[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/Append_Data/LAML-TB/15082450/LAML-TB.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LAML-TB/15087095/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 23 to 20."
[1]  20 191
[1] "AMP PEAK 1(1P33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 1(1P33) MUTATED AMP PEAK 1(1P33) WILD-TYPE 
                         7                        184 
  AMP PEAK 1(1P33) MUTATED AMP PEAK 1(1P33) WILD-TYPE 
                         7                        184 
[1] "AMP PEAK 2(1Q43) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 2(1Q43) MUTATED AMP PEAK 2(1Q43) WILD-TYPE 
                         7                        184 
  AMP PEAK 2(1Q43) MUTATED AMP PEAK 2(1Q43) WILD-TYPE 
                         7                        184 
[1] "AMP PEAK 3(11Q23.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 3(11Q23.3) MUTATED AMP PEAK 3(11Q23.3) WILD-TYPE 
                           17                           174 
  AMP PEAK 3(11Q23.3) MUTATED AMP PEAK 3(11Q23.3) WILD-TYPE 
                           17                           174 
[1] "AMP PEAK 4(13Q31.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 4(13Q31.3) MUTATED AMP PEAK 4(13Q31.3) WILD-TYPE 
                            7                           184 
  AMP PEAK 4(13Q31.3) MUTATED AMP PEAK 4(13Q31.3) WILD-TYPE 
                            7                           184 
[1] "AMP PEAK 5(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 5(19P13.2) MUTATED AMP PEAK 5(19P13.2) WILD-TYPE 
                            6                           185 
  AMP PEAK 5(19P13.2) MUTATED AMP PEAK 5(19P13.2) WILD-TYPE 
                            6                           185 
[1] "AMP PEAK 6(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 6(20Q11.21) MUTATED AMP PEAK 6(20Q11.21) WILD-TYPE 
                             3                            188 
  AMP PEAK 6(20Q11.21) MUTATED AMP PEAK 6(20Q11.21) WILD-TYPE 
                             3                            188 
[1] "AMP PEAK 7(21Q22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 7(21Q22.2) MUTATED AMP PEAK 7(21Q22.2) WILD-TYPE 
                           14                           177 
  AMP PEAK 7(21Q22.2) MUTATED AMP PEAK 7(21Q22.2) WILD-TYPE 
                           14                           177 
[1] "DEL PEAK  2(3P13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(3P13) MUTATED DEL PEAK  2(3P13) WILD-TYPE 
                          8                         183 
  DEL PEAK  2(3P13) MUTATED DEL PEAK  2(3P13) WILD-TYPE 
                          8                         183 
[1] "DEL PEAK  3(5Q31.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(5Q31.2) MUTATED DEL PEAK  3(5Q31.2) WILD-TYPE 
                           18                           173 
  DEL PEAK  3(5Q31.2) MUTATED DEL PEAK  3(5Q31.2) WILD-TYPE 
                           18                           173 
[1] "DEL PEAK  4(7P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(7P12.1) MUTATED DEL PEAK  4(7P12.1) WILD-TYPE 
                           16                           175 
  DEL PEAK  4(7P12.1) MUTATED DEL PEAK  4(7P12.1) WILD-TYPE 
                           16                           175 
[1] "DEL PEAK  5(7Q34) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(7Q34) MUTATED DEL PEAK  5(7Q34) WILD-TYPE 
                         24                         167 
  DEL PEAK  5(7Q34) MUTATED DEL PEAK  5(7Q34) WILD-TYPE 
                         24                         167 
[1] "DEL PEAK  6(7Q34) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(7Q34) MUTATED DEL PEAK  6(7Q34) WILD-TYPE 
                         24                         167 
  DEL PEAK  6(7Q34) MUTATED DEL PEAK  6(7Q34) WILD-TYPE 
                         24                         167 
[1] "DEL PEAK  8(9Q21.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(9Q21.32) MUTATED DEL PEAK  8(9Q21.32) WILD-TYPE 
                             5                            186 
  DEL PEAK  8(9Q21.32) MUTATED DEL PEAK  8(9Q21.32) WILD-TYPE 
                             5                            186 
[1] "DEL PEAK 10(12P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(12P13.2) MUTATED DEL PEAK 10(12P13.2) WILD-TYPE 
                            10                            181 
  DEL PEAK 10(12P13.2) MUTATED DEL PEAK 10(12P13.2) WILD-TYPE 
                            10                            181 
[1] "DEL PEAK 11(12Q21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(12Q21.33) MUTATED DEL PEAK 11(12Q21.33) WILD-TYPE 
                              3                             188 
  DEL PEAK 11(12Q21.33) MUTATED DEL PEAK 11(12Q21.33) WILD-TYPE 
                              3                             188 
[1] "DEL PEAK 12(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(16Q23.1) MUTATED DEL PEAK 12(16Q23.1) WILD-TYPE 
                             9                            182 
  DEL PEAK 12(16Q23.1) MUTATED DEL PEAK 12(16Q23.1) WILD-TYPE 
                             9                            182 
[1] "DEL PEAK 13(17P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(17P13.2) MUTATED DEL PEAK 13(17P13.2) WILD-TYPE 
                            15                            176 
  DEL PEAK 13(17P13.2) MUTATED DEL PEAK 13(17P13.2) WILD-TYPE 
                            15                            176 
[1] "DEL PEAK 14(17Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(17Q11.2) MUTATED DEL PEAK 14(17Q11.2) WILD-TYPE 
                            13                            178 
  DEL PEAK 14(17Q11.2) MUTATED DEL PEAK 14(17Q11.2) WILD-TYPE 
                            13                            178 
[1] "DEL PEAK 15(18P11.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(18P11.21) MUTATED DEL PEAK 15(18P11.21) WILD-TYPE 
                              9                             182 
  DEL PEAK 15(18P11.21) MUTATED DEL PEAK 15(18P11.21) WILD-TYPE 
                              9                             182 
[1] "DEL PEAK 16(20Q13.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(20Q13.13) MUTATED DEL PEAK 16(20Q13.13) WILD-TYPE 
                              4                             187 
  DEL PEAK 16(20Q13.13) MUTATED DEL PEAK 16(20Q13.13) WILD-TYPE 
                              4                             187 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "PRIMARY_SITE_OF_DISEASE"             
 [6] "DCC_UPLOAD_DATE"                     
 [7] "GENDER"                              
 [8] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
 [9] "DAYS_TO_LAST_KNOWN_ALIVE"            
[10] "KARNOFSKY_PERFORMANCE_SCORE"         
[11] "RACE"                                
[12] "ETHNICITY"                           
[13] "BATCH_NUMBER"                        

Input Data has 13 rows and 191 columns.

[1] "Batch" "13"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=63,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=60,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'DCC_UPLOAD_DATE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 9:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DAYS_TO_LAST_KNOWN_ALIVE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "KARNOFSKY_PERFORMANCE_SCORE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 11:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'BATCH_NUMBER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "BATCH_NUMBER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
[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"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 191 columns, 1 survival variables, and 4 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH" "GENDER"         "RACE"           "ETHNICITY"     
YEARS_TO_BIRTH, nv=63, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK 1(1P33) MUTATION ANALYSIS
D1V1, survival
                            sevent
clus2                          0   1
  AMP PEAK 1(1P33) MUTATED     1   5
  AMP PEAK 1(1P33) WILD-TYPE  61 111
  AMP PEAK 1(1P33) MUTATED AMP PEAK 1(1P33) WILD-TYPE 
                         6                        172 
  AMP PEAK 1(1P33) MUTATED AMP PEAK 1(1P33) WILD-TYPE 
                         5                        111 
$`AMP PEAK 1(1P33) MUTATED`
TCGA-AB-2820 TCGA-AB-2822 TCGA-AB-2878 TCGA-AB-2904 TCGA-AB-2934 TCGA-AB-2952 
        0.00        31.99        12.00        17.00         0.92         1.02 

$`AMP PEAK 1(1P33) WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
        2.04         1.02         7.99        12.03         1.02        26.04 
TCGA-AB-2815 TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2821 
       27.02         8.05         8.98         9.96        82.06        27.02 
TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 TCGA-AB-2828 
        0.00         0.99         6.97        24.03         8.98        75.09 
TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 TCGA-AB-2835 
        8.98         9.04        21.04        12.00         8.05        55.00 
TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 
       17.03         0.00        12.00        15.98         0.92        46.06 
TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 TCGA-AB-2849 
        0.00         4.01         9.99        46.09        14.96        72.99 
TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2856 
        2.01         7.96         2.93        12.03         6.97         4.93 
TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 
       10.06        18.97         9.99        14.04         0.00        47.01 
TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 
        1.02        18.97         2.01         5.03         6.05         4.96 
TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 
        7.99         5.03         5.03        20.98         8.98        13.02 
TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 
        6.97        20.98         8.05        12.92        12.00        24.00 
TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 
       24.03         7.04         5.95        10.98         9.99         0.00 
TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 
       31.00         6.97         5.95         5.03         7.04         7.99 
TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2905 
       12.92        22.06         6.05         1.94         0.00        52.96 
TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 
       18.97         1.02         0.99         0.00        38.99         9.01 
TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2919 
       39.98        26.04         0.00        29.00        39.98         2.01 
TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 
       12.03         0.00         1.02         2.96         7.99        15.02 
TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2935 TCGA-AB-2936 
        2.96         4.04         0.00         4.01         2.01         1.94 
TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2942 TCGA-AB-2945 
        7.07         9.99        14.96         0.00        21.07         7.99 
TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2954 TCGA-AB-2955 
        1.02        19.07        22.98        10.06        49.05        16.08 
TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 
        6.02        20.02        16.08        53.98        41.98        11.01 
TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 
       28.08        34.03        15.06        37.05        10.03        26.04 
TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 
        0.99        20.02         3.02        30.08         1.02        22.98 
TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 
       22.98         4.93        11.01        38.04         8.98         6.97 
TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 
        6.05         0.99        12.00        15.02        60.03        56.09 
TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 
       25.02        59.11        50.99        51.98         1.02        57.04 
TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 
       41.06        51.98        47.05        69.04        15.95        51.98 
TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       27.02        18.97        61.97        62.04 

  AMP PEAK 1(1P33) MUTATED AMP PEAK 1(1P33) WILD-TYPE 
                         0                          0 
  AMP PEAK 1(1P33) MUTATED AMP PEAK 1(1P33) WILD-TYPE 
                     31.99                      94.06 
  AMP PEAK 1(1P33) MUTATED AMP PEAK 1(1P33) WILD-TYPE 
                      6.51                      11.01 
[1] "0.0 - 32.0 (6.5)"  "0.0 - 94.1 (11.0)"
[1] "hr=" "1.8"
D1V2, continuous
D1V3, binary
                            cls
clus                           0   1
  AMP PEAK 1(1P33) MUTATED     3   4
  AMP PEAK 1(1P33) WILD-TYPE  84 100
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 1(1P33) MUTATED      3    4
  AMP PEAK 1(1P33) WILD-TYPE   84  100
        clus
vv       AMP PEAK 1(1P33) MUTATED AMP PEAK 1(1P33) WILD-TYPE
  FEMALE                        3                         84
  MALE                          4                        100
[1] 2 2
[1] FALSE
                            vv
clus                         ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 1(1P33) MUTATED       0                         0     7
  AMP PEAK 1(1P33) WILD-TYPE     2                        14   166
D1V4, multiclass
                           clus
vv                          AMP PEAK 1(1P33) MUTATED AMP PEAK 1(1P33) WILD-TYPE
  ASIAN                                            0                          2
  BLACK OR AFRICAN AMERICAN                        0                         14
  WHITE                                            7                        166
[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"
D1V5, binary
                            cls
clus                           0   1
  AMP PEAK 1(1P33) MUTATED     0   7
  AMP PEAK 1(1P33) WILD-TYPE   3 178
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 1(1P33) MUTATED      0    7
  AMP PEAK 1(1P33) WILD-TYPE    3  178
                        clus
vv                       AMP PEAK 1(1P33) MUTATED AMP PEAK 1(1P33) WILD-TYPE
  HISPANIC OR LATINO                            0                          3
  NOT HISPANIC OR LATINO                        7                        178
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK 2(1Q43) MUTATION ANALYSIS
D2V1, survival
                            sevent
clus2                          0   1
  AMP PEAK 2(1Q43) MUTATED     1   5
  AMP PEAK 2(1Q43) WILD-TYPE  61 111
  AMP PEAK 2(1Q43) MUTATED AMP PEAK 2(1Q43) WILD-TYPE 
                         6                        172 
  AMP PEAK 2(1Q43) MUTATED AMP PEAK 2(1Q43) WILD-TYPE 
                         5                        111 
$`AMP PEAK 2(1Q43) MUTATED`
TCGA-AB-2820 TCGA-AB-2915 TCGA-AB-2920 TCGA-AB-2929 TCGA-AB-2938 TCGA-AB-2995 
        0.00         0.00        12.03         4.04         9.99        50.99 

