[1] "ofn"        "-oTPCPG-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/PCPG-TP/15087180/PCPG-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PCPG-TP/15096462/transformed.cor.cli.txt"

nPatients in clinical file=179, in cluster file=162, common to both=162
[1]  28 162
[1] "AMP PEAK 1(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 1(1Q21.3) MUTATED AMP PEAK 1(1Q21.3) WILD-TYPE 
                          30                          132 
  AMP PEAK 1(1Q21.3) MUTATED AMP PEAK 1(1Q21.3) WILD-TYPE 
                          30                          132 
[1] "AMP PEAK 2(4Q25) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 2(4Q25) MUTATED AMP PEAK 2(4Q25) WILD-TYPE 
                         6                        156 
  AMP PEAK 2(4Q25) MUTATED AMP PEAK 2(4Q25) WILD-TYPE 
                         6                        156 
[1] "AMP PEAK 3(4Q31.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 3(4Q31.1) MUTATED AMP PEAK 3(4Q31.1) WILD-TYPE 
                          13                          149 
  AMP PEAK 3(4Q31.1) MUTATED AMP PEAK 3(4Q31.1) WILD-TYPE 
                          13                          149 
[1] "AMP PEAK 4(11P15.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 4(11P15.2) MUTATED AMP PEAK 4(11P15.2) WILD-TYPE 
                            8                           154 
  AMP PEAK 4(11P15.2) MUTATED AMP PEAK 4(11P15.2) WILD-TYPE 
                            8                           154 
[1] "AMP PEAK 5(12Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 5(12Q13.3) MUTATED AMP PEAK 5(12Q13.3) WILD-TYPE 
                           16                           146 
  AMP PEAK 5(12Q13.3) MUTATED AMP PEAK 5(12Q13.3) WILD-TYPE 
                           16                           146 
[1] "AMP PEAK 6(14Q24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 6(14Q24.3) MUTATED AMP PEAK 6(14Q24.3) WILD-TYPE 
                           10                           152 
  AMP PEAK 6(14Q24.3) MUTATED AMP PEAK 6(14Q24.3) WILD-TYPE 
                           10                           152 
[1] "AMP PEAK 7(17Q21.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 7(17Q21.31) MUTATED AMP PEAK 7(17Q21.31) WILD-TYPE 
                            16                            146 
  AMP PEAK 7(17Q21.31) MUTATED AMP PEAK 7(17Q21.31) WILD-TYPE 
                            16                            146 
[1] "DEL PEAK  1(1P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P12) MUTATED DEL PEAK  1(1P12) WILD-TYPE 
                        113                          49 
  DEL PEAK  1(1P12) MUTATED DEL PEAK  1(1P12) WILD-TYPE 
                        113                          49 
[1] "DEL PEAK  2(1Q42.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE 
                            18                            144 
  DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE 
                            18                            144 
[1] "DEL PEAK  3(3P24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(3P24.1) MUTATED DEL PEAK  3(3P24.1) WILD-TYPE 
                           64                            98 
  DEL PEAK  3(3P24.1) MUTATED DEL PEAK  3(3P24.1) WILD-TYPE 
                           64                            98 
[1] "DEL PEAK  4(3Q26.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(3Q26.1) MUTATED DEL PEAK  4(3Q26.1) WILD-TYPE 
                           93                            69 
  DEL PEAK  4(3Q26.1) MUTATED DEL PEAK  4(3Q26.1) WILD-TYPE 
                           93                            69 
[1] "DEL PEAK  5(4Q28.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(4Q28.3) MUTATED DEL PEAK  5(4Q28.3) WILD-TYPE 
                           10                           152 
  DEL PEAK  5(4Q28.3) MUTATED DEL PEAK  5(4Q28.3) WILD-TYPE 
                           10                           152 
[1] "DEL PEAK  6(5Q15) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(5Q15) MUTATED DEL PEAK  6(5Q15) WILD-TYPE 
                         12                         150 
  DEL PEAK  6(5Q15) MUTATED DEL PEAK  6(5Q15) WILD-TYPE 
                         12                         150 
[1] "DEL PEAK  7(6P12.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(6P12.3) MUTATED DEL PEAK  7(6P12.3) WILD-TYPE 
                           10                           152 
  DEL PEAK  7(6P12.3) MUTATED DEL PEAK  7(6P12.3) WILD-TYPE 
                           10                           152 
[1] "DEL PEAK  8(6Q16.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(6Q16.1) MUTATED DEL PEAK  8(6Q16.1) WILD-TYPE 
                           24                           138 
  DEL PEAK  8(6Q16.1) MUTATED DEL PEAK  8(6Q16.1) WILD-TYPE 
                           24                           138 
[1] "DEL PEAK  9(8P22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(8P22) MUTATED DEL PEAK  9(8P22) WILD-TYPE 
                         25                         137 
  DEL PEAK  9(8P22) MUTATED DEL PEAK  9(8P22) WILD-TYPE 
                         25                         137 
[1] "DEL PEAK 10(8Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(8Q23.3) MUTATED DEL PEAK 10(8Q23.3) WILD-TYPE 
                           13                           149 
  DEL PEAK 10(8Q23.3) MUTATED DEL PEAK 10(8Q23.3) WILD-TYPE 
                           13                           149 
[1] "DEL PEAK 11(9P24.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(9P24.2) MUTATED DEL PEAK 11(9P24.2) WILD-TYPE 
                           15                           147 
  DEL PEAK 11(9P24.2) MUTATED DEL PEAK 11(9P24.2) WILD-TYPE 
                           15                           147 
[1] "DEL PEAK 12(9Q21.12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(9Q21.12) MUTATED DEL PEAK 12(9Q21.12) WILD-TYPE 
                            14                            148 
  DEL PEAK 12(9Q21.12) MUTATED DEL PEAK 12(9Q21.12) WILD-TYPE 
                            14                            148 
[1] "DEL PEAK 13(11P15.4) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(11P15.4) MUTATED DEL PEAK 13(11P15.4) WILD-TYPE 
                            58                            104 
  DEL PEAK 13(11P15.4) MUTATED DEL PEAK 13(11P15.4) WILD-TYPE 
                            58                            104 
[1] "DEL PEAK 14(11Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(11Q22.1) MUTATED DEL PEAK 14(11Q22.1) WILD-TYPE 
                            48                            114 
  DEL PEAK 14(11Q22.1) MUTATED DEL PEAK 14(11Q22.1) WILD-TYPE 
                            48                            114 
[1] "DEL PEAK 15(12Q21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(12Q21.33) MUTATED DEL PEAK 15(12Q21.33) WILD-TYPE 
                              8                             154 
  DEL PEAK 15(12Q21.33) MUTATED DEL PEAK 15(12Q21.33) WILD-TYPE 
                              8                             154 
[1] "DEL PEAK 16(13Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(13Q22.3) MUTATED DEL PEAK 16(13Q22.3) WILD-TYPE 
                             8                            154 
  DEL PEAK 16(13Q22.3) MUTATED DEL PEAK 16(13Q22.3) WILD-TYPE 
                             8                            154 
[1] "DEL PEAK 17(16Q21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(16Q21) MUTATED DEL PEAK 17(16Q21) WILD-TYPE 
                           5                          157 
  DEL PEAK 17(16Q21) MUTATED DEL PEAK 17(16Q21) WILD-TYPE 
                           5                          157 
[1] "DEL PEAK 18(17P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(17P13.2) MUTATED DEL PEAK 18(17P13.2) WILD-TYPE 
                            64                             98 
  DEL PEAK 18(17P13.2) MUTATED DEL PEAK 18(17P13.2) WILD-TYPE 
                            64                             98 
[1] "DEL PEAK 19(17Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(17Q11.2) MUTATED DEL PEAK 19(17Q11.2) WILD-TYPE 
                            42                            120 
  DEL PEAK 19(17Q11.2) MUTATED DEL PEAK 19(17Q11.2) WILD-TYPE 
                            42                            120 
[1] "DEL PEAK 20(22Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(22Q13.31) MUTATED DEL PEAK 20(22Q13.31) WILD-TYPE 
                             65                              97 
  DEL PEAK 20(22Q13.31) MUTATED DEL PEAK 20(22Q13.31) WILD-TYPE 
                             65                              97 
[1] "DEL PEAK 21(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(XP21.1) MUTATED DEL PEAK 21(XP21.1) WILD-TYPE 
                           46                           116 
  DEL PEAK 21(XP21.1) MUTATED DEL PEAK 21(XP21.1) WILD-TYPE 
                           46                           116 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "DCC_UPLOAD_DATE"                       
 [6] "GENDER"                                
 [7] "RADIATION_THERAPY"                     
 [8] "RADIATIONS_RADIATION_REGIMENINDICATION"
 [9] "RACE"                                  
[10] "ETHNICITY"                             
[11] "BATCH_NUMBER"                          

Input Data has 11 rows and 162 columns.

[1] "Batch" "11"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=6,	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=147,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'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 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 8:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY excluded in the analysis because there is no case of (both >= 3) in the table below"
              HISPANIC OR LATINO NOT HISPANIC OR LATINO
freq.values   "2"                "128"                 
freq.contrast "128"              "2"                   
both >= 3     "FALSE"            "FALSE"               
Variable 11:'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 162 columns, 1 survival variables, and 3 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"          
YEARS_TO_BIRTH, nv=57, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK 1(1Q21.3) MUTATION ANALYSIS
D1V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 1(1Q21.3) MUTATED    26   4
  AMP PEAK 1(1Q21.3) WILD-TYPE 130   2
  AMP PEAK 1(1Q21.3) MUTATED AMP PEAK 1(1Q21.3) WILD-TYPE 
                          30                          132 
  AMP PEAK 1(1Q21.3) MUTATED AMP PEAK 1(1Q21.3) WILD-TYPE 
                           4                            2 
$`AMP PEAK 1(1Q21.3) MUTATED`
TCGA-P7-A5NY TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A702 TCGA-QR-A70D TCGA-QR-A70K 
       31.46       137.59        19.04         1.28         0.23         9.01 
TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70X TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A686 
      117.14        14.20         6.02        33.30        23.80        13.32 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-SP-A6QC TCGA-SP-A6QD 
        2.89        20.09        31.59        30.21       114.77       109.25 
TCGA-SR-A6MS TCGA-SR-A6MV TCGA-SR-A6MZ TCGA-WB-A80L TCGA-WB-A80P TCGA-WB-A815 
       81.93       121.05        19.76        34.26       316.73         5.98 
TCGA-WB-A819 TCGA-WB-A81G TCGA-WB-A81Q TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 
       33.90        38.76        24.82        71.05        78.21        10.16 

$`AMP PEAK 1(1Q21.3) WILD-TYPE`
TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG 
       29.03         2.27        17.75         5.88        17.95        81.70 
TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GU TCGA-QR-A6GY 
       28.08        35.01        23.11         1.25        58.88         1.05 
TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 
       30.51         9.21        14.17         9.93        14.27        31.53 
TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G 
       15.58        32.15         4.11       116.19         6.31         2.33 
TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70W TCGA-QR-A7IN 
       26.83        29.92        13.12         1.41        41.79        12.39 
TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN 
       17.95        36.23         6.94         1.81         0.72        25.18 
TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W 
        2.30         4.41         0.79        13.08        77.98         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
      108.26        50.63         8.09        86.89        19.86         2.93 
TCGA-RW-A67Y TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A 
        7.10         1.05         0.85         1.22        11.70        13.05 
TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ 
        7.96         6.28        72.79        15.02        41.88         4.41 
TCGA-RW-A7D0 TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR 
        1.78        37.25        35.51        31.04        26.96        40.70 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       37.58        30.51        27.91        20.58        25.32        12.66 
TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI 
       18.94        18.08         9.73        82.62        67.50       110.04 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
       15.52       111.25         1.41         0.10        51.22        68.61 
TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6N0 TCGA-TT-A6YJ 
      106.75       110.53         3.12        24.66        49.61         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 
       25.15        19.92        13.32        25.32        14.20        17.16 
TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF 
        1.18        19.86        12.03        12.49        16.60        17.69 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       25.61        10.65        34.82         4.47         4.73         4.21 
TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A816 TCGA-WB-A817 
      127.56        29.16        19.59        32.88        41.23        32.61 
TCGA-WB-A818 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81H 
       34.03        24.16        35.84        37.18        57.11        42.54 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
       22.32        24.36        40.04        45.83        53.69        12.99 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
        1.61        23.77        18.28        93.11       103.17        20.19 

  AMP PEAK 1(1Q21.3) MUTATED AMP PEAK 1(1Q21.3) WILD-TYPE 
                        0.23                         0.10 
  AMP PEAK 1(1Q21.3) MUTATED AMP PEAK 1(1Q21.3) WILD-TYPE 
                      316.73                       127.56 
  AMP PEAK 1(1Q21.3) MUTATED AMP PEAK 1(1Q21.3) WILD-TYPE 
                      30.835                       19.890 
[1] "0.2 - 316.7 (30.8)" "0.1 - 127.6 (19.9)"
[1] "hr=" "5.9"
D1V2, continuous
D1V3, binary
                              cls
clus                            0  1
  AMP PEAK 1(1Q21.3) MUTATED   13 17
  AMP PEAK 1(1Q21.3) WILD-TYPE 75 57
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(1Q21.3) MUTATED     13   17
  AMP PEAK 1(1Q21.3) WILD-TYPE   75   57
        clus
vv       AMP PEAK 1(1Q21.3) MUTATED AMP PEAK 1(1Q21.3) WILD-TYPE
  FEMALE                         13                           75
  MALE                           17                           57
[1] 2 2
[1] FALSE
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 1(1Q21.3) MUTATED                                  0     0
  AMP PEAK 1(1Q21.3) WILD-TYPE                                1     5
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 1(1Q21.3) MUTATED                           3    26
  AMP PEAK 1(1Q21.3) WILD-TYPE                        16   108
D1V4, multiclass
                                  clus
vv                                 AMP PEAK 1(1Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     0
  BLACK OR AFRICAN AMERICAN                                 3
  WHITE                                                    26
                                  clus
vv                                 AMP PEAK 1(1Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  16
  WHITE                                                     108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = AMP PEAK 2(4Q25) MUTATION ANALYSIS
D2V1, survival
                            sevent
clus2                          0   1
  AMP PEAK 2(4Q25) MUTATED     6   0
  AMP PEAK 2(4Q25) WILD-TYPE 150   6
  AMP PEAK 2(4Q25) MUTATED AMP PEAK 2(4Q25) WILD-TYPE 
                         6                        156 
  AMP PEAK 2(4Q25) MUTATED AMP PEAK 2(4Q25) WILD-TYPE 
                         0                          6 
$`AMP PEAK 2(4Q25) MUTATED`
TCGA-QT-A5XJ TCGA-RW-A688 TCGA-RW-A68G TCGA-SP-A6QI TCGA-WB-A80K TCGA-WB-A81J 
       36.23         1.22        41.88       110.04        34.82        24.36 

$`AMP PEAK 2(4Q25) WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 
       58.88        19.04         1.05        30.51         9.21        14.17 
TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 
        9.93        14.27        31.53        15.58        32.15         1.28 
TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        4.11       116.19         0.23         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R 
       29.92        13.12         9.01         1.41       117.14        14.20 
TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XK TCGA-QT-A5XL 
       41.79         6.02        12.39        17.95         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
        0.72        25.18         2.30         4.41         0.79        13.08 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       77.98         0.92       108.26        50.63         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 
       19.86         2.93         7.10        33.30        23.80         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C 
        0.85        13.32        11.70        13.05         7.96         6.28 
TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ 
       72.79        15.02         4.41         1.78         2.89        20.09 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
       31.59        30.21        37.25        35.51        31.04        26.96 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       40.70        37.58        30.51        27.91        20.58        25.32 
TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD 
       12.66        18.94        18.08         9.73       114.77       109.25 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 
       82.62        67.50        15.52       111.25         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV 
       51.22        68.61        81.93       106.75       110.53       121.05 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK 
        3.12        24.66        19.76        49.61         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA 
       19.92        13.32        25.32        14.20        17.16         1.18 
TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH 
       19.86        12.03        12.49        16.60        17.69        25.61 
TCGA-W2-A7UY TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
       10.65        34.26         4.47         4.73         4.21       316.73 
TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 
      127.56        29.16        19.59        32.88         5.98        41.23 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E 
       32.61        34.03        33.90        24.16        35.84        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81K TCGA-WB-A81M 
       57.11        38.76        42.54        22.32        40.04        45.83 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       53.69        12.99        24.82         1.61        23.77        18.28 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       71.05        78.21        10.16        93.11       103.17        20.19 

