                     TCGA-AB-2874 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2875                     TCGA-AB-2877 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2879                     TCGA-AB-2880 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2881                     TCGA-AB-2882 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2884                     TCGA-AB-2885 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2886                     TCGA-AB-2887 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2888                     TCGA-AB-2889 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2890                     TCGA-AB-2895 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2896                     TCGA-AB-2897 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2898                     TCGA-AB-2899 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2900                     TCGA-AB-2901 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2903                     TCGA-AB-2908 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2909                     TCGA-AB-2910 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2911                     TCGA-AB-2912 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2913                     TCGA-AB-2914 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2915                     TCGA-AB-2916 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2917                     TCGA-AB-2919 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2920                     TCGA-AB-2921 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2924                     TCGA-AB-2925 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2927                     TCGA-AB-2928 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2929                     TCGA-AB-2930 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2931                     TCGA-AB-2932 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2933                     TCGA-AB-2934 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2935                     TCGA-AB-2936 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2937                     TCGA-AB-2938 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2939                     TCGA-AB-2940 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2941                     TCGA-AB-2942 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2943                     TCGA-AB-2944 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2946                     TCGA-AB-2948 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2949                     TCGA-AB-2950 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2952                     TCGA-AB-2954 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2955                     TCGA-AB-2956 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2959                     TCGA-AB-2963 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2964                     TCGA-AB-2965 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2966                     TCGA-AB-2967 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2969                     TCGA-AB-2970 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2971                     TCGA-AB-2972 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2973                     TCGA-AB-2975 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2976                     TCGA-AB-2977 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2978                     TCGA-AB-2980 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2982                     TCGA-AB-2983 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2984                     TCGA-AB-2985 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2986                     TCGA-AB-2987 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2988                     TCGA-AB-2990 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2991                     TCGA-AB-2992 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2993                     TCGA-AB-2994 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2995                     TCGA-AB-2996 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2998                     TCGA-AB-2999 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3000                     TCGA-AB-3001 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3002                     TCGA-AB-3005 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3006                     TCGA-AB-3007 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3008                     TCGA-AB-3009 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3011                     TCGA-AB-3012 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AMP PEAK 3(20Q11.21) MUTATED        0      1      0      0      1
  AMP PEAK 3(20Q11.21) WILD-TYPE     57     30     39     33     18
D3V5, multiclass
[1] "Remove cluster labels:"       "AMP PEAK 3(20Q11.21) MUTATED"
clus
  AMP PEAK 3(20Q11.21) MUTATED AMP PEAK 3(20Q11.21) WILD-TYPE 
                             2                            177 
                    TCGA-AB-2803                     TCGA-AB-2805 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2806                     TCGA-AB-2807 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2808                     TCGA-AB-2810 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2811                     TCGA-AB-2812 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2813                     TCGA-AB-2814 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2815                     TCGA-AB-2816 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2817                     TCGA-AB-2818 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2819                     TCGA-AB-2820 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2821                     TCGA-AB-2822 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2823                     TCGA-AB-2824 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2825                     TCGA-AB-2826 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2828                     TCGA-AB-2830 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2832                     TCGA-AB-2834 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2835                     TCGA-AB-2836 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2837                     TCGA-AB-2838 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2839                     TCGA-AB-2840 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2841                     TCGA-AB-2842 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2844                     TCGA-AB-2845 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2846                     TCGA-AB-2848 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2849                     TCGA-AB-2851 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2853                     TCGA-AB-2854 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2855                     TCGA-AB-2856 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2857                     TCGA-AB-2858 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2859                     TCGA-AB-2860 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2861                     TCGA-AB-2862 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2863                     TCGA-AB-2865 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2866                     TCGA-AB-2867 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2869                     TCGA-AB-2870 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2871                     TCGA-AB-2872 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2873                     TCGA-AB-2874 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2875                     TCGA-AB-2877 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2878                     TCGA-AB-2879 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2880                     TCGA-AB-2881 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2882                     TCGA-AB-2883 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2884                     TCGA-AB-2885 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2886                     TCGA-AB-2887 