$`AMP PEAK 2(1Q43) WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
        2.04         1.02         7.99        12.03         1.02        26.04 
TCGA-AB-2815 TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2821 
       27.02         8.05         8.98         9.96        82.06        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 
       31.99         0.00         0.99         6.97        24.03         8.98 
TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 
       75.09         8.98         9.04        21.04        12.00         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 
       55.00        17.03         0.00        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 
       46.06         0.00         4.01         9.99        46.09        14.96 
TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 
       72.99         2.01         7.96         2.93        12.03         6.97 
TCGA-AB-2856 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 
        4.93        10.06        18.97         9.99        14.04         0.00 
TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 
       47.01         1.02        18.97         2.01         5.03         6.05 
TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 
        4.96         7.99         5.03         5.03        20.98         8.98 
TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 
       13.02         6.97        20.98        12.00         8.05        12.92 
TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 
       12.00        24.00        24.03         7.04         5.95        10.98 
TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 
        9.99         0.00        31.00         6.97         5.95         5.03 
TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 
        7.04         7.99        12.92        22.06         6.05         1.94 
TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 
        0.00        17.00        52.96        18.97         1.02         0.99 
TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2916 
        0.00        38.99         9.01        39.98        26.04        29.00 
TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 
       39.98         2.01         0.00         1.02         2.96         7.99 
TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 
       15.02         2.96         0.00         4.01         0.92         2.01 
TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2942 TCGA-AB-2945 
        1.94         7.07        14.96         0.00        21.07         7.99 
TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 
        1.02        19.07        22.98        10.06         1.02        49.05 
TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 
       16.08         6.02        20.02        16.08        53.98        41.98 
TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2969 TCGA-AB-2970 
       11.01        28.08        34.03        15.06        37.05        10.03 
TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 
       26.04         0.99        20.02         3.02        30.08         1.02 
TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 
       22.98        22.98         4.93        11.01        38.04         8.98 
TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 
        6.97         6.05         0.99        12.00        15.02        60.03 
TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 
       56.09        25.02        59.11        51.98         1.02        57.04 
TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 
       41.06        51.98        47.05        69.04        15.95        51.98 
TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       27.02        18.97        61.97        62.04 

  AMP PEAK 2(1Q43) MUTATED AMP PEAK 2(1Q43) WILD-TYPE 
                         0                          0 
  AMP PEAK 2(1Q43) MUTATED AMP PEAK 2(1Q43) WILD-TYPE 
                     50.99                      94.06 
  AMP PEAK 2(1Q43) MUTATED AMP PEAK 2(1Q43) WILD-TYPE 
                     7.015                     11.505 
[1] "0.0 - 51.0 (7.0)"  "0.0 - 94.1 (11.5)"
[1] "hr=" "1.8"
D2V2, continuous
D2V3, binary
                            cls
clus                           0   1
  AMP PEAK 2(1Q43) MUTATED     3   4
  AMP PEAK 2(1Q43) WILD-TYPE  84 100
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 2(1Q43) MUTATED      3    4
  AMP PEAK 2(1Q43) WILD-TYPE   84  100
        clus
vv       AMP PEAK 2(1Q43) MUTATED AMP PEAK 2(1Q43) WILD-TYPE
  FEMALE                        3                         84
  MALE                          4                        100
[1] 2 2
[1] FALSE
                            vv
clus                         ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 2(1Q43) MUTATED       0                         0     7
  AMP PEAK 2(1Q43) WILD-TYPE     2                        14   166
D2V4, multiclass
                           clus
vv                          AMP PEAK 2(1Q43) MUTATED AMP PEAK 2(1Q43) WILD-TYPE
  ASIAN                                            0                          2
  BLACK OR AFRICAN AMERICAN                        0                         14
  WHITE                                            7                        166
[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"
D2V5, binary
                            cls
clus                           0   1
  AMP PEAK 2(1Q43) MUTATED     0   7
  AMP PEAK 2(1Q43) WILD-TYPE   3 178
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 2(1Q43) MUTATED      0    7
  AMP PEAK 2(1Q43) WILD-TYPE    3  178
                        clus
vv                       AMP PEAK 2(1Q43) MUTATED AMP PEAK 2(1Q43) WILD-TYPE
  HISPANIC OR LATINO                            0                          3
  NOT HISPANIC OR LATINO                        7                        178
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK 3(11Q23.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 3(11Q23.3) MUTATED     3  12
  AMP PEAK 3(11Q23.3) WILD-TYPE  59 104
  AMP PEAK 3(11Q23.3) MUTATED AMP PEAK 3(11Q23.3) WILD-TYPE 
                           15                           163 
  AMP PEAK 3(11Q23.3) MUTATED AMP PEAK 3(11Q23.3) WILD-TYPE 
                           12                           104 
$`AMP PEAK 3(11Q23.3) MUTATED`
TCGA-AB-2805 TCGA-AB-2820 TCGA-AB-2830 TCGA-AB-2838 TCGA-AB-2866 TCGA-AB-2885 
       18.97         0.00         9.04        12.00         5.03         7.04 
TCGA-AB-2904 TCGA-AB-2916 TCGA-AB-2923 TCGA-AB-2934 TCGA-AB-2948 TCGA-AB-2964 
       17.00        29.00         1.02         0.92        19.07        41.98 
TCGA-AB-2970 TCGA-AB-2977 TCGA-AB-2983 
       10.03         1.02        11.01 

$`AMP PEAK 3(11Q23.3) WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 TCGA-AB-2809 
       26.04        84.07        31.07         5.95        94.06         2.04 
TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 TCGA-AB-2815 
        1.02         7.99        12.03         1.02        26.04        27.02 
TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2821 TCGA-AB-2822 
        8.05         8.98         9.96        82.06        27.02        31.99 
TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 TCGA-AB-2828 
        0.00         0.99         6.97        24.03         8.98        75.09 
TCGA-AB-2829 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 
        8.98        21.04        12.00         8.05        55.00        17.03 
TCGA-AB-2837 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 
        0.00        15.98         0.92        46.06         0.00         4.01 
TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 
        9.99        46.09        14.96        72.99         2.01         7.96 
TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2856 TCGA-AB-2857 TCGA-AB-2858 
        2.93        12.03         6.97         4.93        10.06        18.97 
TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 
        9.99        14.04         0.00        47.01         1.02        18.97 
TCGA-AB-2865 TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 
        2.01         6.05         4.96         7.99         5.03         5.03 
TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 
       20.98         8.98        13.02         6.97        20.98        12.00 
TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2886 
        8.05        12.92        12.00        24.00        24.03         5.95 
TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 
       10.98         9.99         0.00        31.00         6.97         5.95 
TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 
        5.03         7.04         7.99        12.92        22.06         6.05 
TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 
        1.94         0.00        52.96        18.97         1.02         0.99 
TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 
        0.00        38.99         9.01        39.98        26.04         0.00 
TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2924 TCGA-AB-2925 
       39.98         2.01        12.03         0.00         2.96         7.99 
TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2935 
       15.02         2.96         4.04         0.00         4.01         2.01 
TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2942 
        1.94         7.07         9.99        14.96         0.00        21.07 
TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 
        7.99         1.02        22.98        10.06         1.02        49.05 
TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2965 
       16.08         6.02        20.02        16.08        53.98        11.01 
TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2969 TCGA-AB-2971 TCGA-AB-2972 
       28.08        34.03        15.06        37.05        26.04         0.99 
TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 
       20.02         3.02        30.08        22.98        22.98         4.93 
TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 
       38.04         8.98         6.97         6.05         0.99        12.00 
TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 
       15.02        60.03        56.09        25.02        59.11        50.99 
TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 
       51.98         1.02        57.04        41.06        51.98        47.05 
TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 
       69.04        15.95        51.98        27.02        18.97        61.97 
TCGA-AB-3012 
       62.04 

  AMP PEAK 3(11Q23.3) MUTATED AMP PEAK 3(11Q23.3) WILD-TYPE 
                            0                             0 
  AMP PEAK 3(11Q23.3) MUTATED AMP PEAK 3(11Q23.3) WILD-TYPE 
                        41.98                         94.06 
  AMP PEAK 3(11Q23.3) MUTATED AMP PEAK 3(11Q23.3) WILD-TYPE 
                        10.03                         12.00 
[1] "0.0 - 42.0 (10.0)" "0.0 - 94.1 (12.0)"
[1] "hr=" "1.6"
D3V2, continuous
D3V3, binary
                               cls
clus                             0  1
  AMP PEAK 3(11Q23.3) MUTATED    6 11
  AMP PEAK 3(11Q23.3) WILD-TYPE 81 93
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 3(11Q23.3) MUTATED      6   11
  AMP PEAK 3(11Q23.3) WILD-TYPE   81   93
        clus
vv       AMP PEAK 3(11Q23.3) MUTATED AMP PEAK 3(11Q23.3) WILD-TYPE
  FEMALE                           6                            81
  MALE                            11                            93
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 3(11Q23.3) MUTATED       0                         1    16
  AMP PEAK 3(11Q23.3) WILD-TYPE     2                        13   157
D3V4, multiclass
                           clus
vv                          AMP PEAK 3(11Q23.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              16
                           clus
vv                          AMP PEAK 3(11Q23.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                            13
  WHITE                                               157
[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"
D3V5, binary
                               cls
clus                              0   1
  AMP PEAK 3(11Q23.3) MUTATED     1  16
  AMP PEAK 3(11Q23.3) WILD-TYPE   2 169
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 3(11Q23.3) MUTATED      1   16
  AMP PEAK 3(11Q23.3) WILD-TYPE    2  169
                        clus
vv                       AMP PEAK 3(11Q23.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          16
                        clus
vv                       AMP PEAK 3(11Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           169
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK 4(13Q31.3) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 4(13Q31.3) MUTATED     2   5
  AMP PEAK 4(13Q31.3) WILD-TYPE  60 111
  AMP PEAK 4(13Q31.3) MUTATED AMP PEAK 4(13Q31.3) WILD-TYPE 
                            7                           171 
  AMP PEAK 4(13Q31.3) MUTATED AMP PEAK 4(13Q31.3) WILD-TYPE 
                            5                           111 
$`AMP PEAK 4(13Q31.3) MUTATED`
TCGA-AB-2820 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2904 TCGA-AB-2917 TCGA-AB-2933 
        0.00        12.92        22.06        17.00        39.98         4.01 
TCGA-AB-2959 
       16.08 

$`AMP PEAK 4(13Q31.3) WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
        2.04         1.02         7.99        12.03         1.02        26.04 
TCGA-AB-2815 TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2821 
       27.02         8.05         8.98         9.96        82.06        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 
       31.99         0.00         0.99         6.97        24.03         8.98 
TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 
       75.09         8.98         9.04        21.04        12.00         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 
       55.00        17.03         0.00        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 
       46.06         0.00         4.01         9.99        46.09        14.96 
TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 
       72.99         2.01         7.96         2.93        12.03         6.97 
TCGA-AB-2856 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 
        4.93        10.06        18.97         9.99        14.04         0.00 
TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 
       47.01         1.02        18.97         2.01         5.03         6.05 
TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 
        4.96         7.99         5.03         5.03        20.98         8.98 
TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 
       13.02         6.97        20.98        12.00         8.05        12.92 
TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 
       12.00        24.00        24.03         7.04         5.95        10.98 
TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 
        9.99         0.00        31.00         6.97         5.95         5.03 
TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2905 
        7.04         7.99         6.05         1.94         0.00        52.96 
TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 
       18.97         1.02         0.99         0.00        38.99         9.01 
TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2919 TCGA-AB-2920 
       39.98        26.04         0.00        29.00         2.01        12.03 
TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 
        0.00         1.02         2.96         7.99        15.02         2.96 
TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 
        4.04         0.00         0.92         2.01         1.94         7.07 
TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 
        9.99        14.96         0.00        21.07         7.99         1.02 
TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 
       19.07        22.98        10.06         1.02        49.05        16.08 
TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 
        6.02        20.02        53.98        41.98        11.01        28.08 
TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 
       34.03        15.06        37.05        10.03        26.04         0.99 
TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 
       20.02         3.02        30.08         1.02        22.98        22.98 
TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 
        4.93        11.01        38.04         8.98         6.97         6.05 
TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 
        0.99        12.00        15.02        60.03        56.09        25.02 
TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 
       59.11        50.99        51.98         1.02        57.04        41.06 
TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 
       51.98        47.05        69.04        15.95        51.98        27.02 
TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       18.97        61.97        62.04 

  AMP PEAK 4(13Q31.3) MUTATED AMP PEAK 4(13Q31.3) WILD-TYPE 
                            0                             0 
  AMP PEAK 4(13Q31.3) MUTATED AMP PEAK 4(13Q31.3) WILD-TYPE 
                        39.98                         94.06 
  AMP PEAK 4(13Q31.3) MUTATED AMP PEAK 4(13Q31.3) WILD-TYPE 
                        16.08                         10.98 
[1] "0.0 - 40.0 (16.1)" "0.0 - 94.1 (11.0)"
[1] "hr=" "1.1"
D4V2, continuous
D4V3, binary
                               cls
clus                              0   1
  AMP PEAK 4(13Q31.3) MUTATED     3   4
  AMP PEAK 4(13Q31.3) WILD-TYPE  84 100
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 4(13Q31.3) MUTATED      3    4
  AMP PEAK 4(13Q31.3) WILD-TYPE   84  100
        clus
vv       AMP PEAK 4(13Q31.3) MUTATED AMP PEAK 4(13Q31.3) WILD-TYPE
  FEMALE                           3                            84
  MALE                             4                           100
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 4(13Q31.3) MUTATED       0                         0     7
  AMP PEAK 4(13Q31.3) WILD-TYPE     2                        14   166
D4V4, multiclass
                           clus
vv                          AMP PEAK 4(13Q31.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               7
                           clus
vv                          AMP PEAK 4(13Q31.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                            14
  WHITE                                               166
[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"
D4V5, binary
                               cls
clus                              0   1
  AMP PEAK 4(13Q31.3) MUTATED     0   7
  AMP PEAK 4(13Q31.3) WILD-TYPE   3 178
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 4(13Q31.3) MUTATED      0    7
  AMP PEAK 4(13Q31.3) WILD-TYPE    3  178
                        clus
vv                       AMP PEAK 4(13Q31.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           7
                        clus
vv                       AMP PEAK 4(13Q31.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           178
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK 5(19P13.2) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 5(19P13.2) MUTATED     2   4
  AMP PEAK 5(19P13.2) WILD-TYPE  60 112
  AMP PEAK 5(19P13.2) MUTATED AMP PEAK 5(19P13.2) WILD-TYPE 
                            6                           172 
  AMP PEAK 5(19P13.2) MUTATED AMP PEAK 5(19P13.2) WILD-TYPE 
                            4                           112 
$`AMP PEAK 5(19P13.2) MUTATED`
TCGA-AB-2820 TCGA-AB-2855 TCGA-AB-2883 TCGA-AB-2917 TCGA-AB-2938 TCGA-AB-2956 
        0.00         6.97        24.00        39.98         9.99         6.02 