  AMP PEAK 2(4Q25) MUTATED AMP PEAK 2(4Q25) WILD-TYPE 
                      1.22                       0.10 
  AMP PEAK 2(4Q25) MUTATED AMP PEAK 2(4Q25) WILD-TYPE 
                    110.04                     316.73 
  AMP PEAK 2(4Q25) MUTATED AMP PEAK 2(4Q25) WILD-TYPE 
                    35.525                     20.140 
[1] "1.2 - 110.0 (35.5)" "0.1 - 316.7 (20.1)"
[1] "hr="     "2.6e+07"
D2V2, continuous
D2V3, binary
                            cls
clus                          0  1
  AMP PEAK 2(4Q25) MUTATED    2  4
  AMP PEAK 2(4Q25) WILD-TYPE 86 70
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 2(4Q25) MUTATED      2    4
  AMP PEAK 2(4Q25) WILD-TYPE   86   70
        clus
vv       AMP PEAK 2(4Q25) MUTATED AMP PEAK 2(4Q25) WILD-TYPE
  FEMALE                        2                         86
  MALE                          4                         70
[1] 2 2
[1] FALSE
                            vv
clus                         AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 2(4Q25) MUTATED                                  0     0
  AMP PEAK 2(4Q25) WILD-TYPE                                1     5
                            vv
clus                         BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 2(4Q25) MUTATED                           1     5
  AMP PEAK 2(4Q25) WILD-TYPE                        18   129
D2V4, multiclass
                                  clus
vv                                 AMP PEAK 2(4Q25) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                        0
  ASIAN                                                   0
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                   5
                                  clus
vv                                 AMP PEAK 2(4Q25) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     5
  BLACK OR AFRICAN AMERICAN                                18
  WHITE                                                   129
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = AMP PEAK 3(4Q31.1) MUTATION ANALYSIS
D3V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 3(4Q31.1) MUTATED    13   0
  AMP PEAK 3(4Q31.1) WILD-TYPE 143   6
  AMP PEAK 3(4Q31.1) MUTATED AMP PEAK 3(4Q31.1) WILD-TYPE 
                          13                          149 
  AMP PEAK 3(4Q31.1) MUTATED AMP PEAK 3(4Q31.1) WILD-TYPE 
                           0                            6 
$`AMP PEAK 3(4Q31.1) MUTATED`
TCGA-PR-A5PF TCGA-PR-A5PH TCGA-QR-A70C TCGA-QR-A70H TCGA-RW-A686 TCGA-RW-A688 
       17.95        28.08       116.19        26.83        13.32         1.22 
TCGA-RW-A68G TCGA-SP-A6QI TCGA-TT-A6YN TCGA-W2-A7H5 TCGA-W2-A7HC TCGA-WB-A80K 
       41.88       110.04        19.92        14.20        12.03        34.82 
TCGA-WB-A80Q 
      127.56 

$`AMP PEAK 3(4Q31.1) WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PG 
       31.46        29.03         2.27        17.75         5.88        81.70 
TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GU TCGA-QR-A6GX 
       35.01        23.11         1.25       137.59        58.88        19.04 
TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 
        1.05        30.51         9.21        14.17         9.93        14.27 
TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70D 
       31.53        15.58        32.15         1.28         4.11         0.23 
TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N 
        6.31         2.33        29.92        13.12         9.01         1.41 
TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP 
      117.14        14.20        41.79         6.02        12.39        17.95 
TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO 
       36.23         6.94         1.81         0.72        25.18         2.30 
TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 
        4.41         0.79        13.08        77.98         0.92       108.26 
TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y 
       50.63         8.09        86.89        19.86         2.93         7.10 
TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A689 TCGA-RW-A68A 
       33.30        23.80         1.05         0.85        11.70        13.05 
TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A7CZ TCGA-RW-A7D0 
        7.96         6.28        72.79        15.02         4.41         1.78 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
        2.89        20.09        31.59        30.21        37.25        35.51 
TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV 
       31.04        26.96        40.70        37.58        30.51        27.91 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 
       20.58        25.32        12.66        18.94        18.08         9.73 
TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QJ TCGA-SP-A6QK 
      114.77       109.25        82.62        67.50        15.52       111.25 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT 
        1.41         0.10        51.22        68.61        81.93       106.75 
TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
      110.53       121.05         3.12        24.66        19.76        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA 
        4.34        25.15        13.32        25.32        17.16         1.18 
TCGA-W2-A7HB TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY 
       19.86        12.49        16.60        17.69        25.61        10.65 
TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80V 
       34.26         4.47         4.73         4.21       316.73        29.16 
TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 
       19.59        32.88         5.98        41.23        32.61        34.03 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G 
       33.90        24.16        35.84        37.18        57.11        38.76 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       42.54        22.32        24.36        40.04        45.83        53.69 
TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       12.99        24.82         1.61        23.77        18.28        71.05 
TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       78.21        10.16        93.11       103.17        20.19 

  AMP PEAK 3(4Q31.1) MUTATED AMP PEAK 3(4Q31.1) WILD-TYPE 
                        1.22                         0.10 
  AMP PEAK 3(4Q31.1) MUTATED AMP PEAK 3(4Q31.1) WILD-TYPE 
                      127.56                       316.73 
  AMP PEAK 3(4Q31.1) MUTATED AMP PEAK 3(4Q31.1) WILD-TYPE 
                       26.83                        20.58 
[1] "1.2 - 127.6 (26.8)" "0.1 - 316.7 (20.6)"
[1] "hr="     "8.1e+07"
D3V2, continuous
D3V3, binary
                              cls
clus                            0  1
  AMP PEAK 3(4Q31.1) MUTATED    6  7
  AMP PEAK 3(4Q31.1) WILD-TYPE 82 67
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 3(4Q31.1) MUTATED      6    7
  AMP PEAK 3(4Q31.1) WILD-TYPE   82   67
        clus
vv       AMP PEAK 3(4Q31.1) MUTATED AMP PEAK 3(4Q31.1) WILD-TYPE
  FEMALE                          6                           82
  MALE                            7                           67
[1] 2 2
[1] FALSE
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 3(4Q31.1) MUTATED                                  0     0
  AMP PEAK 3(4Q31.1) WILD-TYPE                                1     5
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 3(4Q31.1) MUTATED                           1    12
  AMP PEAK 3(4Q31.1) WILD-TYPE                        18   122
D3V4, multiclass
                                  clus
vv                                 AMP PEAK 3(4Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     0
  BLACK OR AFRICAN AMERICAN                                 1
  WHITE                                                    12
                                  clus
vv                                 AMP PEAK 3(4Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  18
  WHITE                                                     122
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = AMP PEAK 4(11P15.2) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 4(11P15.2) MUTATED     8   0
  AMP PEAK 4(11P15.2) WILD-TYPE 148   6
  AMP PEAK 4(11P15.2) MUTATED AMP PEAK 4(11P15.2) WILD-TYPE 
                            8                           154 
  AMP PEAK 4(11P15.2) MUTATED AMP PEAK 4(11P15.2) WILD-TYPE 
                            0                             6 
$`AMP PEAK 4(11P15.2) MUTATED`
TCGA-P8-A5KD TCGA-PR-A5PF TCGA-PR-A5PG TCGA-RW-A689 TCGA-RW-A68D TCGA-SP-A6QF 
        2.27        17.95        81.70        11.70        72.79        82.62 
TCGA-TT-A6YN TCGA-WB-A80O 
       19.92         4.21 

$`AMP PEAK 4(11P15.2) WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PH TCGA-QR-A6GO 
       31.46        29.03        17.75         5.88        28.08        35.01 
TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY 
       23.11         1.25       137.59        58.88        19.04         1.05 
TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 
       30.51         9.21        14.17         9.93        14.27        31.53 
TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D 
       15.58        32.15         1.28         4.11       116.19         0.23 
TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K 
        6.31         2.33        26.83        29.92        13.12         9.01 
TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN 
        1.41       117.14        14.20        41.79         6.02        12.39 
TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN 
       17.95        36.23         6.94         1.81         0.72        25.18 
TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W 
        2.30         4.41         0.79        13.08        77.98         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
      108.26        50.63         8.09        86.89        19.86         2.93 
TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 
        7.10        33.30        23.80         1.05         0.85        13.32 
TCGA-RW-A688 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68F TCGA-RW-A68G 
        1.22        13.05         7.96         6.28        15.02        41.88 
TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
        4.41         1.78         2.89        20.09        31.59        30.21 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT 
       37.25        35.51        31.04        26.96        40.70        37.58 
TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 
       30.51        27.91        20.58        25.32        12.66        18.94 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SP-A6QI 
       18.08         9.73       114.77       109.25        67.50       110.04 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
       15.52       111.25         1.41         0.10        51.22        68.61 
TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY 
       81.93       106.75       110.53       121.05         3.12        24.66 
TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YO TCGA-TT-A6YP 
       19.76        49.61         4.34        25.15        13.32        25.32 
TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD 
       14.20        17.16         1.18        19.86        12.03        12.49 
TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L 
       16.60        17.69        25.61        10.65        34.82        34.26 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.47         4.73       316.73       127.56        29.16        19.59 
TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 
       32.88         5.98        41.23        32.61        34.03        33.90 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       24.16        35.84        37.18        57.11        38.76        42.54 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
       22.32        24.36        40.04        45.83        53.69        12.99 
TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       24.82         1.61        23.77        18.28        71.05        78.21 
TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       10.16        93.11       103.17        20.19 

  AMP PEAK 4(11P15.2) MUTATED AMP PEAK 4(11P15.2) WILD-TYPE 
                         2.27                          0.10 
  AMP PEAK 4(11P15.2) MUTATED AMP PEAK 4(11P15.2) WILD-TYPE 
                        82.62                        316.73 
  AMP PEAK 4(11P15.2) MUTATED AMP PEAK 4(11P15.2) WILD-TYPE 
                       18.935                        22.715 
[1] "2.3 - 82.6 (18.9)"  "0.1 - 316.7 (22.7)"
[1] "hr="     "2.6e+07"
D4V2, continuous
D4V3, binary
                               cls
clus                             0  1
  AMP PEAK 4(11P15.2) MUTATED    6  2
  AMP PEAK 4(11P15.2) WILD-TYPE 82 72
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 4(11P15.2) MUTATED      6    2
  AMP PEAK 4(11P15.2) WILD-TYPE   82   72
        clus
vv       AMP PEAK 4(11P15.2) MUTATED AMP PEAK 4(11P15.2) WILD-TYPE
  FEMALE                           6                            82
  MALE                             2                            72
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 4(11P15.2) MUTATED                                  0     2
  AMP PEAK 4(11P15.2) WILD-TYPE                                1     3
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 4(11P15.2) MUTATED                           0     6
  AMP PEAK 4(11P15.2) WILD-TYPE                        19   128
D4V4, multiclass
                                  clus
vv                                 AMP PEAK 4(11P15.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      6
                                  clus
vv                                 AMP PEAK 4(11P15.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   19
  WHITE                                                      128
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = AMP PEAK 5(12Q13.3) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 5(12Q13.3) MUTATED    16   0
  AMP PEAK 5(12Q13.3) WILD-TYPE 140   6
  AMP PEAK 5(12Q13.3) MUTATED AMP PEAK 5(12Q13.3) WILD-TYPE 
                           16                           146 
  AMP PEAK 5(12Q13.3) MUTATED AMP PEAK 5(12Q13.3) WILD-TYPE 
                            0                             6 
$`AMP PEAK 5(12Q13.3) MUTATED`
TCGA-QR-A6GX TCGA-QR-A6GZ TCGA-QR-A700 TCGA-QR-A70N TCGA-QT-A5XJ TCGA-RT-A6YC 
       19.04        30.51        32.15         1.41        36.23         8.09 
TCGA-RW-A681 TCGA-RW-A68D TCGA-S7-A7X1 TCGA-SR-A6MP TCGA-SR-A6MT TCGA-SR-A6MZ 
       23.80        72.79        18.94        51.22       106.75        19.76 
TCGA-W2-A7H5 TCGA-W2-A7HB TCGA-W2-A7HD TCGA-WB-A821 
       14.20        19.86        12.49        93.11 

$`AMP PEAK 5(12Q13.3) WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 
       58.88         1.05         9.21        14.17         9.93        14.27 
TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D 
       31.53        15.58         1.28         4.11       116.19         0.23 
TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K 
        6.31         2.33        26.83        29.92        13.12         9.01 
TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP 
      117.14        14.20        41.79         6.02        12.39        17.95 
TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP 
        6.94         1.81         0.72        25.18         2.30         4.41 
TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA 
        0.79        13.08        77.98         0.92       108.26        50.63 
TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A684 
       86.89        19.86         2.93         7.10        33.30         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B 
        0.85        13.32         1.22        11.70        13.05         7.96 
TCGA-RW-A68C TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ 
        6.28        15.02        41.88         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
       20.09        31.59        30.21        37.25        35.51        31.04 
TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW 
       26.96        40.70        37.58        30.51        27.91        20.58 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD 
       25.32        12.66        18.08         9.73       114.77       109.25 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
       82.62        67.50       110.04        15.52       111.25         1.41 
TCGA-SQ-A6I6 TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX 
        0.10        68.61        81.93       110.53       121.05         3.12 
TCGA-SR-A6MY TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO 
       24.66        49.61         4.34        25.15        19.92        13.32 
TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HE TCGA-W2-A7HF 
       25.32        17.16         1.18        12.03        16.60        17.69 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N 
       25.61        10.65        34.82        34.26         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 
        4.21       316.73       127.56        29.16        19.59        32.88 
TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A 
        5.98        41.23        32.61        34.03        33.90        24.16 
TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       35.84        37.18        57.11        38.76        42.54        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q 
       24.36        40.04        45.83        53.69        12.99        24.82 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 
        1.61        23.77        18.28        71.05        78.21        10.16 
TCGA-WB-A822 TCGA-XG-A823 
      103.17        20.19 

  AMP PEAK 5(12Q13.3) MUTATED AMP PEAK 5(12Q13.3) WILD-TYPE 
                         1.41                          0.10 
  AMP PEAK 5(12Q13.3) MUTATED AMP PEAK 5(12Q13.3) WILD-TYPE 
                       106.75                        316.73 
  AMP PEAK 5(12Q13.3) MUTATED AMP PEAK 5(12Q13.3) WILD-TYPE 
                        21.83                         21.45 
[1] "1.4 - 106.8 (21.8)" "0.1 - 316.7 (21.4)"
[1] "hr="     "7.9e+07"
D5V2, continuous
D5V3, binary
                               cls
clus                             0  1
  AMP PEAK 5(12Q13.3) MUTATED    9  7
  AMP PEAK 5(12Q13.3) WILD-TYPE 79 67
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 5(12Q13.3) MUTATED      9    7
  AMP PEAK 5(12Q13.3) WILD-TYPE   79   67
        clus
vv       AMP PEAK 5(12Q13.3) MUTATED AMP PEAK 5(12Q13.3) WILD-TYPE
  FEMALE                           9                            79
  MALE                             7                            67
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 5(12Q13.3) MUTATED                                  0     1
  AMP PEAK 5(12Q13.3) WILD-TYPE                                1     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 5(12Q13.3) MUTATED                           3    12
  AMP PEAK 5(12Q13.3) WILD-TYPE                        16   122
D5V4, multiclass
                                  clus
vv                                 AMP PEAK 5(12Q13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  3
  WHITE                                                     12
                                  clus
vv                                 AMP PEAK 5(12Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   16
  WHITE                                                      122
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = AMP PEAK 6(14Q24.3) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 6(14Q24.3) MUTATED     9   1
  AMP PEAK 6(14Q24.3) WILD-TYPE 147   5
  AMP PEAK 6(14Q24.3) MUTATED AMP PEAK 6(14Q24.3) WILD-TYPE 
                           10                           152 
  AMP PEAK 6(14Q24.3) MUTATED AMP PEAK 6(14Q24.3) WILD-TYPE 
                            1                             5 
$`AMP PEAK 6(14Q24.3) MUTATED`
TCGA-QR-A700 TCGA-QR-A70N TCGA-QT-A5XJ TCGA-QT-A5XL TCGA-QT-A5XN TCGA-QT-A5XO 
       32.15         1.41        36.23         1.81        25.18         2.30 
TCGA-RW-A681 TCGA-S7-A7WT TCGA-SR-A6MT TCGA-WB-A820 
       23.80        37.58       106.75        10.16 

$`AMP PEAK 6(14Q24.3) WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 
       58.88        19.04         1.05        30.51         9.21        14.17 
TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 
        9.93        14.27        31.53        15.58         1.28         4.11 
TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I 
      116.19         0.23         6.31         2.33        26.83        29.92 
TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X 
       13.12         9.01       117.14        14.20        41.79         6.02 
TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XK TCGA-QT-A5XM TCGA-QT-A5XP TCGA-QT-A69Q 
       12.39        17.95         6.94         0.72         4.41         0.79 
TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC 
       13.08        77.98         0.92       108.26        50.63         8.09 
TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A684 
       86.89        19.86         2.93         7.10        33.30         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B 
        0.85        13.32         1.22        11.70        13.05         7.96 
TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 
        6.28        72.79        15.02        41.88         4.41         1.78 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
        2.89        20.09        31.59        30.21        37.25        35.51 
TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW 
       31.04        26.96        40.70        30.51        27.91        20.58 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC 
       25.32        12.66        18.94        18.08         9.73       114.77 
TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
      109.25        82.62        67.50       110.04        15.52       111.25 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU 
        1.41         0.10        51.22        68.61        81.93       110.53 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ 
      121.05         3.12        24.66        19.76        49.61         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 
       25.15        19.92        13.32        25.32        14.20        17.16 
TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF 
        1.18        19.86        12.03        12.49        16.60        17.69 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N 
       25.61        10.65        34.82        34.26         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 
        4.21       316.73       127.56        29.16        19.59        32.88 
TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A 
        5.98        41.23        32.61        34.03        33.90        24.16 
TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       35.84        37.18        57.11        38.76        42.54        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q 
       24.36        40.04        45.83        53.69        12.99        24.82 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 
        1.61        23.77        18.28        71.05        78.21        93.11 
TCGA-WB-A822 TCGA-XG-A823 
      103.17        20.19 

