[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/22529564/transformed.cor.cli.txt"

nPatients in clinical file=200, in cluster file=191, common to both=191
[1] "Reduce the number of clustering variables from 82 to 32."
[1]  32 191
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                3               188 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                3               188 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                4               187 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                4               187 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                4               187 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                4               187 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               22               169 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               22               169 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               23               168 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               23               168 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                188 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                188 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                186 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                186 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 7                184 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 7                184 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 6                185 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 6                185 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 3                188 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 3                188 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 5                186 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 5                186 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 5                186 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 5                186 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 8                183 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 8                183 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 9                182 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 9                182 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                3               188 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                3               188 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                3               188 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                3               188 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                3               188 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                3               188 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3               188 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3               188 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                6               185 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                6               185 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               17               174 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               17               174 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               20               171 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               20               171 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 4                187 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 4                187 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 4                187 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 4                187 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                187 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                187 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                13                178 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                13                178 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 7                184 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 7                184 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 5                186 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 5                186 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                187 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                187 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                188 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                188 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                188 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                188 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                5               186 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                5               186 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                5               186 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                5               186 
[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 = 1P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P GAIN MUTATED        0      1      2      0
  1P GAIN WILD-TYPE     49     43     53     43
D1V1, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               0                49
  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
  1P GAIN MUTATED        0      0      3      0      0
  1P GAIN WILD-TYPE     23     25     57     35     42
D1V2, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN 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
  1P GAIN MUTATED        3      0      0
  1P GAIN WILD-TYPE     68     50     45
D1V3, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN 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
  1P GAIN MUTATED        0      0      0      3      0      0
  1P GAIN WILD-TYPE     16     13     14     52     26     42
D1V4, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN 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
  1P GAIN MUTATED        0      0      0      0      3
  1P GAIN WILD-TYPE     57     31     39     33     16
D1V5, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               0                57
  CLUS_2               0                31
  CLUS_3               0                39
  CLUS_4               0                33
  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
  1P GAIN MUTATED        0      2      1
  1P GAIN WILD-TYPE     67     32     77
D1V6, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               0                67
  CLUS_2               2                32
  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(2) Variable = 4P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4P GAIN MUTATED        0      3      0      1
  4P GAIN WILD-TYPE     49     41     55     42
D2V1, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               0                49
  CLUS_2               3                41
  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
  4P GAIN MUTATED        2      0      0      2      0
  4P GAIN WILD-TYPE     21     25     60     33     42
D2V2, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               2                21
  CLUS_2               0                25
  CLUS_3               0                60
  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
  4P GAIN MUTATED        1      0      1
  4P GAIN WILD-TYPE     70     50     44
D2V3, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2               164 
       TCGA-AB-2803        TCGA-AB-2805        TCGA-AB-2806        TCGA-AB-2807 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2808        TCGA-AB-2810        TCGA-AB-2811        TCGA-AB-2812 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2813        TCGA-AB-2814        TCGA-AB-2815        TCGA-AB-2816 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2817        TCGA-AB-2818        TCGA-AB-2819        TCGA-AB-2820 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2821        TCGA-AB-2822        TCGA-AB-2823        TCGA-AB-2824 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2825        TCGA-AB-2826        TCGA-AB-2828        TCGA-AB-2830 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2832        TCGA-AB-2834        TCGA-AB-2835        TCGA-AB-2836 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2837        TCGA-AB-2838        TCGA-AB-2839        TCGA-AB-2840 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2841        TCGA-AB-2842        TCGA-AB-2844        TCGA-AB-2845 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2846        TCGA-AB-2848        TCGA-AB-2851        TCGA-AB-2853 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2854        TCGA-AB-2856        TCGA-AB-2857        TCGA-AB-2858 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2859        TCGA-AB-2860        TCGA-AB-2861        TCGA-AB-2862 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2863        TCGA-AB-2865        TCGA-AB-2866        TCGA-AB-2867 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2868        TCGA-AB-2869        TCGA-AB-2870        TCGA-AB-2871 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2872        TCGA-AB-2873        TCGA-AB-2874        TCGA-AB-2875 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2877        TCGA-AB-2879        TCGA-AB-2880        TCGA-AB-2881 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2882        TCGA-AB-2884        TCGA-AB-2885        TCGA-AB-2886 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2887        TCGA-AB-2888        TCGA-AB-2889        TCGA-AB-2890 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2895        TCGA-AB-2896        TCGA-AB-2897        TCGA-AB-2898 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2899        TCGA-AB-2900        TCGA-AB-2901        TCGA-AB-2903 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2904        TCGA-AB-2908        TCGA-AB-2909        TCGA-AB-2910 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2911        TCGA-AB-2912        TCGA-AB-2913        TCGA-AB-2914 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2915        TCGA-AB-2916        TCGA-AB-2917        TCGA-AB-2919 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2920        TCGA-AB-2921        TCGA-AB-2924        TCGA-AB-2925 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2927        TCGA-AB-2928        TCGA-AB-2929        TCGA-AB-2930 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2931        TCGA-AB-2932        TCGA-AB-2933        TCGA-AB-2934 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2935        TCGA-AB-2936        TCGA-AB-2937        TCGA-AB-2938 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2939        TCGA-AB-2940        TCGA-AB-2941        TCGA-AB-2942 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2943        TCGA-AB-2944        TCGA-AB-2946        TCGA-AB-2948 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2949        TCGA-AB-2950        TCGA-AB-2952        TCGA-AB-2954 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2955        TCGA-AB-2956        TCGA-AB-2959        TCGA-AB-2963 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2964        TCGA-AB-2965        TCGA-AB-2966        TCGA-AB-2967 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2969        TCGA-AB-2970        TCGA-AB-2971        TCGA-AB-2972 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2973        TCGA-AB-2975        TCGA-AB-2976        TCGA-AB-2977 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2978        TCGA-AB-2980        TCGA-AB-2982        TCGA-AB-2983 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2984        TCGA-AB-2985        TCGA-AB-2986        TCGA-AB-2987 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2988        TCGA-AB-2990        TCGA-AB-2991        TCGA-AB-2992 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2993        TCGA-AB-2994        TCGA-AB-2995        TCGA-AB-2996 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2998        TCGA-AB-2999        TCGA-AB-3000        TCGA-AB-3001 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-3002        TCGA-AB-3005        TCGA-AB-3006        TCGA-AB-3007 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-3008        TCGA-AB-3009        TCGA-AB-3011        TCGA-AB-3012 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  4P GAIN MUTATED        0      0      0      2      0      0
  4P GAIN WILD-TYPE     16     13     14     53     26     42
D2V4, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2               164 