$`AMP PEAK 5(19P13.2) WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
        2.04         1.02         7.99        12.03         1.02        26.04 
TCGA-AB-2815 TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2821 
       27.02         8.05         8.98         9.96        82.06        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 
       31.99         0.00         0.99         6.97        24.03         8.98 
TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 
       75.09         8.98         9.04        21.04        12.00         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 
       55.00        17.03         0.00        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 
       46.06         0.00         4.01         9.99        46.09        14.96 
TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2856 
       72.99         2.01         7.96         2.93        12.03         4.93 
TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 
       10.06        18.97         9.99        14.04         0.00        47.01 
TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 
        1.02        18.97         2.01         5.03         6.05         4.96 
TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 
        7.99         5.03         5.03        20.98         8.98        13.02 
TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 
        6.97        20.98        12.00         8.05        12.92        12.00 
TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 
       24.03         7.04         5.95        10.98         9.99         0.00 
TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 
       31.00         6.97         5.95         5.03         7.04         7.99 
TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 
       12.92        22.06         6.05         1.94         0.00        17.00 
TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 
       52.96        18.97         1.02         0.99         0.00        38.99 
TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2919 
        9.01        39.98        26.04         0.00        29.00         2.01 
TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 
       12.03         0.00         1.02         2.96         7.99        15.02 
TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 
        2.96         4.04         0.00         4.01         0.92         2.01 
TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2942 TCGA-AB-2945 
        1.94         7.07        14.96         0.00        21.07         7.99 
TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 
        1.02        19.07        22.98        10.06         1.02        49.05 
TCGA-AB-2955 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 
       16.08        20.02        16.08        53.98        41.98        11.01 
TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 
       28.08        34.03        15.06        37.05        10.03        26.04 
TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 
        0.99        20.02         3.02        30.08         1.02        22.98 
TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 
       22.98         4.93        11.01        38.04         8.98         6.97 
TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 
        6.05         0.99        12.00        15.02        60.03        56.09 
TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 
       25.02        59.11        50.99        51.98         1.02        57.04 
TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 
       41.06        51.98        47.05        69.04        15.95        51.98 
TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       27.02        18.97        61.97        62.04 

  AMP PEAK 5(19P13.2) MUTATED AMP PEAK 5(19P13.2) WILD-TYPE 
                            0                             0 
  AMP PEAK 5(19P13.2) MUTATED AMP PEAK 5(19P13.2) WILD-TYPE 
                        39.98                         94.06 
  AMP PEAK 5(19P13.2) MUTATED AMP PEAK 5(19P13.2) WILD-TYPE 
                        8.480                        11.505 
[1] "0.0 - 40.0 (8.5)"  "0.0 - 94.1 (11.5)"
[1] "hr=" "1.2"
D5V2, continuous
D5V3, binary
                               cls
clus                             0  1
  AMP PEAK 5(19P13.2) MUTATED    1  5
  AMP PEAK 5(19P13.2) WILD-TYPE 86 99
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 5(19P13.2) MUTATED      1    5
  AMP PEAK 5(19P13.2) WILD-TYPE   86   99
        clus
vv       AMP PEAK 5(19P13.2) MUTATED AMP PEAK 5(19P13.2) WILD-TYPE
  FEMALE                           1                            86
  MALE                             5                            99
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 5(19P13.2) MUTATED       0                         0     6
  AMP PEAK 5(19P13.2) WILD-TYPE     2                        14   167
D5V4, multiclass
                           clus
vv                          AMP PEAK 5(19P13.2) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               6
                           clus
vv                          AMP PEAK 5(19P13.2) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                            14
  WHITE                                               167
[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"
D5V5, binary
                               cls
clus                              0   1
  AMP PEAK 5(19P13.2) MUTATED     0   6
  AMP PEAK 5(19P13.2) WILD-TYPE   3 179
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 5(19P13.2) MUTATED      0    6
  AMP PEAK 5(19P13.2) WILD-TYPE    3  179
                        clus
vv                       AMP PEAK 5(19P13.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           6
                        clus
vv                       AMP PEAK 5(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           179
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK 6(20Q11.21) MUTATION ANALYSIS
D6V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 6(20Q11.21) MUTATED     0   3
  AMP PEAK 6(20Q11.21) WILD-TYPE  62 113
  AMP PEAK 6(20Q11.21) MUTATED AMP PEAK 6(20Q11.21) WILD-TYPE 
                             3                            175 
  AMP PEAK 6(20Q11.21) MUTATED AMP PEAK 6(20Q11.21) WILD-TYPE 
                             3                            113 
$`AMP PEAK 6(20Q11.21) MUTATED`
TCGA-AB-2829 TCGA-AB-2868 TCGA-AB-2904 
        8.98         4.96        17.00 

$`AMP PEAK 6(20Q11.21) WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
        2.04         1.02         7.99        12.03         1.02        26.04 
TCGA-AB-2815 TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 
       27.02         8.05         8.98         9.96        82.06         0.00 
TCGA-AB-2821 TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 
       27.02        31.99         0.00         0.99         6.97        24.03 
TCGA-AB-2827 TCGA-AB-2828 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 
        8.98        75.09         9.04        21.04        12.00         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 
       55.00        17.03         0.00        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 
       46.06         0.00         4.01         9.99        46.09        14.96 
TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 
       72.99         2.01         7.96         2.93        12.03         6.97 
TCGA-AB-2856 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 
        4.93        10.06        18.97         9.99        14.04         0.00 
TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 
       47.01         1.02        18.97         2.01         5.03         6.05 
TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 
        7.99         5.03         5.03        20.98         8.98        13.02 
TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 
        6.97        20.98        12.00         8.05        12.92        12.00 
TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 
       24.00        24.03         7.04         5.95        10.98         9.99 
TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 
        0.00        31.00         6.97         5.95         5.03         7.04 
TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 
        7.99        12.92        22.06         6.05         1.94         0.00 
TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 
       52.96        18.97         1.02         0.99         0.00        38.99 
TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 
        9.01        39.98        26.04         0.00        29.00        39.98 
TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 
        2.01        12.03         0.00         1.02         2.96         7.99 
TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 
       15.02         2.96         4.04         0.00         4.01         0.92 
TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2941 
        2.01         1.94         7.07         9.99        14.96         0.00 
TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 
       21.07         7.99         1.02        19.07        22.98        10.06 
TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 
        1.02        49.05        16.08         6.02        20.02        16.08 
TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 
       53.98        41.98        11.01        28.08        34.03        15.06 
TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 
       37.05        10.03        26.04         0.99        20.02         3.02 
TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 
       30.08         1.02        22.98        22.98         4.93        11.01 
TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 
       38.04         8.98         6.97         6.05         0.99        12.00 
TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 
       15.02        60.03        56.09        25.02        59.11        50.99 
TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 
       51.98         1.02        57.04        41.06        51.98        47.05 
TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 
       69.04        15.95        51.98        27.02        18.97        61.97 
TCGA-AB-3012 
       62.04 

  AMP PEAK 6(20Q11.21) MUTATED AMP PEAK 6(20Q11.21) WILD-TYPE 
                          4.96                           0.00 
  AMP PEAK 6(20Q11.21) MUTATED AMP PEAK 6(20Q11.21) WILD-TYPE 
                         17.00                          94.06 
  AMP PEAK 6(20Q11.21) MUTATED AMP PEAK 6(20Q11.21) WILD-TYPE 
                          8.98                          11.01 
[1] "5.0 - 17.0 (9.0)"  "0.0 - 94.1 (11.0)"
[1] "hr=" "2.1"
D6V2, continuous
D6V3, binary
                                cls
clus                               0   1
  AMP PEAK 6(20Q11.21) MUTATED     0   3
  AMP PEAK 6(20Q11.21) WILD-TYPE  87 101
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 6(20Q11.21) MUTATED      0    3
  AMP PEAK 6(20Q11.21) WILD-TYPE   87  101
        clus
vv       AMP PEAK 6(20Q11.21) MUTATED AMP PEAK 6(20Q11.21) WILD-TYPE
  FEMALE                            0                             87
  MALE                              3                            101
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 6(20Q11.21) MUTATED       0                         1     2
  AMP PEAK 6(20Q11.21) WILD-TYPE     2                        13   171
D6V4, multiclass
                           clus
vv                          AMP PEAK 6(20Q11.21) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                                2
                           clus
vv                          AMP PEAK 6(20Q11.21) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                             13
  WHITE                                                171
[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"
D6V5, binary
                                cls
clus                               0   1
  AMP PEAK 6(20Q11.21) MUTATED     0   3
  AMP PEAK 6(20Q11.21) WILD-TYPE   3 182
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 6(20Q11.21) MUTATED      0    3
  AMP PEAK 6(20Q11.21) WILD-TYPE    3  182
                        clus
vv                       AMP PEAK 6(20Q11.21) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            3
                        clus
vv                       AMP PEAK 6(20Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            182
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK 7(21Q22.2) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 7(21Q22.2) MUTATED     2  10
  AMP PEAK 7(21Q22.2) WILD-TYPE  60 106
  AMP PEAK 7(21Q22.2) MUTATED AMP PEAK 7(21Q22.2) WILD-TYPE 
                           12                           166 
  AMP PEAK 7(21Q22.2) MUTATED AMP PEAK 7(21Q22.2) WILD-TYPE 
                           10                           106 
$`AMP PEAK 7(21Q22.2) MUTATED`
TCGA-AB-2807 TCGA-AB-2813 TCGA-AB-2829 TCGA-AB-2860 TCGA-AB-2865 TCGA-AB-2868 
        5.95         1.02         8.98        14.04         2.01         4.96 
TCGA-AB-2883 TCGA-AB-2901 TCGA-AB-2908 TCGA-AB-2935 TCGA-AB-2938 TCGA-AB-2968 
       24.00         1.94         1.02         2.01         9.99        15.06 

$`AMP PEAK 7(21Q22.2) WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2808 TCGA-AB-2809 
       26.04        84.07        18.97        31.07        94.06         2.04 
TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2814 TCGA-AB-2815 TCGA-AB-2816 
        1.02         7.99        12.03        26.04        27.02         8.05 
TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 TCGA-AB-2822 
        8.98         9.96        82.06         0.00        27.02        31.99 
TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 TCGA-AB-2828 
        0.00         0.99         6.97        24.03         8.98        75.09 
TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 
        9.04        21.04        12.00         8.05        55.00        17.03 
TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 
        0.00        12.00        15.98         0.92        46.06         0.00 
TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 TCGA-AB-2849 TCGA-AB-2850 
        4.01         9.99        46.09        14.96        72.99         2.01 
TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2856 TCGA-AB-2857 
        7.96         2.93        12.03         6.97         4.93        10.06 
TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 
       18.97         9.99         0.00        47.01         1.02        18.97 
TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 
        5.03         6.05         7.99         5.03         5.03        20.98 
TCGA-AB-2873 TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 
        8.98        13.02         6.97        20.98        12.00         8.05 
TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 
       12.92        12.00        24.03         7.04         5.95        10.98 
TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 
        9.99         0.00        31.00         6.97         5.95         5.03 
TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2903 
        7.04         7.99        12.92        22.06         6.05         0.00 
TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 
       17.00        52.96        18.97         0.99         0.00        38.99 
TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 
        9.01        39.98        26.04         0.00        29.00        39.98 
TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 
        2.01        12.03         0.00         1.02         2.96         7.99 
TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 
       15.02         2.96         4.04         0.00         4.01         0.92 
TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2942 TCGA-AB-2945 
        1.94         7.07        14.96         0.00        21.07         7.99 
TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 
        1.02        19.07        22.98        10.06         1.02        49.05 
TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 
       16.08         6.02        20.02        16.08        53.98        41.98 
TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 
       11.01        28.08        34.03        37.05        10.03        26.04 
TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 
        0.99        20.02         3.02        30.08         1.02        22.98 
TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 
       22.98         4.93        11.01        38.04         8.98         6.97 
TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 
        6.05         0.99        12.00        15.02        60.03        56.09 
TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 
       25.02        59.11        50.99        51.98         1.02        57.04 
TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 
       41.06        51.98        47.05        69.04        15.95        51.98 
TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       27.02        18.97        61.97        62.04 

  AMP PEAK 7(21Q22.2) MUTATED AMP PEAK 7(21Q22.2) WILD-TYPE 
                         1.02                          0.00 
  AMP PEAK 7(21Q22.2) MUTATED AMP PEAK 7(21Q22.2) WILD-TYPE 
                        24.00                         94.06 
  AMP PEAK 7(21Q22.2) MUTATED AMP PEAK 7(21Q22.2) WILD-TYPE 
                        5.455                        12.000 
[1] "1.0 - 24.0 (5.5)"  "0.0 - 94.1 (12.0)"
[1] "hr=" "2.4"
D7V2, continuous
D7V3, binary
                               cls
clus                             0  1
  AMP PEAK 7(21Q22.2) MUTATED    3 11
  AMP PEAK 7(21Q22.2) WILD-TYPE 84 93
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 7(21Q22.2) MUTATED      3   11
  AMP PEAK 7(21Q22.2) WILD-TYPE   84   93
        clus
vv       AMP PEAK 7(21Q22.2) MUTATED AMP PEAK 7(21Q22.2) WILD-TYPE
  FEMALE                           3                            84
  MALE                            11                            93
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 7(21Q22.2) MUTATED       0                         2    12
  AMP PEAK 7(21Q22.2) WILD-TYPE     2                        12   161
D7V4, multiclass
                           clus
vv                          AMP PEAK 7(21Q22.2) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              12
                           clus
vv                          AMP PEAK 7(21Q22.2) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                            12
  WHITE                                               161
[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"
D7V5, binary
                               cls
clus                              0   1
  AMP PEAK 7(21Q22.2) MUTATED     0  14
  AMP PEAK 7(21Q22.2) WILD-TYPE   3 171
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 7(21Q22.2) MUTATED      0   14
  AMP PEAK 7(21Q22.2) WILD-TYPE    3  171
                        clus
vv                       AMP PEAK 7(21Q22.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          14
                        clus
vv                       AMP PEAK 7(21Q22.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           171
[1] 2 2
[1] FALSE