  AMP PEAK 6(14Q24.3) MUTATED AMP PEAK 6(14Q24.3) WILD-TYPE 
                         1.41                          0.10 
  AMP PEAK 6(14Q24.3) MUTATED AMP PEAK 6(14Q24.3) WILD-TYPE 
                       106.75                        316.73 
  AMP PEAK 6(14Q24.3) MUTATED AMP PEAK 6(14Q24.3) WILD-TYPE 
                       24.490                        20.385 
[1] "1.4 - 106.8 (24.5)" "0.1 - 316.7 (20.4)"
[1] "hr=" "4"  
D6V2, continuous
D6V3, binary
                               cls
clus                             0  1
  AMP PEAK 6(14Q24.3) MUTATED    4  6
  AMP PEAK 6(14Q24.3) WILD-TYPE 84 68
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(14Q24.3) MUTATED      4    6
  AMP PEAK 6(14Q24.3) WILD-TYPE   84   68
        clus
vv       AMP PEAK 6(14Q24.3) MUTATED AMP PEAK 6(14Q24.3) WILD-TYPE
  FEMALE                           4                            84
  MALE                             6                            68
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 6(14Q24.3) MUTATED                                  0     0
  AMP PEAK 6(14Q24.3) WILD-TYPE                                1     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 6(14Q24.3) MUTATED                           4     6
  AMP PEAK 6(14Q24.3) WILD-TYPE                        15   128
D6V4, multiclass
                                  clus
vv                                 AMP PEAK 6(14Q24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  4
  WHITE                                                      6
                                  clus
vv                                 AMP PEAK 6(14Q24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   15
  WHITE                                                      128
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = AMP PEAK 7(17Q21.31) MUTATION ANALYSIS
D7V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 7(17Q21.31) MUTATED    14   2
  AMP PEAK 7(17Q21.31) WILD-TYPE 142   4
  AMP PEAK 7(17Q21.31) MUTATED AMP PEAK 7(17Q21.31) WILD-TYPE 
                            16                            146 
  AMP PEAK 7(17Q21.31) MUTATED AMP PEAK 7(17Q21.31) WILD-TYPE 
                             2                              4 
$`AMP PEAK 7(17Q21.31) MUTATED`
TCGA-P8-A5KC TCGA-PR-A5PF TCGA-PR-A5PH TCGA-QR-A70C TCGA-QR-A70H TCGA-QR-A70K 
       29.03        17.95        28.08       116.19        26.83         9.01 
TCGA-RW-A681 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A8AZ TCGA-WB-A80K TCGA-WB-A80P 
       23.80        13.32         1.22         2.89        34.82       316.73 
TCGA-WB-A80Q TCGA-WB-A81J TCGA-WB-A81Q TCGA-WB-A81W 
      127.56        24.36        24.82        78.21 

$`AMP PEAK 7(17Q21.31) WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PG TCGA-QR-A6GO 
       31.46         2.27        17.75         5.88        81.70        35.01 
TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY 
       23.11         1.25       137.59        58.88        19.04         1.05 
TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 
       30.51         9.21        14.17         9.93        14.27        31.53 
TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70D TCGA-QR-A70E 
       15.58        32.15         1.28         4.11         0.23         6.31 
TCGA-QR-A70G TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R 
        2.33        29.92        13.12         1.41       117.14        14.20 
TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK 
       41.79         6.02        12.39        17.95        36.23         6.94 
TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q 
        1.81         0.72        25.18         2.30         4.41         0.79 
TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC 
       13.08        77.98         0.92       108.26        50.63         8.09 
TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A684 
       86.89        19.86         2.93         7.10        33.30         1.05 
TCGA-RW-A685 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D 
        0.85        11.70        13.05         7.96         6.28        72.79 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RX-A8JQ TCGA-S7-A7WL 
       15.02        41.88         4.41         1.78        20.09        31.59 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR 
       30.21        37.25        35.51        31.04        26.96        40.70 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       37.58        30.51        27.91        20.58        25.32        12.66 
TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
       18.94        18.08         9.73       114.77       109.25        82.62 
TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 
       67.50       110.04        15.52       111.25         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV 
       51.22        68.61        81.93       106.75       110.53       121.05 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK 
        3.12        24.66        19.76        49.61         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA 
       19.92        13.32        25.32        14.20        17.16         1.18 
TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH 
       19.86        12.03        12.49        16.60        17.69        25.61 
TCGA-W2-A7UY TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80V 
       10.65        34.26         4.47         4.73         4.21        29.16 
TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 
       19.59        32.88         5.98        41.23        32.61        34.03 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G 
       33.90        24.16        35.84        37.18        57.11        38.76 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
       42.54        22.32        40.04        45.83        53.69        12.99 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A820 TCGA-WB-A821 
        1.61        23.77        18.28        71.05        10.16        93.11 
TCGA-WB-A822 TCGA-XG-A823 
      103.17        20.19 

  AMP PEAK 7(17Q21.31) MUTATED AMP PEAK 7(17Q21.31) WILD-TYPE 
                          1.22                           0.10 
  AMP PEAK 7(17Q21.31) MUTATED AMP PEAK 7(17Q21.31) WILD-TYPE 
                        316.73                         137.59 
  AMP PEAK 7(17Q21.31) MUTATED AMP PEAK 7(17Q21.31) WILD-TYPE 
                        25.825                         20.005 
[1] "1.2 - 316.7 (25.8)" "0.1 - 137.6 (20.0)"
[1] "hr=" "2.9"
D7V2, continuous
D7V3, binary
                                cls
clus                              0  1
  AMP PEAK 7(17Q21.31) MUTATED    4 12
  AMP PEAK 7(17Q21.31) WILD-TYPE 84 62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 7(17Q21.31) MUTATED      4   12
  AMP PEAK 7(17Q21.31) WILD-TYPE   84   62
        clus
vv       AMP PEAK 7(17Q21.31) MUTATED AMP PEAK 7(17Q21.31) WILD-TYPE
  FEMALE                            4                             84
  MALE                             12                             62
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 7(17Q21.31) MUTATED                                  0     0
  AMP PEAK 7(17Q21.31) WILD-TYPE                                1     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 7(17Q21.31) MUTATED                           1    15
  AMP PEAK 7(17Q21.31) WILD-TYPE                        18   119
D7V4, multiclass
                                  clus
vv                                 AMP PEAK 7(17Q21.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                      15
                                  clus
vv                                 AMP PEAK 7(17Q21.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    18
  WHITE                                                       119
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = DEL PEAK  1(1P12) MUTATION ANALYSIS
D8V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  1(1P12) MUTATED   109   4
  DEL PEAK  1(1P12) WILD-TYPE  47   2
  DEL PEAK  1(1P12) MUTATED DEL PEAK  1(1P12) WILD-TYPE 
                        113                          49 
  DEL PEAK  1(1P12) MUTATED DEL PEAK  1(1P12) WILD-TYPE 
                          4                           2 
$`DEL PEAK  1(1P12) MUTATED`
TCGA-P7-A5NY TCGA-P8-A5KD TCGA-P8-A6RX TCGA-PR-A5PF TCGA-PR-A5PG TCGA-QR-A6GO 
       31.46         2.27        17.75        17.95        81.70        35.01 
TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A6H1 TCGA-QR-A6H2 
       23.11         1.25       137.59        19.04        14.17         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A70D TCGA-QR-A70E 
       14.27        15.58        32.15         1.28         0.23         6.31 
TCGA-QR-A70H TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W 
       26.83        13.12         9.01       117.14        14.20        41.79 
TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       12.39        17.95        36.23         6.94         1.81         0.72 
TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-RM-A68T TCGA-RT-A6YA TCGA-RW-A67V 
        2.30         4.41         0.79        77.98        50.63        86.89 
TCGA-RW-A67W TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 
       19.86         7.10        33.30        23.80         1.05         0.85 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68D TCGA-RW-A7D0 
        1.22        11.70        13.05         7.96        72.79         1.78 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WQ 
        2.89        20.09        31.59        30.21        37.25        26.96 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 
       40.70        37.58        25.32        12.66        18.94        18.08 
TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
      114.77       109.25        82.62        67.50       110.04        15.52 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT 
      111.25         1.41        51.22        68.61        81.93       106.75 
TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ 
      110.53       121.05         3.12        24.66        19.76         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB 
       25.15        19.92        14.20        17.16         1.18        19.86 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HF TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80M 
       12.03        12.49        17.69        10.65        34.82         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80V TCGA-WB-A816 TCGA-WB-A818 
        4.73         4.21       316.73        29.16        41.23        34.03 
TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       33.90        35.84        37.18        57.11        38.76        42.54 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       40.04        45.83        12.99         1.61        23.77        18.28 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 
       71.05        78.21        10.16        93.11       103.17 

$`DEL PEAK  1(1P12) WILD-TYPE`
TCGA-P8-A5KC TCGA-P8-A6RY TCGA-PR-A5PH TCGA-QR-A6GU TCGA-QR-A6GY TCGA-QR-A6GZ 
       29.03         5.88        28.08        58.88         1.05        30.51 
TCGA-QR-A6H0 TCGA-QR-A6H5 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70G TCGA-QR-A70I 
        9.21        31.53         4.11       116.19         2.33        29.92 
TCGA-QR-A70N TCGA-QR-A70X TCGA-QT-A5XN TCGA-QT-A7U0 TCGA-RM-A68W TCGA-RT-A6Y9 
        1.41         6.02        25.18        13.08         0.92       108.26 
TCGA-RT-A6YC TCGA-RW-A67X TCGA-RW-A686 TCGA-RW-A68C TCGA-RW-A68F TCGA-RW-A68G 
        8.09         2.93        13.32         6.28        15.02        41.88 
TCGA-RW-A7CZ TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW 
        4.41        35.51        31.04        30.51        27.91        20.58 
TCGA-SA-A6C2 TCGA-SQ-A6I6 TCGA-SR-A6N0 TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7HE 
        9.73         0.10        49.61        13.32        25.32        16.60 
TCGA-W2-A7HH TCGA-WB-A80L TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
       25.61        34.26       127.56        19.59        32.88         5.98 
TCGA-WB-A817 TCGA-WB-A81A TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81N TCGA-WB-A81Q 
       32.61        24.16        22.32        24.36        53.69        24.82 
TCGA-XG-A823 
       20.19 

  DEL PEAK  1(1P12) MUTATED DEL PEAK  1(1P12) WILD-TYPE 
                       0.23                        0.10 
  DEL PEAK  1(1P12) MUTATED DEL PEAK  1(1P12) WILD-TYPE 
                     316.73                      127.56 
  DEL PEAK  1(1P12) MUTATED DEL PEAK  1(1P12) WILD-TYPE 
                      19.92                       24.16 
[1] "0.2 - 316.7 (19.9)" "0.1 - 127.6 (24.2)"
[1] "hr=" "1.2"
D8V2, continuous
D8V3, binary
                             cls
clus                           0  1
  DEL PEAK  1(1P12) MUTATED   61 52
  DEL PEAK  1(1P12) WILD-TYPE 27 22
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  1(1P12) MUTATED     61   52
  DEL PEAK  1(1P12) WILD-TYPE   27   22
        clus
vv       DEL PEAK  1(1P12) MUTATED DEL PEAK  1(1P12) WILD-TYPE
  FEMALE                        61                          27
  MALE                          52                          22
[1] 2 2
[1] FALSE
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  1(1P12) MUTATED                                  1     5
  DEL PEAK  1(1P12) WILD-TYPE                                0     0
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P12) MUTATED                           9    95
  DEL PEAK  1(1P12) WILD-TYPE                        10    39
D8V4, multiclass
                                  clus
vv                                 DEL PEAK  1(1P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    5
  BLACK OR AFRICAN AMERICAN                                9
  WHITE                                                   95
                                  clus
vv                                 DEL PEAK  1(1P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                 10
  WHITE                                                     39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = DEL PEAK  2(1Q42.13) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  2(1Q42.13) MUTATED    17   1
  DEL PEAK  2(1Q42.13) WILD-TYPE 139   5
  DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE 
                            18                            144 
  DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE 
                             1                              5 
$`DEL PEAK  2(1Q42.13) MUTATED`
TCGA-QR-A6H3 TCGA-QR-A700 TCGA-QR-A70E TCGA-QR-A70X TCGA-QR-A7IN TCGA-QT-A69Q 
       14.27        32.15         6.31         6.02        12.39         0.79 
TCGA-RM-A68T TCGA-RW-A681 TCGA-RW-A68A TCGA-S7-A7WQ TCGA-S7-A7X1 TCGA-SR-A6MT 
       77.98        23.80        13.05        26.96        18.94       106.75 
TCGA-TT-A6YJ TCGA-W2-A7H7 TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A820 TCGA-WB-A821 
        4.34        17.16        37.18        57.11        10.16        93.11 

$`DEL PEAK  2(1Q42.13) WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 
       58.88        19.04         1.05        30.51         9.21        14.17 
TCGA-QR-A6H2 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C 
        9.93        31.53        15.58         1.28         4.11       116.19 
TCGA-QR-A70D TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K 
        0.23         2.33        26.83        29.92        13.12         9.01 
TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A7IP TCGA-QT-A5XJ 
        1.41       117.14        14.20        41.79        17.95        36.23 
TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP 
        6.94         1.81         0.72        25.18         2.30         4.41 
TCGA-QT-A7U0 TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       13.08         0.92       108.26        50.63         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A685 
       19.86         2.93         7.10        33.30         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D 
       13.32         1.22        11.70         7.96         6.28        72.79 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ 
       15.02        41.88         4.41         1.78         2.89        20.09 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR 
       31.59        30.21        37.25        35.51        31.04        40.70 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       37.58        30.51        27.91        20.58        25.32        12.66 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
       18.08         9.73       114.77       109.25        82.62        67.50 
TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP 
      110.04        15.52       111.25         1.41         0.10        51.22 
TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY 
       68.61        81.93       110.53       121.05         3.12        24.66 
TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       19.76        49.61        25.15        19.92        13.32        25.32 
TCGA-W2-A7H5 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       14.20         1.18        19.86        12.03        12.49        16.60 
TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M 
       17.69        25.61        10.65        34.82        34.26         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73         4.21       316.73       127.56        29.16        19.59 
TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 
       32.88         5.98        41.23        32.61        34.03        33.90 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       24.16        35.84        38.76        42.54        22.32        24.36 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R 
       40.04        45.83        53.69        12.99        24.82         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A822 TCGA-XG-A823 
       23.77        18.28        71.05        78.21       103.17        20.19 

  DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE 
                          0.79                           0.10 
  DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE 
                        106.75                         316.73 
  DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE 
                        18.050                         22.715 
[1] "0.8 - 106.8 (18.1)" "0.1 - 316.7 (22.7)"
[1] "hr=" "2.1"
D9V2, continuous
D9V3, binary
                                cls
clus                              0  1
  DEL PEAK  2(1Q42.13) MUTATED    8 10
  DEL PEAK  2(1Q42.13) WILD-TYPE 80 64
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1Q42.13) MUTATED      8   10
  DEL PEAK  2(1Q42.13) WILD-TYPE   80   64
        clus
vv       DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE
  FEMALE                            8                             80
  MALE                             10                             64
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  2(1Q42.13) MUTATED                                  0     0
  DEL PEAK  2(1Q42.13) WILD-TYPE                                1     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1Q42.13) MUTATED                           3    14
  DEL PEAK  2(1Q42.13) WILD-TYPE                        16   120
D9V4, multiclass
                                  clus
vv                                 DEL PEAK  2(1Q42.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      14
                                  clus
vv                                 DEL PEAK  2(1Q42.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    16
  WHITE                                                       120
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = DEL PEAK  3(3P24.1) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  3(3P24.1) MUTATED   62  2
  DEL PEAK  3(3P24.1) WILD-TYPE 94  4
  DEL PEAK  3(3P24.1) MUTATED DEL PEAK  3(3P24.1) WILD-TYPE 
                           64                            98 
  DEL PEAK  3(3P24.1) MUTATED DEL PEAK  3(3P24.1) WILD-TYPE 
                            2                             4 
$`DEL PEAK  3(3P24.1) MUTATED`
TCGA-P8-A6RX TCGA-PR-A5PF TCGA-QR-A6GT TCGA-QR-A6GU TCGA-QR-A6GY TCGA-QR-A6GZ 
       17.75        17.95       137.59        58.88         1.05        30.51 
TCGA-QR-A6H5 TCGA-QR-A700 TCGA-QR-A706 TCGA-QR-A70D TCGA-QR-A70J TCGA-QR-A70N 
       31.53        32.15         4.11         0.23        13.12         1.41 
TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ 
      117.14        14.20         6.02        12.39        17.95        36.23 
TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XN TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RW-A67X 
        6.94         1.81        25.18       108.26        50.63         2.93 
TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68C TCGA-RW-A68D 
        7.10        33.30        11.70        13.05         6.28        72.79 
TCGA-RW-A7CZ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR 
        4.41        31.59        30.21        31.04        26.96        40.70 
TCGA-S7-A7WT TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SQ-A6I6 
       37.58        12.66        18.94       109.25        67.50         0.10 
TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YP 
      106.75       110.53       121.05         4.34        25.15        25.32 
TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HF TCGA-W2-A7UY TCGA-WB-A80P 
       14.20        17.16         1.18        17.69        10.65       316.73 
TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A819 TCGA-WB-A81E 
       29.16        19.59        32.88         5.98        33.90        37.18 
TCGA-WB-A81K TCGA-WB-A81W TCGA-WB-A821 TCGA-XG-A823 
       40.04        78.21        93.11        20.19 