       TCGA-AB-2803        TCGA-AB-2805        TCGA-AB-2806        TCGA-AB-2807 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2808        TCGA-AB-2810        TCGA-AB-2811        TCGA-AB-2812 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2813        TCGA-AB-2814        TCGA-AB-2815        TCGA-AB-2816 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2817        TCGA-AB-2818        TCGA-AB-2819        TCGA-AB-2820 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2821        TCGA-AB-2822        TCGA-AB-2823        TCGA-AB-2824 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2825        TCGA-AB-2826        TCGA-AB-2828        TCGA-AB-2830 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2832        TCGA-AB-2834        TCGA-AB-2835        TCGA-AB-2836 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2837        TCGA-AB-2838        TCGA-AB-2839        TCGA-AB-2840 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2841        TCGA-AB-2842        TCGA-AB-2844        TCGA-AB-2845 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2846        TCGA-AB-2848        TCGA-AB-2851        TCGA-AB-2853 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2854        TCGA-AB-2856        TCGA-AB-2857        TCGA-AB-2858 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2859        TCGA-AB-2860        TCGA-AB-2861        TCGA-AB-2862 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2863        TCGA-AB-2865        TCGA-AB-2866        TCGA-AB-2867 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2868        TCGA-AB-2869        TCGA-AB-2870        TCGA-AB-2871 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2872        TCGA-AB-2873        TCGA-AB-2874        TCGA-AB-2875 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2877        TCGA-AB-2879        TCGA-AB-2880        TCGA-AB-2881 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2882        TCGA-AB-2884        TCGA-AB-2885        TCGA-AB-2886 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2887        TCGA-AB-2888        TCGA-AB-2889        TCGA-AB-2890 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2895        TCGA-AB-2896        TCGA-AB-2897        TCGA-AB-2898 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2899        TCGA-AB-2900        TCGA-AB-2901        TCGA-AB-2903 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2904        TCGA-AB-2908        TCGA-AB-2909        TCGA-AB-2910 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2911        TCGA-AB-2912        TCGA-AB-2913        TCGA-AB-2914 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2915        TCGA-AB-2916        TCGA-AB-2917        TCGA-AB-2919 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2920        TCGA-AB-2921        TCGA-AB-2924        TCGA-AB-2925 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2927        TCGA-AB-2928        TCGA-AB-2929        TCGA-AB-2930 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2931        TCGA-AB-2932        TCGA-AB-2933        TCGA-AB-2934 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2935        TCGA-AB-2936        TCGA-AB-2937        TCGA-AB-2938 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2939        TCGA-AB-2940        TCGA-AB-2941        TCGA-AB-2942 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2943        TCGA-AB-2944        TCGA-AB-2946        TCGA-AB-2948 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2949        TCGA-AB-2950        TCGA-AB-2952        TCGA-AB-2954 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2955        TCGA-AB-2956        TCGA-AB-2959        TCGA-AB-2963 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2964        TCGA-AB-2965        TCGA-AB-2966        TCGA-AB-2967 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2969        TCGA-AB-2970        TCGA-AB-2971        TCGA-AB-2972 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2973        TCGA-AB-2975        TCGA-AB-2976        TCGA-AB-2977 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2978        TCGA-AB-2980        TCGA-AB-2982        TCGA-AB-2983 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2984        TCGA-AB-2985        TCGA-AB-2986        TCGA-AB-2987 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2988        TCGA-AB-2990        TCGA-AB-2991        TCGA-AB-2992 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2993        TCGA-AB-2994        TCGA-AB-2995        TCGA-AB-2996 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2998        TCGA-AB-2999        TCGA-AB-3000        TCGA-AB-3001 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-3002        TCGA-AB-3005        TCGA-AB-3006        TCGA-AB-3007 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-3008        TCGA-AB-3009        TCGA-AB-3011        TCGA-AB-3012 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  4P GAIN MUTATED        3      0      1      0      0
  4P GAIN WILD-TYPE     54     31     38     33     19
D2V5, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               3                54
  CLUS_2               0                31
  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
  4P GAIN MUTATED        2      0      2
  4P GAIN WILD-TYPE     65     34     76
D2V6, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               2                65
  CLUS_2               0                34
  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(3) Variable = 4Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4Q GAIN MUTATED        0      3      0      1
  4Q GAIN WILD-TYPE     49     41     55     42
D3V1, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               0                49
  CLUS_2               3                41
  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
  4Q GAIN MUTATED        2      0      0      2      0
  4Q GAIN WILD-TYPE     21     25     60     33     42
D3V2, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               2                21
  CLUS_2               0                25
  CLUS_3               0                60
  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
  4Q GAIN MUTATED        1      0      1
  4Q GAIN WILD-TYPE     70     50     44
D3V3, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2               164 
       TCGA-AB-2803        TCGA-AB-2805        TCGA-AB-2806        TCGA-AB-2807 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2808        TCGA-AB-2810        TCGA-AB-2811        TCGA-AB-2812 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2813        TCGA-AB-2814        TCGA-AB-2815        TCGA-AB-2816 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2817        TCGA-AB-2818        TCGA-AB-2819        TCGA-AB-2820 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2821        TCGA-AB-2822        TCGA-AB-2823        TCGA-AB-2824 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2825        TCGA-AB-2826        TCGA-AB-2828        TCGA-AB-2830 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2832        TCGA-AB-2834        TCGA-AB-2835        TCGA-AB-2836 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2837        TCGA-AB-2838        TCGA-AB-2839        TCGA-AB-2840 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2841        TCGA-AB-2842        TCGA-AB-2844        TCGA-AB-2845 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2846        TCGA-AB-2848        TCGA-AB-2851        TCGA-AB-2853 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2854        TCGA-AB-2856        TCGA-AB-2857        TCGA-AB-2858 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2859        TCGA-AB-2860        TCGA-AB-2861        TCGA-AB-2862 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2863        TCGA-AB-2865        TCGA-AB-2866        TCGA-AB-2867 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2868        TCGA-AB-2869        TCGA-AB-2870        TCGA-AB-2871 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2872        TCGA-AB-2873        TCGA-AB-2874        TCGA-AB-2875 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2877        TCGA-AB-2879        TCGA-AB-2880        TCGA-AB-2881 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2882        TCGA-AB-2884        TCGA-AB-2885        TCGA-AB-2886 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2887        TCGA-AB-2888        TCGA-AB-2889        TCGA-AB-2890 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2895        TCGA-AB-2896        TCGA-AB-2897        TCGA-AB-2898 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2899        TCGA-AB-2900        TCGA-AB-2901        TCGA-AB-2903 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2904        TCGA-AB-2908        TCGA-AB-2909        TCGA-AB-2910 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2911        TCGA-AB-2912        TCGA-AB-2913        TCGA-AB-2914 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2915        TCGA-AB-2916        TCGA-AB-2917        TCGA-AB-2919 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2920        TCGA-AB-2921        TCGA-AB-2924        TCGA-AB-2925 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2927        TCGA-AB-2928        TCGA-AB-2929        TCGA-AB-2930 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2931        TCGA-AB-2932        TCGA-AB-2933        TCGA-AB-2934 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2935        TCGA-AB-2936        TCGA-AB-2937        TCGA-AB-2938 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2939        TCGA-AB-2940        TCGA-AB-2941        TCGA-AB-2942 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2943        TCGA-AB-2944        TCGA-AB-2946        TCGA-AB-2948 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2949        TCGA-AB-2950        TCGA-AB-2952        TCGA-AB-2954 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2955        TCGA-AB-2956        TCGA-AB-2959        TCGA-AB-2963 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2964        TCGA-AB-2965        TCGA-AB-2966        TCGA-AB-2967 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2969        TCGA-AB-2970        TCGA-AB-2971        TCGA-AB-2972 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2973        TCGA-AB-2975        TCGA-AB-2976        TCGA-AB-2977 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2978        TCGA-AB-2980        TCGA-AB-2982        TCGA-AB-2983 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2984        TCGA-AB-2985        TCGA-AB-2986        TCGA-AB-2987 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2988        TCGA-AB-2990        TCGA-AB-2991        TCGA-AB-2992 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2993        TCGA-AB-2994        TCGA-AB-2995        TCGA-AB-2996 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2998        TCGA-AB-2999        TCGA-AB-3000        TCGA-AB-3001 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-3002        TCGA-AB-3005        TCGA-AB-3006        TCGA-AB-3007 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-3008        TCGA-AB-3009        TCGA-AB-3011        TCGA-AB-3012 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  4Q GAIN MUTATED        0      0      0      2      0      0
  4Q GAIN WILD-TYPE     16     13     14     53     26     42
D3V4, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2               164 