Clustering(8) Variable = DEL PEAK  2(3P13) MUTATION ANALYSIS
D8V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  2(3P13) MUTATED     1   7
  DEL PEAK  2(3P13) WILD-TYPE  61 109
  DEL PEAK  2(3P13) MUTATED DEL PEAK  2(3P13) WILD-TYPE 
                          8                         170 
  DEL PEAK  2(3P13) MUTATED DEL PEAK  2(3P13) WILD-TYPE 
                          7                         109 
$`DEL PEAK  2(3P13) MUTATED`
TCGA-AB-2809 TCGA-AB-2813 TCGA-AB-2857 TCGA-AB-2860 TCGA-AB-2885 TCGA-AB-2908 
        2.04         1.02        10.06        14.04         7.04         1.02 
TCGA-AB-2909 TCGA-AB-2941 
        0.99         0.00 

$`DEL PEAK  2(3P13) WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2814 TCGA-AB-2815 TCGA-AB-2816 
        1.02         7.99        12.03        26.04        27.02         8.05 
TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 TCGA-AB-2822 
        8.98         9.96        82.06         0.00        27.02        31.99 
TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 TCGA-AB-2828 
        0.00         0.99         6.97        24.03         8.98        75.09 
TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 TCGA-AB-2835 
        8.98         9.04        21.04        12.00         8.05        55.00 
TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 
       17.03         0.00        12.00        15.98         0.92        46.06 
TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 TCGA-AB-2849 
        0.00         4.01         9.99        46.09        14.96        72.99 
TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2856 
        2.01         7.96         2.93        12.03         6.97         4.93 
TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 
       18.97         9.99         0.00        47.01         1.02        18.97 
TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 
        2.01         5.03         6.05         4.96         7.99         5.03 
TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2877 
        5.03        20.98         8.98        13.02         6.97        20.98 
TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884 
       12.00         8.05        12.92        12.00        24.00        24.03 
TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 
        5.95        10.98         9.99         0.00        31.00         6.97 
TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 
        5.95         5.03         7.04         7.99        12.92        22.06 
TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 
        6.05         1.94         0.00        17.00        52.96        18.97 
TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 
        0.00        38.99         9.01        39.98        26.04         0.00 
TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 
       29.00        39.98         2.01        12.03         0.00         1.02 
TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 
        2.96         7.99        15.02         2.96         4.04         0.00 
TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 
        4.01         0.92         2.01         1.94         7.07         9.99 
TCGA-AB-2939 TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 
       14.96        21.07         7.99         1.02        19.07        22.98 
TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 
       10.06         1.02        49.05        16.08         6.02        20.02 
TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 
       16.08        53.98        41.98        11.01        28.08        34.03 
TCGA-AB-2968 TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 
       15.06        37.05        10.03        26.04         0.99        20.02 
TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 
        3.02        30.08         1.02        22.98        22.98         4.93 
TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 
       11.01        38.04         8.98         6.97         6.05         0.99 
TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 
       12.00        15.02        60.03        56.09        25.02        59.11 
TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 
       50.99        51.98         1.02        57.04        41.06        51.98 
TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 
       47.05        69.04        15.95        51.98        27.02        18.97 
TCGA-AB-3011 TCGA-AB-3012 
       61.97        62.04 

  DEL PEAK  2(3P13) MUTATED DEL PEAK  2(3P13) WILD-TYPE 
                          0                           0 
  DEL PEAK  2(3P13) MUTATED DEL PEAK  2(3P13) WILD-TYPE 
                      14.04                       94.06 
  DEL PEAK  2(3P13) MUTATED DEL PEAK  2(3P13) WILD-TYPE 
                       1.53                       12.00 
[1] "0.0 - 14.0 (1.5)"  "0.0 - 94.1 (12.0)"
[1] "hr=" "3.6"
D8V2, continuous
D8V3, binary
                             cls
clus                           0  1
  DEL PEAK  2(3P13) MUTATED    2  6
  DEL PEAK  2(3P13) WILD-TYPE 85 98
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(3P13) MUTATED      2    6
  DEL PEAK  2(3P13) WILD-TYPE   85   98
        clus
vv       DEL PEAK  2(3P13) MUTATED DEL PEAK  2(3P13) WILD-TYPE
  FEMALE                         2                          85
  MALE                           6                          98
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(3P13) MUTATED       1                         0     7
  DEL PEAK  2(3P13) WILD-TYPE     1                        14   166
D8V4, multiclass
                           clus
vv                          DEL PEAK  2(3P13) MUTATED
  ASIAN                                             1
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                             7
                           clus
vv                          DEL PEAK  2(3P13) WILD-TYPE
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                          14
  WHITE                                             166
[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"
D8V5, binary
                             cls
clus                            0   1
  DEL PEAK  2(3P13) MUTATED     0   8
  DEL PEAK  2(3P13) WILD-TYPE   3 177
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(3P13) MUTATED      0    8
  DEL PEAK  2(3P13) WILD-TYPE    3  177
                        clus
vv                       DEL PEAK  2(3P13) MUTATED DEL PEAK  2(3P13) WILD-TYPE
  HISPANIC OR LATINO                             0                           3
  NOT HISPANIC OR LATINO                         8                         177
[1] 2 2
[1] FALSE

Clustering(9) Variable = DEL PEAK  3(5Q31.2) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(5Q31.2) MUTATED     2  15
  DEL PEAK  3(5Q31.2) WILD-TYPE  60 101
  DEL PEAK  3(5Q31.2) MUTATED DEL PEAK  3(5Q31.2) WILD-TYPE 
                           17                           161 
  DEL PEAK  3(5Q31.2) MUTATED DEL PEAK  3(5Q31.2) WILD-TYPE 
                           15                           101 
$`DEL PEAK  3(5Q31.2) MUTATED`
TCGA-AB-2811 TCGA-AB-2813 TCGA-AB-2829 TCGA-AB-2838 TCGA-AB-2849 TCGA-AB-2857 
        7.99         1.02         8.98        12.00        72.99        10.06 
TCGA-AB-2860 TCGA-AB-2868 TCGA-AB-2878 TCGA-AB-2885 TCGA-AB-2904 TCGA-AB-2908 
       14.04         4.96        12.00         7.04        17.00         1.02 
TCGA-AB-2920 TCGA-AB-2935 TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2952 
       12.03         2.01         9.99        14.96         1.02 

$`DEL PEAK  3(5Q31.2) WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2812 TCGA-AB-2814 TCGA-AB-2815 TCGA-AB-2816 
        2.04         1.02        12.03        26.04        27.02         8.05 
TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 TCGA-AB-2822 
        8.98         9.96        82.06         0.00        27.02        31.99 
TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 TCGA-AB-2828 
        0.00         0.99         6.97        24.03         8.98        75.09 
TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 
        9.04        21.04        12.00         8.05        55.00        17.03 
TCGA-AB-2837 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 
        0.00        15.98         0.92        46.06         0.00         4.01 
TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 
        9.99        46.09        14.96         2.01         7.96         2.93 
TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2856 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2861 
       12.03         6.97         4.93        18.97         9.99         0.00 
TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 
       47.01         1.02        18.97         2.01         5.03         6.05 
TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 
        7.99         5.03         5.03        20.98         8.98        13.02 
TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 
        6.97        20.98         8.05        12.92        12.00        24.00 
TCGA-AB-2884 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 
       24.03         5.95        10.98         9.99         0.00        31.00 
TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 
        6.97         5.95         5.03         7.04         7.99        12.92 
TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2905 TCGA-AB-2906 
       22.06         6.05         1.94         0.00        52.96        18.97 
TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 
        0.99         0.00        38.99         9.01        39.98        26.04 
TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2922 TCGA-AB-2923 
        0.00        29.00        39.98         2.01         0.00         1.02 
TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 
        2.96         7.99        15.02         2.96         4.04         0.00 
TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2941 TCGA-AB-2942 
        4.01         0.92         1.94         7.07         0.00        21.07 
TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2954 
        7.99         1.02        19.07        22.98        10.06        49.05 
TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 
       16.08         6.02        20.02        16.08        53.98        41.98 
TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2969 TCGA-AB-2970 
       11.01        28.08        34.03        15.06        37.05        10.03 
TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 
       26.04         0.99        20.02         3.02        30.08         1.02 
TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 
       22.98        22.98         4.93        11.01        38.04         8.98 
TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 
        6.97         6.05         0.99        12.00        15.02        60.03 
TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 
       56.09        25.02        59.11        50.99        51.98         1.02 
TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 
       57.04        41.06        51.98        47.05        69.04        15.95 
TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       51.98        27.02        18.97        61.97        62.04 

  DEL PEAK  3(5Q31.2) MUTATED DEL PEAK  3(5Q31.2) WILD-TYPE 
                         1.02                          0.00 
  DEL PEAK  3(5Q31.2) MUTATED DEL PEAK  3(5Q31.2) WILD-TYPE 
                        72.99                         94.06 
  DEL PEAK  3(5Q31.2) MUTATED DEL PEAK  3(5Q31.2) WILD-TYPE 
                         9.99                         12.00 
[1] "1.0 - 73.0 (10.0)" "0.0 - 94.1 (12.0)"
[1] "hr=" "1.9"
D9V2, continuous
D9V3, binary
                               cls
clus                             0  1
  DEL PEAK  3(5Q31.2) MUTATED    4 14
  DEL PEAK  3(5Q31.2) WILD-TYPE 83 90
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(5Q31.2) MUTATED      4   14
  DEL PEAK  3(5Q31.2) WILD-TYPE   83   90
        clus
vv       DEL PEAK  3(5Q31.2) MUTATED DEL PEAK  3(5Q31.2) WILD-TYPE
  FEMALE                           4                            83
  MALE                            14                            90
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(5Q31.2) MUTATED       0                         1    17
  DEL PEAK  3(5Q31.2) WILD-TYPE     2                        13   156
D9V4, multiclass
                           clus
vv                          DEL PEAK  3(5Q31.2) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              17
                           clus
vv                          DEL PEAK  3(5Q31.2) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                            13
  WHITE                                               156
[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"
D9V5, binary
                               cls
clus                              0   1
  DEL PEAK  3(5Q31.2) MUTATED     0  18
  DEL PEAK  3(5Q31.2) WILD-TYPE   3 167
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(5Q31.2) MUTATED      0   18
  DEL PEAK  3(5Q31.2) WILD-TYPE    3  167
                        clus
vv                       DEL PEAK  3(5Q31.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          18
                        clus
vv                       DEL PEAK  3(5Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           167
[1] 2 2
[1] FALSE

Clustering(10) Variable = DEL PEAK  4(7P12.1) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(7P12.1) MUTATED     3  11
  DEL PEAK  4(7P12.1) WILD-TYPE  59 105
  DEL PEAK  4(7P12.1) MUTATED DEL PEAK  4(7P12.1) WILD-TYPE 
                           14                           164 
  DEL PEAK  4(7P12.1) MUTATED DEL PEAK  4(7P12.1) WILD-TYPE 
                           11                           105 
$`DEL PEAK  4(7P12.1) MUTATED`
TCGA-AB-2817 TCGA-AB-2838 TCGA-AB-2857 TCGA-AB-2874 TCGA-AB-2882 TCGA-AB-2885 
        8.98        12.00        10.06        13.02        12.00         7.04 
TCGA-AB-2894 TCGA-AB-2904 TCGA-AB-2917 TCGA-AB-2920 TCGA-AB-2929 TCGA-AB-2941 
        5.95        17.00        39.98        12.03         4.04         0.00 
TCGA-AB-2949 TCGA-AB-2952 
       22.98         1.02 

$`DEL PEAK  4(7P12.1) WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
        2.04         1.02         7.99        12.03         1.02        26.04 
TCGA-AB-2815 TCGA-AB-2816 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 
       27.02         8.05         9.96        82.06         0.00        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 
       31.99         0.00         0.99         6.97        24.03         8.98 
TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 
       75.09         8.98         9.04        21.04        12.00         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 
       55.00        17.03         0.00        15.98         0.92        46.06 
TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 TCGA-AB-2849 
        0.00         4.01         9.99        46.09        14.96        72.99 
TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2856 
        2.01         7.96         2.93        12.03         6.97         4.93 
TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 
       18.97         9.99        14.04         0.00        47.01         1.02 
TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2869 
       18.97         2.01         5.03         6.05         4.96         7.99 
TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2875 TCGA-AB-2877 
        5.03         5.03        20.98         8.98         6.97        20.98 
TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2886 
       12.00         8.05        12.92        24.00        24.03         5.95 
TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2895 
       10.98         9.99         0.00        31.00         6.97         5.03 
TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 
        7.04         7.99        12.92        22.06         6.05         1.94 
TCGA-AB-2903 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 
        0.00        52.96        18.97         1.02         0.99         0.00 
TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 
       38.99         9.01        39.98        26.04         0.00        29.00 
TCGA-AB-2919 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 
        2.01         0.00         1.02         2.96         7.99        15.02 
TCGA-AB-2927 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 
        2.96         0.00         4.01         0.92         2.01         1.94 
TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 
        7.07         9.99        14.96        21.07         7.99         1.02 
TCGA-AB-2948 TCGA-AB-2950 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 
       19.07        10.06        49.05        16.08         6.02        20.02 
TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 
       16.08        53.98        41.98        11.01        28.08        34.03 
TCGA-AB-2968 TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 
       15.06        37.05        10.03        26.04         0.99        20.02 
TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 
        3.02        30.08         1.02        22.98        22.98         4.93 
TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 
       11.01        38.04         8.98         6.97         6.05         0.99 
TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 
       12.00        15.02        60.03        56.09        25.02        59.11 
TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 
       50.99        51.98         1.02        57.04        41.06        51.98 
TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 
       47.05        69.04        15.95        51.98        27.02        18.97 
TCGA-AB-3011 TCGA-AB-3012 
       61.97        62.04 