$`DEL PEAK  3(3P24.1) WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RY TCGA-PR-A5PG TCGA-PR-A5PH 
       31.46        29.03         2.27         5.88        81.70        28.08 
TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GX TCGA-QR-A6H0 TCGA-QR-A6H1 
       35.01        23.11         1.25        19.04         9.21        14.17 
TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A70C TCGA-QR-A70E 
        9.93        14.27        15.58         1.28       116.19         6.31 
TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70K TCGA-QR-A70W TCGA-QT-A5XM 
        2.33        26.83        29.92         9.01        41.79         0.72 
TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W 
        2.30         4.41         0.79        13.08        77.98         0.92 
TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 
        8.09        86.89        19.86        23.80         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7D0 
       13.32         1.22         7.96        15.02        41.88         1.78 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WU TCGA-S7-A7WV 
        2.89        20.09        37.25        35.51        30.51        27.91 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QF 
       20.58        25.32        18.08         9.73       114.77        82.62 
TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SR-A6MP TCGA-SR-A6MQ 
      110.04        15.52       111.25         1.41        51.22        68.61 
TCGA-SR-A6MS TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YN 
       81.93         3.12        24.66        19.76        49.61        19.92 
TCGA-TT-A6YO TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH 
       13.32        19.86        12.03        12.49        16.60        25.61 
TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80Q 
       34.82        34.26         4.47         4.73         4.21       127.56 
TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F 
       41.23        32.61        34.03        24.16        35.84        57.11 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81M TCGA-WB-A81N 
       38.76        42.54        22.32        24.36        45.83        53.69 
TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       12.99        24.82         1.61        23.77        18.28        71.05 
TCGA-WB-A820 TCGA-WB-A822 
       10.16       103.17 

  DEL PEAK  3(3P24.1) MUTATED DEL PEAK  3(3P24.1) WILD-TYPE 
                         0.10                          0.72 
  DEL PEAK  3(3P24.1) MUTATED DEL PEAK  3(3P24.1) WILD-TYPE 
                       316.73                        127.56 
  DEL PEAK  3(3P24.1) MUTATED DEL PEAK  3(3P24.1) WILD-TYPE 
                       25.165                        20.335 
[1] "0.1 - 316.7 (25.2)" "0.7 - 127.6 (20.3)"
[1] "hr=" "1.9"
D10V2, continuous
D10V3, binary
                               cls
clus                             0  1
  DEL PEAK  3(3P24.1) MUTATED   40 24
  DEL PEAK  3(3P24.1) WILD-TYPE 48 50
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(3P24.1) MUTATED     40   24
  DEL PEAK  3(3P24.1) WILD-TYPE   48   50
        clus
vv       DEL PEAK  3(3P24.1) MUTATED DEL PEAK  3(3P24.1) WILD-TYPE
  FEMALE                          40                            48
  MALE                            24                            50
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  3(3P24.1) MUTATED                                  1     1
  DEL PEAK  3(3P24.1) WILD-TYPE                                0     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(3P24.1) MUTATED                          10    50
  DEL PEAK  3(3P24.1) WILD-TYPE                         9    84
D10V4, multiclass
                                  clus
vv                                 DEL PEAK  3(3P24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 10
  WHITE                                                     50
                                  clus
vv                                 DEL PEAK  3(3P24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                    9
  WHITE                                                       84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = DEL PEAK  4(3Q26.1) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  4(3Q26.1) MUTATED   91  2
  DEL PEAK  4(3Q26.1) WILD-TYPE 65  4
  DEL PEAK  4(3Q26.1) MUTATED DEL PEAK  4(3Q26.1) WILD-TYPE 
                           93                            69 
  DEL PEAK  4(3Q26.1) MUTATED DEL PEAK  4(3Q26.1) WILD-TYPE 
                            2                             4 
$`DEL PEAK  4(3Q26.1) MUTATED`
TCGA-P8-A5KD TCGA-P8-A6RX TCGA-QR-A6GO TCGA-QR-A6GT TCGA-QR-A6GU TCGA-QR-A6GZ 
        2.27        17.75        35.01       137.59        58.88        30.51 
TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 
        9.21        14.17        31.53        15.58        32.15         1.28 
TCGA-QR-A70D TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A7IN 
        0.23        13.12         1.41        14.20        41.79        12.39 
TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO 
       17.95        36.23         6.94         0.72        25.18         2.30 
TCGA-QT-A5XP TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y 
        4.41       108.26        50.63        19.86         2.93         7.10 
TCGA-RW-A680 TCGA-RW-A685 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B 
       33.30         0.85         1.22        11.70        13.05         7.96 
TCGA-RW-A68C TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-S7-A7WL TCGA-S7-A7WP TCGA-S7-A7WQ 
        6.28         4.41         1.78        31.59        31.04        26.96 
TCGA-S7-A7WR TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QD 
       40.70        25.32        12.66        18.94        18.08       109.25 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
       82.62        67.50       110.04        15.52       111.25         1.41 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV 
        0.10        51.22        68.61       106.75       110.53       121.05 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
        3.12        24.66        19.76         4.34        25.15        19.92 
TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC 
       25.32        14.20        17.16         1.18        19.86        12.03 
TCGA-W2-A7HD TCGA-W2-A7HF TCGA-W2-A7UY TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80P 
       12.49        17.69        10.65         4.47         4.73       316.73 
TCGA-WB-A80V TCGA-WB-A814 TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81F 
       29.16        32.88        41.23        34.03        33.90        57.11 
TCGA-WB-A81G TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81W TCGA-WB-A820 
       38.76         1.61        23.77        18.28        78.21        10.16 
TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       93.11       103.17        20.19 

$`DEL PEAK  4(3Q26.1) WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH 
       31.46        29.03         5.88        17.95        81.70        28.08 
TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H2 TCGA-QR-A6H3 
       23.11         1.25        19.04         1.05         9.93        14.27 
TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I 
        4.11       116.19         6.31         2.33        26.83        29.92 
TCGA-QR-A70K TCGA-QR-A70P TCGA-QR-A70X TCGA-QT-A5XL TCGA-QT-A69Q TCGA-QT-A7U0 
        9.01       117.14         6.02         1.81         0.79        13.08 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A681 TCGA-RW-A684 
       77.98         0.92         8.09        86.89        23.80         1.05 
TCGA-RW-A686 TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A8AZ TCGA-RX-A8JQ 
       13.32        72.79        15.02        41.88         2.89        20.09 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV 
       30.21        37.25        35.51        37.58        30.51        27.91 
TCGA-S7-A7WW TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SR-A6MS TCGA-SR-A6N0 TCGA-TT-A6YO 
       20.58         9.73       114.77        81.93        49.61        13.32 
TCGA-W2-A7HE TCGA-W2-A7HH TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80O TCGA-WB-A80Q 
       16.60        25.61        34.82        34.26         4.21       127.56 
TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A817 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E 
       19.59         5.98        32.61        24.16        35.84        37.18 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       42.54        22.32        24.36        40.04        45.83        53.69 
TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81V 
       12.99        24.82        71.05 

  DEL PEAK  4(3Q26.1) MUTATED DEL PEAK  4(3Q26.1) WILD-TYPE 
                         0.10                          0.79 
  DEL PEAK  4(3Q26.1) MUTATED DEL PEAK  4(3Q26.1) WILD-TYPE 
                       316.73                        127.56 
  DEL PEAK  4(3Q26.1) MUTATED DEL PEAK  4(3Q26.1) WILD-TYPE 
                        19.76                         24.36 
[1] "0.1 - 316.7 (19.8)" "0.8 - 127.6 (24.4)"
[1] "hr=" "2.6"
D11V2, continuous
D11V3, binary
                               cls
clus                             0  1
  DEL PEAK  4(3Q26.1) MUTATED   51 42
  DEL PEAK  4(3Q26.1) WILD-TYPE 37 32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3Q26.1) MUTATED     51   42
  DEL PEAK  4(3Q26.1) WILD-TYPE   37   32
        clus
vv       DEL PEAK  4(3Q26.1) MUTATED DEL PEAK  4(3Q26.1) WILD-TYPE
  FEMALE                          51                            37
  MALE                            42                            32
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  4(3Q26.1) MUTATED                                  1     3
  DEL PEAK  4(3Q26.1) WILD-TYPE                                0     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(3Q26.1) MUTATED                          11    75
  DEL PEAK  4(3Q26.1) WILD-TYPE                         8    59
D11V4, multiclass
                                  clus
vv                                 DEL PEAK  4(3Q26.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 11
  WHITE                                                     75
                                  clus
vv                                 DEL PEAK  4(3Q26.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                    8
  WHITE                                                       59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = DEL PEAK  5(4Q28.3) MUTATION ANALYSIS
D12V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(4Q28.3) MUTATED    10   0
  DEL PEAK  5(4Q28.3) WILD-TYPE 146   6
  DEL PEAK  5(4Q28.3) MUTATED DEL PEAK  5(4Q28.3) WILD-TYPE 
                           10                           152 
  DEL PEAK  5(4Q28.3) MUTATED DEL PEAK  5(4Q28.3) WILD-TYPE 
                            0                             6 
$`DEL PEAK  5(4Q28.3) MUTATED`
TCGA-QR-A700 TCGA-QR-A70N TCGA-QT-A5XO TCGA-QT-A69Q TCGA-RT-A6YA TCGA-RW-A67X 
       32.15         1.41         2.30         0.79        50.63         2.93 
TCGA-RW-A68C TCGA-TT-A6YP TCGA-WB-A81J TCGA-WB-A821 
        6.28        25.32        24.36        93.11 

$`DEL PEAK  5(4Q28.3) WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 
       58.88        19.04         1.05        30.51         9.21        14.17 
TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 
        9.93        14.27        31.53        15.58         1.28         4.11 
TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I 
      116.19         0.23         6.31         2.33        26.83        29.92 
TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X 
       13.12         9.01       117.14        14.20        41.79         6.02 
TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       12.39        17.95        36.23         6.94         1.81         0.72 
TCGA-QT-A5XN TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 
       25.18         4.41        13.08        77.98         0.92       108.26 
TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 
        8.09        86.89        19.86         7.10        33.30        23.80 
TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A 
        1.05         0.85        13.32         1.22        11.70        13.05 
TCGA-RW-A68B TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 
        7.96        72.79        15.02        41.88         4.41         1.78 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
        2.89        20.09        31.59        30.21        37.25        35.51 
TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV 
       31.04        26.96        40.70        37.58        30.51        27.91 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 
       20.58        25.32        12.66        18.94        18.08         9.73 
TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
      114.77       109.25        82.62        67.50       110.04        15.52 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS 
      111.25         1.41         0.10        51.22        68.61        81.93 
TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ 
      106.75       110.53       121.05         3.12        24.66        19.76 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-W2-A7H5 
       49.61         4.34        25.15        19.92        13.32        14.20 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       17.16         1.18        19.86        12.03        12.49        16.60 
TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M 
       17.69        25.61        10.65        34.82        34.26         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73         4.21       316.73       127.56        29.16        19.59 
TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 
       32.88         5.98        41.23        32.61        34.03        33.90 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       24.16        35.84        37.18        57.11        38.76        42.54 
TCGA-WB-A81I TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q 
       22.32        40.04        45.83        53.69        12.99        24.82 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 
        1.61        23.77        18.28        71.05        78.21        10.16 
TCGA-WB-A822 TCGA-XG-A823 
      103.17        20.19 

  DEL PEAK  5(4Q28.3) MUTATED DEL PEAK  5(4Q28.3) WILD-TYPE 
                         0.79                          0.10 
  DEL PEAK  5(4Q28.3) MUTATED DEL PEAK  5(4Q28.3) WILD-TYPE 
                        93.11                        316.73 
  DEL PEAK  5(4Q28.3) MUTATED DEL PEAK  5(4Q28.3) WILD-TYPE 
                        15.32                         21.45 
[1] "0.8 - 93.1 (15.3)"  "0.1 - 316.7 (21.4)"
[1] "hr="     "2.6e+07"
D12V2, continuous
D12V3, binary
                               cls
clus                             0  1
  DEL PEAK  5(4Q28.3) MUTATED    4  6
  DEL PEAK  5(4Q28.3) WILD-TYPE 84 68
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(4Q28.3) MUTATED      4    6
  DEL PEAK  5(4Q28.3) WILD-TYPE   84   68
        clus
vv       DEL PEAK  5(4Q28.3) MUTATED DEL PEAK  5(4Q28.3) WILD-TYPE
  FEMALE                           4                            84
  MALE                             6                            68
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  5(4Q28.3) MUTATED                                  0     0
  DEL PEAK  5(4Q28.3) WILD-TYPE                                1     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(4Q28.3) MUTATED                           2     8
  DEL PEAK  5(4Q28.3) WILD-TYPE                        17   126
D12V4, multiclass
                                  clus
vv                                 DEL PEAK  5(4Q28.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  2
  WHITE                                                      8
                                  clus
vv                                 DEL PEAK  5(4Q28.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   17
  WHITE                                                      126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = DEL PEAK  6(5Q15) MUTATION ANALYSIS
D13V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  6(5Q15) MUTATED    12   0
  DEL PEAK  6(5Q15) WILD-TYPE 144   6
  DEL PEAK  6(5Q15) MUTATED DEL PEAK  6(5Q15) WILD-TYPE 
                         12                         150 
  DEL PEAK  6(5Q15) MUTATED DEL PEAK  6(5Q15) WILD-TYPE 
                          0                           6 
$`DEL PEAK  6(5Q15) MUTATED`
TCGA-P8-A6RX TCGA-QR-A7IN TCGA-QT-A5XJ TCGA-QT-A69Q TCGA-RW-A67Y TCGA-RW-A68C 
       17.75        12.39        36.23         0.79         7.10         6.28 
TCGA-SR-A6MQ TCGA-SR-A6MY TCGA-WB-A80M TCGA-WB-A81K TCGA-WB-A81S TCGA-WB-A81W 
       68.61        24.66         4.47        40.04        23.77        78.21 

$`DEL PEAK  6(5Q15) WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG 
       31.46        29.03         2.27         5.88        17.95        81.70 
TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GU 
       28.08        35.01        23.11         1.25       137.59        58.88 
TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 
       19.04         1.05        30.51         9.21        14.17         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 
       14.27        31.53        15.58        32.15         1.28         4.11 
TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I 
      116.19         0.23         6.31         2.33        26.83        29.92 
TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W 
       13.12         9.01         1.41       117.14        14.20        41.79 
TCGA-QR-A70X TCGA-QR-A7IP TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN 
        6.02        17.95         6.94         1.81         0.72        25.18 
TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 
        2.30         4.41        13.08        77.98         0.92       108.26 
TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A680 
       50.63         8.09        86.89        19.86         2.93        33.30 
TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 
       23.80         1.05         0.85        13.32         1.22        11.70 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ 
       13.05         7.96        72.79        15.02        41.88         4.41 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
        1.78         2.89        20.09        31.59        30.21        37.25 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU 
       35.51        31.04        26.96        40.70        37.58        30.51 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 
       27.91        20.58        25.32        12.66        18.94        18.08 
TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI 
        9.73       114.77       109.25        82.62        67.50       110.04 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MS 
       15.52       111.25         1.41         0.10        51.22        81.93 
TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MZ TCGA-SR-A6N0 
      106.75       110.53       121.05         3.12        19.76        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 
        4.34        25.15        19.92        13.32        25.32        14.20 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       17.16         1.18        19.86        12.03        12.49        16.60 
TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80N 
       17.69        25.61        10.65        34.82        34.26         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 
        4.21       316.73       127.56        29.16        19.59        32.88 
TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A 
        5.98        41.23        32.61        34.03        33.90        24.16 
TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       35.84        37.18        57.11        38.76        42.54        22.32 
TCGA-WB-A81J TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R 
       24.36        45.83        53.69        12.99        24.82         1.61 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       18.28        71.05        10.16        93.11       103.17        20.19 

  DEL PEAK  6(5Q15) MUTATED DEL PEAK  6(5Q15) WILD-TYPE 
                       0.79                        0.10 
  DEL PEAK  6(5Q15) MUTATED DEL PEAK  6(5Q15) WILD-TYPE 
                      78.21                      316.73 
  DEL PEAK  6(5Q15) MUTATED DEL PEAK  6(5Q15) WILD-TYPE 
                      20.76                       21.45 
[1] "0.8 - 78.2 (20.8)"  "0.1 - 316.7 (21.4)"
[1] "hr="     "2.7e+07"
D13V2, continuous
D13V3, binary
                             cls
clus                           0  1
  DEL PEAK  6(5Q15) MUTATED    6  6
  DEL PEAK  6(5Q15) WILD-TYPE 82 68
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  6(5Q15) MUTATED      6    6
  DEL PEAK  6(5Q15) WILD-TYPE   82   68
        clus
vv       DEL PEAK  6(5Q15) MUTATED DEL PEAK  6(5Q15) WILD-TYPE
  FEMALE                         6                          82
  MALE                           6                          68
[1] 2 2
[1] FALSE
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  6(5Q15) MUTATED                                  0     1
  DEL PEAK  6(5Q15) WILD-TYPE                                1     4
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(5Q15) MUTATED                           2     9
  DEL PEAK  6(5Q15) WILD-TYPE                        17   125
D13V4, multiclass
                                  clus
vv                                 DEL PEAK  6(5Q15) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    1
  BLACK OR AFRICAN AMERICAN                                2
  WHITE                                                    9
                                  clus
vv                                 DEL PEAK  6(5Q15) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 17
  WHITE                                                    125
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = DEL PEAK  7(6P12.3) MUTATION ANALYSIS
D14V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(6P12.3) MUTATED    10   0
  DEL PEAK  7(6P12.3) WILD-TYPE 146   6
  DEL PEAK  7(6P12.3) MUTATED DEL PEAK  7(6P12.3) WILD-TYPE 
                           10                           152 
  DEL PEAK  7(6P12.3) MUTATED DEL PEAK  7(6P12.3) WILD-TYPE 
                            0                             6 
$`DEL PEAK  7(6P12.3) MUTATED`
TCGA-QR-A700 TCGA-QR-A706 TCGA-QR-A70R TCGA-QR-A70X TCGA-SR-A6MU TCGA-SR-A6MV 
       32.15         4.11        14.20         6.02       110.53       121.05 
TCGA-TT-A6YJ TCGA-TT-A6YO TCGA-WB-A81S TCGA-XG-A823 
        4.34        13.32        23.77        20.19 