       TCGA-AB-2803        TCGA-AB-2805        TCGA-AB-2806        TCGA-AB-2807 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2808        TCGA-AB-2810        TCGA-AB-2811        TCGA-AB-2812 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2813        TCGA-AB-2814        TCGA-AB-2815        TCGA-AB-2816 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2817        TCGA-AB-2818        TCGA-AB-2819        TCGA-AB-2820 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2821        TCGA-AB-2822        TCGA-AB-2823        TCGA-AB-2824 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2825        TCGA-AB-2826        TCGA-AB-2828        TCGA-AB-2830 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2832        TCGA-AB-2834        TCGA-AB-2835        TCGA-AB-2836 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2837        TCGA-AB-2838        TCGA-AB-2839        TCGA-AB-2840 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2841        TCGA-AB-2842        TCGA-AB-2844        TCGA-AB-2845 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2846        TCGA-AB-2848        TCGA-AB-2851        TCGA-AB-2853 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2854        TCGA-AB-2856        TCGA-AB-2857        TCGA-AB-2858 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2859        TCGA-AB-2860        TCGA-AB-2861        TCGA-AB-2862 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2863        TCGA-AB-2865        TCGA-AB-2866        TCGA-AB-2867 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2868        TCGA-AB-2869        TCGA-AB-2870        TCGA-AB-2871 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2872        TCGA-AB-2873        TCGA-AB-2874        TCGA-AB-2875 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2877        TCGA-AB-2879        TCGA-AB-2880        TCGA-AB-2881 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2882        TCGA-AB-2884        TCGA-AB-2885        TCGA-AB-2886 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2887        TCGA-AB-2888        TCGA-AB-2889        TCGA-AB-2890 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2895        TCGA-AB-2896        TCGA-AB-2897        TCGA-AB-2898 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2899        TCGA-AB-2900        TCGA-AB-2901        TCGA-AB-2903 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2904        TCGA-AB-2908        TCGA-AB-2909        TCGA-AB-2910 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2911        TCGA-AB-2912        TCGA-AB-2913        TCGA-AB-2914 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2915        TCGA-AB-2916        TCGA-AB-2917        TCGA-AB-2919 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2920        TCGA-AB-2921        TCGA-AB-2924        TCGA-AB-2925 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2927        TCGA-AB-2928        TCGA-AB-2929        TCGA-AB-2930 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2931        TCGA-AB-2932        TCGA-AB-2933        TCGA-AB-2934 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2935        TCGA-AB-2936        TCGA-AB-2937        TCGA-AB-2938 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2939        TCGA-AB-2940        TCGA-AB-2941        TCGA-AB-2942 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2943        TCGA-AB-2944        TCGA-AB-2946        TCGA-AB-2948 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2949        TCGA-AB-2950        TCGA-AB-2952        TCGA-AB-2954 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2955        TCGA-AB-2956        TCGA-AB-2959        TCGA-AB-2963 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2964        TCGA-AB-2965        TCGA-AB-2966        TCGA-AB-2967 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2969        TCGA-AB-2970        TCGA-AB-2971        TCGA-AB-2972 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2973        TCGA-AB-2975        TCGA-AB-2976        TCGA-AB-2977 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2978        TCGA-AB-2980        TCGA-AB-2982        TCGA-AB-2983 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2984        TCGA-AB-2985        TCGA-AB-2986        TCGA-AB-2987 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2988        TCGA-AB-2990        TCGA-AB-2991        TCGA-AB-2992 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2993        TCGA-AB-2994        TCGA-AB-2995        TCGA-AB-2996 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2998        TCGA-AB-2999        TCGA-AB-3000        TCGA-AB-3001 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-3002        TCGA-AB-3005        TCGA-AB-3006        TCGA-AB-3007 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-3008        TCGA-AB-3009        TCGA-AB-3011        TCGA-AB-3012 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  4Q GAIN MUTATED        3      0      1      0      0
  4Q GAIN WILD-TYPE     54     31     38     33     19
D3V5, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               3                54
  CLUS_2               0                31
  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
  4Q GAIN MUTATED        2      0      2
  4Q GAIN WILD-TYPE     65     34     76
D3V6, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               2                65
  CLUS_2               0                34
  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(4) Variable = 8P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8P GAIN MUTATED        6      4      7      5
  8P GAIN WILD-TYPE     43     40     48     38
D4V1, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               6                43
  CLUS_2               4                40
  CLUS_3               7                48
  CLUS_4               5                38
[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
  8P GAIN MUTATED        2      2     15      1      1
  8P GAIN WILD-TYPE     21     23     45     34     41
D4V2, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               2                21
  CLUS_2               2                23
  CLUS_3              15                45
  CLUS_4               1                34
  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
  8P GAIN MUTATED       13      2      3
  8P GAIN WILD-TYPE     58     48     42
D4V3, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              13                58
  CLUS_2               2                48
  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
  8P GAIN MUTATED        1      0      0     15      1      1
  8P GAIN WILD-TYPE     15     13     14     40     25     41
D4V4, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1                15
  CLUS_2               0                13
  CLUS_3               0                14
  CLUS_4              15                40
  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
  8P GAIN MUTATED        2      7      5      4      3
  8P GAIN WILD-TYPE     55     24     34     29     16
D4V5, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               2                55
  CLUS_2               7                24
  CLUS_3               5                34
  CLUS_4               4                29
  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
  8P GAIN MUTATED        3      8     10
  8P GAIN WILD-TYPE     64     26     68
D4V6, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               3                64
  CLUS_2               8                26
  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(5) Variable = 8Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8Q GAIN MUTATED        6      4      8      5
  8Q GAIN WILD-TYPE     43     40     47     38
D5V1, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               6                43
  CLUS_2               4                40
  CLUS_3               8                47
  CLUS_4               5                38
[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
  8Q GAIN MUTATED        2      2     15      2      1
  8Q GAIN WILD-TYPE     21     23     45     33     41
D5V2, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               2                21
  CLUS_2               2                23
  CLUS_3              15                45
  CLUS_4               2                33
  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
  8Q GAIN MUTATED       14      2      3
  8Q GAIN WILD-TYPE     57     48     42
D5V3, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              14                57
  CLUS_2               2                48
  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
  8Q GAIN MUTATED        1      0      1     15      1      1
  8Q GAIN WILD-TYPE     15     13     13     40     25     41
D5V4, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               1                15
  CLUS_2               0                13
  CLUS_3               1                13
  CLUS_4              15                40
  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
  8Q GAIN MUTATED        2      7      6      4      3
  8Q GAIN WILD-TYPE     55     24     33     29     16
D5V5, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               2                55
  CLUS_2               7                24
  CLUS_3               6                33
  CLUS_4               4                29
  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
  8Q GAIN MUTATED        3      8     11
  8Q GAIN WILD-TYPE     64     26     67
D5V6, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               3                64
  CLUS_2               8                26
  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(6) Variable = 10Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10Q GAIN MUTATED        0      0      2      1
  10Q GAIN WILD-TYPE     49     44     53     42
D6V1, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                0                 49
  CLUS_2                0                 44
  CLUS_3                2                 53
  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
  10Q GAIN MUTATED        0      0      3      0      0
  10Q GAIN WILD-TYPE     23     25     57     35     42
D6V2, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN 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
  10Q GAIN MUTATED        3      0      0
  10Q GAIN WILD-TYPE     68     50     45
D6V3, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN 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
  10Q GAIN MUTATED        0      0      0      3      0      0
  10Q GAIN WILD-TYPE     16     13     14     52     26     42
D6V4, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN 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
  10Q GAIN MUTATED        0      1      0      1      1
  10Q GAIN WILD-TYPE     57     30     39     32     18
D6V5, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                0                 57
  CLUS_2                1                 30
  CLUS_3                0                 39
  CLUS_4                1                 32
  CLUS_5                1                 18
[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
  10Q GAIN MUTATED        0      2      1
  10Q GAIN WILD-TYPE     67     32     77
D6V6, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                0                 67
  CLUS_2                2                 32
  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(7) Variable = 11P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11P GAIN MUTATED        0      1      3      1
  11P GAIN WILD-TYPE     49     43     52     42
D7V1, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                 49
  CLUS_2                1                 43
  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
  11P GAIN MUTATED        0      0      4      1      0
  11P GAIN WILD-TYPE     23     25     56     34     42
D7V2, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                 23
  CLUS_2                0                 25
  CLUS_3                4                 56
  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
  11P GAIN MUTATED        4      1      0
  11P GAIN WILD-TYPE     67     49     45
D7V3, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                4                 67
  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
  11P GAIN MUTATED        0      1      0      4      0      0
  11P GAIN WILD-TYPE     16     12     14     51     26     42
D7V4, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                 16
  CLUS_2                1                 12
  CLUS_3                0                 14
  CLUS_4                4                 51
  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
  11P GAIN MUTATED        1      1      0      0      3
  11P GAIN WILD-TYPE     56     30     39     33     16
D7V5, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                1                 56
  CLUS_2                1                 30
  CLUS_3                0                 39
  CLUS_4                0                 33
  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
  11P GAIN MUTATED        0      3      2
  11P GAIN WILD-TYPE     67     31     76
D7V6, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                 67
  CLUS_2                3                 31
  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(8) Variable = 11Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11Q GAIN MUTATED        0      2      4      1
  11Q GAIN WILD-TYPE     49     42     51     42
D8V1, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                 49
  CLUS_2                2                 42
  CLUS_3                4                 51
  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
  11Q GAIN MUTATED        0      0      6      1      0
  11Q GAIN WILD-TYPE     23     25     54     34     42
D8V2, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                 23
  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
  11Q GAIN MUTATED        6      1      0
  11Q GAIN WILD-TYPE     65     49     45
D8V3, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN 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
  11Q GAIN MUTATED        0      1      0      6      0      0
  11Q GAIN WILD-TYPE     16     12     14     49     26     42
D8V4, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                 16
  CLUS_2                1                 12
  CLUS_3                0                 14
  CLUS_4                6                 49
  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
  11Q GAIN MUTATED        1      2      0      0      4
  11Q GAIN WILD-TYPE     56     29     39     33     15
D8V5, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                1                 56