  DEL PEAK  4(7P12.1) MUTATED DEL PEAK  4(7P12.1) WILD-TYPE 
                            0                             0 
  DEL PEAK  4(7P12.1) MUTATED DEL PEAK  4(7P12.1) WILD-TYPE 
                        39.98                         94.06 
  DEL PEAK  4(7P12.1) MUTATED DEL PEAK  4(7P12.1) WILD-TYPE 
                        11.03                         11.01 
[1] "0.0 - 40.0 (11.0)" "0.0 - 94.1 (11.0)"
[1] "hr=" "1.6"
D10V2, continuous
D10V3, binary
                               cls
clus                             0  1
  DEL PEAK  4(7P12.1) MUTATED    6 10
  DEL PEAK  4(7P12.1) WILD-TYPE 81 94
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(7P12.1) MUTATED      6   10
  DEL PEAK  4(7P12.1) WILD-TYPE   81   94
        clus
vv       DEL PEAK  4(7P12.1) MUTATED DEL PEAK  4(7P12.1) WILD-TYPE
  FEMALE                           6                            81
  MALE                            10                            94
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(7P12.1) MUTATED       0                         1    15
  DEL PEAK  4(7P12.1) WILD-TYPE     2                        13   158
D10V4, multiclass
                           clus
vv                          DEL PEAK  4(7P12.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              15
                           clus
vv                          DEL PEAK  4(7P12.1) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                            13
  WHITE                                               158
[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"
D10V5, binary
                               cls
clus                              0   1
  DEL PEAK  4(7P12.1) MUTATED     0  15
  DEL PEAK  4(7P12.1) WILD-TYPE   3 170
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(7P12.1) MUTATED      0   15
  DEL PEAK  4(7P12.1) WILD-TYPE    3  170
                        clus
vv                       DEL PEAK  4(7P12.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          15
                        clus
vv                       DEL PEAK  4(7P12.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           170
[1] 2 2
[1] FALSE

Clustering(11) Variable = DEL PEAK  5(7Q34) MUTATION ANALYSIS
D11V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  5(7Q34) MUTATED     5  16
  DEL PEAK  5(7Q34) WILD-TYPE  57 100
  DEL PEAK  5(7Q34) MUTATED DEL PEAK  5(7Q34) WILD-TYPE 
                         21                         157 
  DEL PEAK  5(7Q34) MUTATED DEL PEAK  5(7Q34) WILD-TYPE 
                         16                         100 
$`DEL PEAK  5(7Q34) MUTATED`
TCGA-AB-2805 TCGA-AB-2817 TCGA-AB-2829 TCGA-AB-2838 TCGA-AB-2857 TCGA-AB-2874 
       18.97         8.98         8.98        12.00        10.06        13.02 
TCGA-AB-2878 TCGA-AB-2882 TCGA-AB-2885 TCGA-AB-2894 TCGA-AB-2915 TCGA-AB-2917 
       12.00        12.00         7.04         5.95         0.00        39.98 
TCGA-AB-2920 TCGA-AB-2923 TCGA-AB-2929 TCGA-AB-2935 TCGA-AB-2939 TCGA-AB-2941 
       12.03         1.02         4.04         2.01        14.96         0.00 
TCGA-AB-2949 TCGA-AB-2952 TCGA-AB-3007 
       22.98         1.02        51.98 

$`DEL PEAK  5(7Q34) WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 TCGA-AB-2809 
       26.04        84.07        31.07         5.95        94.06         2.04 
TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 TCGA-AB-2815 
        1.02         7.99        12.03         1.02        26.04        27.02 
TCGA-AB-2816 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 TCGA-AB-2822 
        8.05         9.96        82.06         0.00        27.02        31.99 
TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 TCGA-AB-2828 
        0.00         0.99         6.97        24.03         8.98        75.09 
TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 
        9.04        21.04        12.00         8.05        55.00        17.03 
TCGA-AB-2837 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 
        0.00        15.98         0.92        46.06         0.00         4.01 
TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 
        9.99        46.09        14.96        72.99         2.01         7.96 
TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2856 TCGA-AB-2858 TCGA-AB-2859 
        2.93        12.03         6.97         4.93        18.97         9.99 
TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 
       14.04         0.00        47.01         1.02        18.97         2.01 
TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 
        5.03         6.05         4.96         7.99         5.03         5.03 
TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2879 TCGA-AB-2881 
       20.98         8.98         6.97        20.98         8.05        12.92 
TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 
       24.00        24.03         5.95        10.98         9.99         0.00 
TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 
       31.00         6.97         5.03         7.04         7.99        12.92 
TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 
       22.06         6.05         1.94         0.00        17.00        52.96 
TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 
       18.97         1.02         0.99         0.00        38.99         9.01 
TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2916 TCGA-AB-2919 TCGA-AB-2922 TCGA-AB-2924 
       39.98        26.04        29.00         2.01         0.00         2.96 
TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 
        7.99        15.02         2.96         0.00         4.01         0.92 
TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 
        1.94         7.07         9.99        21.07         7.99         1.02 
TCGA-AB-2948 TCGA-AB-2950 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 
       19.07        10.06        49.05        16.08         6.02        20.02 
TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 
       16.08        53.98        41.98        11.01        28.08        34.03 
TCGA-AB-2968 TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 
       15.06        37.05        10.03        26.04         0.99        20.02 
TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 
        3.02        30.08         1.02        22.98        22.98         4.93 
TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 
       11.01        38.04         8.98         6.97         6.05         0.99 
TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 
       12.00        15.02        60.03        56.09        25.02        59.11 
TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 
       50.99        51.98         1.02        57.04        41.06        51.98 
TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 
       47.05        69.04        15.95        27.02        18.97        61.97 
TCGA-AB-3012 
       62.04 

  DEL PEAK  5(7Q34) MUTATED DEL PEAK  5(7Q34) WILD-TYPE 
                          0                           0 
  DEL PEAK  5(7Q34) MUTATED DEL PEAK  5(7Q34) WILD-TYPE 
                      51.98                       94.06 
  DEL PEAK  5(7Q34) MUTATED DEL PEAK  5(7Q34) WILD-TYPE 
                      10.06                       11.01 
[1] "0.0 - 52.0 (10.1)" "0.0 - 94.1 (11.0)"
[1] "hr=" "1.6"
D11V2, continuous
D11V3, binary
                             cls
clus                           0  1
  DEL PEAK  5(7Q34) MUTATED    9 15
  DEL PEAK  5(7Q34) WILD-TYPE 78 89
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(7Q34) MUTATED      9   15
  DEL PEAK  5(7Q34) WILD-TYPE   78   89
        clus
vv       DEL PEAK  5(7Q34) MUTATED DEL PEAK  5(7Q34) WILD-TYPE
  FEMALE                         9                          78
  MALE                          15                          89
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(7Q34) MUTATED       0                         2    22
  DEL PEAK  5(7Q34) WILD-TYPE     2                        12   151
D11V4, multiclass
                           clus
vv                          DEL PEAK  5(7Q34) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         2
  WHITE                                            22
                           clus
vv                          DEL PEAK  5(7Q34) WILD-TYPE
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                          12
  WHITE                                             151
[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"
D11V5, binary
                             cls
clus                            0   1
  DEL PEAK  5(7Q34) MUTATED     0  23
  DEL PEAK  5(7Q34) WILD-TYPE   3 162
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(7Q34) MUTATED      0   23
  DEL PEAK  5(7Q34) WILD-TYPE    3  162
                        clus
vv                       DEL PEAK  5(7Q34) MUTATED DEL PEAK  5(7Q34) WILD-TYPE
  HISPANIC OR LATINO                             0                           3
  NOT HISPANIC OR LATINO                        23                         162
[1] 2 2
[1] FALSE

Clustering(12) Variable = DEL PEAK  6(7Q34) MUTATION ANALYSIS
D12V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  6(7Q34) MUTATED     5  16
  DEL PEAK  6(7Q34) WILD-TYPE  57 100
  DEL PEAK  6(7Q34) MUTATED DEL PEAK  6(7Q34) WILD-TYPE 
                         21                         157 
  DEL PEAK  6(7Q34) MUTATED DEL PEAK  6(7Q34) WILD-TYPE 
                         16                         100 
$`DEL PEAK  6(7Q34) MUTATED`
TCGA-AB-2805 TCGA-AB-2817 TCGA-AB-2829 TCGA-AB-2838 TCGA-AB-2857 TCGA-AB-2874 
       18.97         8.98         8.98        12.00        10.06        13.02 
TCGA-AB-2878 TCGA-AB-2882 TCGA-AB-2885 TCGA-AB-2894 TCGA-AB-2915 TCGA-AB-2917 
       12.00        12.00         7.04         5.95         0.00        39.98 
TCGA-AB-2920 TCGA-AB-2923 TCGA-AB-2929 TCGA-AB-2935 TCGA-AB-2939 TCGA-AB-2941 
       12.03         1.02         4.04         2.01        14.96         0.00 
TCGA-AB-2949 TCGA-AB-2952 TCGA-AB-3007 
       22.98         1.02        51.98 

$`DEL PEAK  6(7Q34) WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 TCGA-AB-2809 
       26.04        84.07        31.07         5.95        94.06         2.04 
TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 TCGA-AB-2815 
        1.02         7.99        12.03         1.02        26.04        27.02 
TCGA-AB-2816 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 TCGA-AB-2822 
        8.05         9.96        82.06         0.00        27.02        31.99 
TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 TCGA-AB-2828 
        0.00         0.99         6.97        24.03         8.98        75.09 
TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 
        9.04        21.04        12.00         8.05        55.00        17.03 
TCGA-AB-2837 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 
        0.00        15.98         0.92        46.06         0.00         4.01 
TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 
        9.99        46.09        14.96        72.99         2.01         7.96 
TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2856 TCGA-AB-2858 TCGA-AB-2859 
        2.93        12.03         6.97         4.93        18.97         9.99 
TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 
       14.04         0.00        47.01         1.02        18.97         2.01 
TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 
        5.03         6.05         4.96         7.99         5.03         5.03 
TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2879 TCGA-AB-2881 
       20.98         8.98         6.97        20.98         8.05        12.92 
TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 
       24.00        24.03         5.95        10.98         9.99         0.00 
TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 
       31.00         6.97         5.03         7.04         7.99        12.92 
TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 
       22.06         6.05         1.94         0.00        17.00        52.96 
TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 
       18.97         1.02         0.99         0.00        38.99         9.01 
TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2916 TCGA-AB-2919 TCGA-AB-2922 TCGA-AB-2924 
       39.98        26.04        29.00         2.01         0.00         2.96 
TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 
        7.99        15.02         2.96         0.00         4.01         0.92 
TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 
        1.94         7.07         9.99        21.07         7.99         1.02 
TCGA-AB-2948 TCGA-AB-2950 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 
       19.07        10.06        49.05        16.08         6.02        20.02 
TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 
       16.08        53.98        41.98        11.01        28.08        34.03 
TCGA-AB-2968 TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 
       15.06        37.05        10.03        26.04         0.99        20.02 
TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 
        3.02        30.08         1.02        22.98        22.98         4.93 
TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 
       11.01        38.04         8.98         6.97         6.05         0.99 
TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 
       12.00        15.02        60.03        56.09        25.02        59.11 
TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 
       50.99        51.98         1.02        57.04        41.06        51.98 
TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 
       47.05        69.04        15.95        27.02        18.97        61.97 
TCGA-AB-3012 
       62.04 

  DEL PEAK  6(7Q34) MUTATED DEL PEAK  6(7Q34) WILD-TYPE 
                          0                           0 
  DEL PEAK  6(7Q34) MUTATED DEL PEAK  6(7Q34) WILD-TYPE 
                      51.98                       94.06 
  DEL PEAK  6(7Q34) MUTATED DEL PEAK  6(7Q34) WILD-TYPE 
                      10.06                       11.01 
[1] "0.0 - 52.0 (10.1)" "0.0 - 94.1 (11.0)"
[1] "hr=" "1.6"
D12V2, continuous
D12V3, binary
                             cls
clus                           0  1
  DEL PEAK  6(7Q34) MUTATED    9 15
  DEL PEAK  6(7Q34) WILD-TYPE 78 89
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  6(7Q34) MUTATED      9   15
  DEL PEAK  6(7Q34) WILD-TYPE   78   89
        clus
vv       DEL PEAK  6(7Q34) MUTATED DEL PEAK  6(7Q34) WILD-TYPE
  FEMALE                         9                          78
  MALE                          15                          89
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(7Q34) MUTATED       0                         2    22
  DEL PEAK  6(7Q34) WILD-TYPE     2                        12   151
D12V4, multiclass
                           clus
vv                          DEL PEAK  6(7Q34) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         2
  WHITE                                            22
                           clus
vv                          DEL PEAK  6(7Q34) WILD-TYPE
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                          12
  WHITE                                             151
[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"
D12V5, binary
                             cls
clus                            0   1
  DEL PEAK  6(7Q34) MUTATED     0  23
  DEL PEAK  6(7Q34) WILD-TYPE   3 162
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  6(7Q34) MUTATED      0   23
  DEL PEAK  6(7Q34) WILD-TYPE    3  162
                        clus
vv                       DEL PEAK  6(7Q34) MUTATED DEL PEAK  6(7Q34) WILD-TYPE
  HISPANIC OR LATINO                             0                           3
  NOT HISPANIC OR LATINO                        23                         162
[1] 2 2
[1] FALSE