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2888                     TCGA-AB-2889 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2890                     TCGA-AB-2892 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2893                     TCGA-AB-2894 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2895                     TCGA-AB-2896 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2897                     TCGA-AB-2898 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2899                     TCGA-AB-2900 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2901                     TCGA-AB-2903 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2908                     TCGA-AB-2909 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2910                     TCGA-AB-2911 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2912                     TCGA-AB-2913 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2914                     TCGA-AB-2915 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2916                     TCGA-AB-2917 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2919                     TCGA-AB-2920 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2921                     TCGA-AB-2922 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2923                     TCGA-AB-2924 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2925                     TCGA-AB-2926 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2927                     TCGA-AB-2928 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2929                     TCGA-AB-2930 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2931                     TCGA-AB-2932 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2933                     TCGA-AB-2934 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2935                     TCGA-AB-2936 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2937                     TCGA-AB-2938 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2939                     TCGA-AB-2940 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2941                     TCGA-AB-2942 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2943                     TCGA-AB-2944 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2945                     TCGA-AB-2946 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2947                     TCGA-AB-2948 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2949                     TCGA-AB-2950 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2952                     TCGA-AB-2954 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2955                     TCGA-AB-2956 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2957                     TCGA-AB-2959 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2963                     TCGA-AB-2964 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2965                     TCGA-AB-2966 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2967                     TCGA-AB-2969 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2970                     TCGA-AB-2971 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2972                     TCGA-AB-2973 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2975                     TCGA-AB-2976 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2977                     TCGA-AB-2978 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2980                     TCGA-AB-2982 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2983                     TCGA-AB-2984 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2985                     TCGA-AB-2986 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2987                     TCGA-AB-2988 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2989                     TCGA-AB-2990 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2991                     TCGA-AB-2992 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2993                     TCGA-AB-2994 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2995                     TCGA-AB-2996 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2997                     TCGA-AB-2998 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2999                     TCGA-AB-3000 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3001                     TCGA-AB-3002 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3005                     TCGA-AB-3006 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3007                     TCGA-AB-3008 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3009                     TCGA-AB-3011 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3012 
"AMP PEAK 3(20Q11.21) WILD-TYPE" 
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 3(20Q11.21) MUTATED        0      1      1
  AMP PEAK 3(20Q11.21) WILD-TYPE     67     33     77
D3V6, multiclass
[1] "Remove cluster labels:"       "AMP PEAK 3(20Q11.21) MUTATED"
clus
  AMP PEAK 3(20Q11.21) MUTATED AMP PEAK 3(20Q11.21) WILD-TYPE 
                             2                            177 
                    TCGA-AB-2803                     TCGA-AB-2805 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2806                     TCGA-AB-2807 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2808                     TCGA-AB-2810 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2811                     TCGA-AB-2812 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2813                     TCGA-AB-2814 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2815                     TCGA-AB-2816 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2817                     TCGA-AB-2818 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2819                     TCGA-AB-2820 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2821                     TCGA-AB-2822 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2823                     TCGA-AB-2824 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2825                     TCGA-AB-2826 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2828                     TCGA-AB-2830 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2832                     TCGA-AB-2834 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2835                     TCGA-AB-2836 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2837                     TCGA-AB-2838 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2839                     TCGA-AB-2840 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2841                     TCGA-AB-2842 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2844                     TCGA-AB-2845 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2846                     TCGA-AB-2848 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2849                     TCGA-AB-2851 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2853                     TCGA-AB-2854 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2855                     TCGA-AB-2856 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2857                     TCGA-AB-2858 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2859                     TCGA-AB-2860 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2861                     TCGA-AB-2862 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2863                     TCGA-AB-2865 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2866                     TCGA-AB-2867 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2869                     TCGA-AB-2870 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2871                     TCGA-AB-2872 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2873                     TCGA-AB-2874 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2875                     TCGA-AB-2877 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2878                     TCGA-AB-2879 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2880                     TCGA-AB-2881 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2882                     TCGA-AB-2883 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2884                     TCGA-AB-2885 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2886                     TCGA-AB-2887 