  CLUS_2                2                 29
  CLUS_3                0                 39
  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
  11Q GAIN MUTATED        0      4      3
  11Q GAIN WILD-TYPE     67     30     75
D8V6, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                 67
  CLUS_2                4                 30
  CLUS_3                3                 75
[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 = 13Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  13Q GAIN MUTATED        0      2      3      1
  13Q GAIN WILD-TYPE     49     42     52     42
D9V1, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                0                 49
  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
  13Q GAIN MUTATED        0      0      6      0      0
  13Q GAIN WILD-TYPE     23     25     54     35     42
D9V2, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                0                 23
  CLUS_2                0                 25
  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
  13Q GAIN MUTATED        5      1      0
  13Q GAIN WILD-TYPE     66     49     45
D9V3, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN 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
  13Q GAIN MUTATED        0      0      0      6      0      0
  13Q GAIN WILD-TYPE     16     13     14     49     26     42
D9V4, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                0                 16
  CLUS_2                0                 13
  CLUS_3                0                 14
  CLUS_4                6                 49
  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
  13Q GAIN MUTATED        1      1      0      0      4
  13Q GAIN WILD-TYPE     56     30     39     33     15
D9V5, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                1                 56
  CLUS_2                1                 30
  CLUS_3                0                 39
  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
  13Q GAIN MUTATED        0      1      5
  13Q GAIN WILD-TYPE     67     33     73
D9V6, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                0                 67
  CLUS_2                1                 33
  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(10) Variable = 17Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q GAIN MUTATED        0      1      1      1
  17Q GAIN WILD-TYPE     49     43     54     42
D10V1, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                0                 49
  CLUS_2                1                 43
  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
  17Q GAIN MUTATED        0      0      2      1      0
  17Q GAIN WILD-TYPE     23     25     58     34     42
D10V2, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN 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
  17Q GAIN MUTATED        1      1      1
  17Q GAIN WILD-TYPE     70     49     44
D10V3, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                 70
  CLUS_2                1                 49
  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
  17Q GAIN MUTATED        0      0      0      3      0      0
  17Q GAIN WILD-TYPE     16     13     14     52     26     42
D10V4, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN 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
  17Q GAIN MUTATED        2      1      0      0      0
  17Q GAIN WILD-TYPE     55     30     39     33     19
D10V5, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                2                 55
  CLUS_2                1                 30
  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
  17Q GAIN MUTATED        0      0      3
  17Q GAIN WILD-TYPE     67     34     75
D10V6, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                0                 67
  CLUS_2                0                 34
  CLUS_3                3                 75
[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 = 19P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P GAIN MUTATED        0      2      1      2
  19P GAIN WILD-TYPE     49     42     54     41
D11V1, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                 49
  CLUS_2                2                 42
  CLUS_3                1                 54
  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
  19P GAIN MUTATED        2      0      2      1      0
  19P GAIN WILD-TYPE     21     25     58     34     42
D11V2, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                2                 21
  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
  19P GAIN MUTATED        2      1      1
  19P GAIN WILD-TYPE     69     49     44
D11V3, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                2                 69
  CLUS_2                1                 49
  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
  19P GAIN MUTATED        0      0      0      3      0      1
  19P GAIN WILD-TYPE     16     13     14     52     26     41
D11V4, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                 16
  CLUS_2                0                 13
  CLUS_3                0                 14
  CLUS_4                3                 52
  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
  19P GAIN MUTATED        3      1      0      0      1
  19P GAIN WILD-TYPE     54     30     39     33     18
D11V5, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                3                 54
  CLUS_2                1                 30
  CLUS_3                0                 39
  CLUS_4                0                 33
  CLUS_5                1                 18
[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
  19P GAIN MUTATED        2      1      2
  19P GAIN WILD-TYPE     65     33     76
D11V6, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                2                 65
  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"

Clustering(12) Variable = 19Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19Q GAIN MUTATED        0      2      1      2
  19Q GAIN WILD-TYPE     49     42     54     41
D12V1, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                0                 49
  CLUS_2                2                 42
  CLUS_3                1                 54
  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
  19Q GAIN MUTATED        2      0      2      1      0
  19Q GAIN WILD-TYPE     21     25     58     34     42
D12V2, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                 21
  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
  19Q GAIN MUTATED        2      1      1
  19Q GAIN WILD-TYPE     69     49     44
D12V3, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                 69
  CLUS_2                1                 49
  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
  19Q GAIN MUTATED        0      0      0      3      0      1
  19Q GAIN WILD-TYPE     16     13     14     52     26     41
D12V4, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                0                 16
  CLUS_2                0                 13
  CLUS_3                0                 14
  CLUS_4                3                 52
  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
  19Q GAIN MUTATED        3      1      0      0      1
  19Q GAIN WILD-TYPE     54     30     39     33     18
D12V5, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                3                 54
  CLUS_2                1                 30
  CLUS_3                0                 39
  CLUS_4                0                 33
  CLUS_5                1                 18
[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
  19Q GAIN MUTATED        2      1      2
  19Q GAIN WILD-TYPE     65     33     76
D12V6, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                 65
  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"

Clustering(13) Variable = 21Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  21Q GAIN MUTATED        0      4      3      1
  21Q GAIN WILD-TYPE     49     40     52     42
D13V1, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                0                 49
  CLUS_2                4                 40
  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
  21Q GAIN MUTATED        1      0      5      1      0
  21Q GAIN WILD-TYPE     22     25     55     34     42
D13V2, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                 22
  CLUS_2                0                 25
  CLUS_3                5                 55
  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
  21Q GAIN MUTATED        5      1      0
  21Q GAIN WILD-TYPE     66     49     45
D13V3, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN 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
  21Q GAIN MUTATED        0      0      1      4      0      1
  21Q GAIN WILD-TYPE     16     13     13     51     26     41
D13V4, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                0                 16
  CLUS_2                0                 13
  CLUS_3                1                 13
  CLUS_4                4                 51
  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
  21Q GAIN MUTATED        1      2      0      4      0
  21Q GAIN WILD-TYPE     56     29     39     29     19
D13V5, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                 56
  CLUS_2                2                 29
  CLUS_3                0                 39
  CLUS_4                4                 29
  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
  21Q GAIN MUTATED        1      2      4
  21Q GAIN WILD-TYPE     66     32     74
D13V6, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                 66
  CLUS_2                2                 32
  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(14) Variable = 22Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  22Q GAIN MUTATED        0      3      4      2
  22Q GAIN WILD-TYPE     49     41     51     41
D14V1, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                0                 49
  CLUS_2                3                 41
  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
  22Q GAIN MUTATED        0      0      8      1      0
  22Q GAIN WILD-TYPE     23     25     52     34     42
D14V2, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN 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
  22Q GAIN MUTATED        7      1      1
  22Q GAIN WILD-TYPE     64     49     44
D14V3, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                7                 64
  CLUS_2                1                 49
  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
  22Q GAIN MUTATED        0      1      0      8      0      0
  22Q GAIN WILD-TYPE     16     12     14     47     26     42
D14V4, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                0                 16
  CLUS_2                1                 12
  CLUS_3                0                 14
  CLUS_4                8                 47
  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
  22Q GAIN MUTATED        0      2      1      1      5
  22Q GAIN WILD-TYPE     57     29     38     32     14
D14V5, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                0                 57
  CLUS_2                2                 29
  CLUS_3                1                 38
  CLUS_4                1                 32
  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
  22Q GAIN MUTATED        0      4      5
  22Q GAIN WILD-TYPE     67     30     73
D14V6, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                0                 67
  CLUS_2                4                 30
  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(15) Variable = XP GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XP GAIN MUTATED        0      1      1      1
  XP GAIN WILD-TYPE     49     43     54     42
D15V1, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               0                49
  CLUS_2               1                43
  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
  XP GAIN MUTATED        1      0      2      0      0
  XP GAIN WILD-TYPE     22     25     58     35     42
D15V2, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               1                22
  CLUS_2               0                25
  CLUS_3               2                58
  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
  XP GAIN MUTATED        2      0      0
  XP GAIN WILD-TYPE     69     50     45
D15V3, multiclass
[1] "Remove cluster labels:" "XP GAIN MUTATED"       
clus
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                2               164 