Clustering(13) Variable = DEL PEAK  8(9Q21.32) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  8(9Q21.32) MUTATED     2   3
  DEL PEAK  8(9Q21.32) WILD-TYPE  60 113
  DEL PEAK  8(9Q21.32) MUTATED DEL PEAK  8(9Q21.32) WILD-TYPE 
                             5                            173 
  DEL PEAK  8(9Q21.32) MUTATED DEL PEAK  8(9Q21.32) WILD-TYPE 
                             3                            113 
$`DEL PEAK  8(9Q21.32) MUTATED`
TCGA-AB-2868 TCGA-AB-2872 TCGA-AB-2886 TCGA-AB-2941 TCGA-AB-2971 
        4.96        20.98         5.95         0.00        26.04 

$`DEL PEAK  8(9Q21.32) WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
        2.04         1.02         7.99        12.03         1.02        26.04 
TCGA-AB-2815 TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 
       27.02         8.05         8.98         9.96        82.06         0.00 
TCGA-AB-2821 TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 
       27.02        31.99         0.00         0.99         6.97        24.03 
TCGA-AB-2827 TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 
        8.98        75.09         8.98         9.04        21.04        12.00 
TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 
        8.05        55.00        17.03         0.00        12.00        15.98 
TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 
        0.92        46.06         0.00         4.01         9.99        46.09 
TCGA-AB-2848 TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 
       14.96        72.99         2.01         7.96         2.93        12.03 
TCGA-AB-2855 TCGA-AB-2856 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 
        6.97         4.93        10.06        18.97         9.99        14.04 
TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 
        0.00        47.01         1.02        18.97         2.01         5.03 
TCGA-AB-2867 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2873 TCGA-AB-2874 
        6.05         7.99         5.03         5.03         8.98        13.02 
TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 
        6.97        20.98        12.00         8.05        12.92        12.00 
TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 
       24.00        24.03         7.04        10.98         9.99         0.00 
TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 
       31.00         6.97         5.95         5.03         7.04         7.99 
TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 
       12.92        22.06         6.05         1.94         0.00        17.00 
TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 
       52.96        18.97         1.02         0.99         0.00        38.99 
TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 
        9.01        39.98        26.04         0.00        29.00        39.98 
TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 
        2.01        12.03         0.00         1.02         2.96         7.99 
TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 
       15.02         2.96         4.04         0.00         4.01         0.92 
TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2942 
        2.01         1.94         7.07         9.99        14.96        21.07 
TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 
        7.99         1.02        19.07        22.98        10.06         1.02 
TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 
       49.05        16.08         6.02        20.02        16.08        53.98 
TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2969 
       41.98        11.01        28.08        34.03        15.06        37.05 
TCGA-AB-2970 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 
       10.03         0.99        20.02         3.02        30.08         1.02 
TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 
       22.98        22.98         4.93        11.01        38.04         8.98 
TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 
        6.97         6.05         0.99        12.00        15.02        60.03 
TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 
       56.09        25.02        59.11        50.99        51.98         1.02 
TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 
       57.04        41.06        51.98        47.05        69.04        15.95 
TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       51.98        27.02        18.97        61.97        62.04 

  DEL PEAK  8(9Q21.32) MUTATED DEL PEAK  8(9Q21.32) WILD-TYPE 
                             0                              0 
  DEL PEAK  8(9Q21.32) MUTATED DEL PEAK  8(9Q21.32) WILD-TYPE 
                         26.04                          94.06 
  DEL PEAK  8(9Q21.32) MUTATED DEL PEAK  8(9Q21.32) WILD-TYPE 
                          5.95                          11.01 
[1] "0.0 - 26.0 (6.0)"  "0.0 - 94.1 (11.0)"
[1] "hr=" "1.2"
D13V2, continuous
D13V3, binary
                                cls
clus                               0   1
  DEL PEAK  8(9Q21.32) MUTATED     1   4
  DEL PEAK  8(9Q21.32) WILD-TYPE  86 100
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(9Q21.32) MUTATED      1    4
  DEL PEAK  8(9Q21.32) WILD-TYPE   86  100
        clus
vv       DEL PEAK  8(9Q21.32) MUTATED DEL PEAK  8(9Q21.32) WILD-TYPE
  FEMALE                            1                             86
  MALE                              4                            100
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(9Q21.32) MUTATED       0                         1     4
  DEL PEAK  8(9Q21.32) WILD-TYPE     2                        13   169
D13V4, multiclass
                           clus
vv                          DEL PEAK  8(9Q21.32) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                                4
                           clus
vv                          DEL PEAK  8(9Q21.32) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                             13
  WHITE                                                169
[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"
D13V5, binary
                                cls
clus                               0   1
  DEL PEAK  8(9Q21.32) MUTATED     0   5
  DEL PEAK  8(9Q21.32) WILD-TYPE   3 180
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(9Q21.32) MUTATED      0    5
  DEL PEAK  8(9Q21.32) WILD-TYPE    3  180
                        clus
vv                       DEL PEAK  8(9Q21.32) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            5
                        clus
vv                       DEL PEAK  8(9Q21.32) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            180
[1] 2 2
[1] FALSE

Clustering(14) Variable = DEL PEAK 10(12P13.2) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 10(12P13.2) MUTATED     0   9
  DEL PEAK 10(12P13.2) WILD-TYPE  62 107
  DEL PEAK 10(12P13.2) MUTATED DEL PEAK 10(12P13.2) WILD-TYPE 
                             9                            169 
  DEL PEAK 10(12P13.2) MUTATED DEL PEAK 10(12P13.2) WILD-TYPE 
                             9                            107 
$`DEL PEAK 10(12P13.2) MUTATED`
TCGA-AB-2813 TCGA-AB-2855 TCGA-AB-2857 TCGA-AB-2885 TCGA-AB-2899 TCGA-AB-2920 
        1.02         6.97        10.06         7.04        22.06        12.03 
TCGA-AB-2929 TCGA-AB-2941 TCGA-AB-2952 
        4.04         0.00         1.02 

$`DEL PEAK 10(12P13.2) WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2814 TCGA-AB-2815 
        2.04         1.02         7.99        12.03        26.04        27.02 
TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 
        8.05         8.98         9.96        82.06         0.00        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 
       31.99         0.00         0.99         6.97        24.03         8.98 
TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 
       75.09         8.98         9.04        21.04        12.00         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 
       55.00        17.03         0.00        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 
       46.06         0.00         4.01         9.99        46.09        14.96 
TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2856 
       72.99         2.01         7.96         2.93        12.03         4.93 
TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 
       18.97         9.99        14.04         0.00        47.01         1.02 
TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2869 
       18.97         2.01         5.03         6.05         4.96         7.99 
TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 TCGA-AB-2875 
        5.03         5.03        20.98         8.98        13.02         6.97 
TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 
       20.98        12.00         8.05        12.92        12.00        24.00 
TCGA-AB-2884 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 
       24.03         5.95        10.98         9.99         0.00        31.00 
TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 
        6.97         5.95         5.03         7.04         7.99        12.92 
TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 
        6.05         1.94         0.00        17.00        52.96        18.97 
TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 
        1.02         0.99         0.00        38.99         9.01        39.98 
TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2922 
       26.04         0.00        29.00        39.98         2.01         0.00 
TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2931 
        1.02         2.96         7.99        15.02         2.96         0.00 
TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 
        4.01         0.92         2.01         1.94         7.07         9.99 
TCGA-AB-2939 TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 
       14.96        21.07         7.99         1.02        19.07        22.98 
TCGA-AB-2950 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 
       10.06        49.05        16.08         6.02        20.02        16.08 
TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 
       53.98        41.98        11.01        28.08        34.03        15.06 
TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 
       37.05        10.03        26.04         0.99        20.02         3.02 
TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 
       30.08         1.02        22.98        22.98         4.93        11.01 
TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 
       38.04         8.98         6.97         6.05         0.99        12.00 
TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 
       15.02        60.03        56.09        25.02        59.11        50.99 
TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 
       51.98         1.02        57.04        41.06        51.98        47.05 
TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 
       69.04        15.95        51.98        27.02        18.97        61.97 
TCGA-AB-3012 
       62.04 

  DEL PEAK 10(12P13.2) MUTATED DEL PEAK 10(12P13.2) WILD-TYPE 
                             0                              0 
  DEL PEAK 10(12P13.2) MUTATED DEL PEAK 10(12P13.2) WILD-TYPE 
                         22.06                          94.06 
  DEL PEAK 10(12P13.2) MUTATED DEL PEAK 10(12P13.2) WILD-TYPE 
                          6.97                          12.00 
[1] "0.0 - 22.1 (7.0)"  "0.0 - 94.1 (12.0)"
[1] "hr=" "3"  
D14V2, continuous
D14V3, binary
                                cls
clus                              0  1
  DEL PEAK 10(12P13.2) MUTATED    3  7
  DEL PEAK 10(12P13.2) WILD-TYPE 84 97
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(12P13.2) MUTATED      3    7
  DEL PEAK 10(12P13.2) WILD-TYPE   84   97
        clus
vv       DEL PEAK 10(12P13.2) MUTATED DEL PEAK 10(12P13.2) WILD-TYPE
  FEMALE                            3                             84
  MALE                              7                             97
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(12P13.2) MUTATED       0                         0    10
  DEL PEAK 10(12P13.2) WILD-TYPE     2                        14   163
D14V4, multiclass
                           clus
vv                          DEL PEAK 10(12P13.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               10
                           clus
vv                          DEL PEAK 10(12P13.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                             14
  WHITE                                                163
[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"
D14V5, binary
                                cls
clus                               0   1
  DEL PEAK 10(12P13.2) MUTATED     0  10
  DEL PEAK 10(12P13.2) WILD-TYPE   3 175
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(12P13.2) MUTATED      0   10
  DEL PEAK 10(12P13.2) WILD-TYPE    3  175
                        clus
vv                       DEL PEAK 10(12P13.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           10
                        clus
vv                       DEL PEAK 10(12P13.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            175
[1] 2 2
[1] FALSE

Clustering(15) Variable = DEL PEAK 11(12Q21.33) MUTATION ANALYSIS
D15V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 11(12Q21.33) MUTATED     1   2
  DEL PEAK 11(12Q21.33) WILD-TYPE  61 114
  DEL PEAK 11(12Q21.33) MUTATED DEL PEAK 11(12Q21.33) WILD-TYPE 
                              3                             175 
  DEL PEAK 11(12Q21.33) MUTATED DEL PEAK 11(12Q21.33) WILD-TYPE 
                              2                             114 
$`DEL PEAK 11(12Q21.33) MUTATED`
TCGA-AB-2885 TCGA-AB-2939 TCGA-AB-2941 
        7.04        14.96         0.00 

$`DEL PEAK 11(12Q21.33) WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
        2.04         1.02         7.99        12.03         1.02        26.04 
TCGA-AB-2815 TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 
       27.02         8.05         8.98         9.96        82.06         0.00 
TCGA-AB-2821 TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 
       27.02        31.99         0.00         0.99         6.97        24.03 
TCGA-AB-2827 TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 
        8.98        75.09         8.98         9.04        21.04        12.00 
TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 
        8.05        55.00        17.03         0.00        12.00        15.98 
TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 
        0.92        46.06         0.00         4.01         9.99        46.09 
TCGA-AB-2848 TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 
       14.96        72.99         2.01         7.96         2.93        12.03 
TCGA-AB-2855 TCGA-AB-2856 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 
        6.97         4.93        10.06        18.97         9.99        14.04 
TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 
        0.00        47.01         1.02        18.97         2.01         5.03 
TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 
        6.05         4.96         7.99         5.03         5.03        20.98 
TCGA-AB-2873 TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 
        8.98        13.02         6.97        20.98        12.00         8.05 
TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2886 TCGA-AB-2888 
       12.92        12.00        24.00        24.03         5.95        10.98 
TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 
        9.99         0.00        31.00         6.97         5.95         5.03 
TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 
        7.04         7.99        12.92        22.06         6.05         1.94 
TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 
        0.00        17.00        52.96        18.97         1.02         0.99 
TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 
        0.00        38.99         9.01        39.98        26.04         0.00 
TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 
       29.00        39.98         2.01        12.03         0.00         1.02 
TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 
        2.96         7.99        15.02         2.96         4.04         0.00 
TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 
        4.01         0.92         2.01         1.94         7.07         9.99 
TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 
       21.07         7.99         1.02        19.07        22.98        10.06 
TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 
        1.02        49.05        16.08         6.02        20.02        16.08 
TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 
       53.98        41.98        11.01        28.08        34.03        15.06 
TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 
       37.05        10.03        26.04         0.99        20.02         3.02 
TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 
       30.08         1.02        22.98        22.98         4.93        11.01 
TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 
       38.04         8.98         6.97         6.05         0.99        12.00 
TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 
       15.02        60.03        56.09        25.02        59.11        50.99 
TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 
       51.98         1.02        57.04        41.06        51.98        47.05 
TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 
       69.04        15.95        51.98        27.02        18.97        61.97 
TCGA-AB-3012 
       62.04 