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2888                     TCGA-AB-2889 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2890                     TCGA-AB-2892 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2893                     TCGA-AB-2894 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2895                     TCGA-AB-2896 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2897                     TCGA-AB-2898 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2899                     TCGA-AB-2900 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2901                     TCGA-AB-2903 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2908                     TCGA-AB-2909 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2910                     TCGA-AB-2911 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2912                     TCGA-AB-2913 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2914                     TCGA-AB-2915 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2916                     TCGA-AB-2917 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2919                     TCGA-AB-2920 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2921                     TCGA-AB-2922 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2923                     TCGA-AB-2924 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2925                     TCGA-AB-2926 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2927                     TCGA-AB-2928 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2929                     TCGA-AB-2930 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2931                     TCGA-AB-2932 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2933                     TCGA-AB-2934 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2935                     TCGA-AB-2936 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2937                     TCGA-AB-2938 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2939                     TCGA-AB-2940 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2941                     TCGA-AB-2942 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2943                     TCGA-AB-2944 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2945                     TCGA-AB-2946 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2947                     TCGA-AB-2948 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2949                     TCGA-AB-2950 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2952                     TCGA-AB-2954 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2955                     TCGA-AB-2956 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2957                     TCGA-AB-2959 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2963                     TCGA-AB-2964 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2965                     TCGA-AB-2966 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2967                     TCGA-AB-2969 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2970                     TCGA-AB-2971 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2972                     TCGA-AB-2973 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2975                     TCGA-AB-2976 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2977                     TCGA-AB-2978 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2980                     TCGA-AB-2982 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2983                     TCGA-AB-2984 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2985                     TCGA-AB-2986 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2987                     TCGA-AB-2988 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2989                     TCGA-AB-2990 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2991                     TCGA-AB-2992 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2993                     TCGA-AB-2994 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2995                     TCGA-AB-2996 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2997                     TCGA-AB-2998 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2999                     TCGA-AB-3000 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3001                     TCGA-AB-3002 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3005                     TCGA-AB-3006 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3007                     TCGA-AB-3008 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3009                     TCGA-AB-3011 
"AMP PEAK 3(20Q11.21) WILD-TYPE" "AMP PEAK 3(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3012 
"AMP PEAK 3(20Q11.21) WILD-TYPE" 

Clustering(4) Variable = AMP PEAK 4(21Q22.2) MUTATION ANALYSIS
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  AMP PEAK 4(21Q22.2) MUTATED        0      5      5      4
  AMP PEAK 4(21Q22.2) WILD-TYPE     49     39     50     39
D4V1, multiclass
        clus
vv       AMP PEAK 4(21Q22.2) MUTATED AMP PEAK 4(21Q22.2) WILD-TYPE
  CLUS_1                           0                            49
  CLUS_2                           5                            39
  CLUS_3                           5                            50
  CLUS_4                           4                            39
[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(21Q22.2) MUTATED        1      0     11      1      0
  AMP PEAK 4(21Q22.2) WILD-TYPE     22     25     49     34     42
D4V2, multiclass
        clus
vv       AMP PEAK 4(21Q22.2) MUTATED AMP PEAK 4(21Q22.2) WILD-TYPE
  CLUS_1                           1                            22
  CLUS_2                           0                            25
  CLUS_3                          11                            49
  CLUS_4                           1                            34
  CLUS_5                           0                            42
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 4(21Q22.2) MUTATED       10      1      0
  AMP PEAK 4(21Q22.2) WILD-TYPE     61     49     45
D4V3, multiclass
        clus
vv       AMP PEAK 4(21Q22.2) MUTATED AMP PEAK 4(21Q22.2) WILD-TYPE
  CLUS_1                          10                            61
  CLUS_2                           1                            49
  CLUS_3                           0                            45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  AMP PEAK 4(21Q22.2) MUTATED        0      0      1      9      0      1
  AMP PEAK 4(21Q22.2) WILD-TYPE     16     13     13     46     26     41
D4V4, multiclass
        clus
vv       AMP PEAK 4(21Q22.2) MUTATED AMP PEAK 4(21Q22.2) WILD-TYPE
  CLUS_1                           0                            16
  CLUS_2                           0                            13
  CLUS_3                           1                            13
  CLUS_4                           9                            46
  CLUS_5                           0                            26
  CLUS_6                           1                            41
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  AMP PEAK 4(21Q22.2) MUTATED        1      3      0      5      3
  AMP PEAK 4(21Q22.2) WILD-TYPE     56     28     39     28     16
D4V5, multiclass
        clus
vv       AMP PEAK 4(21Q22.2) MUTATED AMP PEAK 4(21Q22.2) WILD-TYPE
  CLUS_1                           1                            56
  CLUS_2                           3                            28
  CLUS_3                           0                            39
  CLUS_4                           5                            28
  CLUS_5                           3                            16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  AMP PEAK 4(21Q22.2) MUTATED        1      3      8
  AMP PEAK 4(21Q22.2) WILD-TYPE     66     31     70
D4V6, multiclass
        clus
vv       AMP PEAK 4(21Q22.2) MUTATED AMP PEAK 4(21Q22.2) WILD-TYPE
  CLUS_1                           1                            66
  CLUS_2                           3                            31
  CLUS_3                           8                            70
[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"

Clustering(5) Variable = DEL PEAK  1(3P13) MUTATION ANALYSIS
                             vv