       TCGA-AB-2803        TCGA-AB-2805        TCGA-AB-2806        TCGA-AB-2807 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2808        TCGA-AB-2810        TCGA-AB-2811        TCGA-AB-2812 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2813        TCGA-AB-2814        TCGA-AB-2815        TCGA-AB-2816 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2817        TCGA-AB-2818        TCGA-AB-2819        TCGA-AB-2821 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2822        TCGA-AB-2823        TCGA-AB-2824        TCGA-AB-2825 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2826        TCGA-AB-2828        TCGA-AB-2830        TCGA-AB-2832 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2834        TCGA-AB-2835        TCGA-AB-2836        TCGA-AB-2837 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2838        TCGA-AB-2839        TCGA-AB-2840        TCGA-AB-2841 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2842        TCGA-AB-2844        TCGA-AB-2845        TCGA-AB-2846 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2848        TCGA-AB-2849        TCGA-AB-2851        TCGA-AB-2853 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2854        TCGA-AB-2855        TCGA-AB-2856        TCGA-AB-2857 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2858        TCGA-AB-2859        TCGA-AB-2860        TCGA-AB-2861 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2862        TCGA-AB-2863        TCGA-AB-2865        TCGA-AB-2866 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2867        TCGA-AB-2868        TCGA-AB-2869        TCGA-AB-2870 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2871        TCGA-AB-2872        TCGA-AB-2873        TCGA-AB-2874 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2875        TCGA-AB-2877        TCGA-AB-2879        TCGA-AB-2880 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2881        TCGA-AB-2882        TCGA-AB-2884        TCGA-AB-2885 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2886        TCGA-AB-2887        TCGA-AB-2888        TCGA-AB-2889 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2890        TCGA-AB-2895        TCGA-AB-2896        TCGA-AB-2897 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2898        TCGA-AB-2899        TCGA-AB-2900        TCGA-AB-2901 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2903        TCGA-AB-2904        TCGA-AB-2908        TCGA-AB-2909 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2910        TCGA-AB-2911        TCGA-AB-2912        TCGA-AB-2913 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2914        TCGA-AB-2915        TCGA-AB-2916        TCGA-AB-2917 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2919        TCGA-AB-2920        TCGA-AB-2921        TCGA-AB-2924 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2925        TCGA-AB-2927        TCGA-AB-2928        TCGA-AB-2930 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2931        TCGA-AB-2932        TCGA-AB-2933        TCGA-AB-2934 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2935        TCGA-AB-2936        TCGA-AB-2937        TCGA-AB-2938 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2939        TCGA-AB-2940        TCGA-AB-2941        TCGA-AB-2942 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2943        TCGA-AB-2944        TCGA-AB-2946        TCGA-AB-2948 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2949        TCGA-AB-2950        TCGA-AB-2952        TCGA-AB-2954 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2955        TCGA-AB-2956        TCGA-AB-2959        TCGA-AB-2963 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2964        TCGA-AB-2965        TCGA-AB-2966        TCGA-AB-2967 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2969        TCGA-AB-2970        TCGA-AB-2971        TCGA-AB-2972 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2973        TCGA-AB-2975        TCGA-AB-2976        TCGA-AB-2977 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2978        TCGA-AB-2980        TCGA-AB-2982        TCGA-AB-2983 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2984        TCGA-AB-2985        TCGA-AB-2986        TCGA-AB-2987 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2988        TCGA-AB-2990        TCGA-AB-2991        TCGA-AB-2992 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2993        TCGA-AB-2994        TCGA-AB-2995        TCGA-AB-2996 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2998        TCGA-AB-2999        TCGA-AB-3000        TCGA-AB-3001 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-3002        TCGA-AB-3005        TCGA-AB-3006        TCGA-AB-3007 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-3008        TCGA-AB-3009        TCGA-AB-3011        TCGA-AB-3012 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  XP GAIN MUTATED        0      0      0      2      0      0
  XP GAIN WILD-TYPE     16     13     14     53     26     42
D15V4, multiclass
[1] "Remove cluster labels:" "XP GAIN MUTATED"       
clus
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                2               164 
       TCGA-AB-2803        TCGA-AB-2805        TCGA-AB-2806        TCGA-AB-2807 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2808        TCGA-AB-2810        TCGA-AB-2811        TCGA-AB-2812 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2813        TCGA-AB-2814        TCGA-AB-2815        TCGA-AB-2816 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2817        TCGA-AB-2818        TCGA-AB-2819        TCGA-AB-2821 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2822        TCGA-AB-2823        TCGA-AB-2824        TCGA-AB-2825 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2826        TCGA-AB-2828        TCGA-AB-2830        TCGA-AB-2832 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2834        TCGA-AB-2835        TCGA-AB-2836        TCGA-AB-2837 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2838        TCGA-AB-2839        TCGA-AB-2840        TCGA-AB-2841 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2842        TCGA-AB-2844        TCGA-AB-2845        TCGA-AB-2846 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2848        TCGA-AB-2849        TCGA-AB-2851        TCGA-AB-2853 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2854        TCGA-AB-2855        TCGA-AB-2856        TCGA-AB-2857 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2858        TCGA-AB-2859        TCGA-AB-2860        TCGA-AB-2861 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2862        TCGA-AB-2863        TCGA-AB-2865        TCGA-AB-2866 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2867        TCGA-AB-2868        TCGA-AB-2869        TCGA-AB-2870 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2871        TCGA-AB-2872        TCGA-AB-2873        TCGA-AB-2874 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2875        TCGA-AB-2877        TCGA-AB-2879        TCGA-AB-2880 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2881        TCGA-AB-2882        TCGA-AB-2884        TCGA-AB-2885 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2886        TCGA-AB-2887        TCGA-AB-2888        TCGA-AB-2889 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2890        TCGA-AB-2895        TCGA-AB-2896        TCGA-AB-2897 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2898        TCGA-AB-2899        TCGA-AB-2900        TCGA-AB-2901 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2903        TCGA-AB-2904        TCGA-AB-2908        TCGA-AB-2909 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2910        TCGA-AB-2911        TCGA-AB-2912        TCGA-AB-2913 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2914        TCGA-AB-2915        TCGA-AB-2916        TCGA-AB-2917 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2919        TCGA-AB-2920        TCGA-AB-2921        TCGA-AB-2924 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2925        TCGA-AB-2927        TCGA-AB-2928        TCGA-AB-2930 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2931        TCGA-AB-2932        TCGA-AB-2933        TCGA-AB-2934 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2935        TCGA-AB-2936        TCGA-AB-2937        TCGA-AB-2938 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2939        TCGA-AB-2940        TCGA-AB-2941        TCGA-AB-2942 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2943        TCGA-AB-2944        TCGA-AB-2946        TCGA-AB-2948 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2949        TCGA-AB-2950        TCGA-AB-2952        TCGA-AB-2954 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2955        TCGA-AB-2956        TCGA-AB-2959        TCGA-AB-2963 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2964        TCGA-AB-2965        TCGA-AB-2966        TCGA-AB-2967 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2969        TCGA-AB-2970        TCGA-AB-2971        TCGA-AB-2972 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2973        TCGA-AB-2975        TCGA-AB-2976        TCGA-AB-2977 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2978        TCGA-AB-2980        TCGA-AB-2982        TCGA-AB-2983 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2984        TCGA-AB-2985        TCGA-AB-2986        TCGA-AB-2987 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2988        TCGA-AB-2990        TCGA-AB-2991        TCGA-AB-2992 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2993        TCGA-AB-2994        TCGA-AB-2995        TCGA-AB-2996 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-2998        TCGA-AB-2999        TCGA-AB-3000        TCGA-AB-3001 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-3002        TCGA-AB-3005        TCGA-AB-3006        TCGA-AB-3007 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-AB-3008        TCGA-AB-3009        TCGA-AB-3011        TCGA-AB-3012 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  XP GAIN MUTATED        1      1      0      0      1
  XP GAIN WILD-TYPE     56     30     39     33     18
D15V5, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               1                56
  CLUS_2               1                30
  CLUS_3               0                39
  CLUS_4               0                33
  CLUS_5               1                18
[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
  XP GAIN MUTATED        1      2      0
  XP GAIN WILD-TYPE     66     32     78
D15V6, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               1                66
  CLUS_2               2                32
  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(16) Variable = XQ GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XQ GAIN MUTATED        0      1      1      1
  XQ GAIN WILD-TYPE     49     43     54     42
D16V1, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               0                49
  CLUS_2               1                43
  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
  XQ GAIN MUTATED        1      0      2      0      0
  XQ GAIN WILD-TYPE     22     25     58     35     42
D16V2, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1                22
  CLUS_2               0                25
  CLUS_3               2                58
  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
  XQ GAIN MUTATED        2      0      0
  XQ GAIN WILD-TYPE     69     50     45
D16V3, multiclass
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                2               164 