  DEL PEAK 11(12Q21.33) MUTATED DEL PEAK 11(12Q21.33) WILD-TYPE 
                              0                               0 
  DEL PEAK 11(12Q21.33) MUTATED DEL PEAK 11(12Q21.33) WILD-TYPE 
                          14.96                           94.06 
  DEL PEAK 11(12Q21.33) MUTATED DEL PEAK 11(12Q21.33) WILD-TYPE 
                           7.04                           11.01 
[1] "0.0 - 15.0 (7.0)"  "0.0 - 94.1 (11.0)"
[1] "hr=" "1.9"
D15V2, continuous
D15V3, binary
                                 cls
clus                                0   1
  DEL PEAK 11(12Q21.33) MUTATED     0   3
  DEL PEAK 11(12Q21.33) WILD-TYPE  87 101
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 11(12Q21.33) MUTATED      0    3
  DEL PEAK 11(12Q21.33) WILD-TYPE   87  101
        clus
vv       DEL PEAK 11(12Q21.33) MUTATED DEL PEAK 11(12Q21.33) WILD-TYPE
  FEMALE                             0                              87
  MALE                               3                             101
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(12Q21.33) MUTATED       0                         0     3
  DEL PEAK 11(12Q21.33) WILD-TYPE     2                        14   170
D15V4, multiclass
                           clus
vv                          DEL PEAK 11(12Q21.33) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                 3
                           clus
vv                          DEL PEAK 11(12Q21.33) WILD-TYPE
  ASIAN                                                   2
  BLACK OR AFRICAN AMERICAN                              14
  WHITE                                                 170
[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"
D15V5, binary
                                 cls
clus                                0   1
  DEL PEAK 11(12Q21.33) MUTATED     0   3
  DEL PEAK 11(12Q21.33) WILD-TYPE   3 182
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 11(12Q21.33) MUTATED      0    3
  DEL PEAK 11(12Q21.33) WILD-TYPE    3  182
                        clus
vv                       DEL PEAK 11(12Q21.33) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                             3
                        clus
vv                       DEL PEAK 11(12Q21.33) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             182
[1] 2 2
[1] FALSE

Clustering(16) Variable = DEL PEAK 12(16Q23.1) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 12(16Q23.1) MUTATED     1   8
  DEL PEAK 12(16Q23.1) WILD-TYPE  61 108
  DEL PEAK 12(16Q23.1) MUTATED DEL PEAK 12(16Q23.1) WILD-TYPE 
                             9                            169 
  DEL PEAK 12(16Q23.1) MUTATED DEL PEAK 12(16Q23.1) WILD-TYPE 
                             8                            108 
$`DEL PEAK 12(16Q23.1) MUTATED`
TCGA-AB-2813 TCGA-AB-2817 TCGA-AB-2829 TCGA-AB-2838 TCGA-AB-2857 TCGA-AB-2878 
        1.02         8.98         8.98        12.00        10.06        12.00 
TCGA-AB-2941 TCGA-AB-2945 TCGA-AB-2954 
        0.00         7.99        49.05 

$`DEL PEAK 12(16Q23.1) WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2814 TCGA-AB-2815 
        2.04         1.02         7.99        12.03        26.04        27.02 
TCGA-AB-2816 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 TCGA-AB-2822 
        8.05         9.96        82.06         0.00        27.02        31.99 
TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 TCGA-AB-2828 
        0.00         0.99         6.97        24.03         8.98        75.09 
TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 
        9.04        21.04        12.00         8.05        55.00        17.03 
TCGA-AB-2837 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 
        0.00        15.98         0.92        46.06         0.00         4.01 
TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 
        9.99        46.09        14.96        72.99         2.01         7.96 
TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2856 TCGA-AB-2858 TCGA-AB-2859 
        2.93        12.03         6.97         4.93        18.97         9.99 
TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 
       14.04         0.00        47.01         1.02        18.97         2.01 
TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 
        5.03         6.05         4.96         7.99         5.03         5.03 
TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2879 
       20.98         8.98        13.02         6.97        20.98         8.05 
TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 
       12.92        12.00        24.00        24.03         7.04         5.95 
TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 
       10.98         9.99         0.00        31.00         6.97         5.95 
TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 
        5.03         7.04         7.99        12.92        22.06         6.05 
TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 
        1.94         0.00        17.00        52.96        18.97         1.02 
TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 
        0.99         0.00        38.99         9.01        39.98        26.04 
TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 
        0.00        29.00        39.98         2.01        12.03         0.00 
TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 
        1.02         2.96         7.99        15.02         2.96         4.04 
TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 
        0.00         4.01         0.92         2.01         1.94         7.07 
TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2942 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 
        9.99        14.96        21.07         1.02        19.07        22.98 
TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 
       10.06         1.02        16.08         6.02        20.02        16.08 
TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 
       53.98        41.98        11.01        28.08        34.03        15.06 
TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 
       37.05        10.03        26.04         0.99        20.02         3.02 
TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 
       30.08         1.02        22.98        22.98         4.93        11.01 
TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 
       38.04         8.98         6.97         6.05         0.99        12.00 
TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 
       15.02        60.03        56.09        25.02        59.11        50.99 
TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 
       51.98         1.02        57.04        41.06        51.98        47.05 
TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 
       69.04        15.95        51.98        27.02        18.97        61.97 
TCGA-AB-3012 
       62.04 

  DEL PEAK 12(16Q23.1) MUTATED DEL PEAK 12(16Q23.1) WILD-TYPE 
                             0                              0 
  DEL PEAK 12(16Q23.1) MUTATED DEL PEAK 12(16Q23.1) WILD-TYPE 
                         49.05                          94.06 
  DEL PEAK 12(16Q23.1) MUTATED DEL PEAK 12(16Q23.1) WILD-TYPE 
                          8.98                          12.00 
[1] "0.0 - 49.0 (9.0)"  "0.0 - 94.1 (12.0)"
[1] "hr=" "1.8"
D16V2, continuous
D16V3, binary
                                cls
clus                              0  1
  DEL PEAK 12(16Q23.1) MUTATED    3  6
  DEL PEAK 12(16Q23.1) WILD-TYPE 84 98
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(16Q23.1) MUTATED      3    6
  DEL PEAK 12(16Q23.1) WILD-TYPE   84   98
        clus
vv       DEL PEAK 12(16Q23.1) MUTATED DEL PEAK 12(16Q23.1) WILD-TYPE
  FEMALE                            3                             84
  MALE                              6                             98
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(16Q23.1) MUTATED       0                         1     8
  DEL PEAK 12(16Q23.1) WILD-TYPE     2                        13   165
D16V4, multiclass
                           clus
vv                          DEL PEAK 12(16Q23.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                                8
                           clus
vv                          DEL PEAK 12(16Q23.1) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                             13
  WHITE                                                165
[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"
D16V5, binary
                                cls
clus                               0   1
  DEL PEAK 12(16Q23.1) MUTATED     0   9
  DEL PEAK 12(16Q23.1) WILD-TYPE   3 176
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(16Q23.1) MUTATED      0    9
  DEL PEAK 12(16Q23.1) WILD-TYPE    3  176
                        clus
vv                       DEL PEAK 12(16Q23.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            9
                        clus
vv                       DEL PEAK 12(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            176
[1] 2 2
[1] FALSE

Clustering(17) Variable = DEL PEAK 13(17P13.2) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 13(17P13.2) MUTATED     2  13
  DEL PEAK 13(17P13.2) WILD-TYPE  60 103
  DEL PEAK 13(17P13.2) MUTATED DEL PEAK 13(17P13.2) WILD-TYPE 
                            15                            163 
  DEL PEAK 13(17P13.2) MUTATED DEL PEAK 13(17P13.2) WILD-TYPE 
                            13                            103 
$`DEL PEAK 13(17P13.2) MUTATED`
TCGA-AB-2813 TCGA-AB-2838 TCGA-AB-2849 TCGA-AB-2855 TCGA-AB-2857 TCGA-AB-2860 
        1.02        12.00        72.99         6.97        10.06        14.04 
TCGA-AB-2868 TCGA-AB-2904 TCGA-AB-2908 TCGA-AB-2917 TCGA-AB-2933 TCGA-AB-2935 
        4.96        17.00         1.02        39.98         4.01         2.01 
TCGA-AB-2938 TCGA-AB-2941 TCGA-AB-2955 
        9.99         0.00        16.08 

$`DEL PEAK 13(17P13.2) WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2814 TCGA-AB-2815 
        2.04         1.02         7.99        12.03        26.04        27.02 
TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 
        8.05         8.98         9.96        82.06         0.00        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 
       31.99         0.00         0.99         6.97        24.03         8.98 
TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 
       75.09         8.98         9.04        21.04        12.00         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 
       55.00        17.03         0.00        15.98         0.92        46.06 
TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 TCGA-AB-2850 
        0.00         4.01         9.99        46.09        14.96         2.01 
TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2856 TCGA-AB-2858 TCGA-AB-2859 
        7.96         2.93        12.03         4.93        18.97         9.99 
TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 
        0.00        47.01         1.02        18.97         2.01         5.03 
TCGA-AB-2867 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 
        6.05         7.99         5.03         5.03        20.98         8.98 
TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 
       13.02         6.97        20.98        12.00         8.05        12.92 
TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 
       12.00        24.00        24.03         7.04         5.95        10.98 
TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 
        9.99         0.00        31.00         6.97         5.95         5.03 
TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 
        7.04         7.99        12.92        22.06         6.05         1.94 
TCGA-AB-2903 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 
        0.00        52.96        18.97         0.99         0.00        38.99 
TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2919 
        9.01        39.98        26.04         0.00        29.00         2.01 
TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 
       12.03         0.00         1.02         2.96         7.99        15.02 
TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2934 TCGA-AB-2936 TCGA-AB-2937 
        2.96         4.04         0.00         0.92         1.94         7.07 
TCGA-AB-2939 TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 
       14.96        21.07         7.99         1.02        19.07        22.98 
TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 
       10.06         1.02        49.05         6.02        20.02        16.08 
TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 
       53.98        41.98        11.01        28.08        34.03        15.06 
TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 
       37.05        10.03        26.04         0.99        20.02         3.02 
TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 
       30.08         1.02        22.98        22.98         4.93        11.01 
TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 
       38.04         8.98         6.97         6.05         0.99        12.00 
TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 
       15.02        60.03        56.09        25.02        59.11        50.99 
TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 
       51.98         1.02        57.04        41.06        51.98        47.05 
TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 
       69.04        15.95        51.98        27.02        18.97        61.97 
TCGA-AB-3012 
       62.04 

  DEL PEAK 13(17P13.2) MUTATED DEL PEAK 13(17P13.2) WILD-TYPE 
                             0                              0 
  DEL PEAK 13(17P13.2) MUTATED DEL PEAK 13(17P13.2) WILD-TYPE 
                         72.99                          94.06 
  DEL PEAK 13(17P13.2) MUTATED DEL PEAK 13(17P13.2) WILD-TYPE 
                          9.99                          12.00 
[1] "0.0 - 73.0 (10.0)" "0.0 - 94.1 (12.0)"
[1] "hr=" "1.8"
D17V2, continuous
D17V3, binary
                                cls
clus                              0  1
  DEL PEAK 13(17P13.2) MUTATED    3 12
  DEL PEAK 13(17P13.2) WILD-TYPE 84 92
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(17P13.2) MUTATED      3   12
  DEL PEAK 13(17P13.2) WILD-TYPE   84   92
        clus
vv       DEL PEAK 13(17P13.2) MUTATED DEL PEAK 13(17P13.2) WILD-TYPE
  FEMALE                            3                             84
  MALE                             12                             92
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(17P13.2) MUTATED       0                         0    15
  DEL PEAK 13(17P13.2) WILD-TYPE     2                        14   158
D17V4, multiclass
                           clus
vv                          DEL PEAK 13(17P13.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               15
                           clus
vv                          DEL PEAK 13(17P13.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                             14
  WHITE                                                158
[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"
D17V5, binary
                                cls
clus                               0   1
  DEL PEAK 13(17P13.2) MUTATED     0  15
  DEL PEAK 13(17P13.2) WILD-TYPE   3 170
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(17P13.2) MUTATED      0   15
  DEL PEAK 13(17P13.2) WILD-TYPE    3  170
                        clus
vv                       DEL PEAK 13(17P13.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           15
                        clus
vv                       DEL PEAK 13(17P13.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            170
[1] 2 2
[1] FALSE

Clustering(18) Variable = DEL PEAK 14(17Q11.2) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 14(17Q11.2) MUTATED     1  11
  DEL PEAK 14(17Q11.2) WILD-TYPE  61 105
  DEL PEAK 14(17Q11.2) MUTATED DEL PEAK 14(17Q11.2) WILD-TYPE 
                            12                            166 
  DEL PEAK 14(17Q11.2) MUTATED DEL PEAK 14(17Q11.2) WILD-TYPE 
                            11                            105 
$`DEL PEAK 14(17Q11.2) MUTATED`
TCGA-AB-2813 TCGA-AB-2820 TCGA-AB-2855 TCGA-AB-2860 TCGA-AB-2908 TCGA-AB-2920 
        1.02         0.00         6.97        14.04         1.02        12.03 
TCGA-AB-2935 TCGA-AB-2941 TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-3009 
        2.01         0.00         1.02        49.05        16.08        18.97 