$`DEL PEAK  7(6P12.3) WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 
       58.88        19.04         1.05        30.51         9.21        14.17 
TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A70C 
        9.93        14.27        31.53        15.58         1.28       116.19 
TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J 
        0.23         6.31         2.33        26.83        29.92        13.12 
TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70W TCGA-QR-A7IN TCGA-QR-A7IP 
        9.01         1.41       117.14        41.79        12.39        17.95 
TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO 
       36.23         6.94         1.81         0.72        25.18         2.30 
TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 
        4.41         0.79        13.08        77.98         0.92       108.26 
TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y 
       50.63         8.09        86.89        19.86         2.93         7.10 
TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 
       33.30        23.80         1.05         0.85        13.32         1.22 
TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F 
       11.70        13.05         7.96         6.28        72.79        15.02 
TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
       41.88         4.41         1.78         2.89        20.09        31.59 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR 
       30.21        37.25        35.51        31.04        26.96        40.70 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       37.58        30.51        27.91        20.58        25.32        12.66 
TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
       18.94        18.08         9.73       114.77       109.25        82.62 
TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 
       67.50       110.04        15.52       111.25         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MX TCGA-SR-A6MY 
       51.22        68.61        81.93       106.75         3.12        24.66 
TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YP TCGA-W2-A7H5 
       19.76        49.61        25.15        19.92        25.32        14.20 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       17.16         1.18        19.86        12.03        12.49        16.60 
TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M 
       17.69        25.61        10.65        34.82        34.26         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73         4.21       316.73       127.56        29.16        19.59 
TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 
       32.88         5.98        41.23        32.61        34.03        33.90 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       24.16        35.84        37.18        57.11        38.76        42.54 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
       22.32        24.36        40.04        45.83        53.69        12.99 
TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 
       24.82         1.61        18.28        71.05        78.21        10.16 
TCGA-WB-A821 TCGA-WB-A822 
       93.11       103.17 

  DEL PEAK  7(6P12.3) MUTATED DEL PEAK  7(6P12.3) WILD-TYPE 
                         4.11                          0.10 
  DEL PEAK  7(6P12.3) MUTATED DEL PEAK  7(6P12.3) WILD-TYPE 
                       121.05                        316.73 
  DEL PEAK  7(6P12.3) MUTATED DEL PEAK  7(6P12.3) WILD-TYPE 
                       17.195                        22.715 
[1] "4.1 - 121.0 (17.2)" "0.1 - 316.7 (22.7)"
[1] "hr="     "8.1e+07"
D14V2, continuous
D14V3, binary
                               cls
clus                             0  1
  DEL PEAK  7(6P12.3) MUTATED    8  2
  DEL PEAK  7(6P12.3) WILD-TYPE 80 72
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(6P12.3) MUTATED      8    2
  DEL PEAK  7(6P12.3) WILD-TYPE   80   72
        clus
vv       DEL PEAK  7(6P12.3) MUTATED DEL PEAK  7(6P12.3) WILD-TYPE
  FEMALE                           8                            80
  MALE                             2                            72
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  7(6P12.3) MUTATED                                  0     0
  DEL PEAK  7(6P12.3) WILD-TYPE                                1     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(6P12.3) MUTATED                           2     7
  DEL PEAK  7(6P12.3) WILD-TYPE                        17   127
D14V4, multiclass
                                  clus
vv                                 DEL PEAK  7(6P12.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  2
  WHITE                                                      7
                                  clus
vv                                 DEL PEAK  7(6P12.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   17
  WHITE                                                      127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = DEL PEAK  8(6Q16.1) MUTATION ANALYSIS
D15V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(6Q16.1) MUTATED    23   1
  DEL PEAK  8(6Q16.1) WILD-TYPE 133   5
  DEL PEAK  8(6Q16.1) MUTATED DEL PEAK  8(6Q16.1) WILD-TYPE 
                           24                           138 
  DEL PEAK  8(6Q16.1) MUTATED DEL PEAK  8(6Q16.1) WILD-TYPE 
                            1                             5 
$`DEL PEAK  8(6Q16.1) MUTATED`
TCGA-P8-A5KD TCGA-QR-A6GO TCGA-QR-A700 TCGA-QR-A706 TCGA-QR-A70W TCGA-QR-A70X 
        2.27        35.01        32.15         4.11        41.79         6.02 
TCGA-QT-A5XN TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WR TCGA-SR-A6MU TCGA-SR-A6MV 
       25.18        30.21        37.25        40.70       110.53       121.05 
TCGA-SR-A6MY TCGA-TT-A6YJ TCGA-TT-A6YO TCGA-W2-A7HC TCGA-W2-A7UY TCGA-WB-A80O 
       24.66         4.34        13.32        12.03        10.65         4.21 
TCGA-WB-A80V TCGA-WB-A819 TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A820 TCGA-XG-A823 
       29.16        33.90         1.61        23.77        10.16        20.19 

$`DEL PEAK  8(6Q16.1) WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG 
       31.46        29.03        17.75         5.88        17.95        81.70 
TCGA-PR-A5PH TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GU TCGA-QR-A6GX 
       28.08        23.11         1.25       137.59        58.88        19.04 
TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 
        1.05        30.51         9.21        14.17         9.93        14.27 
TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E 
       31.53        15.58         1.28       116.19         0.23         6.31 
TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N 
        2.33        26.83        29.92        13.12         9.01         1.41 
TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK 
      117.14        14.20        12.39        17.95        36.23         6.94 
TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
        1.81         0.72         2.30         4.41         0.79        13.08 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       77.98         0.92       108.26        50.63         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 
       19.86         2.93         7.10        33.30        23.80         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B 
        0.85        13.32         1.22        11.70        13.05         7.96 
TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 
        6.28        72.79        15.02        41.88         4.41         1.78 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
        2.89        20.09        31.59        35.51        31.04        26.96 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       37.58        30.51        27.91        20.58        25.32        12.66 
TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
       18.94        18.08         9.73       114.77       109.25        82.62 
TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 
       67.50       110.04        15.52       111.25         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MX TCGA-SR-A6MZ 
       51.22        68.61        81.93       106.75         3.12        19.76 
TCGA-SR-A6N0 TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 
       49.61        25.15        19.92        25.32        14.20        17.16 
TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH 
        1.18        19.86        12.49        16.60        17.69        25.61 
TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80P TCGA-WB-A80Q 
       34.82        34.26         4.47         4.73       316.73       127.56 
TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 
       19.59        32.88         5.98        41.23        32.61        34.03 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       24.16        35.84        37.18        57.11        38.76        42.54 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
       22.32        24.36        40.04        45.83        53.69        12.99 
TCGA-WB-A81Q TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       24.82        18.28        71.05        78.21        93.11       103.17 

  DEL PEAK  8(6Q16.1) MUTATED DEL PEAK  8(6Q16.1) WILD-TYPE 
                         1.61                          0.10 
  DEL PEAK  8(6Q16.1) MUTATED DEL PEAK  8(6Q16.1) WILD-TYPE 
                       121.05                        316.73 
  DEL PEAK  8(6Q16.1) MUTATED DEL PEAK  8(6Q16.1) WILD-TYPE 
                       24.215                        20.335 
[1] "1.6 - 121.0 (24.2)" "0.1 - 316.7 (20.3)"
[1] "hr=" "1"  
D15V2, continuous
D15V3, binary
                               cls
clus                             0  1
  DEL PEAK  8(6Q16.1) MUTATED   16  8
  DEL PEAK  8(6Q16.1) WILD-TYPE 72 66
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(6Q16.1) MUTATED     16    8
  DEL PEAK  8(6Q16.1) WILD-TYPE   72   66
        clus
vv       DEL PEAK  8(6Q16.1) MUTATED DEL PEAK  8(6Q16.1) WILD-TYPE
  FEMALE                          16                            72
  MALE                             8                            66
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  8(6Q16.1) MUTATED                                  0     0
  DEL PEAK  8(6Q16.1) WILD-TYPE                                1     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(6Q16.1) MUTATED                           3    20
  DEL PEAK  8(6Q16.1) WILD-TYPE                        16   114
D15V4, multiclass
                                  clus
vv                                 DEL PEAK  8(6Q16.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  3
  WHITE                                                     20
                                  clus
vv                                 DEL PEAK  8(6Q16.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   16
  WHITE                                                      114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = DEL PEAK  9(8P22) MUTATION ANALYSIS
D16V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  9(8P22) MUTATED    23   2
  DEL PEAK  9(8P22) WILD-TYPE 133   4
  DEL PEAK  9(8P22) MUTATED DEL PEAK  9(8P22) WILD-TYPE 
                         25                         137 
  DEL PEAK  9(8P22) MUTATED DEL PEAK  9(8P22) WILD-TYPE 
                          2                           4 
$`DEL PEAK  9(8P22) MUTATED`
TCGA-PR-A5PF TCGA-PR-A5PG TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A700 TCGA-QR-A70K 
       17.95        81.70       137.59        19.04        32.15         9.01 
TCGA-QT-A5XN TCGA-RT-A6YA TCGA-RW-A68A TCGA-RW-A68D TCGA-S7-A7WL TCGA-S7-A7WR 
       25.18        50.63        13.05        72.79        31.59        40.70 
TCGA-S7-A7WT TCGA-SP-A6QI TCGA-SR-A6MP TCGA-SR-A6MT TCGA-W2-A7H5 TCGA-W2-A7HE 
       37.58       110.04        51.22       106.75        14.20        16.60 
TCGA-WB-A80V TCGA-WB-A81D TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81T 
       29.16        35.84        12.99        24.82         1.61        18.28 
TCGA-WB-A820 
       10.16 

$`DEL PEAK  9(8P22) WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PH 
       31.46        29.03         2.27        17.75         5.88        28.08 
TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GU TCGA-QR-A6GY TCGA-QR-A6GZ 
       35.01        23.11         1.25        58.88         1.05        30.51 
TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 
        9.21        14.17         9.93        14.27        31.53        15.58 
TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G 
        1.28         4.11       116.19         0.23         6.31         2.33 
TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R 
       26.83        29.92        13.12         1.41       117.14        14.20 
TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK 
       41.79         6.02        12.39        17.95        36.23         6.94 
TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
        1.81         0.72         2.30         4.41         0.79        13.08 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
       77.98         0.92       108.26         8.09        86.89        19.86 
TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 
        2.93         7.10        33.30        23.80         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68F 
       13.32         1.22        11.70         7.96         6.28        15.02 
TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WM 
       41.88         4.41         1.78         2.89        20.09        30.21 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WU TCGA-S7-A7WV 
       37.25        35.51        31.04        26.96        30.51        27.91 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 
       20.58        25.32        12.66        18.94        18.08         9.73 
TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QJ TCGA-SP-A6QK 
      114.77       109.25        82.62        67.50        15.52       111.25 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV 
        1.41         0.10        68.61        81.93       110.53       121.05 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK 
        3.12        24.66        19.76        49.61         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB 
       19.92        13.32        25.32        17.16         1.18        19.86 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K 
       12.03        12.49        17.69        25.61        10.65        34.82 
TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q 
       34.26         4.47         4.73         4.21       316.73       127.56 
TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 
       19.59        32.88         5.98        41.23        32.61        34.03 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       33.90        24.16        37.18        57.11        38.76        42.54 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81S 
       22.32        24.36        40.04        45.83        53.69        23.77 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       71.05        78.21        93.11       103.17        20.19 

  DEL PEAK  9(8P22) MUTATED DEL PEAK  9(8P22) WILD-TYPE 
                       1.61                        0.10 
  DEL PEAK  9(8P22) MUTATED DEL PEAK  9(8P22) WILD-TYPE 
                     137.59                      316.73 
  DEL PEAK  9(8P22) MUTATED DEL PEAK  9(8P22) WILD-TYPE 
                      29.16                       20.09 
[1] "1.6 - 137.6 (29.2)" "0.1 - 316.7 (20.1)"
[1] "hr=" "2.2"
D16V2, continuous
D16V3, binary
                             cls
clus                           0  1
  DEL PEAK  9(8P22) MUTATED   16  9
  DEL PEAK  9(8P22) WILD-TYPE 72 65
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  9(8P22) MUTATED     16    9
  DEL PEAK  9(8P22) WILD-TYPE   72   65
        clus
vv       DEL PEAK  9(8P22) MUTATED DEL PEAK  9(8P22) WILD-TYPE
  FEMALE                        16                          72
  MALE                           9                          65
[1] 2 2
[1] FALSE
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  9(8P22) MUTATED                                  0     1
  DEL PEAK  9(8P22) WILD-TYPE                                1     4
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(8P22) MUTATED                           2    22
  DEL PEAK  9(8P22) WILD-TYPE                        17   112
D16V4, multiclass
                                  clus
vv                                 DEL PEAK  9(8P22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    1
  BLACK OR AFRICAN AMERICAN                                2
  WHITE                                                   22
                                  clus
vv                                 DEL PEAK  9(8P22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 17
  WHITE                                                    112
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = DEL PEAK 10(8Q23.3) MUTATION ANALYSIS
D17V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(8Q23.3) MUTATED    12   1
  DEL PEAK 10(8Q23.3) WILD-TYPE 144   5
  DEL PEAK 10(8Q23.3) MUTATED DEL PEAK 10(8Q23.3) WILD-TYPE 
                           13                           149 
  DEL PEAK 10(8Q23.3) MUTATED DEL PEAK 10(8Q23.3) WILD-TYPE 
                            1                             5 
$`DEL PEAK 10(8Q23.3) MUTATED`
TCGA-QR-A6GX TCGA-QR-A700 TCGA-QR-A70K TCGA-RW-A67W TCGA-RW-A68A TCGA-S7-A7WR 
       19.04        32.15         9.01        19.86        13.05        40.70 
TCGA-SR-A6MT TCGA-SR-A6MX TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HD TCGA-WB-A80K 
      106.75         3.12        14.20        17.16        12.49        34.82 
TCGA-WB-A80V 
       29.16 

$`DEL PEAK 10(8Q23.3) WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 
       58.88         1.05        30.51         9.21        14.17         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C 
       14.27        31.53        15.58         1.28         4.11       116.19 
TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J 
        0.23         6.31         2.33        26.83        29.92        13.12 
TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN 
        1.41       117.14        14.20        41.79         6.02        12.39 
TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN 
       17.95        36.23         6.94         1.81         0.72        25.18 
TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W 
        2.30         4.41         0.79        13.08        77.98         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67X TCGA-RW-A67Y 
      108.26        50.63         8.09        86.89         2.93         7.10 
TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 
       33.30        23.80         1.05         0.85        13.32         1.22 
TCGA-RW-A689 TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G 
       11.70         7.96         6.28        72.79        15.02        41.88 
TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
        4.41         1.78         2.89        20.09        31.59        30.21 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WT TCGA-S7-A7WU 
       37.25        35.51        31.04        26.96        37.58        30.51 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 
       27.91        20.58        25.32        12.66        18.94        18.08 
TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI 
        9.73       114.77       109.25        82.62        67.50       110.04 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
       15.52       111.25         1.41         0.10        51.22        68.61 
TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
       81.93       110.53       121.05        24.66        19.76        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7HA 
        4.34        25.15        19.92        13.32        25.32         1.18 
TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY 
       19.86        12.03        16.60        17.69        25.61        10.65 
TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q 
       34.26         4.47         4.73         4.21       316.73       127.56 
TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 
       19.59        32.88         5.98        41.23        32.61        34.03 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G 
       33.90        24.16        35.84        37.18        57.11        38.76 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       42.54        22.32        24.36        40.04        45.83        53.69 
TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       12.99        24.82         1.61        23.77        18.28        71.05 
TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       78.21        10.16        93.11       103.17        20.19 

  DEL PEAK 10(8Q23.3) MUTATED DEL PEAK 10(8Q23.3) WILD-TYPE 
                         3.12                          0.10 
  DEL PEAK 10(8Q23.3) MUTATED DEL PEAK 10(8Q23.3) WILD-TYPE 
                       106.75                        316.73 
  DEL PEAK 10(8Q23.3) MUTATED DEL PEAK 10(8Q23.3) WILD-TYPE 
                        19.04                         23.11 
[1] "3.1 - 106.8 (19.0)" "0.1 - 316.7 (23.1)"
[1] "hr=" "2.8"
D17V2, continuous
D17V3, binary
                               cls
clus                             0  1
  DEL PEAK 10(8Q23.3) MUTATED    8  5
  DEL PEAK 10(8Q23.3) WILD-TYPE 80 69
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(8Q23.3) MUTATED      8    5
  DEL PEAK 10(8Q23.3) WILD-TYPE   80   69
        clus
vv       DEL PEAK 10(8Q23.3) MUTATED DEL PEAK 10(8Q23.3) WILD-TYPE
  FEMALE                           8                            80
  MALE                             5                            69
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 10(8Q23.3) MUTATED                                  0     0
  DEL PEAK 10(8Q23.3) WILD-TYPE                                1     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(8Q23.3) MUTATED                           1    12
  DEL PEAK 10(8Q23.3) WILD-TYPE                        18   122
D17V4, multiclass
                                  clus
vv                                 DEL PEAK 10(8Q23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     12
                                  clus
vv                                 DEL PEAK 10(8Q23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   18
  WHITE                                                      122
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = DEL PEAK 11(9P24.2) MUTATION ANALYSIS
D18V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(9P24.2) MUTATED    12   3
  DEL PEAK 11(9P24.2) WILD-TYPE 144   3
  DEL PEAK 11(9P24.2) MUTATED DEL PEAK 11(9P24.2) WILD-TYPE 
                           15                           147 
  DEL PEAK 11(9P24.2) MUTATED DEL PEAK 11(9P24.2) WILD-TYPE 
                            3                             3 
$`DEL PEAK 11(9P24.2) MUTATED`
TCGA-QR-A6GO TCGA-QR-A70H TCGA-QR-A70R TCGA-QR-A7IP TCGA-QT-A5XP TCGA-RT-A6YA 
       35.01        26.83        14.20        17.95         4.41        50.63 
TCGA-RW-A686 TCGA-RW-A8AZ TCGA-SP-A6QJ TCGA-SR-A6MV TCGA-W2-A7H5 TCGA-WB-A81J 
       13.32         2.89        15.52       121.05        14.20        24.36 
TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A820 
       24.82         1.61        10.16 