       TCGA-AB-2803        TCGA-AB-2805        TCGA-AB-2806        TCGA-AB-2807 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2808        TCGA-AB-2810        TCGA-AB-2811        TCGA-AB-2812 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2813        TCGA-AB-2814        TCGA-AB-2815        TCGA-AB-2816 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2817        TCGA-AB-2818        TCGA-AB-2819        TCGA-AB-2821 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2822        TCGA-AB-2823        TCGA-AB-2824        TCGA-AB-2825 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2826        TCGA-AB-2828        TCGA-AB-2830        TCGA-AB-2832 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2834        TCGA-AB-2835        TCGA-AB-2836        TCGA-AB-2837 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2838        TCGA-AB-2839        TCGA-AB-2840        TCGA-AB-2841 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2842        TCGA-AB-2844        TCGA-AB-2845        TCGA-AB-2846 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2848        TCGA-AB-2849        TCGA-AB-2851        TCGA-AB-2853 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2854        TCGA-AB-2855        TCGA-AB-2856        TCGA-AB-2857 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2858        TCGA-AB-2859        TCGA-AB-2860        TCGA-AB-2861 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2862        TCGA-AB-2863        TCGA-AB-2865        TCGA-AB-2866 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2867        TCGA-AB-2868        TCGA-AB-2869        TCGA-AB-2870 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2871        TCGA-AB-2872        TCGA-AB-2873        TCGA-AB-2874 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2875        TCGA-AB-2877        TCGA-AB-2879        TCGA-AB-2880 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2881        TCGA-AB-2882        TCGA-AB-2884        TCGA-AB-2885 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2886        TCGA-AB-2887        TCGA-AB-2888        TCGA-AB-2889 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2890        TCGA-AB-2895        TCGA-AB-2896        TCGA-AB-2897 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2898        TCGA-AB-2899        TCGA-AB-2900        TCGA-AB-2901 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2903        TCGA-AB-2904        TCGA-AB-2908        TCGA-AB-2909 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2910        TCGA-AB-2911        TCGA-AB-2912        TCGA-AB-2913 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2914        TCGA-AB-2915        TCGA-AB-2916        TCGA-AB-2917 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2919        TCGA-AB-2920        TCGA-AB-2921        TCGA-AB-2924 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2925        TCGA-AB-2927        TCGA-AB-2928        TCGA-AB-2930 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2931        TCGA-AB-2932        TCGA-AB-2933        TCGA-AB-2934 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2935        TCGA-AB-2936        TCGA-AB-2937        TCGA-AB-2938 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2939        TCGA-AB-2940        TCGA-AB-2941        TCGA-AB-2942 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2943        TCGA-AB-2944        TCGA-AB-2946        TCGA-AB-2948 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2949        TCGA-AB-2950        TCGA-AB-2952        TCGA-AB-2954 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2955        TCGA-AB-2956        TCGA-AB-2959        TCGA-AB-2963 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2964        TCGA-AB-2965        TCGA-AB-2966        TCGA-AB-2967 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2969        TCGA-AB-2970        TCGA-AB-2971        TCGA-AB-2972 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2973        TCGA-AB-2975        TCGA-AB-2976        TCGA-AB-2977 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2978        TCGA-AB-2980        TCGA-AB-2982        TCGA-AB-2983 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2984        TCGA-AB-2985        TCGA-AB-2986        TCGA-AB-2987 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2988        TCGA-AB-2990        TCGA-AB-2991        TCGA-AB-2992 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2993        TCGA-AB-2994        TCGA-AB-2995        TCGA-AB-2996 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2998        TCGA-AB-2999        TCGA-AB-3000        TCGA-AB-3001 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-3002        TCGA-AB-3005        TCGA-AB-3006        TCGA-AB-3007 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-3008        TCGA-AB-3009        TCGA-AB-3011        TCGA-AB-3012 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  XQ GAIN MUTATED        0      0      0      2      0      0
  XQ GAIN WILD-TYPE     16     13     14     53     26     42
D16V4, multiclass
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                2               164 
       TCGA-AB-2803        TCGA-AB-2805        TCGA-AB-2806        TCGA-AB-2807 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2808        TCGA-AB-2810        TCGA-AB-2811        TCGA-AB-2812 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2813        TCGA-AB-2814        TCGA-AB-2815        TCGA-AB-2816 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2817        TCGA-AB-2818        TCGA-AB-2819        TCGA-AB-2821 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2822        TCGA-AB-2823        TCGA-AB-2824        TCGA-AB-2825 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2826        TCGA-AB-2828        TCGA-AB-2830        TCGA-AB-2832 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2834        TCGA-AB-2835        TCGA-AB-2836        TCGA-AB-2837 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2838        TCGA-AB-2839        TCGA-AB-2840        TCGA-AB-2841 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2842        TCGA-AB-2844        TCGA-AB-2845        TCGA-AB-2846 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2848        TCGA-AB-2849        TCGA-AB-2851        TCGA-AB-2853 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2854        TCGA-AB-2855        TCGA-AB-2856        TCGA-AB-2857 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2858        TCGA-AB-2859        TCGA-AB-2860        TCGA-AB-2861 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2862        TCGA-AB-2863        TCGA-AB-2865        TCGA-AB-2866 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2867        TCGA-AB-2868        TCGA-AB-2869        TCGA-AB-2870 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2871        TCGA-AB-2872        TCGA-AB-2873        TCGA-AB-2874 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2875        TCGA-AB-2877        TCGA-AB-2879        TCGA-AB-2880 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2881        TCGA-AB-2882        TCGA-AB-2884        TCGA-AB-2885 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2886        TCGA-AB-2887        TCGA-AB-2888        TCGA-AB-2889 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2890        TCGA-AB-2895        TCGA-AB-2896        TCGA-AB-2897 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2898        TCGA-AB-2899        TCGA-AB-2900        TCGA-AB-2901 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2903        TCGA-AB-2904        TCGA-AB-2908        TCGA-AB-2909 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2910        TCGA-AB-2911        TCGA-AB-2912        TCGA-AB-2913 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2914        TCGA-AB-2915        TCGA-AB-2916        TCGA-AB-2917 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2919        TCGA-AB-2920        TCGA-AB-2921        TCGA-AB-2924 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2925        TCGA-AB-2927        TCGA-AB-2928        TCGA-AB-2930 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2931        TCGA-AB-2932        TCGA-AB-2933        TCGA-AB-2934 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2935        TCGA-AB-2936        TCGA-AB-2937        TCGA-AB-2938 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2939        TCGA-AB-2940        TCGA-AB-2941        TCGA-AB-2942 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2943        TCGA-AB-2944        TCGA-AB-2946        TCGA-AB-2948 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2949        TCGA-AB-2950        TCGA-AB-2952        TCGA-AB-2954 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2955        TCGA-AB-2956        TCGA-AB-2959        TCGA-AB-2963 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2964        TCGA-AB-2965        TCGA-AB-2966        TCGA-AB-2967 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2969        TCGA-AB-2970        TCGA-AB-2971        TCGA-AB-2972 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2973        TCGA-AB-2975        TCGA-AB-2976        TCGA-AB-2977 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2978        TCGA-AB-2980        TCGA-AB-2982        TCGA-AB-2983 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2984        TCGA-AB-2985        TCGA-AB-2986        TCGA-AB-2987 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2988        TCGA-AB-2990        TCGA-AB-2991        TCGA-AB-2992 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2993        TCGA-AB-2994        TCGA-AB-2995        TCGA-AB-2996 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2998        TCGA-AB-2999        TCGA-AB-3000        TCGA-AB-3001 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-3002        TCGA-AB-3005        TCGA-AB-3006        TCGA-AB-3007 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-3008        TCGA-AB-3009        TCGA-AB-3011        TCGA-AB-3012 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  XQ GAIN MUTATED        1      1      0      0      1
  XQ GAIN WILD-TYPE     56     30     39     33     18
D16V5, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1                56
  CLUS_2               1                30
  CLUS_3               0                39
  CLUS_4               0                33
  CLUS_5               1                18
[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
  XQ GAIN MUTATED        1      2      0
  XQ GAIN WILD-TYPE     66     32     78
D16V6, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1                66
  CLUS_2               2                32
  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(17) Variable = 3P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P LOSS MUTATED        0      3      0      0
  3P LOSS WILD-TYPE     49     41     55     43
D17V1, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                49
  CLUS_2               3                41
  CLUS_3               0                55
  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
  3P LOSS MUTATED        0      0      3      0      0
  3P LOSS WILD-TYPE     23     25     57     35     42
D17V2, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS 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
  3P LOSS MUTATED        2      1      0
  3P LOSS WILD-TYPE     69     49     45
D17V3, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS 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
  3P LOSS MUTATED        0      0      0      2      0      1
  3P LOSS WILD-TYPE     16     13     14     53     26     41
D17V4, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                16
  CLUS_2               0                13
  CLUS_3               0                14
  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
  3P LOSS MUTATED        0      2      0      1      0
  3P LOSS WILD-TYPE     57     29     39     32     19
D17V5, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                57
  CLUS_2               2                29
  CLUS_3               0                39
  CLUS_4               1                32
  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
  3P LOSS MUTATED        0      2      1
  3P LOSS WILD-TYPE     67     32     77
D17V6, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                67
  CLUS_2               2                32
  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(18) Variable = 3Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3Q LOSS MUTATED        0      3      0      0
  3Q LOSS WILD-TYPE     49     41     55     43
D18V1, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                49
  CLUS_2               3                41
  CLUS_3               0                55
  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
  3Q LOSS MUTATED        0      0      3      0      0
  3Q LOSS WILD-TYPE     23     25     57     35     42
D18V2, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS 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
  3Q LOSS MUTATED        2      1      0
  3Q LOSS WILD-TYPE     69     49     45
D18V3, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS 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
  3Q LOSS MUTATED        0      0      0      2      0      1
  3Q LOSS WILD-TYPE     16     13     14     53     26     41
D18V4, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                16
  CLUS_2               0                13
  CLUS_3               0                14
  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
  3Q LOSS MUTATED        0      2      0      1      0
  3Q LOSS WILD-TYPE     57     29     39     32     19
D18V5, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                57
  CLUS_2               2                29
  CLUS_3               0                39
  CLUS_4               1                32
  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
  3Q LOSS MUTATED        0      2      1
  3Q LOSS WILD-TYPE     67     32     77
D18V6, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                67
  CLUS_2               2                32
  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(19) Variable = 5Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5Q LOSS MUTATED        0      3      2      1
  5Q LOSS WILD-TYPE     49     41     53     42
D19V1, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               0                49
  CLUS_2               3                41
  CLUS_3               2                53
  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
  5Q LOSS MUTATED        0      0      6      0      0
  5Q LOSS WILD-TYPE     23     25     54     35     42
D19V2, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               0                23
  CLUS_2               0                25