$`DEL PEAK 14(17Q11.2) WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2814 TCGA-AB-2815 
        2.04         1.02         7.99        12.03        26.04        27.02 
TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2821 TCGA-AB-2822 
        8.05         8.98         9.96        82.06        27.02        31.99 
TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 TCGA-AB-2828 
        0.00         0.99         6.97        24.03         8.98        75.09 
TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 TCGA-AB-2835 
        8.98         9.04        21.04        12.00         8.05        55.00 
TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 
       17.03         0.00        12.00        15.98         0.92        46.06 
TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 TCGA-AB-2849 
        0.00         4.01         9.99        46.09        14.96        72.99 
TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2856 TCGA-AB-2857 
        2.01         7.96         2.93        12.03         4.93        10.06 
TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 
       18.97         9.99         0.00        47.01         1.02        18.97 
TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 
        2.01         5.03         6.05         4.96         7.99         5.03 
TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2877 
        5.03        20.98         8.98        13.02         6.97        20.98 
TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884 
       12.00         8.05        12.92        12.00        24.00        24.03 
TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 
        7.04         5.95        10.98         9.99         0.00        31.00 
TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 
        6.97         5.95         5.03         7.04         7.99        12.92 
TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 
       22.06         6.05         1.94         0.00        17.00        52.96 
TCGA-AB-2906 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 
       18.97         0.99         0.00        38.99         9.01        39.98 
TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2922 
       26.04         0.00        29.00        39.98         2.01         0.00 
TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 
        1.02         2.96         7.99        15.02         2.96         4.04 
TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 
        0.00         4.01         0.92         1.94         7.07         9.99 
TCGA-AB-2939 TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 
       14.96        21.07         7.99         1.02        19.07        22.98 
TCGA-AB-2950 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 
       10.06         6.02        20.02        16.08        53.98        41.98 
TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2969 TCGA-AB-2970 
       11.01        28.08        34.03        15.06        37.05        10.03 
TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 
       26.04         0.99        20.02         3.02        30.08         1.02 
TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 
       22.98        22.98         4.93        11.01        38.04         8.98 
TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 
        6.97         6.05         0.99        12.00        15.02        60.03 
TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 
       56.09        25.02        59.11        50.99        51.98         1.02 
TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 
       57.04        41.06        51.98        47.05        69.04        15.95 
TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3011 TCGA-AB-3012 
       51.98        27.02        61.97        62.04 

  DEL PEAK 14(17Q11.2) MUTATED DEL PEAK 14(17Q11.2) WILD-TYPE 
                             0                              0 
  DEL PEAK 14(17Q11.2) MUTATED DEL PEAK 14(17Q11.2) WILD-TYPE 
                         49.05                          94.06 
  DEL PEAK 14(17Q11.2) MUTATED DEL PEAK 14(17Q11.2) WILD-TYPE 
                         4.490                         11.505 
[1] "0.0 - 49.0 (4.5)"  "0.0 - 94.1 (11.5)"
[1] "hr=" "2.3"
D18V2, continuous
D18V3, binary
                                cls
clus                              0  1
  DEL PEAK 14(17Q11.2) MUTATED    5  8
  DEL PEAK 14(17Q11.2) WILD-TYPE 82 96
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(17Q11.2) MUTATED      5    8
  DEL PEAK 14(17Q11.2) WILD-TYPE   82   96
        clus
vv       DEL PEAK 14(17Q11.2) MUTATED DEL PEAK 14(17Q11.2) WILD-TYPE
  FEMALE                            5                             82
  MALE                              8                             96
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(17Q11.2) MUTATED       0                         0    12
  DEL PEAK 14(17Q11.2) WILD-TYPE     2                        14   161
D18V4, multiclass
                           clus
vv                          DEL PEAK 14(17Q11.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               12
                           clus
vv                          DEL PEAK 14(17Q11.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                             14
  WHITE                                                161
[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"
D18V5, binary
                                cls
clus                               0   1
  DEL PEAK 14(17Q11.2) MUTATED     0  12
  DEL PEAK 14(17Q11.2) WILD-TYPE   3 173
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(17Q11.2) MUTATED      0   12
  DEL PEAK 14(17Q11.2) WILD-TYPE    3  173
                        clus
vv                       DEL PEAK 14(17Q11.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           12
                        clus
vv                       DEL PEAK 14(17Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            173
[1] 2 2
[1] FALSE

Clustering(19) Variable = DEL PEAK 15(18P11.21) MUTATION ANALYSIS
D19V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 15(18P11.21) MUTATED     0   8
  DEL PEAK 15(18P11.21) WILD-TYPE  62 108
  DEL PEAK 15(18P11.21) MUTATED DEL PEAK 15(18P11.21) WILD-TYPE 
                              8                             170 
  DEL PEAK 15(18P11.21) MUTATED DEL PEAK 15(18P11.21) WILD-TYPE 
                              8                             108 
$`DEL PEAK 15(18P11.21) MUTATED`
TCGA-AB-2813 TCGA-AB-2829 TCGA-AB-2857 TCGA-AB-2860 TCGA-AB-2885 TCGA-AB-2904 
        1.02         8.98        10.06        14.04         7.04        17.00 
TCGA-AB-2920 TCGA-AB-2935 
       12.03         2.01 

$`DEL PEAK 15(18P11.21) WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2814 TCGA-AB-2815 
        2.04         1.02         7.99        12.03        26.04        27.02 
TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 
        8.05         8.98         9.96        82.06         0.00        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 
       31.99         0.00         0.99         6.97        24.03         8.98 
TCGA-AB-2828 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 TCGA-AB-2835 
       75.09         9.04        21.04        12.00         8.05        55.00 
TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 
       17.03         0.00        12.00        15.98         0.92        46.06 
TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 TCGA-AB-2849 
        0.00         4.01         9.99        46.09        14.96        72.99 
TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2856 
        2.01         7.96         2.93        12.03         6.97         4.93 
TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 
       18.97         9.99         0.00        47.01         1.02        18.97 
TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 
        2.01         5.03         6.05         4.96         7.99         5.03 
TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2877 
        5.03        20.98         8.98        13.02         6.97        20.98 
TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884 
       12.00         8.05        12.92        12.00        24.00        24.03 
TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 
        5.95        10.98         9.99         0.00        31.00         6.97 
TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 
        5.95         5.03         7.04         7.99        12.92        22.06 
TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 
        6.05         1.94         0.00        52.96        18.97         1.02 
TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 
        0.99         0.00        38.99         9.01        39.98        26.04 
TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2922 TCGA-AB-2923 
        0.00        29.00        39.98         2.01         0.00         1.02 
TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 
        2.96         7.99        15.02         2.96         4.04         0.00 
TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 
        4.01         0.92         1.94         7.07         9.99        14.96 
TCGA-AB-2941 TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 
        0.00        21.07         7.99         1.02        19.07        22.98 
TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 
       10.06         1.02        49.05        16.08         6.02        20.02 
TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 
       16.08        53.98        41.98        11.01        28.08        34.03 
TCGA-AB-2968 TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 
       15.06        37.05        10.03        26.04         0.99        20.02 
TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 
        3.02        30.08         1.02        22.98        22.98         4.93 
TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 
       11.01        38.04         8.98         6.97         6.05         0.99 
TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 
       12.00        15.02        60.03        56.09        25.02        59.11 
TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 
       50.99        51.98         1.02        57.04        41.06        51.98 
TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 
       47.05        69.04        15.95        51.98        27.02        18.97 
TCGA-AB-3011 TCGA-AB-3012 
       61.97        62.04 

  DEL PEAK 15(18P11.21) MUTATED DEL PEAK 15(18P11.21) WILD-TYPE 
                           1.02                            0.00 
  DEL PEAK 15(18P11.21) MUTATED DEL PEAK 15(18P11.21) WILD-TYPE 
                          17.00                           94.06 
  DEL PEAK 15(18P11.21) MUTATED DEL PEAK 15(18P11.21) WILD-TYPE 
                          9.520                          11.505 
[1] "1.0 - 17.0 (9.5)"  "0.0 - 94.1 (11.5)"
[1] "hr=" "2.3"
D19V2, continuous
D19V3, binary
                                 cls
clus                               0  1
  DEL PEAK 15(18P11.21) MUTATED    2  7
  DEL PEAK 15(18P11.21) WILD-TYPE 85 97
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(18P11.21) MUTATED      2    7
  DEL PEAK 15(18P11.21) WILD-TYPE   85   97
        clus
vv       DEL PEAK 15(18P11.21) MUTATED DEL PEAK 15(18P11.21) WILD-TYPE
  FEMALE                             2                              85
  MALE                               7                              97
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(18P11.21) MUTATED       0                         1     8
  DEL PEAK 15(18P11.21) WILD-TYPE     2                        13   165
D19V4, multiclass
                           clus
vv                          DEL PEAK 15(18P11.21) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                 8
                           clus
vv                          DEL PEAK 15(18P11.21) WILD-TYPE
  ASIAN                                                   2
  BLACK OR AFRICAN AMERICAN                              13
  WHITE                                                 165
[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"
D19V5, binary
                                 cls
clus                                0   1
  DEL PEAK 15(18P11.21) MUTATED     0   9
  DEL PEAK 15(18P11.21) WILD-TYPE   3 176
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(18P11.21) MUTATED      0    9
  DEL PEAK 15(18P11.21) WILD-TYPE    3  176
                        clus
vv                       DEL PEAK 15(18P11.21) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                             9
                        clus
vv                       DEL PEAK 15(18P11.21) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             176
[1] 2 2
[1] FALSE

Clustering(20) Variable = DEL PEAK 16(20Q13.13) MUTATION ANALYSIS
D20V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 16(20Q13.13) MUTATED     0   4
  DEL PEAK 16(20Q13.13) WILD-TYPE  62 112
  DEL PEAK 16(20Q13.13) MUTATED DEL PEAK 16(20Q13.13) WILD-TYPE 
                              4                             174 
  DEL PEAK 16(20Q13.13) MUTATED DEL PEAK 16(20Q13.13) WILD-TYPE 
                              4                             112 
$`DEL PEAK 16(20Q13.13) MUTATED`
TCGA-AB-2829 TCGA-AB-2868 TCGA-AB-2915 TCGA-AB-2938 
        8.98         4.96         0.00         9.99 

$`DEL PEAK 16(20Q13.13) WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
        2.04         1.02         7.99        12.03         1.02        26.04 
TCGA-AB-2815 TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 
       27.02         8.05         8.98         9.96        82.06         0.00 
TCGA-AB-2821 TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 
       27.02        31.99         0.00         0.99         6.97        24.03 
TCGA-AB-2827 TCGA-AB-2828 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 
        8.98        75.09         9.04        21.04        12.00         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 
       55.00        17.03         0.00        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 
       46.06         0.00         4.01         9.99        46.09        14.96 
TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 
       72.99         2.01         7.96         2.93        12.03         6.97 
TCGA-AB-2856 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 
        4.93        10.06        18.97         9.99        14.04         0.00 
TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 
       47.01         1.02        18.97         2.01         5.03         6.05 
TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 
        7.99         5.03         5.03        20.98         8.98        13.02 
TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 
        6.97        20.98        12.00         8.05        12.92        12.00 
TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 
       24.00        24.03         7.04         5.95        10.98         9.99 
TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 
        0.00        31.00         6.97         5.95         5.03         7.04 
TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 
        7.99        12.92        22.06         6.05         1.94         0.00 
TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 
       17.00        52.96        18.97         1.02         0.99         0.00 
TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2916 TCGA-AB-2917 
       38.99         9.01        39.98        26.04        29.00        39.98 
TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 
        2.01        12.03         0.00         1.02         2.96         7.99 
TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 
       15.02         2.96         4.04         0.00         4.01         0.92 
TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2942 
        2.01         1.94         7.07        14.96         0.00        21.07 
TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 
        7.99         1.02        19.07        22.98        10.06         1.02 
TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 
       49.05        16.08         6.02        20.02        16.08        53.98 
TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2969 
       41.98        11.01        28.08        34.03        15.06        37.05 
TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 
       10.03        26.04         0.99        20.02         3.02        30.08 
TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 
        1.02        22.98        22.98         4.93        11.01        38.04 
TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 
        8.98         6.97         6.05         0.99        12.00        15.02 
TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996 
       60.03        56.09        25.02        59.11        50.99        51.98 
TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 
        1.02        57.04        41.06        51.98        47.05        69.04 
TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       15.95        51.98        27.02        18.97        61.97        62.04 

  DEL PEAK 16(20Q13.13) MUTATED DEL PEAK 16(20Q13.13) WILD-TYPE 
                              0                               0 
  DEL PEAK 16(20Q13.13) MUTATED DEL PEAK 16(20Q13.13) WILD-TYPE 
                           9.99                           94.06 
  DEL PEAK 16(20Q13.13) MUTATED DEL PEAK 16(20Q13.13) WILD-TYPE 
                           6.97                           12.00 
[1] "0.0 - 10.0 (7.0)"  "0.0 - 94.1 (12.0)"
[1] "hr=" "3.5"
D20V2, continuous
D20V3, binary
                                 cls
clus                                0   1
  DEL PEAK 16(20Q13.13) MUTATED     1   3
  DEL PEAK 16(20Q13.13) WILD-TYPE  86 101
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(20Q13.13) MUTATED      1    3
  DEL PEAK 16(20Q13.13) WILD-TYPE   86  101
        clus
vv       DEL PEAK 16(20Q13.13) MUTATED DEL PEAK 16(20Q13.13) WILD-TYPE
  FEMALE                             1                              86
  MALE                               3                             101
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(20Q13.13) MUTATED       0                         1     3
  DEL PEAK 16(20Q13.13) WILD-TYPE     2                        13   170
D20V4, multiclass
                           clus
vv                          DEL PEAK 16(20Q13.13) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                 3
                           clus
vv                          DEL PEAK 16(20Q13.13) WILD-TYPE
  ASIAN                                                   2
  BLACK OR AFRICAN AMERICAN                              13
  WHITE                                                 170
[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"
D20V5, binary
                                 cls
clus                                0   1
  DEL PEAK 16(20Q13.13) MUTATED     0   4
  DEL PEAK 16(20Q13.13) WILD-TYPE   3 181
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(20Q13.13) MUTATED      0    4
  DEL PEAK 16(20Q13.13) WILD-TYPE    3  181
                        clus
vv                       DEL PEAK 16(20Q13.13) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                             4
                        clus
vv                       DEL PEAK 16(20Q13.13) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             181
[1] 2 2
[1] FALSE