clus                          CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK  1(3P13) MUTATED        1      5      2      0
  DEL PEAK  1(3P13) WILD-TYPE     48     39     53     43
D5V1, multiclass
        clus
vv       DEL PEAK  1(3P13) MUTATED DEL PEAK  1(3P13) WILD-TYPE
  CLUS_1                         1                          48
  CLUS_2                         5                          39
  CLUS_3                         2                          53
  CLUS_4                         0                          43
[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(3P13) MUTATED        1      0      6      1      0
  DEL PEAK  1(3P13) WILD-TYPE     22     25     54     34     42
D5V2, multiclass
        clus
vv       DEL PEAK  1(3P13) MUTATED DEL PEAK  1(3P13) WILD-TYPE
  CLUS_1                         1                          22
  CLUS_2                         0                          25
  CLUS_3                         6                          54
  CLUS_4                         1                          34
  CLUS_5                         0                          42
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  1(3P13) MUTATED        6      1      0
  DEL PEAK  1(3P13) WILD-TYPE     65     49     45
D5V3, multiclass
        clus
vv       DEL PEAK  1(3P13) MUTATED DEL PEAK  1(3P13) WILD-TYPE
  CLUS_1                         6                          65
  CLUS_2                         1                          49
  CLUS_3                         0                          45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  1(3P13) MUTATED        0      0      0      6      0      1
  DEL PEAK  1(3P13) WILD-TYPE     16     13     14     49     26     41
D5V4, multiclass
        clus
vv       DEL PEAK  1(3P13) MUTATED DEL PEAK  1(3P13) WILD-TYPE
  CLUS_1                         0                          16
  CLUS_2                         0                          13
  CLUS_3                         0                          14
  CLUS_4                         6                          49
  CLUS_5                         0                          26
  CLUS_6                         1                          41
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK  1(3P13) MUTATED        0      3      1      1      2
  DEL PEAK  1(3P13) WILD-TYPE     57     28     38     32     17
D5V5, multiclass
        clus
vv       DEL PEAK  1(3P13) MUTATED DEL PEAK  1(3P13) WILD-TYPE
  CLUS_1                         0                          57
  CLUS_2                         3                          28
  CLUS_3                         1                          38
  CLUS_4                         1                          32
  CLUS_5                         2                          17
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  1(3P13) MUTATED        0      3      4
  DEL PEAK  1(3P13) WILD-TYPE     67     31     74
D5V6, multiclass
        clus
vv       DEL PEAK  1(3P13) MUTATED DEL PEAK  1(3P13) WILD-TYPE
  CLUS_1                         0                          67
  CLUS_2                         3                          31
  CLUS_3                         4                          74
[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"

Clustering(6) Variable = DEL PEAK  2(5Q31.2) MUTATION ANALYSIS
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK  2(5Q31.2) MUTATED        0     10      4      4
  DEL PEAK  2(5Q31.2) WILD-TYPE     49     34     51     39
D6V1, multiclass
        clus
vv       DEL PEAK  2(5Q31.2) MUTATED DEL PEAK  2(5Q31.2) WILD-TYPE
  CLUS_1                           0                            49
  CLUS_2                          10                            34
  CLUS_3                           4                            51
  CLUS_4                           4                            39
[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(5Q31.2) MUTATED        1      0     15      2      0
  DEL PEAK  2(5Q31.2) WILD-TYPE     22     25     45     33     42
D6V2, multiclass
        clus
vv       DEL PEAK  2(5Q31.2) MUTATED DEL PEAK  2(5Q31.2) WILD-TYPE
  CLUS_1                           1                            22
  CLUS_2                           0                            25
  CLUS_3                          15                            45
  CLUS_4                           2                            33
  CLUS_5                           0                            42
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  2(5Q31.2) MUTATED       13      1      2
  DEL PEAK  2(5Q31.2) WILD-TYPE     58     49     43
D6V3, multiclass
        clus
vv       DEL PEAK  2(5Q31.2) MUTATED DEL PEAK  2(5Q31.2) WILD-TYPE
  CLUS_1                          13                            58
  CLUS_2                           1                            49
  CLUS_3                           2                            43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  2(5Q31.2) MUTATED        0      0      0     14      0      2
  DEL PEAK  2(5Q31.2) WILD-TYPE     16     13     14     41     26     40
D6V4, multiclass
        clus
vv       DEL PEAK  2(5Q31.2) MUTATED DEL PEAK  2(5Q31.2) WILD-TYPE
  CLUS_1                           0                            16
  CLUS_2                           0                            13
  CLUS_3                           0                            14
  CLUS_4                          14                            41
  CLUS_5                           0                            26
  CLUS_6                           2                            40
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK  2(5Q31.2) MUTATED        1      7      2      2      5
  DEL PEAK  2(5Q31.2) WILD-TYPE     56     24     37     31     14
D6V5, multiclass
        clus
vv       DEL PEAK  2(5Q31.2) MUTATED DEL PEAK  2(5Q31.2) WILD-TYPE
  CLUS_1                           1                            56
  CLUS_2                           7                            24
  CLUS_3                           2                            37
  CLUS_4                           2                            31
  CLUS_5                           5                            14
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  2(5Q31.2) MUTATED        1      8      8
  DEL PEAK  2(5Q31.2) WILD-TYPE     66     26     70
D6V6, multiclass
        clus
vv       DEL PEAK  2(5Q31.2) MUTATED DEL PEAK  2(5Q31.2) WILD-TYPE
  CLUS_1                           1                            66
  CLUS_2                           8                            26
  CLUS_3                           8                            70
[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"

Clustering(7) Variable = DEL PEAK  3(7P12.1) MUTATION ANALYSIS
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK  3(7P12.1) MUTATED        0      6      0     10
  DEL PEAK  3(7P12.1) WILD-TYPE     49     38     55     33
D7V1, multiclass
        clus
vv       DEL PEAK  3(7P12.1) MUTATED DEL PEAK  3(7P12.1) WILD-TYPE
  CLUS_1                           0                            49
  CLUS_2                           6                            38
  CLUS_3                           0                            55
  CLUS_4                          10                            33
[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(7P12.1) MUTATED        1      1     13      0      1
  DEL PEAK  3(7P12.1) WILD-TYPE     22     24     47     35     41
D7V2, multiclass
        clus
vv       DEL PEAK  3(7P12.1) MUTATED DEL PEAK  3(7P12.1) WILD-TYPE
  CLUS_1                           1                            22
  CLUS_2                           1                            24
  CLUS_3                          13                            47
  CLUS_4                           0                            35
  CLUS_5                           1                            41
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  3(7P12.1) MUTATED       12      0      3
  DEL PEAK  3(7P12.1) WILD-TYPE     59     50     42
D7V3, multiclass
        clus
vv       DEL PEAK  3(7P12.1) MUTATED DEL PEAK  3(7P12.1) WILD-TYPE
  CLUS_1                          12                            59
  CLUS_2                           0                            50
  CLUS_3                           3                            42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  3(7P12.1) MUTATED        0      0      0     15      0      0