  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
  5Q LOSS MUTATED        4      1      0
  5Q LOSS WILD-TYPE     67     49     45
D19V3, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               4                67
  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
  5Q LOSS MUTATED        0      0      0      4      0      1
  5Q LOSS WILD-TYPE     16     13     14     51     26     41
D19V4, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               0                16
  CLUS_2               0                13
  CLUS_3               0                14
  CLUS_4               4                51
  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
  5Q LOSS MUTATED        0      3      0      1      1
  5Q LOSS WILD-TYPE     57     28     39     32     18
D19V5, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               0                57
  CLUS_2               3                28
  CLUS_3               0                39
  CLUS_4               1                32
  CLUS_5               1                18
[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
  5Q LOSS MUTATED        0      3      2
  5Q LOSS WILD-TYPE     67     31     76
D19V6, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               0                67
  CLUS_2               3                31
  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(20) Variable = 7P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7P LOSS MUTATED        0      5      0     12
  7P LOSS WILD-TYPE     49     39     55     31
D20V1, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               0                49
  CLUS_2               5                39
  CLUS_3               0                55
  CLUS_4              12                31
[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
  7P LOSS MUTATED        1      1     14      0      1
  7P LOSS WILD-TYPE     22     24     46     35     41
D20V2, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               1                22
  CLUS_2               1                24
  CLUS_3              14                46
  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
  7P LOSS MUTATED       13      0      3
  7P LOSS WILD-TYPE     58     50     42
D20V3, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1              13                58
  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
  7P LOSS MUTATED        0      0      0     16      0      0
  7P LOSS WILD-TYPE     16     13     14     39     26     42
D20V4, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               0                16
  CLUS_2               0                13
  CLUS_3               0                14
  CLUS_4              16                39
  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
  7P LOSS MUTATED        1      8      4      2      2
  7P LOSS WILD-TYPE     56     23     35     31     17
D20V5, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               1                56
  CLUS_2               8                23
  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
  7P LOSS MUTATED        1      7      9
  7P LOSS WILD-TYPE     66     27     69
D20V6, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               1                66
  CLUS_2               7                27
  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(21) Variable = 7Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7Q LOSS MUTATED        1      6      0     13
  7Q LOSS WILD-TYPE     48     38     55     30
D21V1, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               1                48
  CLUS_2               6                38
  CLUS_3               0                55
  CLUS_4              13                30
[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
  7Q LOSS MUTATED        1      1     17      0      1
  7Q LOSS WILD-TYPE     22     24     43     35     41
D21V2, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               1                22
  CLUS_2               1                24
  CLUS_3              17                43
  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
  7Q LOSS MUTATED       13      1      3
  7Q LOSS WILD-TYPE     58     49     42
D21V3, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1              13                58
  CLUS_2               1                49
  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
  7Q LOSS MUTATED        0      0      0     17      0      0
  7Q LOSS WILD-TYPE     16     13     14     38     26     42
D21V4, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               0                16
  CLUS_2               0                13
  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
  7Q LOSS MUTATED        1      9      4      3      2
  7Q LOSS WILD-TYPE     56     22     35     30     17
D21V5, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               1                56
  CLUS_2               9                22
  CLUS_3               4                35
  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
  7Q LOSS MUTATED        1      8     10
  7Q LOSS WILD-TYPE     66     26     68
D21V6, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               1                66
  CLUS_2               8                26
  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(22) Variable = 12P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12P LOSS MUTATED        0      2      1      1
  12P LOSS WILD-TYPE     49     42     54     42
D22V1, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                0                 49
  CLUS_2                2                 42
  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
  12P LOSS MUTATED        0      0      3      1      0
  12P LOSS WILD-TYPE     23     25     57     34     42
D22V2, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                0                 23
  CLUS_2                0                 25
  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
  12P LOSS MUTATED        3      0      1
  12P LOSS WILD-TYPE     68     50     44
D22V3, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                3                 68
  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
  12P LOSS MUTATED        0      0      1      3      0      0
  12P LOSS WILD-TYPE     16     13     13     52     26     42
D22V4, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                0                 16
  CLUS_2                0                 13
  CLUS_3                1                 13
  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
  12P LOSS MUTATED        1      2      0      1      0
  12P LOSS WILD-TYPE     56     29     39     32     19
D22V5, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                1                 56
  CLUS_2                2                 29
  CLUS_3                0                 39
  CLUS_4                1                 32
  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
  12P LOSS MUTATED        0      2      2
  12P LOSS WILD-TYPE     67     32     76
D22V6, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                0                 67
  CLUS_2                2                 32
  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(23) Variable = 15Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  15Q LOSS MUTATED        0      2      1      1
  15Q LOSS WILD-TYPE     49     42     54     42
D23V1, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                 49
  CLUS_2                2                 42
  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
  15Q LOSS MUTATED        0      0      2      2      0
  15Q LOSS WILD-TYPE     23     25     58     33     42
D23V2, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                 23
  CLUS_2                0                 25
  CLUS_3                2                 58
  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
  15Q LOSS MUTATED        4      0      0
  15Q LOSS WILD-TYPE     67     50     45
D23V3, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                4                 67
  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
  15Q LOSS MUTATED        0      0      0      4      0      0
  15Q LOSS WILD-TYPE     16     13     14     51     26     42
D23V4, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                 16
  CLUS_2                0                 13
  CLUS_3                0                 14
  CLUS_4                4                 51
  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
  15Q LOSS MUTATED        0      2      1      0      1
  15Q LOSS WILD-TYPE     57     29     38     33     18
D23V5, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                 57
  CLUS_2                2                 29
  CLUS_3                1                 38
  CLUS_4                0                 33
  CLUS_5                1                 18
[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
  15Q LOSS MUTATED        0      2      2
  15Q LOSS WILD-TYPE     67     32     76
D23V6, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                 67
  CLUS_2                2                 32
  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(24) Variable = 16Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16Q LOSS MUTATED        0      3      0      1
  16Q LOSS WILD-TYPE     49     41     55     42
D24V1, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                 49
  CLUS_2                3                 41
  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
  16Q LOSS MUTATED        0      0      4      0      0
  16Q LOSS WILD-TYPE     23     25     56     35     42
D24V2, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS 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
  16Q LOSS MUTATED        2      1      0
  16Q LOSS WILD-TYPE     69     49     45
D24V3, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS 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
  16Q LOSS MUTATED        0      0      0      2      0      1
  16Q LOSS WILD-TYPE     16     13     14     53     26     41
D24V4, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                 16
  CLUS_2                0                 13
  CLUS_3                0                 14
  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
  16Q LOSS MUTATED        0      3      0      1      0
  16Q LOSS WILD-TYPE     57     28     39     32     19
D24V5, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                 57
  CLUS_2                3                 28
  CLUS_3                0                 39
  CLUS_4                1                 32
  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
  16Q LOSS MUTATED        0      3      1
  16Q LOSS WILD-TYPE     67     31     77
D24V6, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                 67
  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(25) Variable = 17P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17P LOSS MUTATED        0      7      3      3
  17P LOSS WILD-TYPE     49     37     52     40
D25V1, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                0                 49
  CLUS_2                7                 37
  CLUS_3                3                 52
  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
  17P LOSS MUTATED        0      0     10      3      0
  17P LOSS WILD-TYPE     23     25     50     32     42
D25V2, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                0                 23
  CLUS_2                0                 25
  CLUS_3               10                 50
  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
  17P LOSS MUTATED        9      2      2
  17P LOSS WILD-TYPE     62     48     43
D25V3, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS 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
  17P LOSS MUTATED        0      0      0     12      0      1
  17P LOSS WILD-TYPE     16     13     14     43     26     41
D25V4, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                0                 16
  CLUS_2                0                 13
  CLUS_3                0                 14
  CLUS_4               12                 43
  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
  17P LOSS MUTATED        2      5      3      1      2
  17P LOSS WILD-TYPE     55     26     36     32     17
D25V5, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                2                 55
  CLUS_2                5                 26
  CLUS_3                3                 36
  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
  17P LOSS MUTATED        0      4      9
  17P LOSS WILD-TYPE     67     30     69
D25V6, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS 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(26) Variable = 17Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q LOSS MUTATED        0      4      1      2