$`DEL PEAK 11(9P24.2) WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GU 
       81.70        28.08        23.11         1.25       137.59        58.88 
TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 
       19.04         1.05        30.51         9.21        14.17         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 
       14.27        31.53        15.58        32.15         1.28         4.11 
TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70I TCGA-QR-A70J 
      116.19         0.23         6.31         2.33        29.92        13.12 
TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN 
        9.01         1.41       117.14        41.79         6.02        12.39 
TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO 
       36.23         6.94         1.81         0.72        25.18         2.30 
TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YC 
        0.79        13.08        77.98         0.92       108.26         8.09 
TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 
       86.89        19.86         2.93         7.10        33.30        23.80 
TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B 
        1.05         0.85         1.22        11.70        13.05         7.96 
TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 
        6.28        72.79        15.02        41.88         4.41         1.78 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
       20.09        31.59        30.21        37.25        35.51        31.04 
TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW 
       26.96        40.70        37.58        30.51        27.91        20.58 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC 
       25.32        12.66        18.94        18.08         9.73       114.77 
TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QK TCGA-SQ-A6I4 
      109.25        82.62        67.50       110.04       111.25         1.41 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU 
        0.10        51.22        68.61        81.93       106.75       110.53 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK 
        3.12        24.66        19.76        49.61         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB 
       19.92        13.32        25.32        17.16         1.18        19.86 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY 
       12.03        12.49        16.60        17.69        25.61        10.65 
TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
       34.82        34.26         4.47         4.73         4.21       316.73 
TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 
      127.56        29.16        19.59        32.88         5.98        41.23 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E 
       32.61        34.03        33.90        24.16        35.84        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81K TCGA-WB-A81M 
       57.11        38.76        42.54        22.32        40.04        45.83 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       53.69        12.99        23.77        18.28        71.05        78.21 
TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       93.11       103.17        20.19 

  DEL PEAK 11(9P24.2) MUTATED DEL PEAK 11(9P24.2) WILD-TYPE 
                         1.61                          0.10 
  DEL PEAK 11(9P24.2) MUTATED DEL PEAK 11(9P24.2) WILD-TYPE 
                       121.05                        316.73 
  DEL PEAK 11(9P24.2) MUTATED DEL PEAK 11(9P24.2) WILD-TYPE 
                        15.52                         23.11 
[1] "1.6 - 121.0 (15.5)" "0.1 - 316.7 (23.1)"
[1] "hr=" "9.3"
D18V2, continuous
D18V3, binary
                               cls
clus                             0  1
  DEL PEAK 11(9P24.2) MUTATED    6  9
  DEL PEAK 11(9P24.2) WILD-TYPE 82 65
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(9P24.2) MUTATED      6    9
  DEL PEAK 11(9P24.2) WILD-TYPE   82   65
        clus
vv       DEL PEAK 11(9P24.2) MUTATED DEL PEAK 11(9P24.2) WILD-TYPE
  FEMALE                           6                            82
  MALE                             9                            65
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 11(9P24.2) MUTATED                                  0     0
  DEL PEAK 11(9P24.2) WILD-TYPE                                1     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(9P24.2) MUTATED                           1    14
  DEL PEAK 11(9P24.2) WILD-TYPE                        18   120
D18V4, multiclass
                                  clus
vv                                 DEL PEAK 11(9P24.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     14
                                  clus
vv                                 DEL PEAK 11(9P24.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   18
  WHITE                                                      120
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = DEL PEAK 12(9Q21.12) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 12(9Q21.12) MUTATED    13   1
  DEL PEAK 12(9Q21.12) WILD-TYPE 143   5
  DEL PEAK 12(9Q21.12) MUTATED DEL PEAK 12(9Q21.12) WILD-TYPE 
                            14                            148 
  DEL PEAK 12(9Q21.12) MUTATED DEL PEAK 12(9Q21.12) WILD-TYPE 
                             1                              5 
$`DEL PEAK 12(9Q21.12) MUTATED`
TCGA-QR-A6GO TCGA-QR-A6GY TCGA-QR-A70R TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XP 
       35.01         1.05        14.20        17.95        36.23         4.41 
TCGA-RT-A6YA TCGA-S7-A7WL TCGA-SP-A6QJ TCGA-SR-A6MP TCGA-SR-A6MV TCGA-W2-A7H5 
       50.63        31.59        15.52        51.22       121.05        14.20 
TCGA-W2-A7H7 TCGA-WB-A81Q 
       17.16        24.82 

$`DEL PEAK 12(9Q21.12) WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GU 
       81.70        28.08        23.11         1.25       137.59        58.88 
TCGA-QR-A6GX TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 
       19.04        30.51         9.21        14.17         9.93        14.27 
TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C 
       31.53        15.58        32.15         1.28         4.11       116.19 
TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J 
        0.23         6.31         2.33        26.83        29.92        13.12 
TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN 
        9.01         1.41       117.14        41.79         6.02        12.39 
TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A69Q 
        6.94         1.81         0.72        25.18         2.30         0.79 
TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V 
       13.08        77.98         0.92       108.26         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 
       19.86         2.93         7.10        33.30        23.80         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B 
        0.85        13.32         1.22        11.70        13.05         7.96 
TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 
        6.28        72.79        15.02        41.88         4.41         1.78 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
        2.89        20.09        30.21        37.25        35.51        31.04 
TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW 
       26.96        40.70        37.58        30.51        27.91        20.58 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC 
       25.32        12.66        18.94        18.08         9.73       114.77 
TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QK TCGA-SQ-A6I4 
      109.25        82.62        67.50       110.04       111.25         1.41 
TCGA-SQ-A6I6 TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MX 
        0.10        68.61        81.93       106.75       110.53         3.12 
TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
       24.66        19.76        49.61         4.34        25.15        19.92 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD 
       13.32        25.32         1.18        19.86        12.03        12.49 
TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L 
       16.60        17.69        25.61        10.65        34.82        34.26 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V 
        4.47         4.73         4.21       316.73       127.56        29.16 
TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 
       19.59        32.88         5.98        41.23        32.61        34.03 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G 
       33.90        24.16        35.84        37.18        57.11        38.76 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       42.54        22.32        24.36        40.04        45.83        53.69 
TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       12.99         1.61        23.77        18.28        71.05        78.21 
TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       10.16        93.11       103.17        20.19 

  DEL PEAK 12(9Q21.12) MUTATED DEL PEAK 12(9Q21.12) WILD-TYPE 
                          1.05                           0.10 
  DEL PEAK 12(9Q21.12) MUTATED DEL PEAK 12(9Q21.12) WILD-TYPE 
                        121.05                         316.73 
  DEL PEAK 12(9Q21.12) MUTATED DEL PEAK 12(9Q21.12) WILD-TYPE 
                        21.385                         21.450 
[1] "1.1 - 121.0 (21.4)" "0.1 - 316.7 (21.4)"
[1] "hr=" "1.6"
D19V2, continuous
D19V3, binary
                                cls
clus                              0  1
  DEL PEAK 12(9Q21.12) MUTATED    8  6
  DEL PEAK 12(9Q21.12) WILD-TYPE 80 68
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(9Q21.12) MUTATED      8    6
  DEL PEAK 12(9Q21.12) WILD-TYPE   80   68
        clus
vv       DEL PEAK 12(9Q21.12) MUTATED DEL PEAK 12(9Q21.12) WILD-TYPE
  FEMALE                            8                             80
  MALE                              6                             68
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 12(9Q21.12) MUTATED                                  0     0
  DEL PEAK 12(9Q21.12) WILD-TYPE                                1     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(9Q21.12) MUTATED                           2    12
  DEL PEAK 12(9Q21.12) WILD-TYPE                        17   122
D19V4, multiclass
                                  clus
vv                                 DEL PEAK 12(9Q21.12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      12
                                  clus
vv                                 DEL PEAK 12(9Q21.12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    17
  WHITE                                                       122
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = DEL PEAK 13(11P15.4) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 13(11P15.4) MUTATED   58  0
  DEL PEAK 13(11P15.4) WILD-TYPE 98  6
  DEL PEAK 13(11P15.4) MUTATED DEL PEAK 13(11P15.4) WILD-TYPE 
                            58                            104 
  DEL PEAK 13(11P15.4) MUTATED DEL PEAK 13(11P15.4) WILD-TYPE 
                             0                              6 
$`DEL PEAK 13(11P15.4) MUTATED`
TCGA-P8-A6RX TCGA-P8-A6RY TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H2 TCGA-QR-A6H5 
       17.75         5.88        58.88        30.51         9.93        31.53 
TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N 
       15.58         1.28         4.11        13.12         9.01         1.41 
TCGA-QR-A70R TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XL TCGA-QT-A5XN TCGA-QT-A7U0 
       14.20        12.39        17.95         1.81        25.18        13.08 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6YA TCGA-RW-A67X TCGA-RW-A681 TCGA-RW-A684 
       77.98         0.92        50.63         2.93        23.80         1.05 
TCGA-RW-A68A TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A7CZ TCGA-S7-A7WP 
       13.05         6.28        72.79        15.02         4.41        31.04 
TCGA-S7-A7WQ TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WW TCGA-S7-A7X0 TCGA-S7-A7X1 
       26.96        37.58        30.51        20.58        12.66        18.94 
TCGA-SP-A6QD TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6N0 TCGA-TT-A6YK 
      109.25       106.75       110.53       121.05        49.61        25.15 
TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7UY TCGA-WB-A80M TCGA-WB-A814 
       25.32        14.20        17.16        10.65         4.47        32.88 
TCGA-WB-A816 TCGA-WB-A81I TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81S TCGA-WB-A81V 
       41.23        22.32        40.04        45.83        23.77        71.05 
TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       78.21        93.11       103.17        20.19 

$`DEL PEAK 13(11P15.4) WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH 
       31.46        29.03         2.27        17.95        81.70        28.08 
TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A6GY 
       35.01        23.11         1.25       137.59        19.04         1.05 
TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H3 TCGA-QR-A700 TCGA-QR-A70C TCGA-QR-A70D 
        9.21        14.17        14.27        32.15       116.19         0.23 
TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70P TCGA-QR-A70W 
        6.31         2.33        26.83        29.92       117.14        41.79 
TCGA-QR-A70X TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XM TCGA-QT-A5XO TCGA-QT-A5XP 
        6.02        36.23         6.94         0.72         2.30         4.41 
TCGA-QT-A69Q TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67Y 
        0.79       108.26         8.09        86.89        19.86         7.10 
TCGA-RW-A680 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68B 
       33.30         0.85        13.32         1.22        11.70         7.96 
TCGA-RW-A68G TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
       41.88         1.78         2.89        20.09        31.59        30.21 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WR TCGA-S7-A7WV TCGA-S7-A7WX TCGA-S7-A7X2 
       37.25        35.51        40.70        27.91        25.32        18.08 
TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
        9.73       114.77        82.62        67.50       110.04        15.52 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS 
      111.25         1.41         0.10        51.22        68.61        81.93 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YN TCGA-TT-A6YO 
        3.12        24.66        19.76         4.34        19.92        13.32 
TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF 
        1.18        19.86        12.03        12.49        16.60        17.69 
TCGA-W2-A7HH TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
       25.61        34.82        34.26         4.73         4.21       316.73 
TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A817 TCGA-WB-A818 
      127.56        29.16        19.59         5.98        32.61        34.03 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G 
       33.90        24.16        35.84        37.18        57.11        38.76 
TCGA-WB-A81H TCGA-WB-A81J TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R 
       42.54        24.36        53.69        12.99        24.82         1.61 
TCGA-WB-A81T TCGA-WB-A820 
       18.28        10.16 

  DEL PEAK 13(11P15.4) MUTATED DEL PEAK 13(11P15.4) WILD-TYPE 
                          0.92                           0.10 
  DEL PEAK 13(11P15.4) MUTATED DEL PEAK 13(11P15.4) WILD-TYPE 
                        121.05                         316.73 
  DEL PEAK 13(11P15.4) MUTATED DEL PEAK 13(11P15.4) WILD-TYPE 
                         21.45                          21.60 
[1] "0.9 - 121.0 (21.4)" "0.1 - 316.7 (21.6)"
[1] "hr="     "3.6e+08"
D20V2, continuous
D20V3, binary
                                cls
clus                              0  1
  DEL PEAK 13(11P15.4) MUTATED   29 29
  DEL PEAK 13(11P15.4) WILD-TYPE 59 45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(11P15.4) MUTATED     29   29
  DEL PEAK 13(11P15.4) WILD-TYPE   59   45
        clus
vv       DEL PEAK 13(11P15.4) MUTATED DEL PEAK 13(11P15.4) WILD-TYPE
  FEMALE                           29                             59
  MALE                             29                             45
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(11P15.4) MUTATED                                  0     2
  DEL PEAK 13(11P15.4) WILD-TYPE                                1     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(11P15.4) MUTATED                           6    49
  DEL PEAK 13(11P15.4) WILD-TYPE                        13    85
D20V4, multiclass
                                  clus
vv                                 DEL PEAK 13(11P15.4) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   6
  WHITE                                                      49
                                  clus
vv                                 DEL PEAK 13(11P15.4) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    13
  WHITE                                                        85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = DEL PEAK 14(11Q22.1) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 14(11Q22.1) MUTATED    47   1
  DEL PEAK 14(11Q22.1) WILD-TYPE 109   5
  DEL PEAK 14(11Q22.1) MUTATED DEL PEAK 14(11Q22.1) WILD-TYPE 
                            48                            114 
  DEL PEAK 14(11Q22.1) MUTATED DEL PEAK 14(11Q22.1) WILD-TYPE 
                             1                              5 
$`DEL PEAK 14(11Q22.1) MUTATED`
TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GU 
       17.75         5.88        17.95        23.11         1.25        58.88 
TCGA-QR-A6GZ TCGA-QR-A6H2 TCGA-QR-A6H5 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A70N 
       30.51         9.93        31.53        32.15         1.28         1.41 
TCGA-QR-A7IN TCGA-QT-A5XL TCGA-QT-A5XO TCGA-QT-A69Q TCGA-RM-A68T TCGA-RM-A68W 
       12.39         1.81         2.30         0.79        77.98         0.92 
TCGA-RT-A6YA TCGA-RW-A67X TCGA-RW-A681 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68F 
       50.63         2.93        23.80        11.70         6.28        15.02 
TCGA-RW-A7CZ TCGA-RW-A8AZ TCGA-S7-A7WL TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WU 
        4.41         2.89        31.59        31.04        26.96        30.51 
TCGA-S7-A7WW TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-SR-A6MT TCGA-SR-A6N0 TCGA-TT-A6YJ 
       20.58        12.66        18.94       106.75        49.61         4.34 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7UY TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A81D 
       13.32        25.32        10.65        32.88         5.98        35.84 
TCGA-WB-A81P TCGA-WB-A81S TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-XG-A823 
       12.99        23.77        71.05        78.21        93.11        20.19 

$`DEL PEAK 14(11Q22.1) WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO 
       31.46        29.03         2.27        81.70        28.08        35.01 
TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H3 
      137.59        19.04         1.05         9.21        14.17        14.27 
TCGA-QR-A6H6 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G 
       15.58         4.11       116.19         0.23         6.31         2.33 
TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70P TCGA-QR-A70R 
       26.83        29.92        13.12         9.01       117.14        14.20 
TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XM 
       41.79         6.02        17.95        36.23         6.94         0.72 
TCGA-QT-A5XN TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V 
       25.18         4.41        13.08       108.26         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 
       19.86         7.10        33.30         1.05         0.85        13.32 
TCGA-RW-A688 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68D TCGA-RW-A68G TCGA-RW-A7D0 
        1.22        13.05         7.96        72.79        41.88         1.78 
TCGA-RX-A8JQ TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WR TCGA-S7-A7WT 
       20.09        30.21        37.25        35.51        40.70        37.58 
TCGA-S7-A7WV TCGA-S7-A7WX TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD 
       27.91        25.32        18.08         9.73       114.77       109.25 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
       82.62        67.50       110.04        15.52       111.25         1.41 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV 
        0.10        51.22        68.61        81.93       110.53       121.05 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-W2-A7H5 
        3.12        24.66        19.76        25.15        19.92        14.20 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       17.16         1.18        19.86        12.03        12.49        16.60 
TCGA-W2-A7HF TCGA-W2-A7HH TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N 
       17.69        25.61        34.82        34.26         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A816 
        4.21       316.73       127.56        29.16        19.59        41.23 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81E TCGA-WB-A81F 
       32.61        34.03        33.90        24.16        37.18        57.11 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       38.76        42.54        22.32        24.36        40.04        45.83 
TCGA-WB-A81N TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81T TCGA-WB-A820 TCGA-WB-A822 
       53.69        24.82         1.61        18.28        10.16       103.17 