  DEL PEAK  3(7P12.1) WILD-TYPE     16     13     14     40     26     42
D7V4, multiclass
        clus
vv       DEL PEAK  3(7P12.1) MUTATED DEL PEAK  3(7P12.1) WILD-TYPE
  CLUS_1                           0                            16
  CLUS_2                           0                            13
  CLUS_3                           0                            14
  CLUS_4                          15                            40
  CLUS_5                           0                            26
  CLUS_6                           0                            42
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK  3(7P12.1) MUTATED        1      7      4      2      2
  DEL PEAK  3(7P12.1) WILD-TYPE     56     24     35     31     17
D7V5, multiclass
        clus
vv       DEL PEAK  3(7P12.1) MUTATED DEL PEAK  3(7P12.1) WILD-TYPE
  CLUS_1                           1                            56
  CLUS_2                           7                            24
  CLUS_3                           4                            35
  CLUS_4                           2                            31
  CLUS_5                           2                            17
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  3(7P12.1) MUTATED        1      6      9
  DEL PEAK  3(7P12.1) WILD-TYPE     66     28     69
D7V6, multiclass
        clus
vv       DEL PEAK  3(7P12.1) MUTATED DEL PEAK  3(7P12.1) WILD-TYPE
  CLUS_1                           1                            66
  CLUS_2                           6                            28
  CLUS_3                           9                            69
[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"

Clustering(8) Variable = DEL PEAK  4(7Q32.3) MUTATION ANALYSIS
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK  4(7Q32.3) MUTATED        2      7      0     14
  DEL PEAK  4(7Q32.3) WILD-TYPE     47     37     55     29
D8V1, multiclass
        clus
vv       DEL PEAK  4(7Q32.3) MUTATED DEL PEAK  4(7Q32.3) WILD-TYPE
  CLUS_1                           2                            47
  CLUS_2                           7                            37
  CLUS_3                           0                            55
  CLUS_4                          14                            29
[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(7Q32.3) MUTATED        1      2     17      1      2
  DEL PEAK  4(7Q32.3) WILD-TYPE     22     23     43     34     40
D8V2, multiclass
        clus
vv       DEL PEAK  4(7Q32.3) MUTATED DEL PEAK  4(7Q32.3) WILD-TYPE
  CLUS_1                           1                            22
  CLUS_2                           2                            23
  CLUS_3                          17                            43
  CLUS_4                           1                            34
  CLUS_5                           2                            40
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  4(7Q32.3) MUTATED       13      2      4
  DEL PEAK  4(7Q32.3) WILD-TYPE     58     48     41
D8V3, multiclass
        clus
vv       DEL PEAK  4(7Q32.3) MUTATED DEL PEAK  4(7Q32.3) WILD-TYPE
  CLUS_1                          13                            58
  CLUS_2                           2                            48
  CLUS_3                           4                            41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  4(7Q32.3) MUTATED        1      1      0     17      0      0
  DEL PEAK  4(7Q32.3) WILD-TYPE     15     12     14     38     26     42
D8V4, multiclass
        clus
vv       DEL PEAK  4(7Q32.3) MUTATED DEL PEAK  4(7Q32.3) WILD-TYPE
  CLUS_1                           1                            15
  CLUS_2                           1                            12
  CLUS_3                           0                            14
  CLUS_4                          17                            38
  CLUS_5                           0                            26
  CLUS_6                           0                            42
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK  4(7Q32.3) MUTATED        2     10      5      3      2
  DEL PEAK  4(7Q32.3) WILD-TYPE     55     21     34     30     17
D8V5, multiclass
        clus
vv       DEL PEAK  4(7Q32.3) MUTATED DEL PEAK  4(7Q32.3) WILD-TYPE
  CLUS_1                           2                            55
  CLUS_2                          10                            21
  CLUS_3                           5                            34
  CLUS_4                           3                            30
  CLUS_5                           2                            17
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  4(7Q32.3) MUTATED        2      9     11
  DEL PEAK  4(7Q32.3) WILD-TYPE     65     25     67
D8V6, multiclass
        clus
vv       DEL PEAK  4(7Q32.3) MUTATED DEL PEAK  4(7Q32.3) WILD-TYPE
  CLUS_1                           2                            65
  CLUS_2                           9                            25
  CLUS_3                          11                            67
[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"

Clustering(9) Variable = DEL PEAK  5(9Q21.32) MUTATION ANALYSIS
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK  5(9Q21.32) MUTATED        1      1      3      0
  DEL PEAK  5(9Q21.32) WILD-TYPE     48     43     52     43
D9V1, multiclass
        clus
vv       DEL PEAK  5(9Q21.32) MUTATED DEL PEAK  5(9Q21.32) WILD-TYPE
  CLUS_1                            1                             48
  CLUS_2                            1                             43
  CLUS_3                            3                             52
  CLUS_4                            0                             43
[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(9Q21.32) MUTATED        0      1      3      1      0
  DEL PEAK  5(9Q21.32) WILD-TYPE     23     24     57     34     42
D9V2, multiclass
        clus
vv       DEL PEAK  5(9Q21.32) MUTATED DEL PEAK  5(9Q21.32) WILD-TYPE
  CLUS_1                            0                             23
  CLUS_2                            1                             24
  CLUS_3                            3                             57
  CLUS_4                            1                             34
  CLUS_5                            0                             42
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  5(9Q21.32) MUTATED        4      0      1
  DEL PEAK  5(9Q21.32) WILD-TYPE     67     50     44
D9V3, multiclass
        clus
vv       DEL PEAK  5(9Q21.32) MUTATED DEL PEAK  5(9Q21.32) WILD-TYPE
  CLUS_1                            4                             67
  CLUS_2                            0                             50
  CLUS_3                            1                             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  5(9Q21.32) MUTATED        1      0      1      2      0      1
  DEL PEAK  5(9Q21.32) WILD-TYPE     15     13     13     53     26     41
D9V4, multiclass
        clus
vv       DEL PEAK  5(9Q21.32) MUTATED DEL PEAK  5(9Q21.32) WILD-TYPE
  CLUS_1                            1                             15
  CLUS_2                            0                             13
  CLUS_3                            1                             13
  CLUS_4                            2                             53
  CLUS_5                            0                             26
  CLUS_6                            1                             41
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK  5(9Q21.32) MUTATED        1      3      1      0      0
  DEL PEAK  5(9Q21.32) WILD-TYPE     56     28     38     33     19
D9V5, multiclass
        clus
vv       DEL PEAK  5(9Q21.32) MUTATED DEL PEAK  5(9Q21.32) WILD-TYPE
  CLUS_1                            1                             56
  CLUS_2                            3                             28
  CLUS_3                            1                             38
  CLUS_4                            0                             33
  CLUS_5                            0                             19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  5(9Q21.32) MUTATED        1      3      1
  DEL PEAK  5(9Q21.32) WILD-TYPE     66     31     77
D9V6, multiclass
        clus
vv       DEL PEAK  5(9Q21.32) MUTATED DEL PEAK  5(9Q21.32) WILD-TYPE