  17Q LOSS WILD-TYPE     49     40     54     41
D26V1, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                 49
  CLUS_2                4                 40
  CLUS_3                1                 54
  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
  17Q LOSS MUTATED        0      0      5      2      0
  17Q LOSS WILD-TYPE     23     25     55     33     42
D26V2, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                 23
  CLUS_2                0                 25
  CLUS_3                5                 55
  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
  17Q LOSS MUTATED        6      1      0
  17Q LOSS WILD-TYPE     65     49     45
D26V3, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS 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
  17Q LOSS MUTATED        0      0      0      6      0      1
  17Q LOSS WILD-TYPE     16     13     14     49     26     41
D26V4, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS 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
  17Q LOSS MUTATED        0      3      2      1      1
  17Q LOSS WILD-TYPE     57     28     37     32     18
D26V5, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                 57
  CLUS_2                3                 28
  CLUS_3                2                 37
  CLUS_4                1                 32
  CLUS_5                1                 18
[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
  17Q LOSS MUTATED        0      3      4
  17Q LOSS WILD-TYPE     67     31     74
D26V6, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS 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(27) Variable = 18P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18P LOSS MUTATED        0      4      0      1
  18P LOSS WILD-TYPE     49     40     55     42
D27V1, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                0                 49
  CLUS_2                4                 40
  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
  18P LOSS MUTATED        0      0      5      0      0
  18P LOSS WILD-TYPE     23     25     55     35     42
D27V2, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                0                 23
  CLUS_2                0                 25
  CLUS_3                5                 55
  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
  18P LOSS MUTATED        2      1      1
  18P LOSS WILD-TYPE     69     49     44
D27V3, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                2                 69
  CLUS_2                1                 49
  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
  18P LOSS MUTATED        0      0      0      3      0      1
  18P LOSS WILD-TYPE     16     13     14     52     26     41
D27V4, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                0                 16
  CLUS_2                0                 13
  CLUS_3                0                 14
  CLUS_4                3                 52
  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
  18P LOSS MUTATED        0      2      1      1      0
  18P LOSS WILD-TYPE     57     29     38     32     19
D27V5, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                0                 57
  CLUS_2                2                 29
  CLUS_3                1                 38
  CLUS_4                1                 32
  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
  18P LOSS MUTATED        0      2      2
  18P LOSS WILD-TYPE     67     32     76
D27V6, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                0                 67
  CLUS_2                2                 32
  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(28) Variable = 18Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18Q LOSS MUTATED        0      2      1      1
  18Q LOSS WILD-TYPE     49     42     54     42
D28V1, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                0                 49
  CLUS_2                2                 42
  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
  18Q LOSS MUTATED        0      0      4      0      0
  18Q LOSS WILD-TYPE     23     25     56     35     42
D28V2, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS 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
  18Q LOSS MUTATED        3      1      0
  18Q LOSS WILD-TYPE     68     49     45
D28V3, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                3                 68
  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
  18Q LOSS MUTATED        0      0      0      3      0      1
  18Q LOSS WILD-TYPE     16     13     14     52     26     41
D28V4, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                0                 16
  CLUS_2                0                 13
  CLUS_3                0                 14
  CLUS_4                3                 52
  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
  18Q LOSS MUTATED        0      2      0      2      0
  18Q LOSS WILD-TYPE     57     29     39     31     19
D28V5, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                0                 57
  CLUS_2                2                 29
  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
  18Q LOSS MUTATED        0      2      2
  18Q LOSS WILD-TYPE     67     32     76
D28V6, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                0                 67
  CLUS_2                2                 32
  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(29) Variable = 19P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P LOSS MUTATED        0      1      2      0
  19P LOSS WILD-TYPE     49     43     53     43
D29V1, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                0                 49
  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
  19P LOSS MUTATED        0      0      2      1      0
  19P LOSS WILD-TYPE     23     25     58     34     42
D29V2, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS 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
  19P LOSS MUTATED        2      1      0
  19P LOSS WILD-TYPE     69     49     45
D29V3, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS 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
  19P LOSS MUTATED        0      0      0      2      0      1
  19P LOSS WILD-TYPE     16     13     14     53     26     41
D29V4, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                0                 16
  CLUS_2                0                 13
  CLUS_3                0                 14
  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
  19P LOSS MUTATED        0      0      1      1      1
  19P LOSS WILD-TYPE     57     31     38     32     18
D29V5, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                0                 57
  CLUS_2                0                 31
  CLUS_3                1                 38
  CLUS_4                1                 32
  CLUS_5                1                 18
[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
  19P LOSS MUTATED        0      1      2
  19P LOSS WILD-TYPE     67     33     76
D29V6, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS 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"

Clustering(30) Variable = 19Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19Q LOSS MUTATED        0      1      2      0
  19Q LOSS WILD-TYPE     49     43     53     43
D30V1, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                0                 49
  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
  19Q LOSS MUTATED        0      0      2      1      0
  19Q LOSS WILD-TYPE     23     25     58     34     42
D30V2, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS 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
  19Q LOSS MUTATED        2      1      0
  19Q LOSS WILD-TYPE     69     49     45
D30V3, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS 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
  19Q LOSS MUTATED        0      0      0      2      0      1
  19Q LOSS WILD-TYPE     16     13     14     53     26     41
D30V4, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                0                 16
  CLUS_2                0                 13
  CLUS_3                0                 14
  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
  19Q LOSS MUTATED        0      0      1      1      1
  19Q LOSS WILD-TYPE     57     31     38     32     18
D30V5, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                0                 57
  CLUS_2                0                 31
  CLUS_3                1                 38
  CLUS_4                1                 32
  CLUS_5                1                 18
[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
  19Q LOSS MUTATED        0      1      2
  19Q LOSS WILD-TYPE     67     33     76
D30V6, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS 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"

Clustering(31) Variable = XP LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XP LOSS MUTATED        0      4      0      1
  XP LOSS WILD-TYPE     49     40     55     42
D31V1, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1               0                49
  CLUS_2               4                40
  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
  XP LOSS MUTATED        0      0      4      1      0
  XP LOSS WILD-TYPE     23     25     56     34     42
D31V2, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1               0                23
  CLUS_2               0                25
  CLUS_3               4                56
  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
  XP LOSS MUTATED        4      1      0
  XP LOSS WILD-TYPE     67     49     45
D31V3, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1               4                67
  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
  XP LOSS MUTATED        0      0      0      4      0      1
  XP LOSS WILD-TYPE     16     13     14     51     26     41
D31V4, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1               0                16
  CLUS_2               0                13
  CLUS_3               0                14
  CLUS_4               4                51
  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
  XP LOSS MUTATED        0      4      0      1      0
  XP LOSS WILD-TYPE     57     27     39     32     19
D31V5, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1               0                57
  CLUS_2               4                27
  CLUS_3               0                39
  CLUS_4               1                32
  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
  XP LOSS MUTATED        0      4      1
  XP LOSS WILD-TYPE     67     30     77
D31V6, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1               0                67
  CLUS_2               4                30
  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(32) Variable = XQ LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XQ LOSS MUTATED        0      4      0      1
  XQ LOSS WILD-TYPE     49     40     55     42
D32V1, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                49
  CLUS_2               4                40
  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
  XQ LOSS MUTATED        0      0      4      1      0
  XQ LOSS WILD-TYPE     23     25     56     34     42
D32V2, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                23
  CLUS_2               0                25
  CLUS_3               4                56
  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
  XQ LOSS MUTATED        4      1      0
  XQ LOSS WILD-TYPE     67     49     45
D32V3, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               4                67
  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
  XQ LOSS MUTATED        0      0      0      4      0      1
  XQ LOSS WILD-TYPE     16     13     14     51     26     41
D32V4, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                16
  CLUS_2               0                13
  CLUS_3               0                14
  CLUS_4               4                51
  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
  XQ LOSS MUTATED        0      4      0      1      0
  XQ LOSS WILD-TYPE     57     27     39     32     19
D32V5, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                57
  CLUS_2               4                27
  CLUS_3               0                39
  CLUS_4               1                32
  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
  XQ LOSS MUTATED        0      4      1
  XQ LOSS WILD-TYPE     67     30     77
D32V6, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                67
  CLUS_2               4                30
  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"