  DEL PEAK 14(11Q22.1) MUTATED DEL PEAK 14(11Q22.1) WILD-TYPE 
                          0.79                           0.10 
  DEL PEAK 14(11Q22.1) MUTATED DEL PEAK 14(11Q22.1) WILD-TYPE 
                        106.75                         316.73 
  DEL PEAK 14(11Q22.1) MUTATED DEL PEAK 14(11Q22.1) WILD-TYPE 
                        18.445                         24.510 
[1] "0.8 - 106.8 (18.4)" "0.1 - 316.7 (24.5)"
[1] "hr=" "1.5"
D21V2, continuous
D21V3, binary
                                cls
clus                              0  1
  DEL PEAK 14(11Q22.1) MUTATED   27 21
  DEL PEAK 14(11Q22.1) WILD-TYPE 61 53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11Q22.1) MUTATED     27   21
  DEL PEAK 14(11Q22.1) WILD-TYPE   61   53
        clus
vv       DEL PEAK 14(11Q22.1) MUTATED DEL PEAK 14(11Q22.1) WILD-TYPE
  FEMALE                           27                             61
  MALE                             21                             53
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 14(11Q22.1) MUTATED                                  0     1
  DEL PEAK 14(11Q22.1) WILD-TYPE                                1     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(11Q22.1) MUTATED                           7    39
  DEL PEAK 14(11Q22.1) WILD-TYPE                        12    95
D21V4, multiclass
                                  clus
vv                                 DEL PEAK 14(11Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      39
                                  clus
vv                                 DEL PEAK 14(11Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    12
  WHITE                                                        95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = DEL PEAK 15(12Q21.33) MUTATION ANALYSIS
D22V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 15(12Q21.33) MUTATED     8   0
  DEL PEAK 15(12Q21.33) WILD-TYPE 148   6
  DEL PEAK 15(12Q21.33) MUTATED DEL PEAK 15(12Q21.33) WILD-TYPE 
                              8                             154 
  DEL PEAK 15(12Q21.33) MUTATED DEL PEAK 15(12Q21.33) WILD-TYPE 
                              0                               6 
$`DEL PEAK 15(12Q21.33) MUTATED`
TCGA-QR-A700 TCGA-QR-A70R TCGA-QR-A70X TCGA-RT-A6YC TCGA-SP-A6QJ TCGA-SR-A6MV 
       32.15        14.20         6.02         8.09        15.52       121.05 
TCGA-TT-A6YJ TCGA-WB-A81S 
        4.34        23.77 

$`DEL PEAK 15(12Q21.33) WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 
       58.88        19.04         1.05        30.51         9.21        14.17 
TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 
        9.93        14.27        31.53        15.58         1.28         4.11 
TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I 
      116.19         0.23         6.31         2.33        26.83        29.92 
TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70W TCGA-QR-A7IN 
       13.12         9.01         1.41       117.14        41.79        12.39 
TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN 
       17.95        36.23         6.94         1.81         0.72        25.18 
TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W 
        2.30         4.41         0.79        13.08        77.98         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y 
      108.26        50.63        86.89        19.86         2.93         7.10 
TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 
       33.30        23.80         1.05         0.85        13.32         1.22 
TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F 
       11.70        13.05         7.96         6.28        72.79        15.02 
TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
       41.88         4.41         1.78         2.89        20.09        31.59 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR 
       30.21        37.25        35.51        31.04        26.96        40.70 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       37.58        30.51        27.91        20.58        25.32        12.66 
TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
       18.94        18.08         9.73       114.77       109.25        82.62 
TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP 
       67.50       110.04       111.25         1.41         0.10        51.22 
TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MX TCGA-SR-A6MY 
       68.61        81.93       106.75       110.53         3.12        24.66 
TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       19.76        49.61        25.15        19.92        13.32        25.32 
TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD 
       14.20        17.16         1.18        19.86        12.03        12.49 
TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L 
       16.60        17.69        25.61        10.65        34.82        34.26 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V 
        4.47         4.73         4.21       316.73       127.56        29.16 
TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 
       19.59        32.88         5.98        41.23        32.61        34.03 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G 
       33.90        24.16        35.84        37.18        57.11        38.76 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       42.54        22.32        24.36        40.04        45.83        53.69 
TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       12.99        24.82         1.61        18.28        71.05        78.21 
TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       10.16        93.11       103.17        20.19 

  DEL PEAK 15(12Q21.33) MUTATED DEL PEAK 15(12Q21.33) WILD-TYPE 
                           4.34                            0.10 
  DEL PEAK 15(12Q21.33) MUTATED DEL PEAK 15(12Q21.33) WILD-TYPE 
                         121.05                          316.73 
  DEL PEAK 15(12Q21.33) MUTATED DEL PEAK 15(12Q21.33) WILD-TYPE 
                         14.860                          22.715 
[1] "4.3 - 121.0 (14.9)" "0.1 - 316.7 (22.7)"
[1] "hr="     "8.1e+07"
D22V2, continuous
D22V3, binary
                                 cls
clus                               0  1
  DEL PEAK 15(12Q21.33) MUTATED    5  3
  DEL PEAK 15(12Q21.33) WILD-TYPE 83 71
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(12Q21.33) MUTATED      5    3
  DEL PEAK 15(12Q21.33) WILD-TYPE   83   71
        clus
vv       DEL PEAK 15(12Q21.33) MUTATED DEL PEAK 15(12Q21.33) WILD-TYPE
  FEMALE                             5                              83
  MALE                               3                              71
[1] 2 2
[1] FALSE
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(12Q21.33) MUTATED                                  0     0
  DEL PEAK 15(12Q21.33) WILD-TYPE                                1     5
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(12Q21.33) MUTATED                           1     6
  DEL PEAK 15(12Q21.33) WILD-TYPE                        18   128
D22V4, multiclass
                                  clus
vv                                 DEL PEAK 15(12Q21.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        0
  BLACK OR AFRICAN AMERICAN                                    1
  WHITE                                                        6
                                  clus
vv                                 DEL PEAK 15(12Q21.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          5
  BLACK OR AFRICAN AMERICAN                                     18
  WHITE                                                        128
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = DEL PEAK 16(13Q22.3) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 16(13Q22.3) MUTATED     8   0
  DEL PEAK 16(13Q22.3) WILD-TYPE 148   6
  DEL PEAK 16(13Q22.3) MUTATED DEL PEAK 16(13Q22.3) WILD-TYPE 
                             8                            154 
  DEL PEAK 16(13Q22.3) MUTATED DEL PEAK 16(13Q22.3) WILD-TYPE 
                             0                              6 
$`DEL PEAK 16(13Q22.3) MUTATED`
TCGA-PR-A5PF TCGA-QR-A700 TCGA-QR-A706 TCGA-QR-A70R TCGA-RW-A68A TCGA-S7-A7WX 
       17.95        32.15         4.11        14.20        13.05        25.32 
TCGA-SP-A6QF TCGA-W2-A7H5 
       82.62        14.20 

$`DEL PEAK 16(13Q22.3) WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PG 
       31.46        29.03         2.27        17.75         5.88        81.70 
TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GU 
       28.08        35.01        23.11         1.25       137.59        58.88 
TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 
       19.04         1.05        30.51         9.21        14.17         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A70C TCGA-QR-A70D 
       14.27        31.53        15.58         1.28       116.19         0.23 
TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K 
        6.31         2.33        26.83        29.92        13.12         9.01 
TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP 
        1.41       117.14        41.79         6.02        12.39        17.95 
TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO 
       36.23         6.94         1.81         0.72        25.18         2.30 
TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 
        4.41         0.79        13.08        77.98         0.92       108.26 
TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y 
       50.63         8.09        86.89        19.86         2.93         7.10 
TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 
       33.30        23.80         1.05         0.85        13.32         1.22 
TCGA-RW-A689 TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G 
       11.70         7.96         6.28        72.79        15.02        41.88 
TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
        4.41         1.78         2.89        20.09        31.59        30.21 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT 
       37.25        35.51        31.04        26.96        40.70        37.58 
TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 
       30.51        27.91        20.58        12.66        18.94        18.08 
TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
        9.73       114.77       109.25        67.50       110.04        15.52 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS 
      111.25         1.41         0.10        51.22        68.61        81.93 
TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ 
      106.75       110.53       121.05         3.12        24.66        19.76 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        25.15        19.92        13.32        25.32 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       17.16         1.18        19.86        12.03        12.49        16.60 
TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M 
       17.69        25.61        10.65        34.82        34.26         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73         4.21       316.73       127.56        29.16        19.59 
TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 
       32.88         5.98        41.23        32.61        34.03        33.90 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       24.16        35.84        37.18        57.11        38.76        42.54 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
       22.32        24.36        40.04        45.83        53.69        12.99 
TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       24.82         1.61        23.77        18.28        71.05        78.21 
TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       10.16        93.11       103.17        20.19 

  DEL PEAK 16(13Q22.3) MUTATED DEL PEAK 16(13Q22.3) WILD-TYPE 
                          4.11                           0.10 
  DEL PEAK 16(13Q22.3) MUTATED DEL PEAK 16(13Q22.3) WILD-TYPE 
                         82.62                         316.73 
  DEL PEAK 16(13Q22.3) MUTATED DEL PEAK 16(13Q22.3) WILD-TYPE 
                        16.075                         22.715 
[1] "4.1 - 82.6 (16.1)"  "0.1 - 316.7 (22.7)"
[1] "hr="     "2.6e+07"
D23V2, continuous
D23V3, binary
                                cls
clus                              0  1
  DEL PEAK 16(13Q22.3) MUTATED    4  4
  DEL PEAK 16(13Q22.3) WILD-TYPE 84 70
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(13Q22.3) MUTATED      4    4
  DEL PEAK 16(13Q22.3) WILD-TYPE   84   70
        clus
vv       DEL PEAK 16(13Q22.3) MUTATED DEL PEAK 16(13Q22.3) WILD-TYPE
  FEMALE                            4                             84
  MALE                              4                             70
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 16(13Q22.3) MUTATED                                  0     1
  DEL PEAK 16(13Q22.3) WILD-TYPE                                1     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(13Q22.3) MUTATED                           0     7
  DEL PEAK 16(13Q22.3) WILD-TYPE                        19   127
D23V4, multiclass
                                  clus
vv                                 DEL PEAK 16(13Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       7
                                  clus
vv                                 DEL PEAK 16(13Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    19
  WHITE                                                       127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = DEL PEAK 17(16Q21) MUTATION ANALYSIS
D24V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 17(16Q21) MUTATED     5   0
  DEL PEAK 17(16Q21) WILD-TYPE 151   6
  DEL PEAK 17(16Q21) MUTATED DEL PEAK 17(16Q21) WILD-TYPE 
                           5                          157 
  DEL PEAK 17(16Q21) MUTATED DEL PEAK 17(16Q21) WILD-TYPE 
                           0                            6 
$`DEL PEAK 17(16Q21) MUTATED`
TCGA-QR-A700 TCGA-QT-A5XJ TCGA-QT-A69Q TCGA-SR-A6MT TCGA-WB-A81S 
       32.15        36.23         0.79       106.75        23.77 

$`DEL PEAK 17(16Q21) WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 
       58.88        19.04         1.05        30.51         9.21        14.17 
TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 
        9.93        14.27        31.53        15.58         1.28         4.11 
TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I 
      116.19         0.23         6.31         2.33        26.83        29.92 
TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W 
       13.12         9.01         1.41       117.14        14.20        41.79 
TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
        6.02        12.39        17.95         6.94         1.81         0.72 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W 
       25.18         2.30         4.41        13.08        77.98         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
      108.26        50.63         8.09        86.89        19.86         2.93 
TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 
        7.10        33.30        23.80         1.05         0.85        13.32 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D 
        1.22        11.70        13.05         7.96         6.28        72.79 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ 
       15.02        41.88         4.41         1.78         2.89        20.09 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
       31.59        30.21        37.25        35.51        31.04        26.96 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       40.70        37.58        30.51        27.91        20.58        25.32 
TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD 
       12.66        18.94        18.08         9.73       114.77       109.25 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
       82.62        67.50       110.04        15.52       111.25         1.41 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV 
        0.10        51.22        68.61        81.93       110.53       121.05 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK 
        3.12        24.66        19.76        49.61         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA 
       19.92        13.32        25.32        14.20        17.16         1.18 
TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH 
       19.86        12.03        12.49        16.60        17.69        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       10.65        34.82        34.26         4.47         4.73         4.21 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
      316.73       127.56        29.16        19.59        32.88         5.98 
TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D 
       41.23        32.61        34.03        33.90        24.16        35.84 
TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       37.18        57.11        38.76        42.54        22.32        24.36 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R 
       40.04        45.83        53.69        12.99        24.82         1.61 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 
       18.28        71.05        78.21        10.16        93.11       103.17 
TCGA-XG-A823 
       20.19 

  DEL PEAK 17(16Q21) MUTATED DEL PEAK 17(16Q21) WILD-TYPE 
                        0.79                         0.10 
  DEL PEAK 17(16Q21) MUTATED DEL PEAK 17(16Q21) WILD-TYPE 
                      106.75                       316.73 
  DEL PEAK 17(16Q21) MUTATED DEL PEAK 17(16Q21) WILD-TYPE 
                       32.15                        20.19 
[1] "0.8 - 106.8 (32.1)" "0.1 - 316.7 (20.2)"
[1] "hr="     "2.6e+07"
D24V2, continuous
D24V3, binary
                              cls
clus                            0  1
  DEL PEAK 17(16Q21) MUTATED    3  2
  DEL PEAK 17(16Q21) WILD-TYPE 85 72
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 17(16Q21) MUTATED      3    2
  DEL PEAK 17(16Q21) WILD-TYPE   85   72
        clus
vv       DEL PEAK 17(16Q21) MUTATED DEL PEAK 17(16Q21) WILD-TYPE
  FEMALE                          3                           85
  MALE                            2                           72
[1] 2 2
[1] FALSE
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 17(16Q21) MUTATED                                  0     0
  DEL PEAK 17(16Q21) WILD-TYPE                                1     5
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(16Q21) MUTATED                           1     4
  DEL PEAK 17(16Q21) WILD-TYPE                        18   130
D24V4, multiclass
                                  clus
vv                                 DEL PEAK 17(16Q21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     0
  BLACK OR AFRICAN AMERICAN                                 1
  WHITE                                                     4
                                  clus
vv                                 DEL PEAK 17(16Q21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  18
  WHITE                                                     130
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = DEL PEAK 18(17P13.2) MUTATION ANALYSIS
D25V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 18(17P13.2) MUTATED   62  2
  DEL PEAK 18(17P13.2) WILD-TYPE 94  4
  DEL PEAK 18(17P13.2) MUTATED DEL PEAK 18(17P13.2) WILD-TYPE 
                            64                             98 
  DEL PEAK 18(17P13.2) MUTATED DEL PEAK 18(17P13.2) WILD-TYPE 
                             2                              4 
$`DEL PEAK 18(17P13.2) MUTATED`
TCGA-PR-A5PG TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GU TCGA-QR-A6GY TCGA-QR-A6H1 
       81.70        23.11         1.25        58.88         1.05        14.17 
TCGA-QR-A6H2 TCGA-QR-A702 TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70R TCGA-QR-A70W 
        9.93         1.28        29.92        13.12        14.20        41.79 
TCGA-QR-A70X TCGA-QT-A5XN TCGA-QT-A5XP TCGA-QT-A69Q TCGA-RW-A67X TCGA-RW-A67Y 
        6.02        25.18         4.41         0.79         2.93         7.10 
TCGA-RW-A681 TCGA-RW-A685 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68C 
       23.80         0.85         1.22        11.70        13.05         6.28 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7D0 TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WQ 
       15.02        41.88         1.78        31.59        30.21        26.96 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X1 TCGA-S7-A7X2 
       40.70        37.58        20.58        25.32        18.94        18.08 
TCGA-SP-A6QD TCGA-SP-A6QJ TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MT 
      109.25        15.52         0.10        51.22        68.61       106.75 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7UY 
        4.34        25.15        19.92         1.18        12.03        10.65 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 
        4.73         4.21       316.73        29.16        19.59         5.98 
TCGA-WB-A818 TCGA-WB-A81J TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q 
       34.03        24.36        45.83        53.69        12.99        24.82 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81W TCGA-WB-A822 
       23.77        18.28        78.21       103.17 

$`DEL PEAK 18(17P13.2) WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27        17.75         5.88        17.95 
TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A6GZ TCGA-QR-A6H0 
       28.08        35.01       137.59        19.04        30.51         9.21 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A706 TCGA-QR-A70C 
       14.27        31.53        15.58        32.15         4.11       116.19 
TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70K TCGA-QR-A70N 
        0.23         6.31         2.33        26.83         9.01         1.41 
TCGA-QR-A70P TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
      117.14        12.39        17.95        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XO TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 
        0.72         2.30        13.08        77.98         0.92       108.26 
TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A680 TCGA-RW-A684 
       50.63         8.09        86.89        19.86        33.30         1.05 
TCGA-RW-A686 TCGA-RW-A68B TCGA-RW-A68D TCGA-RW-A7CZ TCGA-RW-A8AZ TCGA-RX-A8JQ 
       13.32         7.96        72.79         4.41         2.89        20.09 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7X0 
       37.25        35.51        31.04        30.51        27.91        12.66 
TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QK 
        9.73       114.77        82.62        67.50       110.04       111.25 
TCGA-SQ-A6I4 TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY 
        1.41        81.93       110.53       121.05         3.12        24.66 
TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 
       19.76        49.61        13.32        25.32        14.20        17.16 
TCGA-W2-A7HB TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-WB-A80K 
       19.86        12.49        16.60        17.69        25.61        34.82 
TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80Q TCGA-WB-A814 TCGA-WB-A816 TCGA-WB-A817 
       34.26         4.47       127.56        32.88        41.23        32.61 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G 
       33.90        24.16        35.84        37.18        57.11        38.76 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81K TCGA-WB-A81R TCGA-WB-A81V TCGA-WB-A820 
       42.54        22.32        40.04         1.61        71.05        10.16 
TCGA-WB-A821 TCGA-XG-A823 
       93.11        20.19 