  CLUS_1                            1                             66
  CLUS_2                            3                             31
  CLUS_3                            1                             77
[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"

Clustering(10) Variable = DEL PEAK  6(12P13.2) MUTATION ANALYSIS
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK  6(12P13.2) MUTATED        0      8      1      1
  DEL PEAK  6(12P13.2) WILD-TYPE     49     36     54     42
D10V1, multiclass
        clus
vv       DEL PEAK  6(12P13.2) MUTATED DEL PEAK  6(12P13.2) WILD-TYPE
  CLUS_1                            0                             49
  CLUS_2                            8                             36
  CLUS_3                            1                             54
  CLUS_4                            1                             42
[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(12P13.2) MUTATED        0      0      9      1      0
  DEL PEAK  6(12P13.2) WILD-TYPE     23     25     51     34     42
D10V2, multiclass
        clus
vv       DEL PEAK  6(12P13.2) MUTATED DEL PEAK  6(12P13.2) WILD-TYPE
  CLUS_1                            0                             23
  CLUS_2                            0                             25
  CLUS_3                            9                             51
  CLUS_4                            1                             34
  CLUS_5                            0                             42
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  6(12P13.2) MUTATED        7      1      2
  DEL PEAK  6(12P13.2) WILD-TYPE     64     49     43
D10V3, multiclass
        clus
vv       DEL PEAK  6(12P13.2) MUTATED DEL PEAK  6(12P13.2) WILD-TYPE
  CLUS_1                            7                             64
  CLUS_2                            1                             49
  CLUS_3                            2                             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  6(12P13.2) MUTATED        0      0      1      8      0      1
  DEL PEAK  6(12P13.2) WILD-TYPE     16     13     13     47     26     41
D10V4, multiclass
        clus
vv       DEL PEAK  6(12P13.2) MUTATED DEL PEAK  6(12P13.2) WILD-TYPE
  CLUS_1                            0                             16
  CLUS_2                            0                             13
  CLUS_3                            1                             13
  CLUS_4                            8                             47
  CLUS_5                            0                             26
  CLUS_6                            1                             41
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK  6(12P13.2) MUTATED        1      4      1      2      2
  DEL PEAK  6(12P13.2) WILD-TYPE     56     27     38     31     17
D10V5, multiclass
        clus
vv       DEL PEAK  6(12P13.2) MUTATED DEL PEAK  6(12P13.2) WILD-TYPE
  CLUS_1                            1                             56
  CLUS_2                            4                             27
  CLUS_3                            1                             38
  CLUS_4                            2                             31
  CLUS_5                            2                             17
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  6(12P13.2) MUTATED        0      4      6
  DEL PEAK  6(12P13.2) WILD-TYPE     67     30     72
D10V6, multiclass
        clus
vv       DEL PEAK  6(12P13.2) MUTATED DEL PEAK  6(12P13.2) WILD-TYPE
  CLUS_1                            0                             67
  CLUS_2                            4                             30
  CLUS_3                            6                             72
[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"

Clustering(11) Variable = DEL PEAK  7(12Q21.33) MUTATION ANALYSIS
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK  7(12Q21.33) MUTATED        0      2      0      1
  DEL PEAK  7(12Q21.33) WILD-TYPE     49     42     55     42
D11V1, multiclass
        clus
vv       DEL PEAK  7(12Q21.33) MUTATED DEL PEAK  7(12Q21.33) WILD-TYPE
  CLUS_1                             0                              49
  CLUS_2                             2                              42
  CLUS_3                             0                              55
  CLUS_4                             1                              42
[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(12Q21.33) MUTATED        0      0      2      1      0
  DEL PEAK  7(12Q21.33) WILD-TYPE     23     25     58     34     42
D11V2, multiclass
        clus
vv       DEL PEAK  7(12Q21.33) MUTATED DEL PEAK  7(12Q21.33) WILD-TYPE
  CLUS_1                             0                              23
  CLUS_2                             0                              25
  CLUS_3                             2                              58
  CLUS_4                             1                              34
  CLUS_5                             0                              42
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  7(12Q21.33) MUTATED        3      0      0
  DEL PEAK  7(12Q21.33) WILD-TYPE     68     50     45
D11V3, multiclass
        clus
vv       DEL PEAK  7(12Q21.33) MUTATED DEL PEAK  7(12Q21.33) WILD-TYPE
  CLUS_1                             3                              68
  CLUS_2                             0                              50
  CLUS_3                             0                              45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  7(12Q21.33) MUTATED        0      0      0      3      0      0
  DEL PEAK  7(12Q21.33) WILD-TYPE     16     13     14     52     26     42
D11V4, multiclass
        clus
vv       DEL PEAK  7(12Q21.33) MUTATED DEL PEAK  7(12Q21.33) WILD-TYPE
  CLUS_1                             0                              16
  CLUS_2                             0                              13
  CLUS_3                             0                              14
  CLUS_4                             3                              52
  CLUS_5                             0                              26
  CLUS_6                             0                              42
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK  7(12Q21.33) MUTATED        0      3      0      0      0
  DEL PEAK  7(12Q21.33) WILD-TYPE     57     28     39     33     19
D11V5, multiclass
        clus
vv       DEL PEAK  7(12Q21.33) MUTATED DEL PEAK  7(12Q21.33) WILD-TYPE
  CLUS_1                             0                              57
  CLUS_2                             3                              28
  CLUS_3                             0                              39
  CLUS_4                             0                              33
  CLUS_5                             0                              19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  7(12Q21.33) MUTATED        0      3      0
  DEL PEAK  7(12Q21.33) WILD-TYPE     67     31     78
D11V6, multiclass
        clus
vv       DEL PEAK  7(12Q21.33) MUTATED DEL PEAK  7(12Q21.33) WILD-TYPE
  CLUS_1                             0                              67
  CLUS_2                             3                              31
  CLUS_3                             0                              78
[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"

Clustering(12) Variable = DEL PEAK  8(16Q23.1) MUTATION ANALYSIS
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK  8(16Q23.1) MUTATED        1      4      0      4
  DEL PEAK  8(16Q23.1) WILD-TYPE     48     40     55     39
D12V1, multiclass
        clus
vv       DEL PEAK  8(16Q23.1) MUTATED DEL PEAK  8(16Q23.1) WILD-TYPE
  CLUS_1                            1                             48
  CLUS_2                            4                             40
  CLUS_3                            0                             55
  CLUS_4                            4                             39
[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(16Q23.1) MUTATED        2      0      6      1      0
  DEL PEAK  8(16Q23.1) WILD-TYPE     21     25     54     34     42
D12V2, multiclass
        clus
vv       DEL PEAK  8(16Q23.1) MUTATED DEL PEAK  8(16Q23.1) WILD-TYPE
  CLUS_1                            2                             21
  CLUS_2                            0                             25