  DEL PEAK 18(17P13.2) MUTATED DEL PEAK 18(17P13.2) WILD-TYPE 
                          0.10                           0.23 
  DEL PEAK 18(17P13.2) MUTATED DEL PEAK 18(17P13.2) WILD-TYPE 
                        316.73                         137.59 
  DEL PEAK 18(17P13.2) MUTATED DEL PEAK 18(17P13.2) WILD-TYPE 
                        19.265                         24.990 
[1] "0.1 - 316.7 (19.3)" "0.2 - 137.6 (25.0)"
[1] "hr=" "1"  
D25V2, continuous
D25V3, binary
                                cls
clus                              0  1
  DEL PEAK 18(17P13.2) MUTATED   33 31
  DEL PEAK 18(17P13.2) WILD-TYPE 55 43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(17P13.2) MUTATED     33   31
  DEL PEAK 18(17P13.2) WILD-TYPE   55   43
        clus
vv       DEL PEAK 18(17P13.2) MUTATED DEL PEAK 18(17P13.2) WILD-TYPE
  FEMALE                           33                             55
  MALE                             31                             43
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 18(17P13.2) MUTATED                                  1     2
  DEL PEAK 18(17P13.2) WILD-TYPE                                0     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(17P13.2) MUTATED                           4    55
  DEL PEAK 18(17P13.2) WILD-TYPE                        15    79
D25V4, multiclass
                                  clus
vv                                 DEL PEAK 18(17P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      55
                                  clus
vv                                 DEL PEAK 18(17P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    15
  WHITE                                                        79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = DEL PEAK 19(17Q11.2) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 19(17Q11.2) MUTATED    39   3
  DEL PEAK 19(17Q11.2) WILD-TYPE 117   3
  DEL PEAK 19(17Q11.2) MUTATED DEL PEAK 19(17Q11.2) WILD-TYPE 
                            42                            120 
  DEL PEAK 19(17Q11.2) MUTATED DEL PEAK 19(17Q11.2) WILD-TYPE 
                             3                              3 
$`DEL PEAK 19(17Q11.2) MUTATED`
TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A70H TCGA-QR-A70J 
       23.11         1.25        32.15         1.28        26.83        13.12 
TCGA-QT-A5XN TCGA-QT-A5XP TCGA-QT-A69Q TCGA-RT-A6YA TCGA-RW-A67W TCGA-RW-A67X 
       25.18         4.41         0.79        50.63        19.86         2.93 
TCGA-RW-A67Y TCGA-RW-A685 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A7D0 
        7.10         0.85         1.22        11.70         6.28         1.78 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WX TCGA-S7-A7X1 
       31.59        30.21        26.96        40.70        25.32        18.94 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MT TCGA-TT-A6YJ TCGA-W2-A7UY TCGA-WB-A80N 
        0.10        51.22       106.75         4.34        10.65         4.73 
TCGA-WB-A80Y TCGA-WB-A818 TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81H 
       19.59        34.03        35.84        37.18        57.11        42.54 
TCGA-WB-A81J TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81S TCGA-WB-A820 
       24.36        53.69        12.99        24.82        23.77        10.16 

$`DEL PEAK 19(17Q11.2) WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GT TCGA-QR-A6GU TCGA-QR-A6GX 
       81.70        28.08        35.01       137.59        58.88        19.04 
TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 
        1.05        30.51         9.21        14.17         9.93        14.27 
TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E 
       31.53        15.58         4.11       116.19         0.23         6.31 
TCGA-QR-A70G TCGA-QR-A70I TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R 
        2.33        29.92         9.01         1.41       117.14        14.20 
TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK 
       41.79         6.02        12.39        17.95        36.23         6.94 
TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XO TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W 
        1.81         0.72         2.30        13.08        77.98         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 
      108.26         8.09        86.89        33.30        23.80         1.05 
TCGA-RW-A686 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G 
       13.32        13.05         7.96        72.79        15.02        41.88 
TCGA-RW-A7CZ TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
        4.41         2.89        20.09        37.25        35.51        31.04 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7X0 TCGA-S7-A7X2 
       37.58        30.51        27.91        20.58        12.66        18.08 
TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI 
        9.73       114.77       109.25        82.62        67.50       110.04 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU 
       15.52       111.25         1.41        68.61        81.93       110.53 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YK 
      121.05         3.12        24.66        19.76        49.61        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA 
       19.92        13.32        25.32        14.20        17.16         1.18 
TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH 
       19.86        12.03        12.49        16.60        17.69        25.61 
TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q 
       34.82        34.26         4.47         4.21       316.73       127.56 
TCGA-WB-A80V TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A819 
       29.16        32.88         5.98        41.23        32.61        33.90 
TCGA-WB-A81A TCGA-WB-A81G TCGA-WB-A81I TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81R 
       24.16        38.76        22.32        40.04        45.83         1.61 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       18.28        71.05        78.21        93.11       103.17        20.19 

  DEL PEAK 19(17Q11.2) MUTATED DEL PEAK 19(17Q11.2) WILD-TYPE 
                          0.10                           0.23 
  DEL PEAK 19(17Q11.2) MUTATED DEL PEAK 19(17Q11.2) WILD-TYPE 
                        106.75                         316.73 
  DEL PEAK 19(17Q11.2) MUTATED DEL PEAK 19(17Q11.2) WILD-TYPE 
                        21.485                         21.450 
[1] "0.1 - 106.8 (21.5)" "0.2 - 316.7 (21.4)"
[1] "hr=" "4.6"
D26V2, continuous
D26V3, binary
                                cls
clus                              0  1
  DEL PEAK 19(17Q11.2) MUTATED   24 18
  DEL PEAK 19(17Q11.2) WILD-TYPE 64 56
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(17Q11.2) MUTATED     24   18
  DEL PEAK 19(17Q11.2) WILD-TYPE   64   56
        clus
vv       DEL PEAK 19(17Q11.2) MUTATED DEL PEAK 19(17Q11.2) WILD-TYPE
  FEMALE                           24                             64
  MALE                             18                             56
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 19(17Q11.2) MUTATED                                  0     0
  DEL PEAK 19(17Q11.2) WILD-TYPE                                1     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(17Q11.2) MUTATED                           2    39
  DEL PEAK 19(17Q11.2) WILD-TYPE                        17    95
D26V4, multiclass
                                  clus
vv                                 DEL PEAK 19(17Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      39
                                  clus
vv                                 DEL PEAK 19(17Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    17
  WHITE                                                        95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = DEL PEAK 20(22Q13.31) MUTATION ANALYSIS
D27V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 20(22Q13.31) MUTATED   60  5
  DEL PEAK 20(22Q13.31) WILD-TYPE 96  1
  DEL PEAK 20(22Q13.31) MUTATED DEL PEAK 20(22Q13.31) WILD-TYPE 
                             65                              97 
  DEL PEAK 20(22Q13.31) MUTATED DEL PEAK 20(22Q13.31) WILD-TYPE 
                              5                               1 
$`DEL PEAK 20(22Q13.31) MUTATED`
TCGA-P8-A5KD TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PH TCGA-QR-A6GR TCGA-QR-A6H6 
        2.27         5.88        17.95        28.08        23.11        15.58 
TCGA-QR-A702 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70K 
        1.28       116.19         6.31         2.33        26.83         9.01 
TCGA-QR-A70P TCGA-QR-A70W TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XO TCGA-QT-A5XP 
      117.14        41.79         6.94         1.81         2.30         4.41 
TCGA-QT-A69Q TCGA-RT-A6Y9 TCGA-RW-A67Y TCGA-RW-A681 TCGA-RW-A686 TCGA-S7-A7WL 
        0.79       108.26         7.10        23.80        13.32        31.59 
TCGA-S7-A7WM TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WX TCGA-S7-A7X2 TCGA-SP-A6QF 
       30.21        26.96        40.70        25.32        18.08        82.62 
TCGA-SP-A6QG TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
       67.50        15.52       111.25         0.10        51.22        68.61 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-TT-A6YK TCGA-W2-A7H5 TCGA-W2-A7HA 
        3.12        24.66        19.76        25.15        14.20         1.18 
TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7UY 
       19.86        12.03        12.49        16.60        17.69        10.65 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A818 
        4.73         4.21        29.16        19.59         5.98        34.03 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81H TCGA-WB-A81N TCGA-WB-A81Q 
       33.90        24.16        35.84        42.54        53.69        24.82 
TCGA-WB-A81R TCGA-WB-A81T TCGA-WB-A81W TCGA-WB-A820 TCGA-XG-A823 
        1.61        18.28        78.21        10.16        20.19 

$`DEL PEAK 20(22Q13.31) WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A6RX TCGA-PR-A5PG TCGA-QR-A6GO TCGA-QR-A6GS 
       31.46        29.03        17.75        81.70        35.01         1.25 
TCGA-QR-A6GT TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 
      137.59        58.88        19.04         1.05        30.51         9.21 
TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A700 TCGA-QR-A706 
       14.17         9.93        14.27        31.53        32.15         4.11 
TCGA-QR-A70D TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70X 
        0.23        29.92        13.12         1.41        14.20         6.02 
TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A7U0 
       12.39        17.95        36.23         0.72        25.18        13.08 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
       77.98         0.92        50.63         8.09        86.89        19.86 
TCGA-RW-A67X TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A688 TCGA-RW-A689 
        2.93        33.30         1.05         0.85         1.22        11.70 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G 
       13.05         7.96         6.28        72.79        15.02        41.88 
TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WN TCGA-S7-A7WO 
        4.41         1.78         2.89        20.09        37.25        35.51 
TCGA-S7-A7WP TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7X0 
       31.04        37.58        30.51        27.91        20.58        12.66 
TCGA-S7-A7X1 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QI TCGA-SQ-A6I4 
       18.94         9.73       114.77       109.25       110.04         1.41 
TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6N0 TCGA-TT-A6YJ 
       81.93       106.75       110.53       121.05        49.61         4.34 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HH TCGA-WB-A80K 
       19.92        13.32        25.32        17.16        25.61        34.82 
TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A814 TCGA-WB-A816 
       34.26         4.47       316.73       127.56        32.88        41.23 
TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81I TCGA-WB-A81J 
       32.61        37.18        57.11        38.76        22.32        24.36 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81P TCGA-WB-A81S TCGA-WB-A81V TCGA-WB-A821 
       40.04        45.83        12.99        23.77        71.05        93.11 
TCGA-WB-A822 
      103.17 

  DEL PEAK 20(22Q13.31) MUTATED DEL PEAK 20(22Q13.31) WILD-TYPE 
                           0.10                            0.23 
  DEL PEAK 20(22Q13.31) MUTATED DEL PEAK 20(22Q13.31) WILD-TYPE 
                         117.14                          316.73 
  DEL PEAK 20(22Q13.31) MUTATED DEL PEAK 20(22Q13.31) WILD-TYPE 
                          19.59                           25.18 
[1] "0.1 - 117.1 (19.6)" "0.2 - 316.7 (25.2)"
[1] "hr=" "9.9"
D27V2, continuous
D27V3, binary
                                 cls
clus                               0  1
  DEL PEAK 20(22Q13.31) MUTATED   36 29
  DEL PEAK 20(22Q13.31) WILD-TYPE 52 45
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(22Q13.31) MUTATED     36   29
  DEL PEAK 20(22Q13.31) WILD-TYPE   52   45
        clus
vv       DEL PEAK 20(22Q13.31) MUTATED DEL PEAK 20(22Q13.31) WILD-TYPE
  FEMALE                            36                              52
  MALE                              29                              45
[1] 2 2
[1] FALSE
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 20(22Q13.31) MUTATED                                  1     3
  DEL PEAK 20(22Q13.31) WILD-TYPE                                0     2
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(22Q13.31) MUTATED                           6    55
  DEL PEAK 20(22Q13.31) WILD-TYPE                        13    79
D27V4, multiclass
                                  clus
vv                                 DEL PEAK 20(22Q13.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                    6
  WHITE                                                       55
                                  clus
vv                                 DEL PEAK 20(22Q13.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          2
  BLACK OR AFRICAN AMERICAN                                     13
  WHITE                                                         79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = DEL PEAK 21(XP21.1) MUTATION ANALYSIS
D28V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 21(XP21.1) MUTATED    45   1
  DEL PEAK 21(XP21.1) WILD-TYPE 111   5
  DEL PEAK 21(XP21.1) MUTATED DEL PEAK 21(XP21.1) WILD-TYPE 
                           46                           116 
  DEL PEAK 21(XP21.1) MUTATED DEL PEAK 21(XP21.1) WILD-TYPE 
                            1                             5 
$`DEL PEAK 21(XP21.1) MUTATED`
TCGA-QR-A6GO TCGA-QR-A6GT TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A70H TCGA-QR-A70K 
       35.01       137.59        15.58         1.28        26.83         9.01 
TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK 
       14.20        41.79        12.39        17.95        36.23         6.94 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A69Q TCGA-RT-A6YA TCGA-RW-A67Y TCGA-RW-A689 
       25.18         2.30         0.79        50.63         7.10        11.70 
TCGA-RW-A68A TCGA-RW-A68C TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-SP-A6QG TCGA-SQ-A6I6 
       13.05         6.28        26.96        40.70        67.50         0.10 
TCGA-SR-A6MQ TCGA-SR-A6MX TCGA-SR-A6MY TCGA-TT-A6YJ TCGA-TT-A6YN TCGA-TT-A6YP 
       68.61         3.12        24.66         4.34        19.92        25.32 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HF 
       17.16         1.18        19.86        12.03        12.49        17.69 
TCGA-W2-A7UY TCGA-WB-A80M TCGA-WB-A80V TCGA-WB-A815 TCGA-WB-A819 TCGA-WB-A81E 
       10.65         4.47        29.16         5.98        33.90        37.18 
TCGA-WB-A81F TCGA-WB-A81K TCGA-WB-A81R TCGA-WB-A81W 
       57.11        40.04         1.61        78.21 

$`DEL PEAK 21(XP21.1) WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GU TCGA-QR-A6GX 
       81.70        28.08        23.11         1.25        58.88        19.04 
TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 
        1.05        30.51         9.21        14.17         9.93        14.27 
TCGA-QR-A6H5 TCGA-QR-A700 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E 
       31.53        32.15         4.11       116.19         0.23         6.31 
TCGA-QR-A70G TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70X 
        2.33        29.92        13.12         1.41       117.14         6.02 
TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W 
        1.81         0.72         4.41        13.08        77.98         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A680 
      108.26         8.09        86.89        19.86         2.93        33.30 
TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A68B 
       23.80         1.05         0.85        13.32         1.22         7.96 
TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ 
       72.79        15.02        41.88         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
       20.09        31.59        30.21        37.25        35.51        31.04 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       37.58        30.51        27.91        20.58        25.32        12.66 
TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
       18.94        18.08         9.73       114.77       109.25        82.62 
TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SR-A6MP TCGA-SR-A6MS 
      110.04        15.52       111.25         1.41        51.22        81.93 
TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YK 
      106.75       110.53       121.05        19.76        49.61        25.15 
TCGA-TT-A6YO TCGA-W2-A7H5 TCGA-W2-A7HE TCGA-W2-A7HH TCGA-WB-A80K TCGA-WB-A80L 
       13.32        14.20        16.60        25.61        34.82        34.26 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A814 
        4.73         4.21       316.73       127.56        19.59        32.88 
TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81G 
       41.23        32.61        34.03        24.16        35.84        38.76 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
       42.54        22.32        24.36        45.83        53.69        12.99 
TCGA-WB-A81Q TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A820 TCGA-WB-A821 
       24.82        23.77        18.28        71.05        10.16        93.11 
TCGA-WB-A822 TCGA-XG-A823 
      103.17        20.19 

  DEL PEAK 21(XP21.1) MUTATED DEL PEAK 21(XP21.1) WILD-TYPE 
                         0.10                          0.23 
  DEL PEAK 21(XP21.1) MUTATED DEL PEAK 21(XP21.1) WILD-TYPE 
                       137.59                        316.73 
  DEL PEAK 21(XP21.1) MUTATED DEL PEAK 21(XP21.1) WILD-TYPE 
                       17.425                        23.980 
[1] "0.1 - 137.6 (17.4)" "0.2 - 316.7 (24.0)"
[1] "hr=" "1.7"
D28V2, continuous
D28V3, binary
                               cls
clus                             0  1
  DEL PEAK 21(XP21.1) MUTATED   25 21
  DEL PEAK 21(XP21.1) WILD-TYPE 63 53
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(XP21.1) MUTATED     25   21
  DEL PEAK 21(XP21.1) WILD-TYPE   63   53
        clus
vv       DEL PEAK 21(XP21.1) MUTATED DEL PEAK 21(XP21.1) WILD-TYPE
  FEMALE                          25                            63
  MALE                            21                            53
[1] 2 2
[1] FALSE
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 21(XP21.1) MUTATED                                  1     1
  DEL PEAK 21(XP21.1) WILD-TYPE                                0     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(XP21.1) MUTATED                           6    37
  DEL PEAK 21(XP21.1) WILD-TYPE                        13    97
D28V4, multiclass
                                  clus
vv                                 DEL PEAK 21(XP21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  6
  WHITE                                                     37
                                  clus
vv                                 DEL PEAK 21(XP21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   13
  WHITE                                                       97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