  CLUS_3                            6                             54
  CLUS_4                            1                             34
  CLUS_5                            0                             42
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  8(16Q23.1) MUTATED        3      2      1
  DEL PEAK  8(16Q23.1) WILD-TYPE     68     48     44
D12V3, multiclass
        clus
vv       DEL PEAK  8(16Q23.1) MUTATED DEL PEAK  8(16Q23.1) WILD-TYPE
  CLUS_1                            3                             68
  CLUS_2                            2                             48
  CLUS_3                            1                             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  8(16Q23.1) MUTATED        0      1      0      3      1      1
  DEL PEAK  8(16Q23.1) WILD-TYPE     16     12     14     52     25     41
D12V4, multiclass
        clus
vv       DEL PEAK  8(16Q23.1) MUTATED DEL PEAK  8(16Q23.1) WILD-TYPE
  CLUS_1                            0                             16
  CLUS_2                            1                             12
  CLUS_3                            0                             14
  CLUS_4                            3                             52
  CLUS_5                            1                             25
  CLUS_6                            1                             41
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK  8(16Q23.1) MUTATED        2      4      0      2      0
  DEL PEAK  8(16Q23.1) WILD-TYPE     55     27     39     31     19
D12V5, multiclass
        clus
vv       DEL PEAK  8(16Q23.1) MUTATED DEL PEAK  8(16Q23.1) WILD-TYPE
  CLUS_1                            2                             55
  CLUS_2                            4                             27
  CLUS_3                            0                             39
  CLUS_4                            2                             31
  CLUS_5                            0                             19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  8(16Q23.1) MUTATED        2      4      2
  DEL PEAK  8(16Q23.1) WILD-TYPE     65     30     76
D12V6, multiclass
        clus
vv       DEL PEAK  8(16Q23.1) MUTATED DEL PEAK  8(16Q23.1) WILD-TYPE
  CLUS_1                            2                             65
  CLUS_2                            4                             30
  CLUS_3                            2                             76
[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"

Clustering(13) Variable = DEL PEAK  9(17P13.2) MUTATION ANALYSIS
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK  9(17P13.2) MUTATED        0      7      5      3
  DEL PEAK  9(17P13.2) WILD-TYPE     49     37     50     40
D13V1, multiclass
        clus
vv       DEL PEAK  9(17P13.2) MUTATED DEL PEAK  9(17P13.2) WILD-TYPE
  CLUS_1                            0                             49
  CLUS_2                            7                             37
  CLUS_3                            5                             50
  CLUS_4                            3                             40
[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(17P13.2) MUTATED        0      0     12      3      0
  DEL PEAK  9(17P13.2) WILD-TYPE     23     25     48     32     42
D13V2, multiclass
        clus
vv       DEL PEAK  9(17P13.2) MUTATED DEL PEAK  9(17P13.2) WILD-TYPE
  CLUS_1                            0                             23
  CLUS_2                            0                             25
  CLUS_3                           12                             48
  CLUS_4                            3                             32
  CLUS_5                            0                             42
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  9(17P13.2) MUTATED       12      2      1
  DEL PEAK  9(17P13.2) WILD-TYPE     59     48     44
D13V3, multiclass
        clus
vv       DEL PEAK  9(17P13.2) MUTATED DEL PEAK  9(17P13.2) WILD-TYPE
  CLUS_1                           12                             59
  CLUS_2                            2                             48
  CLUS_3                            1                             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK  9(17P13.2) MUTATED        0      0      0     14      0      1
  DEL PEAK  9(17P13.2) WILD-TYPE     16     13     14     41     26     41
D13V4, multiclass
        clus
vv       DEL PEAK  9(17P13.2) MUTATED DEL PEAK  9(17P13.2) WILD-TYPE
  CLUS_1                            0                             16
  CLUS_2                            0                             13
  CLUS_3                            0                             14
  CLUS_4                           14                             41
  CLUS_5                            0                             26
  CLUS_6                            1                             41
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK  9(17P13.2) MUTATED        2      6      2      2      3
  DEL PEAK  9(17P13.2) WILD-TYPE     55     25     37     31     16
D13V5, multiclass
        clus
vv       DEL PEAK  9(17P13.2) MUTATED DEL PEAK  9(17P13.2) WILD-TYPE
  CLUS_1                            2                             55
  CLUS_2                            6                             25
  CLUS_3                            2                             37
  CLUS_4                            2                             31
  CLUS_5                            3                             16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK  9(17P13.2) MUTATED        0      5     10
  DEL PEAK  9(17P13.2) WILD-TYPE     67     29     68
D13V6, multiclass
        clus
vv       DEL PEAK  9(17P13.2) MUTATED DEL PEAK  9(17P13.2) WILD-TYPE
  CLUS_1                            0                             67
  CLUS_2                            5                             29
  CLUS_3                           10                             68
[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"

Clustering(14) Variable = DEL PEAK 10(17Q11.2) MUTATION ANALYSIS
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK 10(17Q11.2) MUTATED        0      7      4      2
  DEL PEAK 10(17Q11.2) WILD-TYPE     49     37     51     41
D14V1, multiclass
        clus
vv       DEL PEAK 10(17Q11.2) MUTATED DEL PEAK 10(17Q11.2) WILD-TYPE
  CLUS_1                            0                             49
  CLUS_2                            7                             37
  CLUS_3                            4                             51
  CLUS_4                            2                             41
[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(17Q11.2) MUTATED        0      0      9      4      0
  DEL PEAK 10(17Q11.2) WILD-TYPE     23     25     51     31     42
D14V2, multiclass
        clus
vv       DEL PEAK 10(17Q11.2) MUTATED DEL PEAK 10(17Q11.2) WILD-TYPE
  CLUS_1                            0                             23
  CLUS_2                            0                             25
  CLUS_3                            9                             51
  CLUS_4                            4                             31
  CLUS_5                            0                             42
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 10(17Q11.2) MUTATED        9      2      2
  DEL PEAK 10(17Q11.2) WILD-TYPE     62     48     43
D14V3, multiclass
        clus
vv       DEL PEAK 10(17Q11.2) MUTATED DEL PEAK 10(17Q11.2) WILD-TYPE
  CLUS_1                            9                             62
  CLUS_2                            2                             48
  CLUS_3                            2                             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 10(17Q11.2) MUTATED        0      1      0     11      0      1
  DEL PEAK 10(17Q11.2) WILD-TYPE     16     12     14     44     26     41
D14V4, multiclass
        clus
vv       DEL PEAK 10(17Q11.2) MUTATED DEL PEAK 10(17Q11.2) WILD-TYPE
  CLUS_1                            0                             16
  CLUS_2                            1                             12
  CLUS_3                            0                             14
  CLUS_4                           11                             44
  CLUS_5                            0                             26
  CLUS_6                            1                             41
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK 10(17Q11.2) MUTATED        1      2      3      2      5
  DEL PEAK 10(17Q11.2) WILD-TYPE     56     29     36     31     14
D14V5, multiclass
        clus
vv       DEL PEAK 10(17Q11.2) MUTATED DEL PEAK 10(17Q11.2) WILD-TYPE
  CLUS_1                            1                             56
  CLUS_2                            2                             29
  CLUS_3                            3                             36
  CLUS_4                            2                             31
  CLUS_5                            5                             14
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 10(17Q11.2) MUTATED        0      4      9
  DEL PEAK 10(17Q11.2) WILD-TYPE     67     30     69
D14V6, multiclass
        clus
vv       DEL PEAK 10(17Q11.2) MUTATED DEL PEAK 10(17Q11.2) WILD-TYPE
  CLUS_1                            0                             67
  CLUS_2                            4                             30
  CLUS_3                            9                             69
[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"

Clustering(15) Variable = DEL PEAK 11(18P11.21) MUTATION ANALYSIS
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK 11(18P11.21) MUTATED        0      7      1      1
  DEL PEAK 11(18P11.21) WILD-TYPE     49     37     54     42
D15V1, multiclass
        clus
vv       DEL PEAK 11(18P11.21) MUTATED DEL PEAK 11(18P11.21) WILD-TYPE
  CLUS_1                             0                              49
  CLUS_2                             7                              37
  CLUS_3                             1                              54
  CLUS_4                             1                              42
[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(18P11.21) MUTATED        0      0      8      1      0
  DEL PEAK 11(18P11.21) WILD-TYPE     23     25     52     34     42
D15V2, multiclass
        clus
vv       DEL PEAK 11(18P11.21) MUTATED DEL PEAK 11(18P11.21) WILD-TYPE
  CLUS_1                             0                              23
  CLUS_2                             0                              25
  CLUS_3                             8                              52
  CLUS_4                             1                              34
  CLUS_5                             0                              42
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 11(18P11.21) MUTATED        5      1      2
  DEL PEAK 11(18P11.21) WILD-TYPE     66     49     43
D15V3, multiclass
        clus
vv       DEL PEAK 11(18P11.21) MUTATED DEL PEAK 11(18P11.21) WILD-TYPE
  CLUS_1                             5                              66
  CLUS_2                             1                              49
  CLUS_3                             2                              43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 11(18P11.21) MUTATED        0      0      0      6      0      2
  DEL PEAK 11(18P11.21) WILD-TYPE     16     13     14     49     26     40
D15V4, multiclass
        clus
vv       DEL PEAK 11(18P11.21) MUTATED DEL PEAK 11(18P11.21) WILD-TYPE
  CLUS_1                             0                              16
  CLUS_2                             0                              13
  CLUS_3                             0                              14
  CLUS_4                             6                              49
  CLUS_5                             0                              26
  CLUS_6                             2                              40
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK 11(18P11.21) MUTATED        1      3      1      1      2
  DEL PEAK 11(18P11.21) WILD-TYPE     56     28     38     32     17
D15V5, multiclass
        clus
vv       DEL PEAK 11(18P11.21) MUTATED DEL PEAK 11(18P11.21) WILD-TYPE
  CLUS_1                             1                              56
  CLUS_2                             3                              28
  CLUS_3                             1                              38
  CLUS_4                             1                              32
  CLUS_5                             2                              17
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 11(18P11.21) MUTATED        0      3      5
  DEL PEAK 11(18P11.21) WILD-TYPE     67     31     73
D15V6, multiclass
        clus
vv       DEL PEAK 11(18P11.21) MUTATED DEL PEAK 11(18P11.21) WILD-TYPE
  CLUS_1                             0                              67
  CLUS_2                             3                              31
  CLUS_3                             5                              73
[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"

Clustering(16) Variable = DEL PEAK 12(20Q13.13) MUTATION ANALYSIS
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DEL PEAK 12(20Q13.13) MUTATED        1      1      2      0
  DEL PEAK 12(20Q13.13) WILD-TYPE     48     43     53     43
D16V1, multiclass
        clus
vv       DEL PEAK 12(20Q13.13) MUTATED DEL PEAK 12(20Q13.13) WILD-TYPE
  CLUS_1                             1                              48
  CLUS_2                             1                              43
  CLUS_3                             2                              53
  CLUS_4                             0                              43
[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(20Q13.13) MUTATED        0      0      4      0      0
  DEL PEAK 12(20Q13.13) WILD-TYPE     23     25     56     35     42
D16V2, multiclass
        clus
vv       DEL PEAK 12(20Q13.13) MUTATED DEL PEAK 12(20Q13.13) WILD-TYPE
  CLUS_1                             0                              23
  CLUS_2                             0                              25
  CLUS_3                             4                              56
  CLUS_4                             0                              35
  CLUS_5                             0                              42
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 12(20Q13.13) MUTATED        2      1      0
  DEL PEAK 12(20Q13.13) WILD-TYPE     69     49     45
D16V3, multiclass
        clus
vv       DEL PEAK 12(20Q13.13) MUTATED DEL PEAK 12(20Q13.13) WILD-TYPE
  CLUS_1                             2                              69
  CLUS_2                             1                              49
  CLUS_3                             0                              45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DEL PEAK 12(20Q13.13) MUTATED        0      0      0      3      0      0
  DEL PEAK 12(20Q13.13) WILD-TYPE     16     13     14     52     26     42
D16V4, multiclass
        clus
vv       DEL PEAK 12(20Q13.13) MUTATED DEL PEAK 12(20Q13.13) WILD-TYPE
  CLUS_1                             0                              16
  CLUS_2                             0                              13
  CLUS_3                             0                              14
  CLUS_4                             3                              52
  CLUS_5                             0                              26
  CLUS_6                             0                              42
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DEL PEAK 12(20Q13.13) MUTATED        0      1      0      2      0
  DEL PEAK 12(20Q13.13) WILD-TYPE     57     30     39     31     19
D16V5, multiclass
        clus
vv       DEL PEAK 12(20Q13.13) MUTATED DEL PEAK 12(20Q13.13) WILD-TYPE
  CLUS_1                             0                              57
  CLUS_2                             1                              30
  CLUS_3                             0                              39
  CLUS_4                             2                              31
  CLUS_5                             0                              19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              CLUS_1 CLUS_2 CLUS_3
  DEL PEAK 12(20Q13.13) MUTATED        0      1      2
  DEL PEAK 12(20Q13.13) WILD-TYPE     67     33     76
D16V6, multiclass
        clus
vv       DEL PEAK 12(20Q13.13) MUTATED DEL PEAK 12(20Q13.13) WILD-TYPE
  CLUS_1                             0                              67
  CLUS_2                             1                              33
  CLUS_3                             2                              76
[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"
